finished
This commit is contained in:
2
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/.gitignore
generated
vendored
Normal file
2
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/.gitignore
generated
vendored
Normal file
@@ -0,0 +1,2 @@
|
|||||||
|
# Default ignored files
|
||||||
|
/workspace.xml
|
||||||
21
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/contentModel.xml
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Normal file
21
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/contentModel.xml
generated
Normal file
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|
|||||||
|
<?xml version="1.0" encoding="UTF-8"?>
|
||||||
|
<project version="4">
|
||||||
|
<component name="ContentModelStore">
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||||||
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<e p="$USER_HOME$/Library/Caches/Rider2019.2/extResources" t="IncludeRecursive" />
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||||||
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<e p="$USER_HOME$/Library/Caches/Rider2019.2/resharper-host/local/Transient/ReSharperHost/v192/SolutionCaches/_DNA_Alignment.-1495054751.00" t="ExcludeRecursive" />
|
||||||
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<e p="$PROJECT_DIR$" t="IncludeFlat">
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||||||
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<e p="DNA_Alignment" t="IncludeRecursive">
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||||||
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<e p="bin" t="ExcludeRecursive" />
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||||||
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<e p="DNA_Alignment.csproj" t="IncludeRecursive" />
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||||||
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<e p="obj" t="ExcludeRecursive" />
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||||||
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<e p="Program.cs" t="Include" />
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||||||
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<e p="Properties" t="Include">
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||||||
|
<e p="AssemblyInfo.cs" t="Include" />
|
||||||
|
</e>
|
||||||
|
<e p="writeup.txt" t="Include" />
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||||||
|
</e>
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||||||
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<e p="DNA_Alignment.sln" t="IncludeFlat" />
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||||||
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<e p="packages" t="ExcludeRecursive" />
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||||||
|
</e>
|
||||||
|
</component>
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||||||
|
</project>
|
||||||
4
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/encodings.xml
generated
Normal file
4
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/encodings.xml
generated
Normal file
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|
|||||||
|
<?xml version="1.0" encoding="UTF-8"?>
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||||||
|
<project version="4">
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||||||
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<component name="Encoding" addBOMForNewFiles="with BOM under Windows, with no BOM otherwise" />
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||||||
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</project>
|
||||||
8
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/indexLayout.xml
generated
Normal file
8
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/indexLayout.xml
generated
Normal file
@@ -0,0 +1,8 @@
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|||||||
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<?xml version="1.0" encoding="UTF-8"?>
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||||||
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<project version="4">
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||||||
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<component name="ContentModelUserStore">
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||||||
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<attachedFolders />
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||||||
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<explicitIncludes />
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||||||
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<explicitExcludes />
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||||||
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</component>
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||||||
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</project>
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||||||
8
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/modules.xml
generated
Normal file
8
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/modules.xml
generated
Normal file
@@ -0,0 +1,8 @@
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|||||||
|
<?xml version="1.0" encoding="UTF-8"?>
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||||||
|
<project version="4">
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||||||
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<component name="ProjectModuleManager">
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||||||
|
<modules>
|
||||||
|
<module fileurl="file://$PROJECT_DIR$/.idea/.idea.DNA_Alignment/riderModule.iml" filepath="$PROJECT_DIR$/.idea/.idea.DNA_Alignment/riderModule.iml" />
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||||||
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</modules>
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||||||
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</component>
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||||||
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</project>
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||||||
6
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/projectSettingsUpdater.xml
generated
Normal file
6
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/projectSettingsUpdater.xml
generated
Normal file
@@ -0,0 +1,6 @@
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|||||||
|
<?xml version="1.0" encoding="UTF-8"?>
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||||||
|
<project version="4">
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||||||
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<component name="RiderProjectSettingsUpdater">
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||||||
|
<option name="vcsConfiguration" value="1" />
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||||||
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</component>
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||||||
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</project>
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||||||
6
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/vcs.xml
generated
Normal file
6
DNA_Alignment/.idea/.idea.DNA_Alignment/.idea/vcs.xml
generated
Normal file
@@ -0,0 +1,6 @@
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|||||||
|
<?xml version="1.0" encoding="UTF-8"?>
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||||||
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<project version="4">
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||||||
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<component name="VcsDirectoryMappings">
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||||||
|
<mapping directory="$PROJECT_DIR$/.." vcs="Git" />
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||||||
|
</component>
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||||||
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</project>
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||||||
7
DNA_Alignment/.idea/.idea.DNA_Alignment/riderModule.iml
generated
Normal file
7
DNA_Alignment/.idea/.idea.DNA_Alignment/riderModule.iml
generated
Normal file
@@ -0,0 +1,7 @@
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|||||||
|
<?xml version="1.0" encoding="UTF-8"?>
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||||||
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<module type="RIDER_MODULE" version="4">
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||||||
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<component name="NewModuleRootManager">
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||||||
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<content url="file://$MODULE_DIR$/../.." />
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||||||
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<orderEntry type="sourceFolder" forTests="false" />
|
||||||
|
</component>
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||||||
|
</module>
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||||||
16
DNA_Alignment/DNA_Alignment.sln
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16
DNA_Alignment/DNA_Alignment.sln
Normal file
@@ -0,0 +1,16 @@
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|||||||
|
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||||||
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Microsoft Visual Studio Solution File, Format Version 12.00
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||||||
|
Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "DNA_Alignment", "DNA_Alignment\DNA_Alignment.csproj", "{ED9116C6-3BCE-4B84-89EA-DEE30AE5FBC5}"
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||||||
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EndProject
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||||||
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Global
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||||||
|
GlobalSection(SolutionConfigurationPlatforms) = preSolution
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||||||
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Debug|Any CPU = Debug|Any CPU
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||||||
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Release|Any CPU = Release|Any CPU
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||||||
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EndGlobalSection
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||||||
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GlobalSection(ProjectConfigurationPlatforms) = postSolution
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||||||
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{ED9116C6-3BCE-4B84-89EA-DEE30AE5FBC5}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
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||||||
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{ED9116C6-3BCE-4B84-89EA-DEE30AE5FBC5}.Debug|Any CPU.Build.0 = Debug|Any CPU
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||||||
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{ED9116C6-3BCE-4B84-89EA-DEE30AE5FBC5}.Release|Any CPU.ActiveCfg = Release|Any CPU
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||||||
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{ED9116C6-3BCE-4B84-89EA-DEE30AE5FBC5}.Release|Any CPU.Build.0 = Release|Any CPU
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||||||
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EndGlobalSection
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||||||
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EndGlobal
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||||||
BIN
DNA_Alignment/DNA_Alignment/Archive.zip
Normal file
BIN
DNA_Alignment/DNA_Alignment/Archive.zip
Normal file
Binary file not shown.
55
DNA_Alignment/DNA_Alignment/DNA_Alignment.csproj
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55
DNA_Alignment/DNA_Alignment/DNA_Alignment.csproj
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@@ -0,0 +1,55 @@
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|||||||
|
<?xml version="1.0" encoding="utf-8"?>
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||||||
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<Project ToolsVersion="4.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
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||||||
|
<Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
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||||||
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<PropertyGroup>
|
||||||
|
<Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
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||||||
|
<Platform Condition=" '$(Platform)' == '' ">AnyCPU</Platform>
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||||||
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<ProjectGuid>{ED9116C6-3BCE-4B84-89EA-DEE30AE5FBC5}</ProjectGuid>
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||||||
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<OutputType>Exe</OutputType>
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||||||
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<AppDesignerFolder>Properties</AppDesignerFolder>
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||||||
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<RootNamespace>DNA_Alignment</RootNamespace>
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||||||
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<AssemblyName>DNA_Alignment</AssemblyName>
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||||||
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<TargetFrameworkVersion>v4.7.2</TargetFrameworkVersion>
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||||||
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<FileAlignment>512</FileAlignment>
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||||||
|
</PropertyGroup>
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||||||
|
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
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||||||
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<PlatformTarget>AnyCPU</PlatformTarget>
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||||||
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<DebugSymbols>true</DebugSymbols>
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||||||
|
<DebugType>full</DebugType>
|
||||||
|
<Optimize>false</Optimize>
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||||||
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<OutputPath>bin\Debug\</OutputPath>
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||||||
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<DefineConstants>DEBUG;TRACE</DefineConstants>
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||||||
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<ErrorReport>prompt</ErrorReport>
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||||||
|
<WarningLevel>4</WarningLevel>
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||||||
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</PropertyGroup>
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||||||
|
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
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||||||
|
<PlatformTarget>AnyCPU</PlatformTarget>
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||||||
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<DebugType>pdbonly</DebugType>
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||||||
|
<Optimize>true</Optimize>
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||||||
|
<OutputPath>bin\Release\</OutputPath>
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||||||
|
<DefineConstants>TRACE</DefineConstants>
|
||||||
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<ErrorReport>prompt</ErrorReport>
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||||||
|
<WarningLevel>4</WarningLevel>
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||||||
|
</PropertyGroup>
|
||||||
|
<ItemGroup>
|
||||||
|
<Reference Include="System" />
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||||||
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<Reference Include="System.Core" />
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||||||
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<Reference Include="System.Data" />
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||||||
|
<Reference Include="System.Xml" />
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||||||
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</ItemGroup>
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||||||
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<ItemGroup>
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||||||
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<Compile Include="Program.cs" />
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||||||
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<Compile Include="Properties\AssemblyInfo.cs" />
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||||||
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</ItemGroup>
|
||||||
|
<ItemGroup>
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||||||
|
<Content Include="writeup.txt" />
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||||||
|
</ItemGroup>
|
||||||
|
<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
|
||||||
|
<!-- To modify your build process, add your task inside one of the targets below and uncomment it.
|
||||||
|
Other similar extension points exist, see Microsoft.Common.targets.
|
||||||
|
<Target Name="BeforeBuild">
|
||||||
|
</Target>
|
||||||
|
<Target Name="AfterBuild">
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||||||
|
</Target>
|
||||||
|
-->
|
||||||
|
</Project>
|
||||||
273
DNA_Alignment/DNA_Alignment/GreatApes.txt
Normal file
273
DNA_Alignment/DNA_Alignment/GreatApes.txt
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@@ -0,0 +1,273 @@
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|||||||
|
gtttatgtag cttacctccc caaagcaata cactgaaaat gtttcgacgg gctcacatca
|
||||||
|
ccccataaac aaataggttt ggtcctagcc tttctattaa ctcttagtag gattacacat
|
||||||
|
gcaagcatcc ccgccccagt gaatcaccct ctaaatcacc acgatcaaaa ggaacaagca
|
||||||
|
tcaagtacgc agaaatgcag ctcaaaacgc ttagcctagc cacaccccca cgggggacag
|
||||||
|
cagtgattaa cctttagcaa taaacgaaag tttaactaag ccatactaac cccagggttg
|
||||||
|
gtcaatttcg tgccagccac cgcggtcaca cgattaaccc aagccaatag aaatcggcgt
|
||||||
|
aaagagtgtt ttagatcaat ccccaataaa gctaaaattc acctgagttg taaaaaactc
|
||||||
|
cagctgatat aaaataaact acgaaagtgg ctttaatata tctgaacaca caatagctag
|
||||||
|
gacccaaact gggattagat accccactat gcctagccct aaacttcaac agttaaatta
|
||||||
|
acaagactgc tcgccagaac actacgagcc acagcttaaa actcaaagga cctggcggtg
|
||||||
|
cttcatatcc ctctagagga gcctgttctg taatcgataa accccgatca acctcaccac
|
||||||
|
ctcttgctca gcctatatac cgccatcttc agcaaaccct gatgaaggcc acaaagtaag
|
||||||
|
cacaagtacc cacgtaaaga cgttaggtca aggtgtagcc catgaggtgg caagaaatgg
|
||||||
|
gctacatttt ctacttcaga aaactacgat aacccttatg aaacctaagg gtagaaggtg
|
||||||
|
gatttagcag taaactaaga gtagagtgct tagttgaaca gggccctgaa gcgcgtacac
|
||||||
|
accgcccgtc accctcctca agtatacttc aaaggacatt taactaaaac ccctacgcat
|
||||||
|
ctatatagag gagataagtc gtaacatggt aagtgtactg gaaagtgcac ttggacgaac
|
||||||
|
cagagtgtag cttaacacaa agcacccaac ttacacttag gagatttcaa ctcaacttga
|
||||||
|
ccgctctgag caaaacctag ccccaaaccc accccacatt actaccaaac aactttaatc
|
||||||
|
aaaccattta cccaaataaa gtataggcga tagaaattgt aaatcggcgc aatagatata
|
||||||
|
gtaccgcaag ggaaagatga aaaaatataa ccaagcacga cacagcaagg actaacccct
|
||||||
|
gtaccttctg cataatgaat taactagaaa taactttgca aagagaaccg aagctaagac
|
||||||
|
ccccgaaacc agacgagcta cctaagaaca gctaaaagag cacacccgtc tatgtagcaa
|
||||||
|
aatagtggga agattcctag gtagaggcga caaacctacc gagcctggtg atagctggtt
|
||||||
|
gtccaagaca gaatcttagt tcaactttaa atttacccac agaaccctcc aaatcctccc
|
||||||
|
gtaaatttaa ctgttagtcc aaagaggaac agctctttgg acactaggaa aaaaccttgt
|
||||||
|
aaagtgagta aaaaatttaa tacccatagt aggcctaaaa gcagccacca attaagaaag
|
||||||
|
cgttcaagct caacactatc acccaaaata atcccaaaca cacaactgaa ctccctacac
|
||||||
|
ccaattggac caatctatta ccctatagaa gagctaatgt tagtataagt aacatgaaac
|
||||||
|
cattctcctc cgcataagcc tacatcagac caaaatatta aactgacaat taacaactca
|
||||||
|
atatctacaa ctaaccaaca agctattatt acccccactg ttaacccaac acaggcatgc
|
||||||
|
ccacgaggaa aggttgaaaa aagtaaaagg aactcggcaa attttacccc gcctgtttac
|
||||||
|
caaaaacatc acctctagca ttaccagtat tagaggcacc gcctgcccag tgacatgcgt
|
||||||
|
tcaacggccg cggtacccta accgtgcaaa ggtagcataa tcacttgttc cttaaatagg
|
||||||
|
gactcgtatg aatggctcca cgagggttca gctgtctctt acttttgacc agtgaaattg
|
||||||
|
acctgcccgt gaagaggcgg acataacata acaagacgag aagaccctat ggagctttaa
|
||||||
|
ttcattaatg caagcaacac ttaataaacc cacaggtcct aaactaccaa acctgcatta
|
||||||
|
aaaatttcgg ttggggcgac ctcggagtat aatctaacct ccgaacaaca catgccaaga
|
||||||
|
cttcaccagt caaagcgagc taccacattt aattgatcca atgacttgac caacggaaca
|
||||||
|
agttacccta gggataacag cgcaatccta ttctagagtc catatcaaca gtagggttta
|
||||||
|
cgacctcgat gttggatcag gacatcccga tggtgcagcc gctatcaaag gttcgtttgt
|
||||||
|
tcaacgatta aagtcctacg tgatctgagt tcagaccgga gtaatccagg tcggtttcta
|
||||||
|
tctattccgt gtttctccct gtacgaaagg acaagagaaa cgaggcctac ttcacaaagc
|
||||||
|
gcctcccccc gtaaatgata ctatctcaat ttaatatagc gcccacatct actcaagaat
|
||||||
|
agggtttgtt aagatggcag agcccggtaa tcgcataaaa cttaaaactt tatagtcaga
|
||||||
|
ggttcaattc ctcttcttaa caatatatcc atggctaacc ttctactcct cattgtacct
|
||||||
|
atcctaatcg ccatagcatt cctaatgcta accgaacgaa aaattttagg ctatatacaa
|
||||||
|
ctacgtaaag gccccaacgt cgtaggcccc tacgggctac tacaaccctt cgctgacgcc
|
||||||
|
ataaaactct tcaccaaaga gcccctaaaa ccctcaacat caaccatcac cctctacatc
|
||||||
|
accgccccaa ccttagctct cactattgcc ctactattat gaacccccct ccccataccc
|
||||||
|
aaccccctag tcaatctcaa tctaggcctc ctattcatcc tagccacctc tagcctagcc
|
||||||
|
gtttactcca tcctctgatc agggtgggca tcaaactcaa actacgcctt gatcggcgca
|
||||||
|
ctacgagcag tagcccaaac aatctcatat gaagtcaccc tggccattat cctactatca
|
||||||
|
acactactga tgaatggttc ctttaacctc tccaccctca tcataacaca agaacacctc
|
||||||
|
tgactgctcc taccaacatg acccttagct ataatatgat ttatctccac attagcagaa
|
||||||
|
accaaccgga cccccttcga cctcgctgaa ggagaatctg aactagtctc aggctttaat
|
||||||
|
atcgaatatg ccgcaggccc cctcgcccta tttttcatag ccgagtacat aaatattatc
|
||||||
|
ataataaata ctctcaccac tataattttc ctaggaacaa catacaatgc ccactcccct
|
||||||
|
gaactctaca cagtatgctt catcaccaaa accctgcttc taacctctct attcctatga
|
||||||
|
attcgaactg catatcctcg atttcgctac gaccaactca tgcacctcct gtgaaaaaac
|
||||||
|
ttcttgccac tcaccctggc actactcata tgatatattt ccatacctac cacaatctcc
|
||||||
|
agcattcccc ctcaaaccta agaaatatgt ctgataaaag agttactttg atagagtaaa
|
||||||
|
taatagaggt ttaaaccccc ttatttctag gactatgaga attgaaccca tccctgagaa
|
||||||
|
tccaaaattc tccgtgccac ctgtcacacc ccatcctaaa gtaaggtcag ctaaataagc
|
||||||
|
tatcgggccc ataccccgaa aatgttggtc acatccttcc cgtactaatt aaccccctgg
|
||||||
|
cccaacccat catctactct accatcttcg caggcactct tattacagca ctaagctccc
|
||||||
|
actgattttt tgcctgagta ggcctagaaa taaacatact agcttttatc ccagtcctaa
|
||||||
|
ccaaaaaaat aaatccccgc tccacagaag ccgccatcaa atatttcctc acacaagcaa
|
||||||
|
ctgcatccat aatcctccta atagccatcc tctccaacaa catactctcc ggacaatgaa
|
||||||
|
ccacaaccaa tgccactaat caatactcat cattaatgat cgtagtagct atagctataa
|
||||||
|
aactaggaat agcccccttt cacttctgag tgccagaagt cacccaaggc acccccctaa
|
||||||
|
tgtctggcct actcctcctc acatgacaaa aactagcccc tatgtcaatc atataccaaa
|
||||||
|
tttcctcgtc aacaaatgta agccttctcc tcactctttc aatcctatcc atcctagcag
|
||||||
|
gcagctgagg cggactaaac caaactcaac tacgcaagat tctagcatac tcctcaatca
|
||||||
|
cccatgtagg atgaataata gcagttctac catataaccc taatataact attcttaatc
|
||||||
|
tgaccattta tattatcctc actactacca cattcctatt actcaaccta agctccagca
|
||||||
|
ccacaacctt actactatct cgtacttgaa ataaactgac atgattaaca cctctaatcc
|
||||||
|
cctccaccct cctctcccta ggaggtctac ccccactaac cggcttccta cccaaatggc
|
||||||
|
ttattatcga agaattcaca aaaaataacg acctcattac ccccaccatt atggccatca
|
||||||
|
tcaccctcct caacctctat ttctatctac gcctaattta ctccacctct atcacactac
|
||||||
|
tacccatatc caacaacgta aagataaaat gacagctcga atatactaaa cccactccct
|
||||||
|
tcctccctac acttatcaca ctcaccaccc tacttctacc catctccccc ttcatactaa
|
||||||
|
tagttctata gaaatttagg ttaaacatag accaagagcc ttcaaagccc ttagtaagtt
|
||||||
|
acaacactta atttctgcaa caactaagga ctgcaaaacc ctactctgca tcaactgaac
|
||||||
|
gcaaatcagc cactttaatt aagctaagcc cttactagat caatgggact caaacccaca
|
||||||
|
aacatttagt taacagctaa acaccctagt caactggctt caatctactt ctcccgccgc
|
||||||
|
aagaaaaaaa ggcgggagaa gccccggcag gtttgaagct gcttcttcga atttgcaatt
|
||||||
|
caatatgaaa ttcacctcgg agctggtaaa aagaggccca gcctctgtct ttagatttac
|
||||||
|
agtccaatgc cttactcagc cattttacct ccttttttcc actgatgttc accgaccgct
|
||||||
|
gattattctc tacaaaccat aaagatattg gaacactata tctactattc ggcgcatgag
|
||||||
|
ctggagtcct aggcacagcc ctaagtctcc ttattcgagc agaacttggt caaccaggca
|
||||||
|
accttctagg taacgatcac atctataatg ttatcgtcac agcccatgcg ttcgtaataa
|
||||||
|
ttttcttcat agtaatgcct atcataatcg gaggctttgg caactggcta gtacccttaa
|
||||||
|
taattggtgc ccccgacatg gcattccccc gcataaacaa cataagcttc tgactccttc
|
||||||
|
ccccttcttt cctacttctg ctcgcatccg ctatagtaga agccggcgca gggactggtt
|
||||||
|
ggacagtcta ccctccctta gcaggaaatt attcccaccc cggagcttct gtagacctaa
|
||||||
|
ccattttttc cctacaccta gcaggcatct cctctattct aggggccatc aacttcatta
|
||||||
|
caacaatcat caatataaaa ccccccgcca taacccaata ccaaacaccc cttttcgtct
|
||||||
|
gatccgtcct aatcacagca gtcttacttc ttctatctct cccagtacta gctgctggaa
|
||||||
|
ttaccatatt attaacagac cgtaacctca acaccacctt tttcgaccca gccggaggag
|
||||||
|
gagatcctat cctataccaa cacttattct gattttttgg acaccccgaa gtttacattc
|
||||||
|
taatcctacc aggcttcgga ataatctccc acattgtaac ttattactcc ggaaaaaaag
|
||||||
|
aaccattcgg atatataggt atagtctgag ctataatatc aattggtttc ctgggattta
|
||||||
|
ttgtgtgagc ccaccacata tttacagtag gaatagacgt agatacacga gcctacttca
|
||||||
|
cctccgctac cataatcatc gctatcccca ccggcgtcaa agtattcagc tgactcgcta
|
||||||
|
cactccatgg aagtaatacc aaatgatctg ccgcaatgct ctgagcccta gggttcattt
|
||||||
|
ttctcttcac tgtaggcggc ctaaccggca tcgtactagc aaactcgtca ttagatatcg
|
||||||
|
tgctgcacga cacatattac gtcgtagctc acttccacta tgtcctatct ataggagctg
|
||||||
|
tgttcgccat catagggggc tttattcact gatttcccct attctcaggc tacactctag
|
||||||
|
atcaaaccta cgccaaaatc cactttgcca tcatattcat tggcgttaat ctaaccttct
|
||||||
|
tcccacaaca ctttcttggc ctatctggaa taccccgaca ttactcggac taccccgatg
|
||||||
|
catatactac atgaaatatc ctgtcatccg tgggctcatt catttcccta acagcagtaa
|
||||||
|
tattaataat ttttataatc tgagaagcct tcgcctcaaa acgaaaagtc ctaataatcg
|
||||||
|
aagaaccctc cacaaatctg gagtgactgt atggatgccc tccaccctat catacatttg
|
||||||
|
aagagtctgt atatataaag tctaaacaaa aaaggaagga atcgaacccc ccaaagctgg
|
||||||
|
tttcaagcca accccatgac cttcatgact ttttcaaaaa gatattagaa aaactatttc
|
||||||
|
ataactttgt caaggttaaa ttacgggtta aaccccgtat atcttaatgg cacatgcagc
|
||||||
|
gcaagtaggt ctacaagacg ctacttctcc tatcatagaa gaactaatca tctttcatga
|
||||||
|
tcatgccctc ataatcattt ttctcatctg cttcttagtc ctgtacgccc ttttcctaac
|
||||||
|
actcacaaca aagctaacta acaacaacat ctcagacgcc caagaaatag agaccatctg
|
||||||
|
aaccatcctg cccgctatta tcttagtcct gatcgccctc ccatctctac gaatcctcta
|
||||||
|
tatgacagat gaaatcaatg acccctcctt cactatcaaa tcaatcggtc accaatgata
|
||||||
|
ctgaacctac gaatacaccg actatggtgg attgatcttt aactcctata tactcccccc
|
||||||
|
attattccta gaaccaggtg acctacgact ccttgacgtc gacaaccgag tagtccttcc
|
||||||
|
agttgaagcc cccgtccgta taataattac atcccaagat gtcttacact catgagctgt
|
||||||
|
tcccacatta ggcctaaaaa cagacgcaat ccccgggcgc ctgaaccaaa ccacattcac
|
||||||
|
cgccacacga ccaggagtat actacggcca gtgctcagaa atctgtggag ccaaccacag
|
||||||
|
ttttatgccc attgttctag agctaatccc cctaaaaatc tttgaaatag gacccgtatt
|
||||||
|
cgccctataa tacccctctc atccctctcc agagctcact gtaaagctaa cctagcgtta
|
||||||
|
accttttaag ttaaagatta agagtatcgg cacctctttg cagtgaaatg ccccagctaa
|
||||||
|
ataccaccgt atggcccacc ataattgccc caatactcct cacactattt ctcattaccc
|
||||||
|
aactaaaagt tttaaacaca aattaccacc tacccccctt accaaaaact ataaaaataa
|
||||||
|
aaaacttctg taaaccctga gaaccaaaat gaacgaaaat ttattcgctt cattcattgc
|
||||||
|
ccccacaatc ctaggcttac ccgccgcagt attaattatc ctacttcccc ctctactgat
|
||||||
|
ccccacctcc aaatatctca tcaacaaccg actgattgcc acccaacagt gactaatcca
|
||||||
|
actaacctca aaacaaataa taactataca taacgccaag ggacgaacct gatcccttat
|
||||||
|
gttaatatga ttaattattt ttattgccac aaccaacctc ctcggactct tgccccactc
|
||||||
|
attcacacca actacccagc tatctataaa cctggccata gccatccccc tgtgagcagg
|
||||||
|
cgcagtaact acaggctttc gctccaagac taaaaatgcc ctagcccacc tactaccaca
|
||||||
|
aggcacccct acacccctta tccctatact agtcatcatt gaaaccatca gcctattcat
|
||||||
|
ccaaccaata gccctagctg tacgcctaac cgctaacatc actgcaggtc acctacttat
|
||||||
|
gcacctaatc ggaagcgcca cactagcaat atcaactacc aatcttccct caacactcat
|
||||||
|
tatctttaca gtcctaattt tattaactat actagaaatc gctgtcgccc tcatccaagc
|
||||||
|
ctacgttttc acacttttag tgagcctcta cctgcacgag aacacataat gatccaccaa
|
||||||
|
tcacatgcct atcacatagt aaaacccagc ccatgacccc taacaggggc cctctcagcc
|
||||||
|
ctcctaataa cctcaggctt agccatatga ttccacttcc actctacaac cctactcata
|
||||||
|
ctaggcctac taaccaacat actaactata taccaatgat gacgtgatgt aatgcgagaa
|
||||||
|
agcacgtacc aaggccacca tacactaccc gtccaaaaag gcttacgata tggaatgatc
|
||||||
|
ctatttatta cctcagaagt ctttttcttc gcaggattct tctgagcttt ctaccactcc
|
||||||
|
agcctagccc ctacccctca actaggagca cactgacccc caacaggcat caccccacta
|
||||||
|
aaccccctag aagttccact tttaaataca tctgtactgc tcgcatcagg tgtctcaatt
|
||||||
|
acctgagccc accatagcct aatagaaaat aaccgtaacc aaataattca agcactactt
|
||||||
|
atcacaattt tactgggcct ctacttcacc ctcctacaag cctcagagta ctttgaagcc
|
||||||
|
ccctttacca tttccgatgg tatctatggc tcaacatttt ttgtagccac aggctttcac
|
||||||
|
gggctccacg tcatcattgg gtcaactttc ctcactatct gtcttattcg ccaactaata
|
||||||
|
tttcacttta catccaaaca ccacttcggc ttcgaagccg ccgcttggta ttggcacttc
|
||||||
|
gtagatgtag tctgactatt cctatacgtc tccatctact gatgagggtc ctactctttt
|
||||||
|
agtataatta gtaccgttaa cttccaatta accagttttg gtagtaccca aaaaagagta
|
||||||
|
ataaacttcg ccctgatctt aataaccaac acccttctag ccctactact aataattatt
|
||||||
|
acattttgac taccgcaact taacagctac atagaaaaaa ctaaccccta cgaatgtggt
|
||||||
|
ttcgaccccg tatcccccgc ccgcattcct ttctccataa aatttttcct agtagccatc
|
||||||
|
actttcttac tatttgacct agaaattgcc ctcctattgc ccctgccatg agccctacaa
|
||||||
|
acaaccaact taccactaat agtcatgtca tccctcttat taatcattat cctaacccta
|
||||||
|
agtctagcct acgaatgact gcaaaaagga ctagactgga ccgaattggt acatagttta
|
||||||
|
aacaaaacga atgatttcga ctcattaaat tatgataatc atatttacca aatgcccctt
|
||||||
|
atttacataa acattatact agcatttacc atctcacttc taggaatact agtgtaccgt
|
||||||
|
tcacacctaa tatcctccct actatgccta gaaggaataa tattatcact attcattata
|
||||||
|
gctactctca taaccctcaa tacccacttc ctcttagcta acattgtacc catcaccata
|
||||||
|
ctagtctttg ctgcctgtga agcagcagta ggcctagccc tactagtctc aatctctaac
|
||||||
|
acatatggtc ttgactatgt acaaaaccta aacctgctcc aatgctaaaa ctaatcgccc
|
||||||
|
caacaattat actactaccg ctaacatgac tctccaaaaa acatataatt tgaatcaaca
|
||||||
|
caaccaccca cagcctaatc atcagcatca ttcccctact attttttaac caaattaata
|
||||||
|
acaatctatt tagttactcc ctatcttttt cctccgaccc cctaacgacc cccctcctaa
|
||||||
|
tattaactac ctgactccta ccccttacaa ttatagcaag ccagcgccac ctatccaacg
|
||||||
|
aaccactatc acgaaaaaaa ctctatctct ccatattaat ctccctccaa atctccttaa
|
||||||
|
tcataacatt cacagccaca gaactaatca tattctatat cttcttcgaa gccacactta
|
||||||
|
tccctaccct agttatcatc acccgatgag gcaaccaacc cgaacgtcta aacgcgggta
|
||||||
|
catacttcct attctacacc ctagtaggat ccctccccct acttatcgca ttaatccaca
|
||||||
|
ctcacaacac cttaggctca ctaaatattc tattactcac ccttactgcc caagaactac
|
||||||
|
ctaactcctg agccaacaac ttaatatgac tggcatacac aatagccttt atagtgaaaa
|
||||||
|
taccacttta cgggctccac ctatgactcc ctaaggccca tgttgaggcc cccattgctg
|
||||||
|
gctcaatgat gctcgctgca gtactcttaa aattaggtgg ctatggcata atacgcctca
|
||||||
|
tactcattct taacccccta acaaaacaca tagcttatcc tttcctcgcc ctatctttat
|
||||||
|
ggggtataat cataacaagc tccatctcgc tacggcaaac agatttaaaa tcgctcattg
|
||||||
|
catactcctc aattagccac atagcccttg tagtagcagc tatccttatc caaaccccct
|
||||||
|
gaagcttcac cggcgcagtt gttcttataa ttgcccacgg acttacatca tcattattat
|
||||||
|
tctgcctagc aaactcaaac tacgaacgaa cccacagccg catcataatt ctctctcaag
|
||||||
|
gactccaaac cctactccca ctaatagccc tttgatgact tctggcaagc ctcgccaacc
|
||||||
|
tcgccttacc ccccaccatt aacctactag gagagctctc cgtactagta accacattct
|
||||||
|
cctgatcaaa caccaccctt ttacttacag gatctaacat actaattaca gccctgtact
|
||||||
|
ccctttatat atttaccaca acacaatgag gcccactcac acaccacatc accaacataa
|
||||||
|
aaccctcatt tacacgagaa aacatcctca tattcatgca cctatccccc atcctcctcc
|
||||||
|
tatccctcaa ccccgatatt atcaccgggt ttacctcctg taaatatagt ttaaccaaaa
|
||||||
|
catcagattg tgaatctgat aacagaggct cacaacccct tatttaccga gaaagctcgt
|
||||||
|
aagagctgct aactcatacc cccgtgctta acaacatggc tttctcaact tttaaaggat
|
||||||
|
aacagctatc cattggtctt aggacccaaa aattttggtg caactccaaa taaaagtaat
|
||||||
|
aactatgtac gctaccataa ccaccttagc cctaacttcc ttaattcccc ctatccttac
|
||||||
|
caccttcatc aatcctaaca aaaaaagctc atacccccat tacgtaaaat ctatcgtcgc
|
||||||
|
atccaccttt atcatcagcc tcttccccac aacaatattt ctatgcctag accaagaagc
|
||||||
|
tattatctca agctgacact gagcaacaac ccaaacaatt caactctccc taagctttaa
|
||||||
|
actagattat ttctccataa tatttatccc tgtagcactg ttcgtcacat gatccatcat
|
||||||
|
agaattctca ctatgatata taaactcaga ccccaacatc aaccaattct tcaaatacct
|
||||||
|
gctcatcttt ctaatcacca tactaatcct agtcaccgct aataacctgt ttcaactctt
|
||||||
|
tatcggctga gaaggtgtgg gaattatatc ttttctactc attggctgat gatacgctcg
|
||||||
|
aacagacgcc aacacagcag ccgtccaagc aattctatac aaccgtattg gtgacattgg
|
||||||
|
ttttatccta gccctagcat gatttctcct acactccaac tcatgagacc cacaacaaat
|
||||||
|
atctctctta aacaccaacc ctaaccttat cccacttcta ggtttcctcc tagcagcagc
|
||||||
|
aggcaaatca gctcaactag gcctccaccc ctgactcccc tcggccatag aaggccccac
|
||||||
|
ccccgtctca gccctactcc actcaagcac tatagtcgtg gcaggggtct tcctactcat
|
||||||
|
ccgcttccgc catttagcag aaaacaactc actagctcaa actcttacac tatgcctagg
|
||||||
|
cgctattact actctattcg cggcagtctg cgctctcaca caaaatgata tcaaaaaaat
|
||||||
|
cgtagccttc tccacttcaa gccaattagg gctcatagta gccacaattg gcatcggcca
|
||||||
|
gccacaccta gcatttctac acatctgcac ccacgctttc tttaaagcca tattatttat
|
||||||
|
atgctccgga tccattatcc ataacctcaa taatgagcaa gacatccgaa aaataggagg
|
||||||
|
tctgctcaaa gccatacccc ttacttcaac ctccctagcc attggcagcc tagcactaat
|
||||||
|
aggaatacct tttctcacag gcttctactc caaagacctc atcatcgaaa ccgcaaacat
|
||||||
|
atcacacaca aacgcctggg ccctatcaat cattctcatc gccacctctc ttacgagtgc
|
||||||
|
ctacagcact cgaataatcc ttctcaccct gacaggtcaa cctcgcttcc caacctttgc
|
||||||
|
caacatcaac gaaaactact ccaccctatt aaatcctatt aaacgcctaa caattggaag
|
||||||
|
cctgtttgca ggattcttca tcaccaacaa catcctccct acatccgtac cccaaatgac
|
||||||
|
aatcccactt tacttaaaac ttacagctct aagcatcact ctcctaggac tcctgacagc
|
||||||
|
cctagacctc aactacctca ccaacaaact caaaataaaa cacccaccac acacatttta
|
||||||
|
cttctccaac atactcggat tttaccccaa catcacacac cgcacaattc cctatctagg
|
||||||
|
ccttctcata agtcaaaatc tacccctact cctcctagac ctaatttgac tagaaaaact
|
||||||
|
actacccaaa acaatctcac agcatcaaat ctcagcctcc atcactacct ctacccaaaa
|
||||||
|
aggtttgatc aaactgtact tcctctcttt cttcttccct cttcttttaa tccttcttct
|
||||||
|
aatcacataa cctattaccc cgagcaatct caatcacaat atatacacca acaaataacg
|
||||||
|
tccaaccagt aaccactacc aatcaacgcc cataatcata caaagccccc gcaccaatag
|
||||||
|
gatcttcccg aattaaccct gaaccttccc cctcataaat cattcaactc cccacattat
|
||||||
|
taaaattcac cacaaccacc accccatcat actctttcac ccacaacacc agccccacct
|
||||||
|
ccattgctaa ccccactaag acactcacca agacctcaac cccagacccc cacgcctcag
|
||||||
|
gatactcccc aatggccatc gctgtagtat acccaaaaac aaccatcatc ccccctaaat
|
||||||
|
aaattaaaaa aaccattaaa cccatataac ctcccccaca gtttaaaata atagcacacc
|
||||||
|
caaccacacc actaacaatc aacactaaac ccccataaat aggagaaggc ttagaggaaa
|
||||||
|
accccacaaa ccccattact aaacccacac tcaataaaaa taaaacatat gtcatcattc
|
||||||
|
tcgcacggac cacgaccgcg actaatgata tgaaaaacca tcgttgtact tcaactacaa
|
||||||
|
gaacatcaat gacccctata cgcaaaacta acccactagc aaaactaatt aaccactcat
|
||||||
|
tcattgacct ccctaccccg tccaacatct ccacatgatg aaacttcggc tcactccttg
|
||||||
|
gtgcctgctt aatccttcaa atcaccacag ggctattcct agccatacac tactcacctg
|
||||||
|
atgcctcaac cgccttctca tcaattgccc acatcacccg agatgtaaac tatggctgaa
|
||||||
|
ccatccgcta cctccacgct aacggcgcct caatattctt catttgcctc tttctacaca
|
||||||
|
tcggacgggg cctatactac ggctcatttc tccaccaaga aacctgaaac atcggcatca
|
||||||
|
tcctcctact cacaaccata gcagcagcct tcataggcta tgtcctccca tgaggccaaa
|
||||||
|
tatccttctg aggagccaca gtaatcacaa acttgctatc cgccatcccg tacatcggaa
|
||||||
|
cagacctagt ccaatgagtt tgaggtggtt actcagtaga tagccctacc cttacacgat
|
||||||
|
tctttacctt ccactttatc ctacccttca tcatcacagc cctaacaacc ctccatctcc
|
||||||
|
tatttctaca cgaaacagga tcaaacaacc ctctaggcat cccctcccac tctgacaaaa
|
||||||
|
tcaccttcca cccctactac acaatcaaag acatcctagg cctattcctc tttctcctga
|
||||||
|
ccttgataac attaacacta ttctcaccag acctcctagg agacccagac aactacacct
|
||||||
|
tagccaaccc cctaagcacc ccaccccaca tcaaacccga atgatatttc ctatttgcct
|
||||||
|
acgcaattct ccgatctgtc cccaataaac taggaggcgt cttagctcta ttactatcta
|
||||||
|
ttctcatcct agcaataatt cctattctcc acatatccaa acaacaaagc ataatattcc
|
||||||
|
gcccattaag ccaactactc tactgattcc taatcgcaga cctcttcacc ctaacctgaa
|
||||||
|
tcggaggaca accagtaagc taccccttca tcaccattgg gcaagtagca tccgtactat
|
||||||
|
acttcacgac aatcctattc ctgataccaa tcacatccct gatcgaaaac aaaatactca
|
||||||
|
aatgaacctg cccttgtagt acagaccaat acaccagtct tgtaaaccgg aaacgaagac
|
||||||
|
ctccttccaa gggcatattc agagaaaaag tcctcgactc caccatcagc acccaaagct
|
||||||
|
aatattctaa tttaaactat tctctgttct ttcatgggga gacaaatttg ggtactacca
|
||||||
|
gtattagcta acccatcata attatcatgt atgtcgtgca ttactgccag acaccatgaa
|
||||||
|
taatgtacag taccataaaa cgcccaatca cctgtagcac atcccaacgg aataccaact
|
||||||
|
aacccatccc tcacaaaaag tacataacac ataagatcat ttatcgcaca tagcacatcc
|
||||||
|
cagttaaatc accctcgtcc ccacggatgc cccccctcag atgggaatcc cttgaacacc
|
||||||
|
atcctccgtg aaatcaatat cccgcacaag agtgcactct cctcgctccg ggcccataac
|
||||||
|
acttgggggt agctaaagtg aactgtatcc ggcatctggt tcctacttca gggtcataac
|
||||||
|
acctaaagcg cttcacacgt tccccttaaa taagacatca cgatggatca caggtctatc
|
||||||
|
accctattaa ccactcacgg gagctctcca tgcatttggt atttttcgtc ggggggtgtg
|
||||||
|
cacgcgatag tgagacgctg gaaccggagc accacatgtc gcagtatctg tctttgattc
|
||||||
|
ctgccccatg ctaccattta tcgcacctac gttcaatatt acagccgagc gcacagtgtt
|
||||||
|
catggtgtta attaattcat gcttgttgga cataaaacaa ccaggtggac gtgaacacaa
|
||||||
|
ccacccttca caccaaaaac acaacaaaaa tccaaccccc ccccccgcac tagaaaacag
|
||||||
|
ccccaccaaa ctccaaattt catcttttgg cggtatgcac ttttaacagt cacccctcaa
|
||||||
|
ctaacatagt cagcccacca gtacaacccc cgcccgccct agcaacacac actgctgctg
|
||||||
|
atcctatacc ccgaattaac caaaccccaa agacacccca caca
|
||||||
18669
DNA_Alignment/DNA_Alignment/GreatApes.txt_vs_protypicalHuman.txt.txt
Normal file
18669
DNA_Alignment/DNA_Alignment/GreatApes.txt_vs_protypicalHuman.txt.txt
Normal file
File diff suppressed because it is too large
Load Diff
177
DNA_Alignment/DNA_Alignment/Program.cs
Normal file
177
DNA_Alignment/DNA_Alignment/Program.cs
Normal file
@@ -0,0 +1,177 @@
|
|||||||
|
using System;
|
||||||
|
using System.CodeDom;
|
||||||
|
using System.Collections.Generic;
|
||||||
|
using System.IO;
|
||||||
|
using System.Linq;
|
||||||
|
using System.Text.RegularExpressions;
|
||||||
|
using System.Xml.Schema;
|
||||||
|
|
||||||
|
namespace DNA_Alignment
|
||||||
|
{
|
||||||
|
internal class Program
|
||||||
|
{
|
||||||
|
/// <summary>
|
||||||
|
/// Cost Matrix
|
||||||
|
/// </summary>
|
||||||
|
static readonly int[,] AlignmentMatrix =
|
||||||
|
new int[5, 5] {
|
||||||
|
{5, -1, -2, -1, -3},
|
||||||
|
{-1, 5, -3, -2, -4},
|
||||||
|
{-2, -3, 5, -2, -2},
|
||||||
|
{-1, -2, -2, 5, -1},
|
||||||
|
{-3, -4, -2, -1, 0}
|
||||||
|
};
|
||||||
|
/// <summary>
|
||||||
|
/// Letter LookUP
|
||||||
|
/// </summary>
|
||||||
|
static readonly Dictionary<char, int> LetterLookUp=
|
||||||
|
new Dictionary<char, int>
|
||||||
|
{
|
||||||
|
{'a', 0},
|
||||||
|
{'c', 1},
|
||||||
|
{'g', 2},
|
||||||
|
{'t', 3},
|
||||||
|
{'-', 4}
|
||||||
|
};
|
||||||
|
|
||||||
|
/// <summary>
|
||||||
|
/// Calculates the chage score given two chars.
|
||||||
|
/// </summary>
|
||||||
|
/// <param name="i"></param>
|
||||||
|
/// <param name="j"></param>
|
||||||
|
/// <returns></returns>
|
||||||
|
private static int score(char i, char j)
|
||||||
|
{
|
||||||
|
return AlignmentMatrix[LetterLookUp[i], LetterLookUp[j]];
|
||||||
|
}
|
||||||
|
/// <summary>
|
||||||
|
/// takes a string and reverses it.
|
||||||
|
/// </summary>
|
||||||
|
/// <param name="s"></param>
|
||||||
|
/// <returns></returns>
|
||||||
|
private static string ReverseString(string s)
|
||||||
|
{
|
||||||
|
char[] arr = s.ToCharArray();
|
||||||
|
Array.Reverse(arr);
|
||||||
|
return new string(arr);
|
||||||
|
}
|
||||||
|
|
||||||
|
/// <summary>
|
||||||
|
/// Takes M and reverses the process.
|
||||||
|
/// </summary>
|
||||||
|
/// <param name="M"></param>
|
||||||
|
/// <param name="writeFile"></param>
|
||||||
|
/// <param name="score"></param>
|
||||||
|
/// <returns></returns>
|
||||||
|
private static Tuple<string, string> Traceback(int[,] M, string writeFile, string score)
|
||||||
|
{
|
||||||
|
var xAlign = "";
|
||||||
|
var yAlign = "";
|
||||||
|
var i = A.Length;
|
||||||
|
var j = B.Length;
|
||||||
|
var r = new List<string>();
|
||||||
|
r.Add(score);
|
||||||
|
|
||||||
|
while (i > 0 || j > 0)
|
||||||
|
{
|
||||||
|
var up = M[i - 1, j];
|
||||||
|
var left = M[i, j - 1];
|
||||||
|
var diag = M[i - 1, j - 1];
|
||||||
|
if (i > 0 && up == Math.Max(Math.Max(up, left), diag))//up
|
||||||
|
{
|
||||||
|
r.Add($"{A[i - 1]} => -");
|
||||||
|
// Console.WriteLine(A[j - 1]+" => -");
|
||||||
|
|
||||||
|
xAlign += A[i - 1];
|
||||||
|
yAlign += '-';
|
||||||
|
i -= 1;
|
||||||
|
}
|
||||||
|
else if (j > 0 && left == Math.Max(Math.Max(up, left), diag))//left
|
||||||
|
{
|
||||||
|
r.Add($"- => {B[j - 1]}");
|
||||||
|
// Console.WriteLine("- => "+B[i - 1]);
|
||||||
|
|
||||||
|
xAlign += '-';
|
||||||
|
yAlign += B[j - 1];
|
||||||
|
j -= 1;
|
||||||
|
}else//diag
|
||||||
|
{
|
||||||
|
r.Add($"{A[i - 1]} = {B[j - 1]}");
|
||||||
|
// Console.WriteLine(A[j - 1]+" = "+B[i - 1]);
|
||||||
|
xAlign += A[i - 1];
|
||||||
|
yAlign += B[j - 1];
|
||||||
|
i -= 1;
|
||||||
|
j -= 1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
File.WriteAllLines(writeFile, r);
|
||||||
|
//reverse the strings
|
||||||
|
xAlign = ReverseString(xAlign);
|
||||||
|
yAlign = ReverseString(yAlign);
|
||||||
|
return new Tuple<string, string>(xAlign, yAlign);
|
||||||
|
}
|
||||||
|
|
||||||
|
/// <summary>
|
||||||
|
/// Creates the array M
|
||||||
|
/// </summary>
|
||||||
|
/// <returns></returns>
|
||||||
|
private static int[,] DPmed()
|
||||||
|
{
|
||||||
|
var m = A.Length+1;
|
||||||
|
var n = B.Length+1;
|
||||||
|
var M = new int [m, n];
|
||||||
|
|
||||||
|
for (var x = 1; x < m; x++)
|
||||||
|
{
|
||||||
|
M[x, 0] = M[x-1, 0] + AlignmentMatrix[LetterLookUp[A[x-1]], LetterLookUp['-']];
|
||||||
|
}
|
||||||
|
|
||||||
|
for (var y = 1; y < n; y++)
|
||||||
|
{
|
||||||
|
M[0, y] = M[0, y-1] + AlignmentMatrix[LetterLookUp['-'], LetterLookUp[B[y-1]]];
|
||||||
|
}
|
||||||
|
|
||||||
|
for (var x = 1; x < m; x++)
|
||||||
|
{
|
||||||
|
for (var y = 1; y < n; y++)
|
||||||
|
{
|
||||||
|
//sets up the cache
|
||||||
|
M[x, y] = Math.Max(Math.Max(M[x-1, y-1] + score(A[x - 1], B[y - 1]),
|
||||||
|
M[x-1, y] + score(A[x-1], '-')),
|
||||||
|
M[x, y-1] + score('-', B[y-1]));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return M;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
public static void Main(string[] args)
|
||||||
|
{
|
||||||
|
// Debug mode from ../DNA_Alignment/bin/Debug/
|
||||||
|
// Release mode from ../DNA_Alignment/bin/Release/
|
||||||
|
var f1 = File.ReadAllText(Path.Combine(Environment.CurrentDirectory, args[0]));
|
||||||
|
var f2 = File.ReadAllText(Path.Combine(Environment.CurrentDirectory, args[1]));
|
||||||
|
A = Regex.Replace(f1, @"(\r\n|\r|\n)|n|[ ]|[1234567890]", "");
|
||||||
|
B = Regex.Replace(f2, @"(\r\n|\r|\n)|n|[ ]", "");
|
||||||
|
var M = DPmed();
|
||||||
|
var writeFile = Path.Combine(Environment.CurrentDirectory, $"{args[0]}_vs_{args[1]}.txt");
|
||||||
|
Console.WriteLine("Score: " + M[A.Length,B.Length]);
|
||||||
|
var results = Traceback(M, writeFile, $"Score: {M[A.Length,B.Length].ToString()}");
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
/// <summary>
|
||||||
|
/// String 1
|
||||||
|
/// </summary>
|
||||||
|
public static string A { get; set; }
|
||||||
|
|
||||||
|
/// <summary>
|
||||||
|
/// String 2
|
||||||
|
/// </summary>
|
||||||
|
public static string B { get; set; }
|
||||||
|
}
|
||||||
|
}
|
||||||
35
DNA_Alignment/DNA_Alignment/Properties/AssemblyInfo.cs
Normal file
35
DNA_Alignment/DNA_Alignment/Properties/AssemblyInfo.cs
Normal file
@@ -0,0 +1,35 @@
|
|||||||
|
using System.Reflection;
|
||||||
|
using System.Runtime.InteropServices;
|
||||||
|
|
||||||
|
// General Information about an assembly is controlled through the following
|
||||||
|
// set of attributes. Change these attribute values to modify the information
|
||||||
|
// associated with an assembly.
|
||||||
|
[assembly: AssemblyTitle("DNA_Alignment")]
|
||||||
|
[assembly: AssemblyDescription("")]
|
||||||
|
[assembly: AssemblyConfiguration("")]
|
||||||
|
[assembly: AssemblyCompany("")]
|
||||||
|
[assembly: AssemblyProduct("DNA_Alignment")]
|
||||||
|
[assembly: AssemblyCopyright("Copyright © 2020")]
|
||||||
|
[assembly: AssemblyTrademark("")]
|
||||||
|
[assembly: AssemblyCulture("")]
|
||||||
|
|
||||||
|
// Setting ComVisible to false makes the types in this assembly not visible
|
||||||
|
// to COM components. If you need to access a type in this assembly from
|
||||||
|
// COM, set the ComVisible attribute to true on that type.
|
||||||
|
[assembly: ComVisible(false)]
|
||||||
|
|
||||||
|
// The following GUID is for the ID of the typelib if this project is exposed to COM
|
||||||
|
[assembly: Guid("ED9116C6-3BCE-4B84-89EA-DEE30AE5FBC5")]
|
||||||
|
|
||||||
|
// Version information for an assembly consists of the following four values:
|
||||||
|
//
|
||||||
|
// Major Version
|
||||||
|
// Minor Version
|
||||||
|
// Build Number
|
||||||
|
// Revision
|
||||||
|
//
|
||||||
|
// You can specify all the values or you can default the Build and Revision Numbers
|
||||||
|
// by using the '*' as shown below:
|
||||||
|
// [assembly: AssemblyVersion("1.0.*")]
|
||||||
|
[assembly: AssemblyVersion("1.0.0.0")]
|
||||||
|
[assembly: AssemblyFileVersion("1.0.0.0")]
|
||||||
BIN
DNA_Alignment/DNA_Alignment/bin/Debug/DNA_Alignment.exe
Normal file
BIN
DNA_Alignment/DNA_Alignment/bin/Debug/DNA_Alignment.exe
Normal file
Binary file not shown.
BIN
DNA_Alignment/DNA_Alignment/bin/Debug/DNA_Alignment.pdb
Normal file
BIN
DNA_Alignment/DNA_Alignment/bin/Debug/DNA_Alignment.pdb
Normal file
Binary file not shown.
@@ -0,0 +1,273 @@
|
|||||||
|
gtttatgtag cttacctccc caaagcaata cactgaaaat gtttcgacgg gctcacatca
|
||||||
|
ccccataaac aaataggttt ggtcctagcc tttctattaa ctcttagtag gattacacat
|
||||||
|
gcaagcatcc ccgccccagt gaatcaccct ctaaatcacc acgatcaaaa ggaacaagca
|
||||||
|
tcaagtacgc agaaatgcag ctcaaaacgc ttagcctagc cacaccccca cgggggacag
|
||||||
|
cagtgattaa cctttagcaa taaacgaaag tttaactaag ccatactaac cccagggttg
|
||||||
|
gtcaatttcg tgccagccac cgcggtcaca cgattaaccc aagccaatag aaatcggcgt
|
||||||
|
aaagagtgtt ttagatcaat ccccaataaa gctaaaattc acctgagttg taaaaaactc
|
||||||
|
cagctgatat aaaataaact acgaaagtgg ctttaatata tctgaacaca caatagctag
|
||||||
|
gacccaaact gggattagat accccactat gcctagccct aaacttcaac agttaaatta
|
||||||
|
acaagactgc tcgccagaac actacgagcc acagcttaaa actcaaagga cctggcggtg
|
||||||
|
cttcatatcc ctctagagga gcctgttctg taatcgataa accccgatca acctcaccac
|
||||||
|
ctcttgctca gcctatatac cgccatcttc agcaaaccct gatgaaggcc acaaagtaag
|
||||||
|
cacaagtacc cacgtaaaga cgttaggtca aggtgtagcc catgaggtgg caagaaatgg
|
||||||
|
gctacatttt ctacttcaga aaactacgat aacccttatg aaacctaagg gtagaaggtg
|
||||||
|
gatttagcag taaactaaga gtagagtgct tagttgaaca gggccctgaa gcgcgtacac
|
||||||
|
accgcccgtc accctcctca agtatacttc aaaggacatt taactaaaac ccctacgcat
|
||||||
|
ctatatagag gagataagtc gtaacatggt aagtgtactg gaaagtgcac ttggacgaac
|
||||||
|
cagagtgtag cttaacacaa agcacccaac ttacacttag gagatttcaa ctcaacttga
|
||||||
|
ccgctctgag caaaacctag ccccaaaccc accccacatt actaccaaac aactttaatc
|
||||||
|
aaaccattta cccaaataaa gtataggcga tagaaattgt aaatcggcgc aatagatata
|
||||||
|
gtaccgcaag ggaaagatga aaaaatataa ccaagcacga cacagcaagg actaacccct
|
||||||
|
gtaccttctg cataatgaat taactagaaa taactttgca aagagaaccg aagctaagac
|
||||||
|
ccccgaaacc agacgagcta cctaagaaca gctaaaagag cacacccgtc tatgtagcaa
|
||||||
|
aatagtggga agattcctag gtagaggcga caaacctacc gagcctggtg atagctggtt
|
||||||
|
gtccaagaca gaatcttagt tcaactttaa atttacccac agaaccctcc aaatcctccc
|
||||||
|
gtaaatttaa ctgttagtcc aaagaggaac agctctttgg acactaggaa aaaaccttgt
|
||||||
|
aaagtgagta aaaaatttaa tacccatagt aggcctaaaa gcagccacca attaagaaag
|
||||||
|
cgttcaagct caacactatc acccaaaata atcccaaaca cacaactgaa ctccctacac
|
||||||
|
ccaattggac caatctatta ccctatagaa gagctaatgt tagtataagt aacatgaaac
|
||||||
|
cattctcctc cgcataagcc tacatcagac caaaatatta aactgacaat taacaactca
|
||||||
|
atatctacaa ctaaccaaca agctattatt acccccactg ttaacccaac acaggcatgc
|
||||||
|
ccacgaggaa aggttgaaaa aagtaaaagg aactcggcaa attttacccc gcctgtttac
|
||||||
|
caaaaacatc acctctagca ttaccagtat tagaggcacc gcctgcccag tgacatgcgt
|
||||||
|
tcaacggccg cggtacccta accgtgcaaa ggtagcataa tcacttgttc cttaaatagg
|
||||||
|
gactcgtatg aatggctcca cgagggttca gctgtctctt acttttgacc agtgaaattg
|
||||||
|
acctgcccgt gaagaggcgg acataacata acaagacgag aagaccctat ggagctttaa
|
||||||
|
ttcattaatg caagcaacac ttaataaacc cacaggtcct aaactaccaa acctgcatta
|
||||||
|
aaaatttcgg ttggggcgac ctcggagtat aatctaacct ccgaacaaca catgccaaga
|
||||||
|
cttcaccagt caaagcgagc taccacattt aattgatcca atgacttgac caacggaaca
|
||||||
|
agttacccta gggataacag cgcaatccta ttctagagtc catatcaaca gtagggttta
|
||||||
|
cgacctcgat gttggatcag gacatcccga tggtgcagcc gctatcaaag gttcgtttgt
|
||||||
|
tcaacgatta aagtcctacg tgatctgagt tcagaccgga gtaatccagg tcggtttcta
|
||||||
|
tctattccgt gtttctccct gtacgaaagg acaagagaaa cgaggcctac ttcacaaagc
|
||||||
|
gcctcccccc gtaaatgata ctatctcaat ttaatatagc gcccacatct actcaagaat
|
||||||
|
agggtttgtt aagatggcag agcccggtaa tcgcataaaa cttaaaactt tatagtcaga
|
||||||
|
ggttcaattc ctcttcttaa caatatatcc atggctaacc ttctactcct cattgtacct
|
||||||
|
atcctaatcg ccatagcatt cctaatgcta accgaacgaa aaattttagg ctatatacaa
|
||||||
|
ctacgtaaag gccccaacgt cgtaggcccc tacgggctac tacaaccctt cgctgacgcc
|
||||||
|
ataaaactct tcaccaaaga gcccctaaaa ccctcaacat caaccatcac cctctacatc
|
||||||
|
accgccccaa ccttagctct cactattgcc ctactattat gaacccccct ccccataccc
|
||||||
|
aaccccctag tcaatctcaa tctaggcctc ctattcatcc tagccacctc tagcctagcc
|
||||||
|
gtttactcca tcctctgatc agggtgggca tcaaactcaa actacgcctt gatcggcgca
|
||||||
|
ctacgagcag tagcccaaac aatctcatat gaagtcaccc tggccattat cctactatca
|
||||||
|
acactactga tgaatggttc ctttaacctc tccaccctca tcataacaca agaacacctc
|
||||||
|
tgactgctcc taccaacatg acccttagct ataatatgat ttatctccac attagcagaa
|
||||||
|
accaaccgga cccccttcga cctcgctgaa ggagaatctg aactagtctc aggctttaat
|
||||||
|
atcgaatatg ccgcaggccc cctcgcccta tttttcatag ccgagtacat aaatattatc
|
||||||
|
ataataaata ctctcaccac tataattttc ctaggaacaa catacaatgc ccactcccct
|
||||||
|
gaactctaca cagtatgctt catcaccaaa accctgcttc taacctctct attcctatga
|
||||||
|
attcgaactg catatcctcg atttcgctac gaccaactca tgcacctcct gtgaaaaaac
|
||||||
|
ttcttgccac tcaccctggc actactcata tgatatattt ccatacctac cacaatctcc
|
||||||
|
agcattcccc ctcaaaccta agaaatatgt ctgataaaag agttactttg atagagtaaa
|
||||||
|
taatagaggt ttaaaccccc ttatttctag gactatgaga attgaaccca tccctgagaa
|
||||||
|
tccaaaattc tccgtgccac ctgtcacacc ccatcctaaa gtaaggtcag ctaaataagc
|
||||||
|
tatcgggccc ataccccgaa aatgttggtc acatccttcc cgtactaatt aaccccctgg
|
||||||
|
cccaacccat catctactct accatcttcg caggcactct tattacagca ctaagctccc
|
||||||
|
actgattttt tgcctgagta ggcctagaaa taaacatact agcttttatc ccagtcctaa
|
||||||
|
ccaaaaaaat aaatccccgc tccacagaag ccgccatcaa atatttcctc acacaagcaa
|
||||||
|
ctgcatccat aatcctccta atagccatcc tctccaacaa catactctcc ggacaatgaa
|
||||||
|
ccacaaccaa tgccactaat caatactcat cattaatgat cgtagtagct atagctataa
|
||||||
|
aactaggaat agcccccttt cacttctgag tgccagaagt cacccaaggc acccccctaa
|
||||||
|
tgtctggcct actcctcctc acatgacaaa aactagcccc tatgtcaatc atataccaaa
|
||||||
|
tttcctcgtc aacaaatgta agccttctcc tcactctttc aatcctatcc atcctagcag
|
||||||
|
gcagctgagg cggactaaac caaactcaac tacgcaagat tctagcatac tcctcaatca
|
||||||
|
cccatgtagg atgaataata gcagttctac catataaccc taatataact attcttaatc
|
||||||
|
tgaccattta tattatcctc actactacca cattcctatt actcaaccta agctccagca
|
||||||
|
ccacaacctt actactatct cgtacttgaa ataaactgac atgattaaca cctctaatcc
|
||||||
|
cctccaccct cctctcccta ggaggtctac ccccactaac cggcttccta cccaaatggc
|
||||||
|
ttattatcga agaattcaca aaaaataacg acctcattac ccccaccatt atggccatca
|
||||||
|
tcaccctcct caacctctat ttctatctac gcctaattta ctccacctct atcacactac
|
||||||
|
tacccatatc caacaacgta aagataaaat gacagctcga atatactaaa cccactccct
|
||||||
|
tcctccctac acttatcaca ctcaccaccc tacttctacc catctccccc ttcatactaa
|
||||||
|
tagttctata gaaatttagg ttaaacatag accaagagcc ttcaaagccc ttagtaagtt
|
||||||
|
acaacactta atttctgcaa caactaagga ctgcaaaacc ctactctgca tcaactgaac
|
||||||
|
gcaaatcagc cactttaatt aagctaagcc cttactagat caatgggact caaacccaca
|
||||||
|
aacatttagt taacagctaa acaccctagt caactggctt caatctactt ctcccgccgc
|
||||||
|
aagaaaaaaa ggcgggagaa gccccggcag gtttgaagct gcttcttcga atttgcaatt
|
||||||
|
caatatgaaa ttcacctcgg agctggtaaa aagaggccca gcctctgtct ttagatttac
|
||||||
|
agtccaatgc cttactcagc cattttacct ccttttttcc actgatgttc accgaccgct
|
||||||
|
gattattctc tacaaaccat aaagatattg gaacactata tctactattc ggcgcatgag
|
||||||
|
ctggagtcct aggcacagcc ctaagtctcc ttattcgagc agaacttggt caaccaggca
|
||||||
|
accttctagg taacgatcac atctataatg ttatcgtcac agcccatgcg ttcgtaataa
|
||||||
|
ttttcttcat agtaatgcct atcataatcg gaggctttgg caactggcta gtacccttaa
|
||||||
|
taattggtgc ccccgacatg gcattccccc gcataaacaa cataagcttc tgactccttc
|
||||||
|
ccccttcttt cctacttctg ctcgcatccg ctatagtaga agccggcgca gggactggtt
|
||||||
|
ggacagtcta ccctccctta gcaggaaatt attcccaccc cggagcttct gtagacctaa
|
||||||
|
ccattttttc cctacaccta gcaggcatct cctctattct aggggccatc aacttcatta
|
||||||
|
caacaatcat caatataaaa ccccccgcca taacccaata ccaaacaccc cttttcgtct
|
||||||
|
gatccgtcct aatcacagca gtcttacttc ttctatctct cccagtacta gctgctggaa
|
||||||
|
ttaccatatt attaacagac cgtaacctca acaccacctt tttcgaccca gccggaggag
|
||||||
|
gagatcctat cctataccaa cacttattct gattttttgg acaccccgaa gtttacattc
|
||||||
|
taatcctacc aggcttcgga ataatctccc acattgtaac ttattactcc ggaaaaaaag
|
||||||
|
aaccattcgg atatataggt atagtctgag ctataatatc aattggtttc ctgggattta
|
||||||
|
ttgtgtgagc ccaccacata tttacagtag gaatagacgt agatacacga gcctacttca
|
||||||
|
cctccgctac cataatcatc gctatcccca ccggcgtcaa agtattcagc tgactcgcta
|
||||||
|
cactccatgg aagtaatacc aaatgatctg ccgcaatgct ctgagcccta gggttcattt
|
||||||
|
ttctcttcac tgtaggcggc ctaaccggca tcgtactagc aaactcgtca ttagatatcg
|
||||||
|
tgctgcacga cacatattac gtcgtagctc acttccacta tgtcctatct ataggagctg
|
||||||
|
tgttcgccat catagggggc tttattcact gatttcccct attctcaggc tacactctag
|
||||||
|
atcaaaccta cgccaaaatc cactttgcca tcatattcat tggcgttaat ctaaccttct
|
||||||
|
tcccacaaca ctttcttggc ctatctggaa taccccgaca ttactcggac taccccgatg
|
||||||
|
catatactac atgaaatatc ctgtcatccg tgggctcatt catttcccta acagcagtaa
|
||||||
|
tattaataat ttttataatc tgagaagcct tcgcctcaaa acgaaaagtc ctaataatcg
|
||||||
|
aagaaccctc cacaaatctg gagtgactgt atggatgccc tccaccctat catacatttg
|
||||||
|
aagagtctgt atatataaag tctaaacaaa aaaggaagga atcgaacccc ccaaagctgg
|
||||||
|
tttcaagcca accccatgac cttcatgact ttttcaaaaa gatattagaa aaactatttc
|
||||||
|
ataactttgt caaggttaaa ttacgggtta aaccccgtat atcttaatgg cacatgcagc
|
||||||
|
gcaagtaggt ctacaagacg ctacttctcc tatcatagaa gaactaatca tctttcatga
|
||||||
|
tcatgccctc ataatcattt ttctcatctg cttcttagtc ctgtacgccc ttttcctaac
|
||||||
|
actcacaaca aagctaacta acaacaacat ctcagacgcc caagaaatag agaccatctg
|
||||||
|
aaccatcctg cccgctatta tcttagtcct gatcgccctc ccatctctac gaatcctcta
|
||||||
|
tatgacagat gaaatcaatg acccctcctt cactatcaaa tcaatcggtc accaatgata
|
||||||
|
ctgaacctac gaatacaccg actatggtgg attgatcttt aactcctata tactcccccc
|
||||||
|
attattccta gaaccaggtg acctacgact ccttgacgtc gacaaccgag tagtccttcc
|
||||||
|
agttgaagcc cccgtccgta taataattac atcccaagat gtcttacact catgagctgt
|
||||||
|
tcccacatta ggcctaaaaa cagacgcaat ccccgggcgc ctgaaccaaa ccacattcac
|
||||||
|
cgccacacga ccaggagtat actacggcca gtgctcagaa atctgtggag ccaaccacag
|
||||||
|
ttttatgccc attgttctag agctaatccc cctaaaaatc tttgaaatag gacccgtatt
|
||||||
|
cgccctataa tacccctctc atccctctcc agagctcact gtaaagctaa cctagcgtta
|
||||||
|
accttttaag ttaaagatta agagtatcgg cacctctttg cagtgaaatg ccccagctaa
|
||||||
|
ataccaccgt atggcccacc ataattgccc caatactcct cacactattt ctcattaccc
|
||||||
|
aactaaaagt tttaaacaca aattaccacc tacccccctt accaaaaact ataaaaataa
|
||||||
|
aaaacttctg taaaccctga gaaccaaaat gaacgaaaat ttattcgctt cattcattgc
|
||||||
|
ccccacaatc ctaggcttac ccgccgcagt attaattatc ctacttcccc ctctactgat
|
||||||
|
ccccacctcc aaatatctca tcaacaaccg actgattgcc acccaacagt gactaatcca
|
||||||
|
actaacctca aaacaaataa taactataca taacgccaag ggacgaacct gatcccttat
|
||||||
|
gttaatatga ttaattattt ttattgccac aaccaacctc ctcggactct tgccccactc
|
||||||
|
attcacacca actacccagc tatctataaa cctggccata gccatccccc tgtgagcagg
|
||||||
|
cgcagtaact acaggctttc gctccaagac taaaaatgcc ctagcccacc tactaccaca
|
||||||
|
aggcacccct acacccctta tccctatact agtcatcatt gaaaccatca gcctattcat
|
||||||
|
ccaaccaata gccctagctg tacgcctaac cgctaacatc actgcaggtc acctacttat
|
||||||
|
gcacctaatc ggaagcgcca cactagcaat atcaactacc aatcttccct caacactcat
|
||||||
|
tatctttaca gtcctaattt tattaactat actagaaatc gctgtcgccc tcatccaagc
|
||||||
|
ctacgttttc acacttttag tgagcctcta cctgcacgag aacacataat gatccaccaa
|
||||||
|
tcacatgcct atcacatagt aaaacccagc ccatgacccc taacaggggc cctctcagcc
|
||||||
|
ctcctaataa cctcaggctt agccatatga ttccacttcc actctacaac cctactcata
|
||||||
|
ctaggcctac taaccaacat actaactata taccaatgat gacgtgatgt aatgcgagaa
|
||||||
|
agcacgtacc aaggccacca tacactaccc gtccaaaaag gcttacgata tggaatgatc
|
||||||
|
ctatttatta cctcagaagt ctttttcttc gcaggattct tctgagcttt ctaccactcc
|
||||||
|
agcctagccc ctacccctca actaggagca cactgacccc caacaggcat caccccacta
|
||||||
|
aaccccctag aagttccact tttaaataca tctgtactgc tcgcatcagg tgtctcaatt
|
||||||
|
acctgagccc accatagcct aatagaaaat aaccgtaacc aaataattca agcactactt
|
||||||
|
atcacaattt tactgggcct ctacttcacc ctcctacaag cctcagagta ctttgaagcc
|
||||||
|
ccctttacca tttccgatgg tatctatggc tcaacatttt ttgtagccac aggctttcac
|
||||||
|
gggctccacg tcatcattgg gtcaactttc ctcactatct gtcttattcg ccaactaata
|
||||||
|
tttcacttta catccaaaca ccacttcggc ttcgaagccg ccgcttggta ttggcacttc
|
||||||
|
gtagatgtag tctgactatt cctatacgtc tccatctact gatgagggtc ctactctttt
|
||||||
|
agtataatta gtaccgttaa cttccaatta accagttttg gtagtaccca aaaaagagta
|
||||||
|
ataaacttcg ccctgatctt aataaccaac acccttctag ccctactact aataattatt
|
||||||
|
acattttgac taccgcaact taacagctac atagaaaaaa ctaaccccta cgaatgtggt
|
||||||
|
ttcgaccccg tatcccccgc ccgcattcct ttctccataa aatttttcct agtagccatc
|
||||||
|
actttcttac tatttgacct agaaattgcc ctcctattgc ccctgccatg agccctacaa
|
||||||
|
acaaccaact taccactaat agtcatgtca tccctcttat taatcattat cctaacccta
|
||||||
|
agtctagcct acgaatgact gcaaaaagga ctagactgga ccgaattggt acatagttta
|
||||||
|
aacaaaacga atgatttcga ctcattaaat tatgataatc atatttacca aatgcccctt
|
||||||
|
atttacataa acattatact agcatttacc atctcacttc taggaatact agtgtaccgt
|
||||||
|
tcacacctaa tatcctccct actatgccta gaaggaataa tattatcact attcattata
|
||||||
|
gctactctca taaccctcaa tacccacttc ctcttagcta acattgtacc catcaccata
|
||||||
|
ctagtctttg ctgcctgtga agcagcagta ggcctagccc tactagtctc aatctctaac
|
||||||
|
acatatggtc ttgactatgt acaaaaccta aacctgctcc aatgctaaaa ctaatcgccc
|
||||||
|
caacaattat actactaccg ctaacatgac tctccaaaaa acatataatt tgaatcaaca
|
||||||
|
caaccaccca cagcctaatc atcagcatca ttcccctact attttttaac caaattaata
|
||||||
|
acaatctatt tagttactcc ctatcttttt cctccgaccc cctaacgacc cccctcctaa
|
||||||
|
tattaactac ctgactccta ccccttacaa ttatagcaag ccagcgccac ctatccaacg
|
||||||
|
aaccactatc acgaaaaaaa ctctatctct ccatattaat ctccctccaa atctccttaa
|
||||||
|
tcataacatt cacagccaca gaactaatca tattctatat cttcttcgaa gccacactta
|
||||||
|
tccctaccct agttatcatc acccgatgag gcaaccaacc cgaacgtcta aacgcgggta
|
||||||
|
catacttcct attctacacc ctagtaggat ccctccccct acttatcgca ttaatccaca
|
||||||
|
ctcacaacac cttaggctca ctaaatattc tattactcac ccttactgcc caagaactac
|
||||||
|
ctaactcctg agccaacaac ttaatatgac tggcatacac aatagccttt atagtgaaaa
|
||||||
|
taccacttta cgggctccac ctatgactcc ctaaggccca tgttgaggcc cccattgctg
|
||||||
|
gctcaatgat gctcgctgca gtactcttaa aattaggtgg ctatggcata atacgcctca
|
||||||
|
tactcattct taacccccta acaaaacaca tagcttatcc tttcctcgcc ctatctttat
|
||||||
|
ggggtataat cataacaagc tccatctcgc tacggcaaac agatttaaaa tcgctcattg
|
||||||
|
catactcctc aattagccac atagcccttg tagtagcagc tatccttatc caaaccccct
|
||||||
|
gaagcttcac cggcgcagtt gttcttataa ttgcccacgg acttacatca tcattattat
|
||||||
|
tctgcctagc aaactcaaac tacgaacgaa cccacagccg catcataatt ctctctcaag
|
||||||
|
gactccaaac cctactccca ctaatagccc tttgatgact tctggcaagc ctcgccaacc
|
||||||
|
tcgccttacc ccccaccatt aacctactag gagagctctc cgtactagta accacattct
|
||||||
|
cctgatcaaa caccaccctt ttacttacag gatctaacat actaattaca gccctgtact
|
||||||
|
ccctttatat atttaccaca acacaatgag gcccactcac acaccacatc accaacataa
|
||||||
|
aaccctcatt tacacgagaa aacatcctca tattcatgca cctatccccc atcctcctcc
|
||||||
|
tatccctcaa ccccgatatt atcaccgggt ttacctcctg taaatatagt ttaaccaaaa
|
||||||
|
catcagattg tgaatctgat aacagaggct cacaacccct tatttaccga gaaagctcgt
|
||||||
|
aagagctgct aactcatacc cccgtgctta acaacatggc tttctcaact tttaaaggat
|
||||||
|
aacagctatc cattggtctt aggacccaaa aattttggtg caactccaaa taaaagtaat
|
||||||
|
aactatgtac gctaccataa ccaccttagc cctaacttcc ttaattcccc ctatccttac
|
||||||
|
caccttcatc aatcctaaca aaaaaagctc atacccccat tacgtaaaat ctatcgtcgc
|
||||||
|
atccaccttt atcatcagcc tcttccccac aacaatattt ctatgcctag accaagaagc
|
||||||
|
tattatctca agctgacact gagcaacaac ccaaacaatt caactctccc taagctttaa
|
||||||
|
actagattat ttctccataa tatttatccc tgtagcactg ttcgtcacat gatccatcat
|
||||||
|
agaattctca ctatgatata taaactcaga ccccaacatc aaccaattct tcaaatacct
|
||||||
|
gctcatcttt ctaatcacca tactaatcct agtcaccgct aataacctgt ttcaactctt
|
||||||
|
tatcggctga gaaggtgtgg gaattatatc ttttctactc attggctgat gatacgctcg
|
||||||
|
aacagacgcc aacacagcag ccgtccaagc aattctatac aaccgtattg gtgacattgg
|
||||||
|
ttttatccta gccctagcat gatttctcct acactccaac tcatgagacc cacaacaaat
|
||||||
|
atctctctta aacaccaacc ctaaccttat cccacttcta ggtttcctcc tagcagcagc
|
||||||
|
aggcaaatca gctcaactag gcctccaccc ctgactcccc tcggccatag aaggccccac
|
||||||
|
ccccgtctca gccctactcc actcaagcac tatagtcgtg gcaggggtct tcctactcat
|
||||||
|
ccgcttccgc catttagcag aaaacaactc actagctcaa actcttacac tatgcctagg
|
||||||
|
cgctattact actctattcg cggcagtctg cgctctcaca caaaatgata tcaaaaaaat
|
||||||
|
cgtagccttc tccacttcaa gccaattagg gctcatagta gccacaattg gcatcggcca
|
||||||
|
gccacaccta gcatttctac acatctgcac ccacgctttc tttaaagcca tattatttat
|
||||||
|
atgctccgga tccattatcc ataacctcaa taatgagcaa gacatccgaa aaataggagg
|
||||||
|
tctgctcaaa gccatacccc ttacttcaac ctccctagcc attggcagcc tagcactaat
|
||||||
|
aggaatacct tttctcacag gcttctactc caaagacctc atcatcgaaa ccgcaaacat
|
||||||
|
atcacacaca aacgcctggg ccctatcaat cattctcatc gccacctctc ttacgagtgc
|
||||||
|
ctacagcact cgaataatcc ttctcaccct gacaggtcaa cctcgcttcc caacctttgc
|
||||||
|
caacatcaac gaaaactact ccaccctatt aaatcctatt aaacgcctaa caattggaag
|
||||||
|
cctgtttgca ggattcttca tcaccaacaa catcctccct acatccgtac cccaaatgac
|
||||||
|
aatcccactt tacttaaaac ttacagctct aagcatcact ctcctaggac tcctgacagc
|
||||||
|
cctagacctc aactacctca ccaacaaact caaaataaaa cacccaccac acacatttta
|
||||||
|
cttctccaac atactcggat tttaccccaa catcacacac cgcacaattc cctatctagg
|
||||||
|
ccttctcata agtcaaaatc tacccctact cctcctagac ctaatttgac tagaaaaact
|
||||||
|
actacccaaa acaatctcac agcatcaaat ctcagcctcc atcactacct ctacccaaaa
|
||||||
|
aggtttgatc aaactgtact tcctctcttt cttcttccct cttcttttaa tccttcttct
|
||||||
|
aatcacataa cctattaccc cgagcaatct caatcacaat atatacacca acaaataacg
|
||||||
|
tccaaccagt aaccactacc aatcaacgcc cataatcata caaagccccc gcaccaatag
|
||||||
|
gatcttcccg aattaaccct gaaccttccc cctcataaat cattcaactc cccacattat
|
||||||
|
taaaattcac cacaaccacc accccatcat actctttcac ccacaacacc agccccacct
|
||||||
|
ccattgctaa ccccactaag acactcacca agacctcaac cccagacccc cacgcctcag
|
||||||
|
gatactcccc aatggccatc gctgtagtat acccaaaaac aaccatcatc ccccctaaat
|
||||||
|
aaattaaaaa aaccattaaa cccatataac ctcccccaca gtttaaaata atagcacacc
|
||||||
|
caaccacacc actaacaatc aacactaaac ccccataaat aggagaaggc ttagaggaaa
|
||||||
|
accccacaaa ccccattact aaacccacac tcaataaaaa taaaacatat gtcatcattc
|
||||||
|
tcgcacggac cacgaccgcg actaatgata tgaaaaacca tcgttgtact tcaactacaa
|
||||||
|
gaacatcaat gacccctata cgcaaaacta acccactagc aaaactaatt aaccactcat
|
||||||
|
tcattgacct ccctaccccg tccaacatct ccacatgatg aaacttcggc tcactccttg
|
||||||
|
gtgcctgctt aatccttcaa atcaccacag ggctattcct agccatacac tactcacctg
|
||||||
|
atgcctcaac cgccttctca tcaattgccc acatcacccg agatgtaaac tatggctgaa
|
||||||
|
ccatccgcta cctccacgct aacggcgcct caatattctt catttgcctc tttctacaca
|
||||||
|
tcggacgggg cctatactac ggctcatttc tccaccaaga aacctgaaac atcggcatca
|
||||||
|
tcctcctact cacaaccata gcagcagcct tcataggcta tgtcctccca tgaggccaaa
|
||||||
|
tatccttctg aggagccaca gtaatcacaa acttgctatc cgccatcccg tacatcggaa
|
||||||
|
cagacctagt ccaatgagtt tgaggtggtt actcagtaga tagccctacc cttacacgat
|
||||||
|
tctttacctt ccactttatc ctacccttca tcatcacagc cctaacaacc ctccatctcc
|
||||||
|
tatttctaca cgaaacagga tcaaacaacc ctctaggcat cccctcccac tctgacaaaa
|
||||||
|
tcaccttcca cccctactac acaatcaaag acatcctagg cctattcctc tttctcctga
|
||||||
|
ccttgataac attaacacta ttctcaccag acctcctagg agacccagac aactacacct
|
||||||
|
tagccaaccc cctaagcacc ccaccccaca tcaaacccga atgatatttc ctatttgcct
|
||||||
|
acgcaattct ccgatctgtc cccaataaac taggaggcgt cttagctcta ttactatcta
|
||||||
|
ttctcatcct agcaataatt cctattctcc acatatccaa acaacaaagc ataatattcc
|
||||||
|
gcccattaag ccaactactc tactgattcc taatcgcaga cctcttcacc ctaacctgaa
|
||||||
|
tcggaggaca accagtaagc taccccttca tcaccattgg gcaagtagca tccgtactat
|
||||||
|
acttcacgac aatcctattc ctgataccaa tcacatccct gatcgaaaac aaaatactca
|
||||||
|
aatgaacctg cccttgtagt acagaccaat acaccagtct tgtaaaccgg aaacgaagac
|
||||||
|
ctccttccaa gggcatattc agagaaaaag tcctcgactc caccatcagc acccaaagct
|
||||||
|
aatattctaa tttaaactat tctctgttct ttcatgggga gacaaatttg ggtactacca
|
||||||
|
gtattagcta acccatcata attatcatgt atgtcgtgca ttactgccag acaccatgaa
|
||||||
|
taatgtacag taccataaaa cgcccaatca cctgtagcac atcccaacgg aataccaact
|
||||||
|
aacccatccc tcacaaaaag tacataacac ataagatcat ttatcgcaca tagcacatcc
|
||||||
|
cagttaaatc accctcgtcc ccacggatgc cccccctcag atgggaatcc cttgaacacc
|
||||||
|
atcctccgtg aaatcaatat cccgcacaag agtgcactct cctcgctccg ggcccataac
|
||||||
|
acttgggggt agctaaagtg aactgtatcc ggcatctggt tcctacttca gggtcataac
|
||||||
|
acctaaagcg cttcacacgt tccccttaaa taagacatca cgatggatca caggtctatc
|
||||||
|
accctattaa ccactcacgg gagctctcca tgcatttggt atttttcgtc ggggggtgtg
|
||||||
|
cacgcgatag tgagacgctg gaaccggagc accacatgtc gcagtatctg tctttgattc
|
||||||
|
ctgccccatg ctaccattta tcgcacctac gttcaatatt acagccgagc gcacagtgtt
|
||||||
|
catggtgtta attaattcat gcttgttgga cataaaacaa ccaggtggac gtgaacacaa
|
||||||
|
ccacccttca caccaaaaac acaacaaaaa tccaaccccc ccccccgcac tagaaaacag
|
||||||
|
ccccaccaaa ctccaaattt catcttttgg cggtatgcac ttttaacagt cacccctcaa
|
||||||
|
ctaacatagt cagcccacca gtacaacccc cgcccgccct agcaacacac actgctgctg
|
||||||
|
atcctatacc ccgaattaac caaaccccaa agacacccca caca
|
||||||
File diff suppressed because it is too large
Load Diff
232
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.0.json
Normal file
232
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.0.json
Normal file
@@ -0,0 +1,232 @@
|
|||||||
|
{
|
||||||
|
"protocol_version" : "0.0.4",
|
||||||
|
"configuration" : {
|
||||||
|
"version" : "(6.4.0.198) (2019-06/fe64a4765e6)",
|
||||||
|
"tlc" : "normal",
|
||||||
|
"sigsgev" : "altstack",
|
||||||
|
"notifications" : "kqueue",
|
||||||
|
"architecture" : "amd64",
|
||||||
|
"disabled_features" : "none",
|
||||||
|
"smallconfig" : "disabled",
|
||||||
|
"bigarrays" : "disabled",
|
||||||
|
"softdebug" : "enabled",
|
||||||
|
"interpreter" : "enabled",
|
||||||
|
"llvm_support" : "0",
|
||||||
|
"suspend" : "hybrid"
|
||||||
|
},
|
||||||
|
"memory" : {
|
||||||
|
"Resident Size" : "37834752",
|
||||||
|
"Virtual Size" : "4466749440",
|
||||||
|
"minor_gc_time" : "0",
|
||||||
|
"major_gc_time" : "0",
|
||||||
|
"minor_gc_count" : "0",
|
||||||
|
"major_gc_count" : "0",
|
||||||
|
"major_gc_time_concurrent" : "0"
|
||||||
|
},
|
||||||
|
"threads" : [
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x11437bdc0",
|
||||||
|
"thread_info_addr" : "0x7f9d2d800000",
|
||||||
|
"thread_name" : "tid_307",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4bace6",
|
||||||
|
"SP" : "0x7ffee4485f08",
|
||||||
|
"BP" : "0x7ffee4485fa0"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : true,
|
||||||
|
"native_thread_id" : "0x70000643a000",
|
||||||
|
"thread_info_addr" : "0x7f9d2e014600",
|
||||||
|
"thread_name" : "Debugger agent",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4be7fa",
|
||||||
|
"SP" : "0x7000064394f8",
|
||||||
|
"BP" : "0x700006439520"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x700006237000",
|
||||||
|
"thread_info_addr" : "0x7f9d2e800e00",
|
||||||
|
"thread_name" : "Finalizer",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4b8296",
|
||||||
|
"SP" : "0x700006236e48",
|
||||||
|
"BP" : "0x700006236ef0"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
}
|
||||||
|
]
|
||||||
|
}
|
||||||
232
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.1.json
Normal file
232
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.1.json
Normal file
@@ -0,0 +1,232 @@
|
|||||||
|
{
|
||||||
|
"protocol_version" : "0.0.4",
|
||||||
|
"configuration" : {
|
||||||
|
"version" : "(6.4.0.198) (2019-06/fe64a4765e6)",
|
||||||
|
"tlc" : "normal",
|
||||||
|
"sigsgev" : "altstack",
|
||||||
|
"notifications" : "kqueue",
|
||||||
|
"architecture" : "amd64",
|
||||||
|
"disabled_features" : "none",
|
||||||
|
"smallconfig" : "disabled",
|
||||||
|
"bigarrays" : "disabled",
|
||||||
|
"softdebug" : "enabled",
|
||||||
|
"interpreter" : "enabled",
|
||||||
|
"llvm_support" : "0",
|
||||||
|
"suspend" : "hybrid"
|
||||||
|
},
|
||||||
|
"memory" : {
|
||||||
|
"Resident Size" : "37117952",
|
||||||
|
"Virtual Size" : "4466745344",
|
||||||
|
"minor_gc_time" : "0",
|
||||||
|
"major_gc_time" : "0",
|
||||||
|
"minor_gc_count" : "0",
|
||||||
|
"major_gc_count" : "0",
|
||||||
|
"major_gc_time_concurrent" : "0"
|
||||||
|
},
|
||||||
|
"threads" : [
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x104ff6dc0",
|
||||||
|
"thread_info_addr" : "0x7fa20c001200",
|
||||||
|
"thread_name" : "tid_307",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4bace6",
|
||||||
|
"SP" : "0x7ffeec355f08",
|
||||||
|
"BP" : "0x7ffeec355fa0"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x700001c9d000",
|
||||||
|
"thread_info_addr" : "0x7fa20b800600",
|
||||||
|
"thread_name" : "Finalizer",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4b8296",
|
||||||
|
"SP" : "0x700001c9ce48",
|
||||||
|
"BP" : "0x700001c9cef0"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : true,
|
||||||
|
"native_thread_id" : "0x700001ea0000",
|
||||||
|
"thread_info_addr" : "0x7fa20c802a00",
|
||||||
|
"thread_name" : "Debugger agent",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4be7fa",
|
||||||
|
"SP" : "0x700001e9f4f8",
|
||||||
|
"BP" : "0x700001e9f520"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
}
|
||||||
|
]
|
||||||
|
}
|
||||||
236
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.2.json
Normal file
236
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.2.json
Normal file
@@ -0,0 +1,236 @@
|
|||||||
|
{
|
||||||
|
"protocol_version" : "0.0.4",
|
||||||
|
"configuration" : {
|
||||||
|
"version" : "(6.4.0.198) (2019-06/fe64a4765e6)",
|
||||||
|
"tlc" : "normal",
|
||||||
|
"sigsgev" : "altstack",
|
||||||
|
"notifications" : "kqueue",
|
||||||
|
"architecture" : "amd64",
|
||||||
|
"disabled_features" : "none",
|
||||||
|
"smallconfig" : "disabled",
|
||||||
|
"bigarrays" : "disabled",
|
||||||
|
"softdebug" : "enabled",
|
||||||
|
"interpreter" : "enabled",
|
||||||
|
"llvm_support" : "0",
|
||||||
|
"suspend" : "hybrid"
|
||||||
|
},
|
||||||
|
"memory" : {
|
||||||
|
"Resident Size" : "39825408",
|
||||||
|
"Virtual Size" : "4467929088",
|
||||||
|
"minor_gc_time" : "0",
|
||||||
|
"major_gc_time" : "0",
|
||||||
|
"minor_gc_count" : "0",
|
||||||
|
"major_gc_count" : "0",
|
||||||
|
"major_gc_time_concurrent" : "0"
|
||||||
|
},
|
||||||
|
"threads" : [
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x700009e42000",
|
||||||
|
"thread_info_addr" : "0x7fbe49816c00",
|
||||||
|
"thread_name" : "Finalizer",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4b8296",
|
||||||
|
"SP" : "0x700009e41e48",
|
||||||
|
"BP" : "0x700009e41ef0"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : true,
|
||||||
|
"native_thread_id" : "0x70000a045000",
|
||||||
|
"thread_info_addr" : "0x7fbe49008400",
|
||||||
|
"thread_name" : "Debugger agent",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4be7fa",
|
||||||
|
"SP" : "0x70000a0444f8",
|
||||||
|
"BP" : "0x70000a044520"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x11db44dc0",
|
||||||
|
"thread_info_addr" : "0x7fbe49801200",
|
||||||
|
"thread_name" : "tid_307",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4bace6",
|
||||||
|
"SP" : "0x7ffedfd4def8",
|
||||||
|
"BP" : "0x7ffedfd4df90"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
}
|
||||||
|
]
|
||||||
|
}
|
||||||
236
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.3.json
Normal file
236
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.3.json
Normal file
@@ -0,0 +1,236 @@
|
|||||||
|
{
|
||||||
|
"protocol_version" : "0.0.4",
|
||||||
|
"configuration" : {
|
||||||
|
"version" : "(6.4.0.198) (2019-06/fe64a4765e6)",
|
||||||
|
"tlc" : "normal",
|
||||||
|
"sigsgev" : "altstack",
|
||||||
|
"notifications" : "kqueue",
|
||||||
|
"architecture" : "amd64",
|
||||||
|
"disabled_features" : "none",
|
||||||
|
"smallconfig" : "disabled",
|
||||||
|
"bigarrays" : "disabled",
|
||||||
|
"softdebug" : "enabled",
|
||||||
|
"interpreter" : "enabled",
|
||||||
|
"llvm_support" : "0",
|
||||||
|
"suspend" : "hybrid"
|
||||||
|
},
|
||||||
|
"memory" : {
|
||||||
|
"Resident Size" : "25600000",
|
||||||
|
"Virtual Size" : "4467929088",
|
||||||
|
"minor_gc_time" : "0",
|
||||||
|
"major_gc_time" : "0",
|
||||||
|
"minor_gc_count" : "0",
|
||||||
|
"major_gc_count" : "0",
|
||||||
|
"major_gc_time_concurrent" : "0"
|
||||||
|
},
|
||||||
|
"threads" : [
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x116c59dc0",
|
||||||
|
"thread_info_addr" : "0x7fd13000f200",
|
||||||
|
"thread_name" : "tid_307",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4bace6",
|
||||||
|
"SP" : "0x7ffee86f6ef8",
|
||||||
|
"BP" : "0x7ffee86f6f90"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x700009fd4000",
|
||||||
|
"thread_info_addr" : "0x7fd13002a600",
|
||||||
|
"thread_name" : "Finalizer",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4b8296",
|
||||||
|
"SP" : "0x700009fd3e48",
|
||||||
|
"BP" : "0x700009fd3ef0"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : true,
|
||||||
|
"native_thread_id" : "0x70000a1d7000",
|
||||||
|
"thread_info_addr" : "0x7fd130041600",
|
||||||
|
"thread_name" : "Debugger agent",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4be7fa",
|
||||||
|
"SP" : "0x70000a1d64f8",
|
||||||
|
"BP" : "0x70000a1d6520"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
}
|
||||||
|
]
|
||||||
|
}
|
||||||
236
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.4.json
Normal file
236
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.4.json
Normal file
@@ -0,0 +1,236 @@
|
|||||||
|
{
|
||||||
|
"protocol_version" : "0.0.4",
|
||||||
|
"configuration" : {
|
||||||
|
"version" : "(6.4.0.198) (2019-06/fe64a4765e6)",
|
||||||
|
"tlc" : "normal",
|
||||||
|
"sigsgev" : "altstack",
|
||||||
|
"notifications" : "kqueue",
|
||||||
|
"architecture" : "amd64",
|
||||||
|
"disabled_features" : "none",
|
||||||
|
"smallconfig" : "disabled",
|
||||||
|
"bigarrays" : "disabled",
|
||||||
|
"softdebug" : "enabled",
|
||||||
|
"interpreter" : "enabled",
|
||||||
|
"llvm_support" : "0",
|
||||||
|
"suspend" : "hybrid"
|
||||||
|
},
|
||||||
|
"memory" : {
|
||||||
|
"Resident Size" : "39002112",
|
||||||
|
"Virtual Size" : "4466749440",
|
||||||
|
"minor_gc_time" : "0",
|
||||||
|
"major_gc_time" : "0",
|
||||||
|
"minor_gc_count" : "0",
|
||||||
|
"major_gc_count" : "0",
|
||||||
|
"major_gc_time_concurrent" : "0"
|
||||||
|
},
|
||||||
|
"threads" : [
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : true,
|
||||||
|
"native_thread_id" : "0x700004db3000",
|
||||||
|
"thread_info_addr" : "0x7fdbd282e200",
|
||||||
|
"thread_name" : "Debugger agent",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4be7fa",
|
||||||
|
"SP" : "0x700004db24f8",
|
||||||
|
"BP" : "0x700004db2520"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x700004bb0000",
|
||||||
|
"thread_info_addr" : "0x7fdbd282d000",
|
||||||
|
"thread_name" : "Finalizer",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4b8296",
|
||||||
|
"SP" : "0x700004bafe48",
|
||||||
|
"BP" : "0x700004bafef0"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x10e36cdc0",
|
||||||
|
"thread_info_addr" : "0x7fdbd3000000",
|
||||||
|
"thread_name" : "tid_307",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4bace6",
|
||||||
|
"SP" : "0x7ffee3b7ceb8",
|
||||||
|
"BP" : "0x7ffee3b7cf50"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
}
|
||||||
|
]
|
||||||
|
}
|
||||||
236
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.5.json
Normal file
236
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.5.json
Normal file
@@ -0,0 +1,236 @@
|
|||||||
|
{
|
||||||
|
"protocol_version" : "0.0.4",
|
||||||
|
"configuration" : {
|
||||||
|
"version" : "(6.4.0.198) (2019-06/fe64a4765e6)",
|
||||||
|
"tlc" : "normal",
|
||||||
|
"sigsgev" : "altstack",
|
||||||
|
"notifications" : "kqueue",
|
||||||
|
"architecture" : "amd64",
|
||||||
|
"disabled_features" : "none",
|
||||||
|
"smallconfig" : "disabled",
|
||||||
|
"bigarrays" : "disabled",
|
||||||
|
"softdebug" : "enabled",
|
||||||
|
"interpreter" : "enabled",
|
||||||
|
"llvm_support" : "0",
|
||||||
|
"suspend" : "hybrid"
|
||||||
|
},
|
||||||
|
"memory" : {
|
||||||
|
"Resident Size" : "38891520",
|
||||||
|
"Virtual Size" : "4467793920",
|
||||||
|
"minor_gc_time" : "0",
|
||||||
|
"major_gc_time" : "0",
|
||||||
|
"minor_gc_count" : "0",
|
||||||
|
"major_gc_count" : "0",
|
||||||
|
"major_gc_time_concurrent" : "0"
|
||||||
|
},
|
||||||
|
"threads" : [
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x700003d13000",
|
||||||
|
"thread_info_addr" : "0x7feb54016c00",
|
||||||
|
"thread_name" : "Finalizer",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4b8296",
|
||||||
|
"SP" : "0x700003d12e48",
|
||||||
|
"BP" : "0x700003d12ef0"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x11a147dc0",
|
||||||
|
"thread_info_addr" : "0x7feb54802000",
|
||||||
|
"thread_name" : "tid_307",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4bace6",
|
||||||
|
"SP" : "0x7ffee2d7aea8",
|
||||||
|
"BP" : "0x7ffee2d7af40"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : true,
|
||||||
|
"native_thread_id" : "0x700003f16000",
|
||||||
|
"thread_info_addr" : "0x7feb5401ca00",
|
||||||
|
"thread_name" : "Debugger agent",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4be7fa",
|
||||||
|
"SP" : "0x700003f154f8",
|
||||||
|
"BP" : "0x700003f15520"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
}
|
||||||
|
]
|
||||||
|
}
|
||||||
260
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.6.json
Normal file
260
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.6.json
Normal file
@@ -0,0 +1,260 @@
|
|||||||
|
{
|
||||||
|
"protocol_version" : "0.0.4",
|
||||||
|
"configuration" : {
|
||||||
|
"version" : "(6.4.0.198) (2019-06/fe64a4765e6)",
|
||||||
|
"tlc" : "normal",
|
||||||
|
"sigsgev" : "altstack",
|
||||||
|
"notifications" : "kqueue",
|
||||||
|
"architecture" : "amd64",
|
||||||
|
"disabled_features" : "none",
|
||||||
|
"smallconfig" : "disabled",
|
||||||
|
"bigarrays" : "disabled",
|
||||||
|
"softdebug" : "enabled",
|
||||||
|
"interpreter" : "enabled",
|
||||||
|
"llvm_support" : "0",
|
||||||
|
"suspend" : "hybrid"
|
||||||
|
},
|
||||||
|
"memory" : {
|
||||||
|
"Resident Size" : "16523264",
|
||||||
|
"Virtual Size" : "4466749440",
|
||||||
|
"minor_gc_time" : "0",
|
||||||
|
"major_gc_time" : "0",
|
||||||
|
"minor_gc_count" : "0",
|
||||||
|
"major_gc_count" : "0",
|
||||||
|
"major_gc_time_concurrent" : "0"
|
||||||
|
},
|
||||||
|
"threads" : [
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x103ab0dc0",
|
||||||
|
"thread_info_addr" : "0x7fedb000f200",
|
||||||
|
"thread_name" : "tid_307",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4bace6",
|
||||||
|
"SP" : "0x7ffeeeb739c8",
|
||||||
|
"BP" : "0x7ffeeeb73a60"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x700003a7a000",
|
||||||
|
"thread_info_addr" : "0x7fedb1007800",
|
||||||
|
"thread_name" : "Finalizer",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4b8296",
|
||||||
|
"SP" : "0x700003a79e48",
|
||||||
|
"BP" : "0x700003a79ef0"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : true,
|
||||||
|
"native_thread_id" : "0x700003c7d000",
|
||||||
|
"thread_info_addr" : "0x7fedb1813400",
|
||||||
|
"thread_name" : "Debugger agent",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4be7fa",
|
||||||
|
"SP" : "0x700003c7c4f8",
|
||||||
|
"BP" : "0x700003c7c520"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
}
|
||||||
|
]
|
||||||
|
}
|
||||||
260
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.7.json
Normal file
260
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.7.json
Normal file
@@ -0,0 +1,260 @@
|
|||||||
|
{
|
||||||
|
"protocol_version" : "0.0.4",
|
||||||
|
"configuration" : {
|
||||||
|
"version" : "(6.4.0.198) (2019-06/fe64a4765e6)",
|
||||||
|
"tlc" : "normal",
|
||||||
|
"sigsgev" : "altstack",
|
||||||
|
"notifications" : "kqueue",
|
||||||
|
"architecture" : "amd64",
|
||||||
|
"disabled_features" : "none",
|
||||||
|
"smallconfig" : "disabled",
|
||||||
|
"bigarrays" : "disabled",
|
||||||
|
"softdebug" : "enabled",
|
||||||
|
"interpreter" : "enabled",
|
||||||
|
"llvm_support" : "0",
|
||||||
|
"suspend" : "hybrid"
|
||||||
|
},
|
||||||
|
"memory" : {
|
||||||
|
"Resident Size" : "19746816",
|
||||||
|
"Virtual Size" : "4459810816",
|
||||||
|
"minor_gc_time" : "0",
|
||||||
|
"major_gc_time" : "0",
|
||||||
|
"minor_gc_count" : "0",
|
||||||
|
"major_gc_count" : "0",
|
||||||
|
"major_gc_time_concurrent" : "0"
|
||||||
|
},
|
||||||
|
"threads" : [
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x10c8b6dc0",
|
||||||
|
"thread_info_addr" : "0x7f8b2780f200",
|
||||||
|
"thread_name" : "tid_307",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4bace6",
|
||||||
|
"SP" : "0x7ffeeed7e998",
|
||||||
|
"BP" : "0x7ffeeed7ea30"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x7000059d5000",
|
||||||
|
"thread_info_addr" : "0x7f8b28800800",
|
||||||
|
"thread_name" : "Finalizer",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4b8296",
|
||||||
|
"SP" : "0x7000059d4e48",
|
||||||
|
"BP" : "0x7000059d4ef0"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : true,
|
||||||
|
"native_thread_id" : "0x700005bd8000",
|
||||||
|
"thread_info_addr" : "0x7f8b27818c00",
|
||||||
|
"thread_name" : "Debugger agent",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4be7fa",
|
||||||
|
"SP" : "0x700005bd74f8",
|
||||||
|
"BP" : "0x700005bd7520"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
}
|
||||||
|
]
|
||||||
|
}
|
||||||
260
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.8.json
Normal file
260
DNA_Alignment/DNA_Alignment/bin/Debug/mono_crash.0.8.json
Normal file
@@ -0,0 +1,260 @@
|
|||||||
|
{
|
||||||
|
"protocol_version" : "0.0.4",
|
||||||
|
"configuration" : {
|
||||||
|
"version" : "(6.4.0.198) (2019-06/fe64a4765e6)",
|
||||||
|
"tlc" : "normal",
|
||||||
|
"sigsgev" : "altstack",
|
||||||
|
"notifications" : "kqueue",
|
||||||
|
"architecture" : "amd64",
|
||||||
|
"disabled_features" : "none",
|
||||||
|
"smallconfig" : "disabled",
|
||||||
|
"bigarrays" : "disabled",
|
||||||
|
"softdebug" : "enabled",
|
||||||
|
"interpreter" : "enabled",
|
||||||
|
"llvm_support" : "0",
|
||||||
|
"suspend" : "hybrid"
|
||||||
|
},
|
||||||
|
"memory" : {
|
||||||
|
"Resident Size" : "31916032",
|
||||||
|
"Virtual Size" : "4459806720",
|
||||||
|
"minor_gc_time" : "0",
|
||||||
|
"major_gc_time" : "0",
|
||||||
|
"minor_gc_count" : "0",
|
||||||
|
"major_gc_count" : "0",
|
||||||
|
"major_gc_time_concurrent" : "0"
|
||||||
|
},
|
||||||
|
"threads" : [
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x70000d300000",
|
||||||
|
"thread_info_addr" : "0x7fa144803600",
|
||||||
|
"thread_name" : "Finalizer",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4b8296",
|
||||||
|
"SP" : "0x70000d2ffe48",
|
||||||
|
"BP" : "0x70000d2ffef0"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : false,
|
||||||
|
"native_thread_id" : "0x111a41dc0",
|
||||||
|
"thread_info_addr" : "0x7fa145805c00",
|
||||||
|
"thread_name" : "tid_307",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4bace6",
|
||||||
|
"SP" : "0x7ffeedc81998",
|
||||||
|
"BP" : "0x7ffeedc81a30"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"is_managed" : false,
|
||||||
|
"offset_free_hash" : "0x0",
|
||||||
|
"offset_rich_hash" : "0x0",
|
||||||
|
"crashed" : true,
|
||||||
|
"native_thread_id" : "0x70000d503000",
|
||||||
|
"thread_info_addr" : "0x7fa14400b200",
|
||||||
|
"thread_name" : "Debugger agent",
|
||||||
|
"ctx" : {
|
||||||
|
"IP" : "0x7fff6c4be7fa",
|
||||||
|
"SP" : "0x70000d5024f8",
|
||||||
|
"BP" : "0x70000d502520"
|
||||||
|
},
|
||||||
|
"unmanaged_frames" : [
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
,
|
||||||
|
{
|
||||||
|
"native_address" : "unregistered"
|
||||||
|
}
|
||||||
|
|
||||||
|
]
|
||||||
|
}
|
||||||
|
]
|
||||||
|
}
|
||||||
@@ -0,0 +1,277 @@
|
|||||||
|
gatcacaggt ctatcaccct attaaccact cacgggagct ctccatgcat ttggtatttt
|
||||||
|
cgtctggggg gtgtgcacgc gatagcattg cgagacgctg gagccggagc accctatgtc
|
||||||
|
gcagtatctg tctttgattc ctgccccatt ccattattta tcgcacctac gttcaatatt
|
||||||
|
acaggcgagc atacttactg aagtgtgtta attaattaat gcttgtagga cataataata
|
||||||
|
acgactaaat gtctgcacag ctgctttcca cacagacatc ataacaaaaa atttccacca
|
||||||
|
aaccccccct cccccgcttc tggccacagc acttaaacac atctctgcca aaccccaaaa
|
||||||
|
acaaagaacc ctaacaccag cctaaccaga tttcaaattt tatcttttgg cggtatacac
|
||||||
|
ttttaacagt caccccctaa ctaacacatt attttcccct cccactccca tactactaat
|
||||||
|
ctcatcaata caacccccgc ccatcctacc cagcacacac cgctgctaac cccatacccc
|
||||||
|
gagccaacca aaccccaaag acacccccca cagtttatgt agcttacctc ctcaaagcaa
|
||||||
|
tacactgaaa atgtttagac gggctcacat caccccataa acaaataggt ttggtcctag
|
||||||
|
cctttctatt agctcttagt aagattacac atgcaagcat ccccattcca gtgagttcac
|
||||||
|
cctctaaatc accacgatca aaagggacaa gcatcaagca cgcaacaatg cagctcaaaa
|
||||||
|
cgcttagcct agccacaccc ccacgggaaa cagcagtgat aagcctttag caataaacga
|
||||||
|
aagtttaact aagctatact aaccccaggg ttggtcaatt tcgtgccagc caccgcggtc
|
||||||
|
acacgattaa cccaagtcaa tagaagccgg cgtaaagagt gttttagatc accccctccc
|
||||||
|
caataaagct aaaactcacc tgagttgtaa aaaactccag ttgacacaaa ataaactacg
|
||||||
|
aaagtggctt taacatatct gaacacacaa tagctaagac ccaaactggg attagatacc
|
||||||
|
ccactatgct tagccctaaa cctcaacagt taaatcaaca aaactgctcg ccagaacact
|
||||||
|
acgagccaca gcttaaaact caaaggacct ggcggtgctt catatccctc tagaggagcc
|
||||||
|
tgttctgtaa tcgataaacc ccgatcaacc tcaccacctc ttgctcagcc tatataccgc
|
||||||
|
catcttcagc aaaccctgat gaaggctaca aagtaagcgc aagtacccac gtaaagacgt
|
||||||
|
taggtcaagg tgtagcccat gaggtggcaa gaaatgggct acattttcta ccccagaaaa
|
||||||
|
ctacgatagc ccttatgaaa cctaagggtc gaaggtggat ttagcagtaa actgagagta
|
||||||
|
gagtgcttag ttgaacaggg ccctgaagcg cgtacacacc gcccgtcacc ctcctcaagt
|
||||||
|
atacttcaaa ggacatttaa ctaaaacccc tacgcattta tatagaggag acaagtcgta
|
||||||
|
acatggtaag tgtactggaa agtgcacttg gacgaaccag agtgtagctt aacacaaagc
|
||||||
|
acccaactta cacttaggag atttcaactt aacttgaccg ctctgagcta aacctagccc
|
||||||
|
caaacccact ccaccttact accaaacaac cttagccaaa ccatttaccc aaataaagta
|
||||||
|
taggcgatag aaattgaaac ctggcgcaat agatgtagta ccgcaaggga aagatgaaaa
|
||||||
|
attataacca agcataatat agcaaggact aacccctata ccttctgcat aatgaattaa
|
||||||
|
ctagaaataa ctttgcaagg agagccaaag ctaagacccc cgaaaccaga cgagctacct
|
||||||
|
aagaacagct aaaagagcac acccgtctat gtagcaaaat agtgggaaga tttataggta
|
||||||
|
gaggcgacaa acctaccgag cctggtgata gctggttgtc caagatagaa tcttagttca
|
||||||
|
actttaaatt tacccacaga accctctaaa tccccttgta aatttaactg ttagtccaaa
|
||||||
|
gaggaacagc tctttggaca ctaggaaaaa accttgtaga gagagtaaaa aatttaacac
|
||||||
|
ccatagtagg cctaaaagca gccaccaatt aagaaagcgt tcaagctcaa cacccactac
|
||||||
|
ctaaaaaatc ccaaacatat aactgaactc ctcacaccca attggaccaa tctatcaccc
|
||||||
|
tatagaagaa ctaatgttag tataagtaac atgaaaacat tctcctccgc ataagcctgc
|
||||||
|
gtcagattaa aacactgaac tgacaattaa cagcccaata tctacaatca accaacaagt
|
||||||
|
cattattacc ctcactgtca acccaacaca ggcatgctca taaggaaagg ttaaaaaaag
|
||||||
|
taaaaggaac tcggcaaatc ttaccccgcc tgtttaccaa aaacatcacc tctagcatta
|
||||||
|
ccagtattag aggcaccgcc tgcccagtga cacatgttta acggccgcgg taccctaacc
|
||||||
|
gtgcaaaggt agcataatca cttgttcctt aaatagggac ctgtatgaat ggctccacga
|
||||||
|
gggttcagct gtctcttact tttaaccagt gaaattgacc tgcccgtgaa gaggcgggca
|
||||||
|
taacacagca agacgagaag accctatgga gctttaattt attaatgcaa acagtaccta
|
||||||
|
acaaacccac aggtcctaaa ctaccaaacc tgcattaaaa atttcggttg gggcgacctc
|
||||||
|
ggagcacaac ccaacctccg agcagtacat gctaagacct caccagtcaa agcgaactac
|
||||||
|
catactcaat tgatccaata acttgaccaa cggaacaagt taccctaggg ataacagcgc
|
||||||
|
aatcctattc tagagtccat atcaacaata gggtttacga cctcgatgtt ggatcaggac
|
||||||
|
atcccaatgg tgcagccgct attaaaggtt cgtttgttca acgattaaag tcctacgtga
|
||||||
|
tctgagttca gaccggagta atccaggtcg gtttctatct acttcaaatt cctccctgta
|
||||||
|
cgaaaggaca agagaaataa ggcctacttc acaaagcgcc ttcccccgta aatgatatca
|
||||||
|
tctcaactta gtattatacc cacacccacc caagaacagg gtttgttaag atggcagagc
|
||||||
|
ccggtaatcg cataaaactt aaaactttac agtcagaggt tcaattcctc ttcttaacaa
|
||||||
|
cacacccatg gccaacctcc tactcctcgt tgtacccatt ctaatcgcaa tggcattcct
|
||||||
|
aatgcttacc gaacgaaaaa ttctaggcta tatgcaacta cgcaaaggtc ccaacgttgt
|
||||||
|
aggcccctac gggctactac aacccttcgc tgacgccata aaactcttca ccaaagaacc
|
||||||
|
cctaaaaccc gccacatcca ccatcaccct ctacatcacc gccccgacct tagctctcac
|
||||||
|
catcgctctt ctactatgaa cccccctccc catacccaac cccctggtta acctcaacct
|
||||||
|
aggcctccta tttattctag ccacctctag cctagccgtt tactcaatcc tctgatcagg
|
||||||
|
gtgagcatca aactcaaact acgccctgat cggcgcactg cgagcagtag cccaaacaat
|
||||||
|
ctcatatgaa gtcaccctag ccatcattct actatcaaca ttactaataa gtggctcctt
|
||||||
|
taacctctcc acccttatca cagcacaaga acacctctga ttactcctgc catcatgacc
|
||||||
|
cttggccata atatgattta tctccacact agcagagacc aaccgaaccc ccttcgacct
|
||||||
|
tgctgaaggg gaatccgaac tagtctcagg ctttaacatc gaatacgccg caggcccctt
|
||||||
|
cgccctattc ttcatagccg aatacacaaa cattattata ataaacaccc tcaccactac
|
||||||
|
aatcttccta ggaacaacat ataacgcact ctcccctgaa ctctacacaa catattttgt
|
||||||
|
caccaagacc ctacttctga cctccctgtt cttatgaatt cgaacagcat acccccgatt
|
||||||
|
ccgctacgac caactcatac acctcctatg aaaaaacttc ctaccactca ccctagcact
|
||||||
|
acttatatga tatgtctcca tacccattac aatctccagc attccccctc aaacctaaga
|
||||||
|
aatatgtctg ataaaagagt tactttgata gagtaaataa taggagttta aaccccctta
|
||||||
|
tttctaggac tatgagaatc gaacccatcc ctgagaatcc aaaattctcc gtgccaccta
|
||||||
|
tcacacccca tcctaaagta aggtcagcta aataagctat cgggcccata ccccgaaaat
|
||||||
|
gttggttata cccttcccgt actaattaat cccctggccc aacccgtcat ctactctacc
|
||||||
|
atctttgcag gcacactcat cacagcacta agctcgcact gattttttac ctgagtgggc
|
||||||
|
ctagaaataa acatgctagc ttttattcca gttctaacca aaaaaataaa ccctcgttcc
|
||||||
|
acagaagctg ccatcaagta tttcctcacg caagcaaccg catccataat ccttctaata
|
||||||
|
gctatcctct tcaacaatat actctccgga caatgaacca taaccaatac taccaatcaa
|
||||||
|
tactcatcat taataatcat aatggctata gcaataaaac taggaatagc cccctttcac
|
||||||
|
ttctgagtcc cagaggttac ccaaggcacc cctctgacat ccggcctgct ccttctcaca
|
||||||
|
tgacaaaaac tagcccccat ctcaatcata taccaaattt ctccctcact aaacgtaagc
|
||||||
|
ctcctcctca ctctttcaat cttatccatc atagcaggca gttgaggtgg attaaaccaa
|
||||||
|
acccagctac gcaaaatctt agcatactcc tcaattaccc acataggatg aataatagca
|
||||||
|
gttctaccgt acaaccctaa cataaccatt cttaatttaa ctatttatat tatcctaact
|
||||||
|
actaccgcat tcctactact caacttaaac tccagcacca cgaccctact actatctcgc
|
||||||
|
acctgaaaca agctaacatg actaacaccc ttaattccat ccaccctcct ctccctagga
|
||||||
|
ggcctgcccc cgctaaccgg ctttttgccc aaatgggcca ttatcgaaga attcacaaaa
|
||||||
|
aacaatagcc tcatcatccc caccatcata gccaccatca ccctccttaa cctctacttc
|
||||||
|
tacctacgcc taatctactc cacctcaatc acactactcc ctatatctaa caacgtaaaa
|
||||||
|
ataaaatgac agtttgaaca tacaaaaccc accccattcc tccccacact catcaccctt
|
||||||
|
accacactac tcctacctat ctcccctttt atactaatag tcttatagaa atttaggtta
|
||||||
|
aatacagacc aagagccttc aaagccctca gtaagttgca atacttaatt tctgcaacag
|
||||||
|
ctaaggactg caaaacccca ctctgcatca actgaacgca aatcagccac tttaattaag
|
||||||
|
ctaagccctt actagaccaa tgggactcaa acccacaaac acttagttaa cagctaagca
|
||||||
|
ccctaatcaa ctggcttcaa tctacttctc ccgccgccgg gaaaaaaggc gggagaagcc
|
||||||
|
ccggcaggtt tgaagctgct tcttcgaatt tgcaattcaa tatgaaaatc acctcagagc
|
||||||
|
tggtaaaaag aggcttaacc cctgtcttta gatttacagt ccaatgcttc actcagccat
|
||||||
|
tttacctcac ccccactgat gttcgccgac cgttgactat tctctacaaa ccacaaagac
|
||||||
|
attggaacac tatacctact attcggcgca tgagctggag tcctaggcac agctctaagc
|
||||||
|
ctccttattc gagccgaact gggccagcca ggcaaccttc taggtaacga ccacatctac
|
||||||
|
aacgttatcg tcacagccca tgcatttgta ataatcttct tcatagtaat acccatcata
|
||||||
|
atcgggggct ttggcaactg actagttccc ttaataatcg gtgcccccga tatggcgttt
|
||||||
|
ccccgcataa acaatataag cttctgactc ttacctccct ctctcctact cctgctcgca
|
||||||
|
tctgctatag tggaagccgg cgcaggaaca ggttgaacag tctaccctcc cttagcaggg
|
||||||
|
aactactccc accctggagc ctccgtagac ctaaccatct tctccttaca cctagcaggt
|
||||||
|
gtctcctcta tcttaggggc catcaatttc atcacaacaa ttattaatat aaaaccccct
|
||||||
|
gccataaccc aataccaaac gccccttttc gtctgatccg tcctaatcac agcagtccta
|
||||||
|
cttctcctat ctctcccagt cctagctgct ggcatcacta tactactaac agaccgcaac
|
||||||
|
ctcaacacca ccttcttcga ccccgccgga ggaggagacc ccattctata ccaacaccta
|
||||||
|
ttctgatttt tcggccaccc tgaagtttat attctcatcc taccaggctt cggaataatc
|
||||||
|
tcccatattg taacttacta ctccggaaaa aaagaaccat ttggatacat aggtatggtc
|
||||||
|
tgagctatga tatcaattgg cttcctaggg tttatcgtgt gagcacacca tatatttaca
|
||||||
|
gtaggaatag acgtagacac acgagcatat ttcacctccg ctaccataat catcgctatc
|
||||||
|
cccaccggcg tcaaagtatt tagctgactc gccacactcc acggaagcaa tatgaaatga
|
||||||
|
tctgctgcag tgctctgagc cctaggattc atctttcttt tcaccgtagg tggcctgact
|
||||||
|
ggcattgtat tagcaaactc atcactagac atcgtactac acgacacgta ctacgttgta
|
||||||
|
gctcacttcc actatgtcct atcaatagga gctgtatttg ccatcatagg aggcttcatt
|
||||||
|
cactgatttc ccctattctc cggctacacc ctagaccaaa cttacgccaa aatccatttc
|
||||||
|
actatcatat tcatcggcgt aaatctaact ttcttcccac aacactttct cggcctatcc
|
||||||
|
ggaatgcccc gacgttactc ggactacccc gatgcataca ccacatgaaa tatcctatca
|
||||||
|
tctgtaggct cattcatttc tctaacagca gtaatattaa taattttcat gatttgagaa
|
||||||
|
gccttcgctt cgaagcgaaa agtcctaata gtagaagaac cctccataaa cctggagtga
|
||||||
|
ctatatggat gccccccacc ctaccacaca ttcgaagagc ccgtatacat aaaatctaga
|
||||||
|
caaaaaagga aggaatcgaa ccccccaaag ctggtttcaa gccaacccca tggcctccat
|
||||||
|
gactttttca aaaagatatt agaaaaacca tttcataact ttgtcaaagt taaattatag
|
||||||
|
gctaaatcct atatatctta atggcacatg cagcgcaagt aggtctacaa gacgctactt
|
||||||
|
cccctatcat agaagagctt atcatctttc atgatcacgc cctcataatc attttcctta
|
||||||
|
tctgcttcct agtcctgtat gcccttttcc taacactcac aacaaaacta actaatacta
|
||||||
|
gcatctcaga cgctcaggaa atagaaaccg tctgaactat cctgcccgcc atcatcctag
|
||||||
|
tcctcatcgc cctcccatcc ctacgcatcc tttacataac agacgaggtc aacgacccct
|
||||||
|
cctttaccat caaatcaatt ggccatcaat ggtactgaac ctacgagtac accgactacg
|
||||||
|
gcggactaat cttcaactcc tacatacttc ccccattatt cctagaacca ggcgacctgc
|
||||||
|
gactccttga cgttgacaat cgagtagtac tcccggttga agcccccatt cgtataataa
|
||||||
|
ttacatcaca agacgtctta cactcatgag ctgtccccac attaggctta aaaacagatg
|
||||||
|
caattcccgg acgtctaaac caaaccactt tcaccgctac acgaccgggg gtatactacg
|
||||||
|
gtcaatgctc tgaaatctgt ggagcaaacc acagtttcat gcccatcgtc ctagaattaa
|
||||||
|
ttcccctaaa aatctttgaa atagggcccg tatttaccct atagcacccc ctctaccccc
|
||||||
|
tctagagccc actgtaaagc taacttagca ttaacctttt aagttaaaga ttaagagaac
|
||||||
|
cagcacctct ttacagtgag atgccccaac taaatactac tgtatggccc accataatta
|
||||||
|
tccccatact ccttacacta ttcctcatca cccaactaaa aatattaaat acaaattacc
|
||||||
|
acttacctcc ctcaccaaag cccataaaaa taaaaaacta taacaaaccc tgagaaccaa
|
||||||
|
aatgaacgaa aatctgttcg cttcattcat tgcccccaca atcctaggcc tacccgccgc
|
||||||
|
agtactgatc attctatttc cccctctatt gatccccacc tccaaatatc tcatcaacaa
|
||||||
|
ccgactaatt accacccaac aatgactaat caaactaacc tcaaaacaaa tgatagccat
|
||||||
|
acacaacact aagggacgaa cctgatctct tatactagta tccttaatca tttttattac
|
||||||
|
cacaactaac ctcctcggac tcctgcctca ctcatttaca ccaaccaccc aactatctat
|
||||||
|
aaacctagcc atggccatcc ccttatgagc gggcgcagtg attataggct ttcgctctaa
|
||||||
|
gattaaaaat gccctagccc acttcttacc acaaggcaca cctacacccc ttatccctat
|
||||||
|
actagttatt atcgaaacca tcagcctact cattcaacca gtagccctgg ccgtacgcct
|
||||||
|
aaccgctaac attactgcag gtcacctact catgcaccta attggaaacg ccaccctagc
|
||||||
|
aatatcaacc attaaccttc cctctacact tatcatcttc acaattctaa ttctactgac
|
||||||
|
tatcctagaa atcgctgtcg ccttaatcca agcctacgtt ttcacacttc tagtaagcct
|
||||||
|
ctacctgcac gacaacacat aatgacccac caatcacatg cctatcatat agtaaaaccc
|
||||||
|
agcccatgac ccctaacagg ggccctctca gccctcctaa tgacctccgg cctagccatg
|
||||||
|
tgatttcact tccactccac aaccctcctc atactaggct tactaaccaa cacactaacc
|
||||||
|
atataccaat gatggcgcga tgtaacacga gaaagcacat accaaggcca ccacacacca
|
||||||
|
cctgtccaaa aaggccttcg atacgggata gtcctattta ttacctcaga agtttttttc
|
||||||
|
ttcgcaggat ttttctgagc cttttaccac tccagcctag cccctacccc ccaactagga
|
||||||
|
gggcactggc ccccaacagg catcaccccg ctaaatcccc tagaagtccc actcctaaac
|
||||||
|
acatccgtat tactcgcatc aggagtatca atcacctgag ctcaccatag tctaatagaa
|
||||||
|
aacaaccgaa accaaataat tcaagcactg cttattacaa ttttactggg tctctatttt
|
||||||
|
accctcctac aagcctcaga gtacttcgaa tctcccttca ccatttccga cggcatctac
|
||||||
|
ggctcaacat tttttgtagc cacaggcttc cacggacttc acgtcattat tggctcaact
|
||||||
|
ttcctcacta tctgcttcat ccgtcaacta atatttcact ttacatccaa acatcacttt
|
||||||
|
ggcttcgaag ccgccgcctg atactggcat tttgtagatg tggtttgact atttctgtat
|
||||||
|
gtctccatct attgatgagg gtcttactct tttagtataa atagtaccgt taacttccaa
|
||||||
|
ttaactagtt ttgacaacat tcaaaaaaga gtaataaact tcgccttaat tttaataatc
|
||||||
|
aacaccctcc tagccctact actaataatt attacatttt gactaccaca actcaacggc
|
||||||
|
tacatagaaa aatccacccc ttacgagtgc ggcttcgacc ctatatcccc cgcccgcgtc
|
||||||
|
cctttctcca taaaattctt cttagtagct attaccttct tattatttga cctagaaatt
|
||||||
|
gccctccttt tacccttacc atgagcccta caaacaacta atctaccact aatagttacg
|
||||||
|
tcatccctct tattaatcat catcctagcc ctaagtctgg cctatgaatg actacaaaaa
|
||||||
|
ggattagact gagccgaatt ggtatatagt ttaaacaaaa cgaatgattt cgactcatta
|
||||||
|
aattatgata atcatattta ccaaatgccc ctcatttaca taaatattat actagcattt
|
||||||
|
accatctcac ttctgggaat actagtgtat cgctcacacc tcatatcctc cctactatgc
|
||||||
|
ctagaaggaa taatactatc gctgttcatt atagctactc tcataaccct caacacccac
|
||||||
|
tccctcttag ccaatattgt gcctattgcc atactagttt ttgccgcctg cgaagcagcg
|
||||||
|
gtaggcctag ccctactagt ctcaatctcc aacacatatg gcctagacta cgtacataac
|
||||||
|
ctaagcctac tccaatgcta aaactaatcg tcccaacaat tatattacta ccactgacat
|
||||||
|
gactctccaa aaaacacata atttgaatca acacaaccac ccacagccta attattagca
|
||||||
|
tcatccccct actatttttt aaccaaatca acaacaacct atttagctgc tccccaacct
|
||||||
|
tttcctccga ccccctaaca acccccctcc taatactaac tacctgactc ctacccctca
|
||||||
|
caatcatggc aagccaacgc cacttatcca gtgaaccact atcacgaaaa aaactctacc
|
||||||
|
tctctatact aatctcccta caaatctcct taattataac attcacagcc acagaactaa
|
||||||
|
tcatatttta tatcttcttc gaaaccacac ttatccccac cttggctatc atcacccgat
|
||||||
|
gaggcaacca gccagaacgc ctgaacgcag gcacatactt cctattctac accctagtag
|
||||||
|
gctcccttcc cctactcatc gcactaattt acactcacaa caccctaggc tcactaaaca
|
||||||
|
ttctactact cactctcact gcccaagaac tatcaaactc ctgagccaac aacttaatat
|
||||||
|
gactagctta cacaatagct tttatagtaa agatacccct ttacggactc cacttatgac
|
||||||
|
tccctaaagc ccatgtcgaa gcccccatcg ctgggtcaat agtacttgcc gctgtactct
|
||||||
|
taaaactagg cggctatggt ataatacgcc tcacactcat tctcaacccc ctgacaaaac
|
||||||
|
atatagccta ccccttcctt gtactatccc tatggggcat aattataaca agctccatct
|
||||||
|
gcctgcgaca aacagaccta aaatcgctca ttgcatattc ttcaatcagc cacatagccc
|
||||||
|
tcgtagtaac agccattctc atccaaaccc cctgaagctt caccggcgca gtcattctca
|
||||||
|
taatcgccca cggacttaca tcctcattac tattctgcct agcaaactca aactacgaac
|
||||||
|
gcacccacag tcgcatcata atcctctctc aaggacttca aactctactc ccactaatag
|
||||||
|
ctttttgatg acttctagca agcctcgcta acctcgcctt accccccact attaacctac
|
||||||
|
tgggagaact ctctgtgcta gtaaccacat tctcctgatc aaatatcact ctcctactta
|
||||||
|
cagggctcaa catactagtc acagccctat actccctcta catatttacc acaacacaat
|
||||||
|
ggggctcact cacccaccac attaacaaca taaaaccctc attcacacga gaaaacaccc
|
||||||
|
tcatattcat acacctatcc cccattctcc tcctatccct caaccccgac atcattaccg
|
||||||
|
ggttttcctc ttgtaaatat agtttaacca aaacatcaga ttgtgaatct gacaacagag
|
||||||
|
gctcacgacc ccttatttac cgagaaagct cacaagaact gctaactcat gcccccatgt
|
||||||
|
ctaacaacat ggctttctca acttttaaag gataacagct atccattggt cttaggcccc
|
||||||
|
aaaaattttg gtgcaactcc aaataaaagt aataaccatg cacaccacta taaccaccct
|
||||||
|
gaccctgact tccctaattc cccccatcct taccaccctc attaacccta acaaaaaaaa
|
||||||
|
ctcatacccc cattatgtaa aatccattgt cgcatccacc tttattatta gtctcttccc
|
||||||
|
cacaacaata ttcatgtgcc tagaccaaga agttattatc tcgaactgac actgagccac
|
||||||
|
aacccaaaca acccagctct ccctaagctt caaactagac tacttctcca taatattcat
|
||||||
|
ccctgtagca ttgttcgtta catggtccat catagaattc tcactgtgat atataaactc
|
||||||
|
agacccaaac attaatcagt tcttcaaata tctactcatt ttcctaatta ccatactaat
|
||||||
|
cttagttacc gctaacaacc tattccaact gttcatcggc tgagagggcg taggaattat
|
||||||
|
atccttcttg ctcatcagtt gatgatacgc ccgagcagat gccaacacag cagccattca
|
||||||
|
agcaatccta tacaaccgca tcggcgatat cggtttcatc ctcgccttag catgatttat
|
||||||
|
cctacactcc aactcatgag acccacaaca aatagccctt ctaaacgcta atccaagcct
|
||||||
|
caccccacta ctaggcctcc tcctagcagc agcaggcaaa tcagcccaat taggtctcca
|
||||||
|
cccctgactc ccctcagcca tagaaggccc caccccagtc tcagccctac tccactcaag
|
||||||
|
cactatagtc gtagcaggag tcttcttact catccgcttc caccccctag cagaaaatag
|
||||||
|
cccactaatc caaactctaa cactatgctt aggcgctatc accactctat tcgcagcagt
|
||||||
|
ctgcgccctt acacaaaatg acatcaaaaa aatcgtagcc ttctccactt caagtcaact
|
||||||
|
agggctcata gtagttacaa tcggcatcaa ccaaccacac ctagcattcc tgcacatctg
|
||||||
|
tacccacgcc ttcttcaaag ccatactatt tatatgctcc gggtccatca tccacaacct
|
||||||
|
taacaatgaa caagatattc gaaaaatagg aggactactc aaaaccatac ctctcacttc
|
||||||
|
aacctccctc accattggca gcctagcatt agcaggaata cctttcctca caggtttcta
|
||||||
|
ctccaaagac cacatcatcg aaaccgcaaa catatcatac acaaacgcct gagccctatc
|
||||||
|
tattactctc atcgctacct ccctgacaag cgcctatagc actcgaataa ttcttctcac
|
||||||
|
cctaacaggt caacctcgct tccccaccct cactaacatt aacgaaaata accctaccct
|
||||||
|
actaaacccc attaaacgcc tagcagccgg aagcctattc gcaggatttc tcattactaa
|
||||||
|
caacatttcc cccgcatccc ccttccaaac aacaatcccc ctctacctaa aactcgcagc
|
||||||
|
cctcgctgtc actttcctag gacttctaac agccctagac ctcaactacc taaccaacaa
|
||||||
|
acttaaaata aaaaccccac tatacacatt ttatttctcc aacatactcg ggttctaccc
|
||||||
|
tagcatcaca caccgcacaa tcccctatct aggccttctt acgagccaaa acctgcccct
|
||||||
|
actcctccta gacctaacct gactagaaaa gctattacct aaaacaattt cacagcacca
|
||||||
|
aatctccgcc tccatcacca cctcaaccca aaaaggcata attaaacttt acttcctctc
|
||||||
|
tttcttcttc ccactcatcc taaccctact cctaatcata taacctattc ccccgagcaa
|
||||||
|
tctcaattac aacatataca ccaacaaaca atgttcaacc agtaactact actaatcaac
|
||||||
|
gcccataatc atacaaagcc cccgcaccaa taggatcctc ccgaatcaac cctgacccct
|
||||||
|
ctccttcata gattattcag cttcctacac tattaaagtt taccacaacc accaccccat
|
||||||
|
catactcttt cacccacagc accaatccta cctccatcgc taaccccact aaaacactca
|
||||||
|
ccaagacctc aacccctgac ccccatgcct caggatactc ctcaatagcc atcgctgtag
|
||||||
|
tatatccaaa gacaaccatc attcccccta aataaattaa aaaaactatt aaacccatat
|
||||||
|
aacctccccc aaaattcaga ataataacac acccaaccac accgctaaca atcaatacta
|
||||||
|
aacccccata aataggagaa ggcttagaag aaaaccccac aaaccccatt actaaaccca
|
||||||
|
cactcaacag aaacaaagca tacatcatta ttctcgcacg gactacaacc acgaccaatg
|
||||||
|
atatgaaaaa ccatcgttgt atttcaacta caagaacacc aatgacccca atacgcaaaa
|
||||||
|
ttaaccccct aataaaatta attaaccact cattcatcga cctccccacc ccatccaaca
|
||||||
|
tctccgcatg atgaaacttc ggctcactcc ttggcgcctg cctgatcctc caaatcacca
|
||||||
|
caggactatt cctagccatg cactactcac cagacgcctc gaccgccttt tcatcaatcg
|
||||||
|
cccacatcac tcgagacgta aattatggct gaatcatccg ctaccttcac gccaatggcg
|
||||||
|
cctcaatatt ctttatctgc ctcttcctac acatcggacg aggcctatat tacggatcat
|
||||||
|
ttctctactc aaaaacctga aacatcggca ttatcctcct gcttgcaact atagcaacag
|
||||||
|
ccttcatagg ctatgtcctc ccatgaggcc aaatatcatt ctgaggggcc acagtaatta
|
||||||
|
caaacctact atccgccatc ccatacattg ggacagacct ggttcagtga atctgaggag
|
||||||
|
gctactcagt agacagtccc accctcacac gattctttac ctttcacttt atcttaccct
|
||||||
|
tcattattgc agccctagca gcactccacc tcctattctt gcacgaaaca ggatcaaaca
|
||||||
|
accccctagg aatcacctcc cattccgata aaatcacctt ccacccttac tacacaatca
|
||||||
|
aagacgccct cggcttattt ctcttccttc tctccttaat gacattaaca ctactctcac
|
||||||
|
cagacctcct aggcgaccca gacaattata ccctagccaa ccccttaaac acccctcccc
|
||||||
|
acatcaagcc cgaatgatat ttcctattcg cctacacaat tctccgatcc gtccctaaca
|
||||||
|
aactaggagg cgtccttgcc ctactactat ccatcctcat cctggcaata atccccatcc
|
||||||
|
ttcatgtatc caaacaacaa agcataatat ttcgcccact aagccaatca ctttattgac
|
||||||
|
tcctagccgc agacctcctc attctaacct gaatcggagg acaaccagta agctaccctt
|
||||||
|
ttatcatcat tggacaagta gcatccgtac tatacttcac aacaatccta atcctaatac
|
||||||
|
caaccatctc cctaattgaa aacaaaatac tcaaatgggc ctgtccttgt agtataaact
|
||||||
|
aatacaccag tcttgtaaac cggagatgaa aacctttttc caaggacaaa tcagagaaaa
|
||||||
|
agtctttaac tccaccatta gcacccaaag ctaagattct aatttaaact attctctgtt
|
||||||
|
ctttcatggg ggagcagatt tgggtaccac ccaagtattg actcacccat cagcaaccgc
|
||||||
|
tatgtatttc gtacattact gccagccacc atgaatattg tacagtacca taattacttg
|
||||||
|
actacctgca gtacataaaa acctaatcca catcaacccc ccccccccat gcttacaagc
|
||||||
|
aagcacagca atcaaccttc aactgtcata catcaactac aactccaaag acgcccttac
|
||||||
|
acccactagg atatcaacaa acctacccac ccttgacagt acatagcaca taaagtcatt
|
||||||
|
taccgtacat agcacattac agtcaaatcc cttctcgccc ccatggatga cccccctcag
|
||||||
|
ataggggtcc cttgatcacc atcctccgtg aaatcaatat cccgcacaag agtgctactc
|
||||||
|
tcctcgctcc gggcccataa cacttggggg tagctaaagt gaactgtatc cgacatctgg
|
||||||
|
ttcctacttc agggccataa agcctaaata gcccacacgt tccccttaaa taagacatca
|
||||||
|
cgatg
|
||||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,277 @@
|
|||||||
|
gatcacaggt ctatcaccct attaaccact cacgggagct ctccatgcat ttggtatttt
|
||||||
|
cgtctggggg gtatgcacgc gatagcattg cgagacgctg gagccggagc accctatgtc
|
||||||
|
gcagtatctg tctttgattc ctgcctcatc ctattattta tcgcacctac gttcaatatt
|
||||||
|
acaggcgaac atacttacta aagtgtgtta attaattaat gcttgtagga cataataata
|
||||||
|
acaattgaat gtctgcacag ccactttcca cacagacatc ataacaaaaa atttccacca
|
||||||
|
aaccccccct cccccgcttc tggccacagc acttaaacac atctctgcca aaccccaaaa
|
||||||
|
acaaagaacc ctaacaccag cctaaccaga tttcaaattt tatcttttgg cggtatgcac
|
||||||
|
ttttaacagt caccccccaa ctaacacatt attttcccct cccactccca tactactaat
|
||||||
|
ctcatcaata caacccccgc ccatcctacc cagcacacac acaccgctgc taaccccata
|
||||||
|
ccccgaacca accaaacccc aaagacaccc cccacagttt atgtagctta cctcctcaaa
|
||||||
|
gcaatacact gaaaatgttt agacgggctc acatcacccc ataaacaaat aggtttggtc
|
||||||
|
ctagcctttc tattagctct tagtaagatt acacatgcaa gcatccccgt tccagtgagt
|
||||||
|
tcaccctcta aatcaccacg atcaaaagga acaagcatca agcacgcagc aatgcagctc
|
||||||
|
aaaacgctta gcctagccac acccccacgg gaaacagcag tgattaacct ttagcaataa
|
||||||
|
acgaaagttt aactaagcta tactaacccc agggttggtc aatttcgtgc cagccaccgc
|
||||||
|
ggtcacacga ttaacccaag tcaatagaag ccggcgtaaa gagtgtttta gatcaccccc
|
||||||
|
tccccaataa agctaaaact cacctgagtt gtaaaaaact ccagttgaca caaaatagac
|
||||||
|
tacgaaagtg gctttaacat atctgaacac acaatagcta agacccaaac tgggattaga
|
||||||
|
taccccacta tgcttagccc taaacctcaa cagttaaatc aacaaaactg ctcgccagaa
|
||||||
|
cactacgagc cacagcttaa aactcaaagg acctggcggt gcttcatatc cctctagagg
|
||||||
|
agcctgttct gtaatcgata aaccccgatc aacctcacca cctcttgctc agcctatata
|
||||||
|
ccgccatctt cagcaaaccc tgatgaaggc tacaaagtaa gcgcaagtac ccacgtaaag
|
||||||
|
acgttaggtc aaggtgtagc ccatgaggtg gcaagaaatg ggctacattt tctaccccag
|
||||||
|
aaaactacga tagcccttat gaaacttaag ggtcgaaggt ggatttagca gtaaactaag
|
||||||
|
agtagagtgc ttagttgaac agggccctga agcgcgtaca caccgcccgt caccctcctc
|
||||||
|
aagtatactt caaaggacat ttaactaaaa cccctacgca tttatataga ggagacaagt
|
||||||
|
cgtaacatgg taagtgtact ggaaagtgca cttggacgaa ccagagtgta gcttaacaca
|
||||||
|
aagcacccaa cttacactta ggagatttca acttaacttg accgctctga gctaaaccta
|
||||||
|
gccccaaacc cactccacct tactaccaga caaccttagc caaaccattt acccaaataa
|
||||||
|
agtataggcg atagaaattg aaacctggcg caatagatat agtaccgcaa gggaaagatg
|
||||||
|
aaaaattata accaagcata atatagcaag gactaacccc tataccttct gcataatgaa
|
||||||
|
ttaactagaa ataactttgc aaggagagcc aaagctaaga cccccgaaac cagacgagct
|
||||||
|
acctaagaac agctaaaaga gcacacccgt ctatgtagca aaatagtggg aagatttata
|
||||||
|
ggtagaggcg acaaacctac cgagcctggt gatagctggt tgtccaagat agaatcttag
|
||||||
|
ttcaacttta aatttgccca cagaaccctc taaatcccct tgtaaattta actgttagtc
|
||||||
|
caaagaggaa cagctctttg gacactagga aaaaaccttg tagagagagt aaaaaattta
|
||||||
|
acacccatag taggcctaaa agcagccacc aattaagaaa gcgttcaagc tcaacaccca
|
||||||
|
ctacctaaaa aatcccaaac atataactga actcctcaca cccaattgga ccaatctatc
|
||||||
|
accctataga agaactaatg ttagtataag taacatgaaa acattctcct ccgcataagc
|
||||||
|
ctgcgtcaga ttaaaacact gaactgacaa ttaacagccc aatatctaca atcaaccaac
|
||||||
|
aagtcattat taccctcact gtcaacccaa cacaggcatg ctcataagga aaggttaaaa
|
||||||
|
aaagtaaaag gaactcggca aatcttaccc cgcctgttta ccaaaaacat cacctctagc
|
||||||
|
atcaccagta ttagaggcac cgcctgccca gtgacacatg tttaacggcc gcggtaccct
|
||||||
|
aaccgtgcaa aggtagcata atcacttgtt ccttaaatag ggacctgtat gaatggctcc
|
||||||
|
acgagggttc agctgtctct tacttttaac cagtgaaatt gacctgcccg tgaagaggcg
|
||||||
|
ggcataacac agcaagacga gaagacccta tggagcttta atttattaat gcaaacagta
|
||||||
|
cctaacaaac ccacaggtcc taaactacca aacctgcatt aaaaatttcg gttggggcga
|
||||||
|
cctcggagca gaacccaacc tccgagcagt acatgctaag acttcaccag tcaaagcgaa
|
||||||
|
ctactatact caattgatcc aataacttga ccaacggaac aagttaccct agggataaca
|
||||||
|
gcgcaatcct attctagagt ccatatcaac aatagggttt acgacctcga tgttggatca
|
||||||
|
ggacatcccg atggtgcagc cgctattaaa ggttcgtttg ttcaacgatt aaagtcctac
|
||||||
|
gtgatctgag ttcagaccgg agtaatccag gtcggtttct atctacnttc aaattcctcc
|
||||||
|
ctgtacgaaa ggacaagaga aataaggcct acttcacaaa gcgccttccc ccgtaaatga
|
||||||
|
tatcatctca acttagtatt atacccacac ccacccaaga acagggtttg ttaagatggc
|
||||||
|
agagcccggt aatcgcataa aacttaaaac tttacagtca gaggttcaat tcctcttctt
|
||||||
|
aacaacatac ccatggccaa cctcctactc ctcattgtac ccattctaat cgcaatggca
|
||||||
|
ttcctaatgc ttaccgaacg aaaaattcta ggctatatac aactacgcaa aggccccaac
|
||||||
|
gttgtaggcc cctacgggct actacaaccc ttcgctgacg ccataaaact cttcaccaaa
|
||||||
|
gagcccctaa aacccgccac atctaccatc accctctaca tcaccgcccc gaccttagct
|
||||||
|
ctcaccatcg ctcttctact atgaaccccc ctccccatac ccaaccccct ggtcaacctc
|
||||||
|
aacctaggcc tcctatttat tctagccacc tctagcctag ccgtttactc aatcctctga
|
||||||
|
tcagggtgag catcaaactc aaactacgcc ctgatcggcg cactgcgagc agtagcccaa
|
||||||
|
acaatctcat atgaagtcac cctagccatc attctactat caacattact aataagtggc
|
||||||
|
tcctttaacc tctccaccct tatcacaaca caagaacacc tctgattact cctgccatca
|
||||||
|
tgacccttgg ccataatatg atttatctcc acactagcag agaccaaccg aacccccttc
|
||||||
|
gaccttgccg aaggggagtc cgaactagtc tcaggcttca acatcgaata cgccgcaggc
|
||||||
|
cccttcgccc tattcttcat agccgaatac acaaacatta ttataataaa caccctcacc
|
||||||
|
actacaatct tcctaggaac aacatatgac gcactctccc ctgaactcta cacaacatat
|
||||||
|
tttgtcacca agaccctact tctaacctcc ctgttcttat gaattcgaac agcatacccc
|
||||||
|
cgattccgct acgaccaact catacacctc ctatgaaaaa acttcctacc actcacccta
|
||||||
|
gcattactta tatgatatgt ctccataccc attacaatct ccagcattcc ccctcaaacc
|
||||||
|
taagaaatat gtctgataaa agagttactt tgatagagta aataatagga gcttaaaccc
|
||||||
|
ccttatttct aggactatga gaatcgaacc catccctgag aatccaaaat tctccgtgcc
|
||||||
|
acctatcaca ccccatccta aagtaaggtc agctaaataa gctatcgggc ccataccccg
|
||||||
|
aaaatgttgg ttataccctt cccgtactaa ttaatcccct ggcccaaccc gtcatctact
|
||||||
|
ctaccatctt tgcaggcaca ctcatcacag cgctaagctc gcactgattt tttacctgag
|
||||||
|
taggcctaga aataaacatg ctagctttta ttccagttct aaccaaaaaa ataaaccctc
|
||||||
|
gttccacaga agctgccatc aagtatttcc tcacgcaagc aaccgcatcc ataatccttc
|
||||||
|
taatagctat cctcttcaac aatatactct ccggacaatg aaccataacc aatactacca
|
||||||
|
atcaatactc atcattaata atcataatag ctatagcaat aaaactagga atagccccct
|
||||||
|
ttcacttctg agtcccagag gttacccaag gcacccctct gacatccggc ctgcttcttc
|
||||||
|
tcacatgaca aaaactagcc cccatctcaa tcatatacca aatctctccc tcactaaacg
|
||||||
|
taagccttct cctcactctc tcaatcttat ccatcatagc aggcagttga ggtggattaa
|
||||||
|
accaaaccca gctacgcaaa atcttagcat actcctcaat tacccacata ggatgaataa
|
||||||
|
tagcagttct accgtacaac cctaacataa ccattcttaa tttaactatt tatattatcc
|
||||||
|
taactactac cgcattccta ctactcaact taaactccag caccacgacc ctactactat
|
||||||
|
ctcgcacctg aaacaagcta acatgactaa cacccttaat tccatccacc ctcctctccc
|
||||||
|
taggaggcct gcccccgcta accggctttt tgcccaaatg ggccattatc gaagaattca
|
||||||
|
caaaaaacaa tagcctcatc atccccacca tcatagccac catcaccctc cttaacctct
|
||||||
|
acttctacct acgcctaatc tactccacct caatcacact actccccata tctaacaacg
|
||||||
|
taaaaataaa atgacagttt gaacatacaa aacccacccc attcctcccc acactcatcg
|
||||||
|
cccttaccac gctactccta cctatctccc cttttatact aataatctta tagaaattta
|
||||||
|
ggttaaatac agaccaagag ccttcaaagc cctcagtaag ttgcaatact taatttctgt
|
||||||
|
aacagctaag gactgcaaaa ccccactctg catcaactga acgcaaatca gccactttaa
|
||||||
|
ttaagctaag cccttactag accaatggga cttaaaccca caaacactta gttaacagct
|
||||||
|
aagcacccta atcaactggc ttcaatctac ttctcccgcc gccgggaaaa aaggcgggag
|
||||||
|
aagccccggc aggtttgaag ctgcttcttc gaatttgcaa ttcaatatga aaatcacctc
|
||||||
|
ggagctggta aaaagaggcc taacccctgt ctttagattt acagtccaat gcttcactca
|
||||||
|
gccattttac ctcaccccca ctgatgttcg ccgaccgttg actattctct acaaaccaca
|
||||||
|
aagacattgg aacactatac ctattattcg gcgcatgagc tggagtccta ggcacagctc
|
||||||
|
taagcctcct tattcgagcc gagctgggcc agccaggcaa ccttctaggt aacgaccaca
|
||||||
|
tctacaacgt tatcgtcaca gcccatgcat ttgtaataat cttcttcata gtaataccca
|
||||||
|
tcataatcgg aggctttggc aactgactag ttcccctaat aatcggtgcc cccgatatgg
|
||||||
|
cgtttccccg cataaacaac ataagcttct gactcttacc tccctctctc ctactcctgc
|
||||||
|
tcgcatctgc tatagtggag gccggagcag gaacaggttg aacagtctac cctcccttag
|
||||||
|
cagggaacta ctcccaccct ggagcctccg tagacctaac catcttctcc ttacacctag
|
||||||
|
caggtgtctc ctctatctta ggggccatca atttcatcac aacaattatc aatataaaac
|
||||||
|
cccctgccat aacccaatac caaacgcccc tcttcgtctg atccgtccta atcacagcag
|
||||||
|
tcctacttct cctatctctc ccagtcctag ctgctggcat cactatacta ctaacagacc
|
||||||
|
gcaacctcaa caccaccttc ttcgaccccg ccggaggagg agaccccatt ctataccaac
|
||||||
|
acctattctg atttttcggt caccctgaag tttatattct tatcctacca ggcttcggaa
|
||||||
|
taatctccca tattgtaact tactactccg gaaaaaaaga accatttgga tacataggta
|
||||||
|
tggtctgagc tatgatatca attggcttcc tagggtttat cgtgtgagca caccatatat
|
||||||
|
ttacagtagg aatagacgta gacacacgag catatttcac ctccgctacc ataatcatcg
|
||||||
|
ctatccccac cggcgtcaaa gtatttagct gactcgccac actccacgga agcaatatga
|
||||||
|
aatgatctgc tgcagtgctc tgagccctag gattcatctt tcttttcacc gtaggtggcc
|
||||||
|
tgactggcat tgtattagca aactcatcac tagacatcgt actacacgac acgtactacg
|
||||||
|
ttgtagccca cttccactat gtcctatcaa taggagctgt atttgccatc ataggaggct
|
||||||
|
tcattcactg atttccccta ttctcaggct acaccctaga ccaaacctac gccaaaatcc
|
||||||
|
atttcactat catattcatc ggcgtaaatc taactttctt cccacaacac tttctcggcc
|
||||||
|
tatccggaat gccccgacgt tactcggact accccgatgc atacaccaca tgaaacatcc
|
||||||
|
tatcatctgt aggctcattc atttctctaa cagcagtaat attaataatt ttcatgattt
|
||||||
|
gagaagcctt cgcttcgaag cgaaaagtcc taatagtaga agaaccctcc ataaacctgg
|
||||||
|
agtgactata tggatgcccc ccaccctacc acacattcga agaacccgta tacataaaat
|
||||||
|
ctagacaaaa aaggaaggaa tcgaaccccc caaagctggt ttcaagccaa ccccatggcc
|
||||||
|
tccatgactt tttcaaaaag gtattagaaa aaccatttca taactttgtc aaagttaaat
|
||||||
|
tataggctaa atcctatata tcttaatggc acatgcagcg caagtaggtc tacaagacgc
|
||||||
|
tacttcccct atcatagaag agcttatcac ctttcatgat cacgccctca taatcatttt
|
||||||
|
ccttatctgc ttcctagtcc tgtatgccct tttcctaaca ctcacaacaa aactaactaa
|
||||||
|
tactaacatc tcagacgctc aggaaataga aaccgtctga actatcctgc ccgccatcat
|
||||||
|
cctagtcctc atcgccctcc catccctacg catcctttac ataacagacg aggtcaacga
|
||||||
|
tccctccctt accatcaaat caattggcca ccaatggtac tgaacctacg agtacaccga
|
||||||
|
ctacggcgga ctaatcttca actcctacat acttccccca ttattcctag aaccaggcga
|
||||||
|
cctgcgactc cttgacgttg acaatcgagt agtactcccg attgaagccc ccattcgtat
|
||||||
|
aataattaca tcacaagacg tcttgcactc atgagctgtc cccacattag gcttaaaaac
|
||||||
|
agatgcaatt cccggacgtc taaaccaaac cactttcacc gctacacgac cgggggtata
|
||||||
|
ctacggtcaa tgctctgaaa tctgtggagc aaaccacagt ttcatgccca tcgtcctaga
|
||||||
|
attaattccc ctaaaaatct ttgaaatagg gcccgtattt accctatagc accccctcta
|
||||||
|
ccccctctag agcccactgt aaagctaact tagcattaac cttttaagtt aaagattaag
|
||||||
|
agaaccaaca cctctttaca gtgaaatgcc ccaactaaat actaccgtat ggcccaccat
|
||||||
|
aattaccccc atactcctta cactattcct catcacccaa ctaaaaatat taaacacaaa
|
||||||
|
ctaccaccta cctccctcac caaagcccat aaaaataaaa aattataaca aaccctgaga
|
||||||
|
accaaaatga acgaaaatct gttcgcttca ttcattgccc ccacaatcct aggcctaccc
|
||||||
|
gccgcagtac tgatcattct atttccccct ctattgatcc ccacctccaa atatctcatc
|
||||||
|
aacaaccgac taatcaccac ccaacaatga ctaatcaaac taacctcaaa acaaatgata
|
||||||
|
accatacaca acactaaagg acgaacctga tctcttatac tagtatcctt aatcattttt
|
||||||
|
attgccacaa ctaacctcct cggactcctg cctcactcat ttacaccaac cacccaacta
|
||||||
|
tctataaacc tagccatggc catcccctta tgagcgggca cagtgattat aggctttcgc
|
||||||
|
tctaagatta aaaatgccct agcccacttc ttaccacaag gcacacctac accccttatc
|
||||||
|
cccatactag ttattatcga aaccatcagc ctactcattc aaccaatagc cctggccgta
|
||||||
|
cgcctaaccg ctaacattac tgcaggccac ctactcatgc acctaattgg aagcgccacc
|
||||||
|
ctagcaatat caaccattaa ccttccctct acacttatca tcttcacaat tctaattcta
|
||||||
|
ctgactatcc tagaaatcgc tgtcgcctta atccaagcct acgttttcac acttctagta
|
||||||
|
agcctctacc tgcacgacaa cacataatga cccaccaatc acatgcctat catatagtaa
|
||||||
|
aacccagccc atgaccccta acaggggccc tctcagccct cctaatgacc tccggcctag
|
||||||
|
ccatgtgatt tcacttccac tccataacgc tcctcatact aggcctacta accaacacac
|
||||||
|
taaccatata ccaatgatgg cgcgatgtaa cacgagaaag cacataccaa ggccaccaca
|
||||||
|
caccacctgt ccaaaaaggc cttcgatacg ggataatcct atttattacc tcagaagttt
|
||||||
|
ttttcttcgc aggatttttc tgagcctttt accactccag cctagcccct accccccaat
|
||||||
|
taggagggca ctggccccca acaggcatca ccccgctaaa tcccctagaa gtcccactcc
|
||||||
|
taaacacatc cgtattactc gcatcaggag tatcaatcac ctgagctcac catagtctaa
|
||||||
|
tagaaaacaa ccgaaaccaa ataattcaag cactgcttat tacaatttta ctgggtctct
|
||||||
|
attttaccct cctacaagcc tcagagtact tcgagtctcc cttcaccatt tccgacggca
|
||||||
|
tctacggctc aacatttttt gtagccacag gcttccacgg acttcacgtc attattggct
|
||||||
|
caactttcct cactatctgc ttcatccgcc aactaatatt tcactttaca tccaaacatc
|
||||||
|
actttggctt cgaagccgcc gcctgatact ggcattttgt agatgtggtt tgactatttc
|
||||||
|
tgtatgtctc catctattga tgagggtctt actcttttag tataaatagt accgttaact
|
||||||
|
tccaattaac tagttttgac aacattcaaa aaagagtaat aaacttcgcc ttaattttaa
|
||||||
|
taatcaacac cctcctagcc ttactactaa taattattac attttgacta ccacaactca
|
||||||
|
acggctacat agaaaaatcc accccttacg agtgcggctt cgaccctata tcccccgccc
|
||||||
|
gcgtcccttt ctccataaaa ttcttcttag tagctattac cttcttatta tttgatctag
|
||||||
|
aaattgccct ccttttaccc ctaccatgag ccctacaaac aactaacctg ccactaatag
|
||||||
|
ttatgtcatc cctcttatta atcatcatcc tagccctaag tctggcctat gagtgactac
|
||||||
|
aaaaaggatt agactgaacc gaattggtat atagtttaaa caaaacgaat gatttcgact
|
||||||
|
cattaaatta tgataatcat atttaccaaa tgcccctcat ttacataaat attatactag
|
||||||
|
catttaccat ctcacttcta ggaatactag tatatcgctc acacctcata tcctccctac
|
||||||
|
tatgcctaga aggaataata ctatcgctgt tcattatagc tactctcata accctcaaca
|
||||||
|
cccactccct cttagccaat attgtgccta ttgccatact agtctttgcc gcctgcgaag
|
||||||
|
cagcggtggg cctagcccta ctagtctcaa tctccaacac atatggccta gactacgtac
|
||||||
|
ataacctaaa cctactccaa tgctaaaact aatcgtccca acaattatat tactaccact
|
||||||
|
gacatgactt tccaaaaaac acataatttg aatcaacaca accacccaca gcctaattat
|
||||||
|
tagcatcatc cctctactat tttttaacca aatcaacaac aacctattta gctgttcccc
|
||||||
|
aaccttttcc tccgaccccc taacaacccc cctcctaata ctaactacct gactcctacc
|
||||||
|
cctcacaatc atggcaagcc aacgccactt atccagtgaa ccactatcac gaaaaaaact
|
||||||
|
ctacctctct atactaatct ccctacaaat ctccttaatt ataacattca cagccacaga
|
||||||
|
actaatcata ttttatatct tcttcgaaac cacacttatc cccaccttgg ctatcatcac
|
||||||
|
ccgatgaggc aaccagccag aacgcctgaa cgcaggcaca tacttcctat tctacaccct
|
||||||
|
agtaggctcc cttcccctac tcatcgcact aatttacact cacaacaccc taggctcact
|
||||||
|
aaacattcta ctactcactc tcactgccca agaactatca aactcctgag ccaacaactt
|
||||||
|
aatatgacta gcttacacaa tagcttttat agtaaagata cctctttacg gactccactt
|
||||||
|
atgactccct aaagcccatg tcgaagcccc catcgctggg tcaatagtac ttgccgcagt
|
||||||
|
actcttaaaa ctaggcggct atggtataat acgcctcaca ctcattctca accccctgac
|
||||||
|
aaaacacata gcctacccct tccttgtact atccctatga ggcataatta taacaagctc
|
||||||
|
catctgccta cgacaaacag acctaaaatc gctcattgca tactcttcaa tcagccacat
|
||||||
|
agccctcgta gtaacagcca ttctcatcca aaccccctga agcttcaccg gcgcagtcat
|
||||||
|
tctcataatc gcccacgggc ttacatcctc attactattc tgcctagcaa actcaaacta
|
||||||
|
cgaacgcact cacagtcgca tcataatcct ctctcaagga cttcaaactc tactcccact
|
||||||
|
aatagctttt tgatgacttc tagcaagcct cgctaacctc gccttacccc ccactattaa
|
||||||
|
cctactggga gaactctctg tgctagtaac cacgttctcc tgatcaaata tcactctcct
|
||||||
|
acttacagga ctcaacatac tagtcacagc cctatactcc ctctacatat ttaccacaac
|
||||||
|
acaatggggc tcactcaccc accacattaa caacataaaa ccctcattca cacgagaaaa
|
||||||
|
caccctcatg ttcatacacc tatcccccat tctcctccta tccctcaacc ccgacatcat
|
||||||
|
taccgggttt tcctcttgta aatatagttt aaccaaaaca tcagattgtg aatctgacaa
|
||||||
|
cagaggctta cgacccctta tttaccgaga aagctcacaa gaactgctaa ctcatgcccc
|
||||||
|
catgtctaac aacatggctt tctcaacttt taaaggataa cagctatcca ttggtcttag
|
||||||
|
gccccaaaaa ttttggtgca actccaaata aaagtaataa ccatgcacac tactataacc
|
||||||
|
accctaaccc tgacttccct aattcccccc atccttacca ccctcgttaa ccctaacaaa
|
||||||
|
aaaaactcat acccccatta tgtaaaatcc attgtcgcat ccacctttat tatcagtctc
|
||||||
|
ttccccacaa caatattcat gtgcctagac caagaagtta ttatctcgaa ctgacactga
|
||||||
|
gccacaaccc aaacaaccca gctctcccta agcttcaaac tagactactt ctccataata
|
||||||
|
ttcatccctg tagcattgtt cgttacatgg tccatcatag aattctcact gtgatatata
|
||||||
|
aactcagacc caaacattaa tcagttcttc aaatatctac tcatcttcct aattaccata
|
||||||
|
ctaatcttag ttaccgctaa caacctattc caactgttca tcggctgaga gggcgtagga
|
||||||
|
attatatcct tcttgctcat cagttgatga tacgcccgag cagatgccaa cacagcagcc
|
||||||
|
attcaagcaa tcctatacaa ccgtatcggc gatatcggtt tcatcctcgc cttagcatga
|
||||||
|
tttatcctac actccaactc atgagaccca caacaaatag cccttctaaa cgctaatcca
|
||||||
|
agcctcaccc cactactagg cctcctccta gcagcagcag gcaaatcagc ccaattaggt
|
||||||
|
ctccacccct gactcccctc agccatagaa ggccccaccc cagtctcagc cctactccac
|
||||||
|
tcaagcacta tagttgtagc aggaatcttc ttactcatcc gcttccaccc cctagcagaa
|
||||||
|
aatagcccac taatccaaac tctaacacta tgcttaggcg ctatcaccac tctgttcgca
|
||||||
|
gcagtctgcg cccttacaca aaatgacatc aaaaaaatcg tagccttctc cacttcaagt
|
||||||
|
caactaggac tcataatagt tacaatcggc atcaaccaac cacacctagc attcctgcac
|
||||||
|
atctgtaccc acgccttctt caaagccata ctatttatgt gctccgggtc catcatccac
|
||||||
|
aaccttaaca atgaacaaga tattcgaaaa ataggaggac tactcaaaac catacctctc
|
||||||
|
acttcaacct ccctcaccat tggcagccta gcattagcag gaataccttt cctcacaggt
|
||||||
|
ttctactcca aagaccacat catcgaaacc gcaaacatat catacacaaa cgcctgagcc
|
||||||
|
ctatctatta ctctcatcgc tacctccctg acaagcgcct atagcactcg aataattctt
|
||||||
|
ctcaccctaa caggtcaacc tcgcttcccc acccttacta acattaacga aaataacccc
|
||||||
|
accctactaa accccattaa acgcctggca gccggaagcc tattcgcagg atttctcatt
|
||||||
|
actaacaaca tttcccccgc atcccccttc caaacaacaa tccccctcta cctaaaactc
|
||||||
|
acagccctcg ctgtcacttt cctaggactt ctaacagccc tagacctcaa ctacctaacc
|
||||||
|
aacaaactta aaataaaatc cccactatgc acattttatt tctccaacat actcggattc
|
||||||
|
taccctagca tcacacaccg cacaatcccc tatctaggcc ttcttacgag ccaaaacctg
|
||||||
|
cccctactcc tcctagacct aacctgacta gaaaagctat tacctaaaac aatttcacag
|
||||||
|
caccaaatct ccacctccat catcacctca acccaaaaag gcataattaa actttacttc
|
||||||
|
ctctctttct tcttcccact catcctaacc ctactcctaa tcacataacc tattcccccg
|
||||||
|
agcaatctca attacaatat atacaccaac aaacaatgtt caaccagtaa ctactactaa
|
||||||
|
tcaacgccca taatcataca aagcccccgc accaatagga tcctcccgaa tcaaccctga
|
||||||
|
cccctctcct tcataaatta ttcagcttcc tacactatta aagtttacca caaccaccac
|
||||||
|
cccatcatac tctttcaccc acagcaccaa tcctacctcc atcgctaacc ccactaaaac
|
||||||
|
actcaccaag acctcaaccc ctgaccccca tgcctcagga tactcctcaa tagccatcgc
|
||||||
|
tgtagtatat ccaaagacaa ccatcattcc ccctaaataa attaaaaaaa ctattaaacc
|
||||||
|
catataacct cccccaaaat tcagaataat aacacacccg accacaccgc taacaatcaa
|
||||||
|
tactaaaccc ccataaatag gagaaggctt agaagaaaac cccacaaacc ccattactaa
|
||||||
|
acccacactc aacagaaaca aagcatacat cattattctc gcacggacta caaccacgac
|
||||||
|
caatgatatg aaaaaccatc gttgtatttc aactacaaga acaccaatga ccccaatacg
|
||||||
|
caaaactaac cccctaataa aattaattaa ccactcattc atcgacctcc ccaccccatc
|
||||||
|
caacatctcc gcatgatgaa acttcggctc actccttggc gcctgcctga tcctccaaat
|
||||||
|
caccacagga ctattcctag ccatgcacta ctcaccagac gcctcaaccg ccttttcatc
|
||||||
|
aatcgcccac atcactcgag acgtaaatta tggctgaatc atccgctacc ttcacgccaa
|
||||||
|
tggcgcctca atattcttta tctgcctctt cctacacatc gggcgaggcc tatattacgg
|
||||||
|
atcatttctc tactcagaaa cctgaaacat cggcattatc ctcctgcttg caactatagc
|
||||||
|
aacagccttc ataggctatg tcctcccgtg aggccaaata tcattctgag gggccacagt
|
||||||
|
aattacaaac ttactatccg ccatcccata cattgggaca gacctagttc aatgaatctg
|
||||||
|
aggaggctac tcagtagaca gtcccaccct cacacgattc tttacctttc acttcatctt
|
||||||
|
gcccttcatt attgcagccc tagcaacact ccacctccta ttcttgcacg aaacgggatc
|
||||||
|
aaacaacccc ctaggaatca cctcccattc cgataaaatc accttccacc cttactacac
|
||||||
|
aatcaaagac gccctcggct tacttctctt ccttctctcc ttaatgacat taacactatt
|
||||||
|
ctcaccagac ctcctaggcg acccagacaa ttatacccta gccaacccct taaacacccc
|
||||||
|
tccccacatc aagcccgaat gatatttcct attcgcctac acaattctcc gatccgtccc
|
||||||
|
taacaaacta ggaggcgtcc ttgccctatt actatccatc ctcatcctag caataatccc
|
||||||
|
catcctccat atatccaaac aacaaagcat aatatttcgc ccactaagcc aatcacttta
|
||||||
|
ttgactccta gccgcagacc tcctcattct aacctgaatc ggaggacaac cagtaagcta
|
||||||
|
cccttttacc atcattggac aagtagcatc cgtactatac ttcacaacaa tcctaatcct
|
||||||
|
aataccaact atctccctaa ttgaaaacaa aatactcaaa tgggcctgtc cttgtagtat
|
||||||
|
aaactaatac accagtcttg taaaccggag atgaaaacct ttttccaagg acaaatcaga
|
||||||
|
gaaaaagtct ttaactccac cattagcacc caaagctaag attctaattt aaactattct
|
||||||
|
ctgttctttc atggggaagc agatttgggt accacccaag tattgactca cccatcaaca
|
||||||
|
accgctatgt atttcgtaca ttactgccag ccaccatgaa tattgtacgg taccataaat
|
||||||
|
acttgaccac ctgtagtaca taaaaaccca atccacatca aaaccccctc cccatgctta
|
||||||
|
caagcaagta cagcaatcaa ccctcaacta tcacacatca actgcaactc caaagccacc
|
||||||
|
cctcacccac taggatacca acaaacctac ccacccttaa cagtacatag tacataaagc
|
||||||
|
catttaccgt acatagcaca ttacagtcaa atcccttctc gtccccatgg atgacccccc
|
||||||
|
tcagataggg gtcccttgac caccatcctc cgtgaaatca atatcccgca caagagtgct
|
||||||
|
actctcctcg ctccgggccc ataacacttg ggggtagcta aagtgaactg tatccgacat
|
||||||
|
ctggttccta cttcagggtc ataaagccta aatagcccac acgttcccct taaataagac
|
||||||
|
atcacgatg
|
||||||
277
DNA_Alignment/DNA_Alignment/neanderthal.txt
Normal file
277
DNA_Alignment/DNA_Alignment/neanderthal.txt
Normal file
@@ -0,0 +1,277 @@
|
|||||||
|
gatcacaggt ctatcaccct attaaccact cacgggagct ctccatgcat ttggtatttt
|
||||||
|
cgtctggggg gtgtgcacgc gatagcattg cgagacgctg gagccggagc accctatgtc
|
||||||
|
gcagtatctg tctttgattc ctgccccatt ccattattta tcgcacctac gttcaatatt
|
||||||
|
acaggcgagc atacttactg aagtgtgtta attaattaat gcttgtagga cataataata
|
||||||
|
acgactaaat gtctgcacag ctgctttcca cacagacatc ataacaaaaa atttccacca
|
||||||
|
aaccccccct cccccgcttc tggccacagc acttaaacac atctctgcca aaccccaaaa
|
||||||
|
acaaagaacc ctaacaccag cctaaccaga tttcaaattt tatcttttgg cggtatacac
|
||||||
|
ttttaacagt caccccctaa ctaacacatt attttcccct cccactccca tactactaat
|
||||||
|
ctcatcaata caacccccgc ccatcctacc cagcacacac cgctgctaac cccatacccc
|
||||||
|
gagccaacca aaccccaaag acacccccca cagtttatgt agcttacctc ctcaaagcaa
|
||||||
|
tacactgaaa atgtttagac gggctcacat caccccataa acaaataggt ttggtcctag
|
||||||
|
cctttctatt agctcttagt aagattacac atgcaagcat ccccattcca gtgagttcac
|
||||||
|
cctctaaatc accacgatca aaagggacaa gcatcaagca cgcaacaatg cagctcaaaa
|
||||||
|
cgcttagcct agccacaccc ccacgggaaa cagcagtgat aagcctttag caataaacga
|
||||||
|
aagtttaact aagctatact aaccccaggg ttggtcaatt tcgtgccagc caccgcggtc
|
||||||
|
acacgattaa cccaagtcaa tagaagccgg cgtaaagagt gttttagatc accccctccc
|
||||||
|
caataaagct aaaactcacc tgagttgtaa aaaactccag ttgacacaaa ataaactacg
|
||||||
|
aaagtggctt taacatatct gaacacacaa tagctaagac ccaaactggg attagatacc
|
||||||
|
ccactatgct tagccctaaa cctcaacagt taaatcaaca aaactgctcg ccagaacact
|
||||||
|
acgagccaca gcttaaaact caaaggacct ggcggtgctt catatccctc tagaggagcc
|
||||||
|
tgttctgtaa tcgataaacc ccgatcaacc tcaccacctc ttgctcagcc tatataccgc
|
||||||
|
catcttcagc aaaccctgat gaaggctaca aagtaagcgc aagtacccac gtaaagacgt
|
||||||
|
taggtcaagg tgtagcccat gaggtggcaa gaaatgggct acattttcta ccccagaaaa
|
||||||
|
ctacgatagc ccttatgaaa cctaagggtc gaaggtggat ttagcagtaa actgagagta
|
||||||
|
gagtgcttag ttgaacaggg ccctgaagcg cgtacacacc gcccgtcacc ctcctcaagt
|
||||||
|
atacttcaaa ggacatttaa ctaaaacccc tacgcattta tatagaggag acaagtcgta
|
||||||
|
acatggtaag tgtactggaa agtgcacttg gacgaaccag agtgtagctt aacacaaagc
|
||||||
|
acccaactta cacttaggag atttcaactt aacttgaccg ctctgagcta aacctagccc
|
||||||
|
caaacccact ccaccttact accaaacaac cttagccaaa ccatttaccc aaataaagta
|
||||||
|
taggcgatag aaattgaaac ctggcgcaat agatgtagta ccgcaaggga aagatgaaaa
|
||||||
|
attataacca agcataatat agcaaggact aacccctata ccttctgcat aatgaattaa
|
||||||
|
ctagaaataa ctttgcaagg agagccaaag ctaagacccc cgaaaccaga cgagctacct
|
||||||
|
aagaacagct aaaagagcac acccgtctat gtagcaaaat agtgggaaga tttataggta
|
||||||
|
gaggcgacaa acctaccgag cctggtgata gctggttgtc caagatagaa tcttagttca
|
||||||
|
actttaaatt tacccacaga accctctaaa tccccttgta aatttaactg ttagtccaaa
|
||||||
|
gaggaacagc tctttggaca ctaggaaaaa accttgtaga gagagtaaaa aatttaacac
|
||||||
|
ccatagtagg cctaaaagca gccaccaatt aagaaagcgt tcaagctcaa cacccactac
|
||||||
|
ctaaaaaatc ccaaacatat aactgaactc ctcacaccca attggaccaa tctatcaccc
|
||||||
|
tatagaagaa ctaatgttag tataagtaac atgaaaacat tctcctccgc ataagcctgc
|
||||||
|
gtcagattaa aacactgaac tgacaattaa cagcccaata tctacaatca accaacaagt
|
||||||
|
cattattacc ctcactgtca acccaacaca ggcatgctca taaggaaagg ttaaaaaaag
|
||||||
|
taaaaggaac tcggcaaatc ttaccccgcc tgtttaccaa aaacatcacc tctagcatta
|
||||||
|
ccagtattag aggcaccgcc tgcccagtga cacatgttta acggccgcgg taccctaacc
|
||||||
|
gtgcaaaggt agcataatca cttgttcctt aaatagggac ctgtatgaat ggctccacga
|
||||||
|
gggttcagct gtctcttact tttaaccagt gaaattgacc tgcccgtgaa gaggcgggca
|
||||||
|
taacacagca agacgagaag accctatgga gctttaattt attaatgcaa acagtaccta
|
||||||
|
acaaacccac aggtcctaaa ctaccaaacc tgcattaaaa atttcggttg gggcgacctc
|
||||||
|
ggagcacaac ccaacctccg agcagtacat gctaagacct caccagtcaa agcgaactac
|
||||||
|
catactcaat tgatccaata acttgaccaa cggaacaagt taccctaggg ataacagcgc
|
||||||
|
aatcctattc tagagtccat atcaacaata gggtttacga cctcgatgtt ggatcaggac
|
||||||
|
atcccaatgg tgcagccgct attaaaggtt cgtttgttca acgattaaag tcctacgtga
|
||||||
|
tctgagttca gaccggagta atccaggtcg gtttctatct acttcaaatt cctccctgta
|
||||||
|
cgaaaggaca agagaaataa ggcctacttc acaaagcgcc ttcccccgta aatgatatca
|
||||||
|
tctcaactta gtattatacc cacacccacc caagaacagg gtttgttaag atggcagagc
|
||||||
|
ccggtaatcg cataaaactt aaaactttac agtcagaggt tcaattcctc ttcttaacaa
|
||||||
|
cacacccatg gccaacctcc tactcctcgt tgtacccatt ctaatcgcaa tggcattcct
|
||||||
|
aatgcttacc gaacgaaaaa ttctaggcta tatgcaacta cgcaaaggtc ccaacgttgt
|
||||||
|
aggcccctac gggctactac aacccttcgc tgacgccata aaactcttca ccaaagaacc
|
||||||
|
cctaaaaccc gccacatcca ccatcaccct ctacatcacc gccccgacct tagctctcac
|
||||||
|
catcgctctt ctactatgaa cccccctccc catacccaac cccctggtta acctcaacct
|
||||||
|
aggcctccta tttattctag ccacctctag cctagccgtt tactcaatcc tctgatcagg
|
||||||
|
gtgagcatca aactcaaact acgccctgat cggcgcactg cgagcagtag cccaaacaat
|
||||||
|
ctcatatgaa gtcaccctag ccatcattct actatcaaca ttactaataa gtggctcctt
|
||||||
|
taacctctcc acccttatca cagcacaaga acacctctga ttactcctgc catcatgacc
|
||||||
|
cttggccata atatgattta tctccacact agcagagacc aaccgaaccc ccttcgacct
|
||||||
|
tgctgaaggg gaatccgaac tagtctcagg ctttaacatc gaatacgccg caggcccctt
|
||||||
|
cgccctattc ttcatagccg aatacacaaa cattattata ataaacaccc tcaccactac
|
||||||
|
aatcttccta ggaacaacat ataacgcact ctcccctgaa ctctacacaa catattttgt
|
||||||
|
caccaagacc ctacttctga cctccctgtt cttatgaatt cgaacagcat acccccgatt
|
||||||
|
ccgctacgac caactcatac acctcctatg aaaaaacttc ctaccactca ccctagcact
|
||||||
|
acttatatga tatgtctcca tacccattac aatctccagc attccccctc aaacctaaga
|
||||||
|
aatatgtctg ataaaagagt tactttgata gagtaaataa taggagttta aaccccctta
|
||||||
|
tttctaggac tatgagaatc gaacccatcc ctgagaatcc aaaattctcc gtgccaccta
|
||||||
|
tcacacccca tcctaaagta aggtcagcta aataagctat cgggcccata ccccgaaaat
|
||||||
|
gttggttata cccttcccgt actaattaat cccctggccc aacccgtcat ctactctacc
|
||||||
|
atctttgcag gcacactcat cacagcacta agctcgcact gattttttac ctgagtgggc
|
||||||
|
ctagaaataa acatgctagc ttttattcca gttctaacca aaaaaataaa ccctcgttcc
|
||||||
|
acagaagctg ccatcaagta tttcctcacg caagcaaccg catccataat ccttctaata
|
||||||
|
gctatcctct tcaacaatat actctccgga caatgaacca taaccaatac taccaatcaa
|
||||||
|
tactcatcat taataatcat aatggctata gcaataaaac taggaatagc cccctttcac
|
||||||
|
ttctgagtcc cagaggttac ccaaggcacc cctctgacat ccggcctgct ccttctcaca
|
||||||
|
tgacaaaaac tagcccccat ctcaatcata taccaaattt ctccctcact aaacgtaagc
|
||||||
|
ctcctcctca ctctttcaat cttatccatc atagcaggca gttgaggtgg attaaaccaa
|
||||||
|
acccagctac gcaaaatctt agcatactcc tcaattaccc acataggatg aataatagca
|
||||||
|
gttctaccgt acaaccctaa cataaccatt cttaatttaa ctatttatat tatcctaact
|
||||||
|
actaccgcat tcctactact caacttaaac tccagcacca cgaccctact actatctcgc
|
||||||
|
acctgaaaca agctaacatg actaacaccc ttaattccat ccaccctcct ctccctagga
|
||||||
|
ggcctgcccc cgctaaccgg ctttttgccc aaatgggcca ttatcgaaga attcacaaaa
|
||||||
|
aacaatagcc tcatcatccc caccatcata gccaccatca ccctccttaa cctctacttc
|
||||||
|
tacctacgcc taatctactc cacctcaatc acactactcc ctatatctaa caacgtaaaa
|
||||||
|
ataaaatgac agtttgaaca tacaaaaccc accccattcc tccccacact catcaccctt
|
||||||
|
accacactac tcctacctat ctcccctttt atactaatag tcttatagaa atttaggtta
|
||||||
|
aatacagacc aagagccttc aaagccctca gtaagttgca atacttaatt tctgcaacag
|
||||||
|
ctaaggactg caaaacccca ctctgcatca actgaacgca aatcagccac tttaattaag
|
||||||
|
ctaagccctt actagaccaa tgggactcaa acccacaaac acttagttaa cagctaagca
|
||||||
|
ccctaatcaa ctggcttcaa tctacttctc ccgccgccgg gaaaaaaggc gggagaagcc
|
||||||
|
ccggcaggtt tgaagctgct tcttcgaatt tgcaattcaa tatgaaaatc acctcagagc
|
||||||
|
tggtaaaaag aggcttaacc cctgtcttta gatttacagt ccaatgcttc actcagccat
|
||||||
|
tttacctcac ccccactgat gttcgccgac cgttgactat tctctacaaa ccacaaagac
|
||||||
|
attggaacac tatacctact attcggcgca tgagctggag tcctaggcac agctctaagc
|
||||||
|
ctccttattc gagccgaact gggccagcca ggcaaccttc taggtaacga ccacatctac
|
||||||
|
aacgttatcg tcacagccca tgcatttgta ataatcttct tcatagtaat acccatcata
|
||||||
|
atcgggggct ttggcaactg actagttccc ttaataatcg gtgcccccga tatggcgttt
|
||||||
|
ccccgcataa acaatataag cttctgactc ttacctccct ctctcctact cctgctcgca
|
||||||
|
tctgctatag tggaagccgg cgcaggaaca ggttgaacag tctaccctcc cttagcaggg
|
||||||
|
aactactccc accctggagc ctccgtagac ctaaccatct tctccttaca cctagcaggt
|
||||||
|
gtctcctcta tcttaggggc catcaatttc atcacaacaa ttattaatat aaaaccccct
|
||||||
|
gccataaccc aataccaaac gccccttttc gtctgatccg tcctaatcac agcagtccta
|
||||||
|
cttctcctat ctctcccagt cctagctgct ggcatcacta tactactaac agaccgcaac
|
||||||
|
ctcaacacca ccttcttcga ccccgccgga ggaggagacc ccattctata ccaacaccta
|
||||||
|
ttctgatttt tcggccaccc tgaagtttat attctcatcc taccaggctt cggaataatc
|
||||||
|
tcccatattg taacttacta ctccggaaaa aaagaaccat ttggatacat aggtatggtc
|
||||||
|
tgagctatga tatcaattgg cttcctaggg tttatcgtgt gagcacacca tatatttaca
|
||||||
|
gtaggaatag acgtagacac acgagcatat ttcacctccg ctaccataat catcgctatc
|
||||||
|
cccaccggcg tcaaagtatt tagctgactc gccacactcc acggaagcaa tatgaaatga
|
||||||
|
tctgctgcag tgctctgagc cctaggattc atctttcttt tcaccgtagg tggcctgact
|
||||||
|
ggcattgtat tagcaaactc atcactagac atcgtactac acgacacgta ctacgttgta
|
||||||
|
gctcacttcc actatgtcct atcaatagga gctgtatttg ccatcatagg aggcttcatt
|
||||||
|
cactgatttc ccctattctc cggctacacc ctagaccaaa cttacgccaa aatccatttc
|
||||||
|
actatcatat tcatcggcgt aaatctaact ttcttcccac aacactttct cggcctatcc
|
||||||
|
ggaatgcccc gacgttactc ggactacccc gatgcataca ccacatgaaa tatcctatca
|
||||||
|
tctgtaggct cattcatttc tctaacagca gtaatattaa taattttcat gatttgagaa
|
||||||
|
gccttcgctt cgaagcgaaa agtcctaata gtagaagaac cctccataaa cctggagtga
|
||||||
|
ctatatggat gccccccacc ctaccacaca ttcgaagagc ccgtatacat aaaatctaga
|
||||||
|
caaaaaagga aggaatcgaa ccccccaaag ctggtttcaa gccaacccca tggcctccat
|
||||||
|
gactttttca aaaagatatt agaaaaacca tttcataact ttgtcaaagt taaattatag
|
||||||
|
gctaaatcct atatatctta atggcacatg cagcgcaagt aggtctacaa gacgctactt
|
||||||
|
cccctatcat agaagagctt atcatctttc atgatcacgc cctcataatc attttcctta
|
||||||
|
tctgcttcct agtcctgtat gcccttttcc taacactcac aacaaaacta actaatacta
|
||||||
|
gcatctcaga cgctcaggaa atagaaaccg tctgaactat cctgcccgcc atcatcctag
|
||||||
|
tcctcatcgc cctcccatcc ctacgcatcc tttacataac agacgaggtc aacgacccct
|
||||||
|
cctttaccat caaatcaatt ggccatcaat ggtactgaac ctacgagtac accgactacg
|
||||||
|
gcggactaat cttcaactcc tacatacttc ccccattatt cctagaacca ggcgacctgc
|
||||||
|
gactccttga cgttgacaat cgagtagtac tcccggttga agcccccatt cgtataataa
|
||||||
|
ttacatcaca agacgtctta cactcatgag ctgtccccac attaggctta aaaacagatg
|
||||||
|
caattcccgg acgtctaaac caaaccactt tcaccgctac acgaccgggg gtatactacg
|
||||||
|
gtcaatgctc tgaaatctgt ggagcaaacc acagtttcat gcccatcgtc ctagaattaa
|
||||||
|
ttcccctaaa aatctttgaa atagggcccg tatttaccct atagcacccc ctctaccccc
|
||||||
|
tctagagccc actgtaaagc taacttagca ttaacctttt aagttaaaga ttaagagaac
|
||||||
|
cagcacctct ttacagtgag atgccccaac taaatactac tgtatggccc accataatta
|
||||||
|
tccccatact ccttacacta ttcctcatca cccaactaaa aatattaaat acaaattacc
|
||||||
|
acttacctcc ctcaccaaag cccataaaaa taaaaaacta taacaaaccc tgagaaccaa
|
||||||
|
aatgaacgaa aatctgttcg cttcattcat tgcccccaca atcctaggcc tacccgccgc
|
||||||
|
agtactgatc attctatttc cccctctatt gatccccacc tccaaatatc tcatcaacaa
|
||||||
|
ccgactaatt accacccaac aatgactaat caaactaacc tcaaaacaaa tgatagccat
|
||||||
|
acacaacact aagggacgaa cctgatctct tatactagta tccttaatca tttttattac
|
||||||
|
cacaactaac ctcctcggac tcctgcctca ctcatttaca ccaaccaccc aactatctat
|
||||||
|
aaacctagcc atggccatcc ccttatgagc gggcgcagtg attataggct ttcgctctaa
|
||||||
|
gattaaaaat gccctagccc acttcttacc acaaggcaca cctacacccc ttatccctat
|
||||||
|
actagttatt atcgaaacca tcagcctact cattcaacca gtagccctgg ccgtacgcct
|
||||||
|
aaccgctaac attactgcag gtcacctact catgcaccta attggaaacg ccaccctagc
|
||||||
|
aatatcaacc attaaccttc cctctacact tatcatcttc acaattctaa ttctactgac
|
||||||
|
tatcctagaa atcgctgtcg ccttaatcca agcctacgtt ttcacacttc tagtaagcct
|
||||||
|
ctacctgcac gacaacacat aatgacccac caatcacatg cctatcatat agtaaaaccc
|
||||||
|
agcccatgac ccctaacagg ggccctctca gccctcctaa tgacctccgg cctagccatg
|
||||||
|
tgatttcact tccactccac aaccctcctc atactaggct tactaaccaa cacactaacc
|
||||||
|
atataccaat gatggcgcga tgtaacacga gaaagcacat accaaggcca ccacacacca
|
||||||
|
cctgtccaaa aaggccttcg atacgggata gtcctattta ttacctcaga agtttttttc
|
||||||
|
ttcgcaggat ttttctgagc cttttaccac tccagcctag cccctacccc ccaactagga
|
||||||
|
gggcactggc ccccaacagg catcaccccg ctaaatcccc tagaagtccc actcctaaac
|
||||||
|
acatccgtat tactcgcatc aggagtatca atcacctgag ctcaccatag tctaatagaa
|
||||||
|
aacaaccgaa accaaataat tcaagcactg cttattacaa ttttactggg tctctatttt
|
||||||
|
accctcctac aagcctcaga gtacttcgaa tctcccttca ccatttccga cggcatctac
|
||||||
|
ggctcaacat tttttgtagc cacaggcttc cacggacttc acgtcattat tggctcaact
|
||||||
|
ttcctcacta tctgcttcat ccgtcaacta atatttcact ttacatccaa acatcacttt
|
||||||
|
ggcttcgaag ccgccgcctg atactggcat tttgtagatg tggtttgact atttctgtat
|
||||||
|
gtctccatct attgatgagg gtcttactct tttagtataa atagtaccgt taacttccaa
|
||||||
|
ttaactagtt ttgacaacat tcaaaaaaga gtaataaact tcgccttaat tttaataatc
|
||||||
|
aacaccctcc tagccctact actaataatt attacatttt gactaccaca actcaacggc
|
||||||
|
tacatagaaa aatccacccc ttacgagtgc ggcttcgacc ctatatcccc cgcccgcgtc
|
||||||
|
cctttctcca taaaattctt cttagtagct attaccttct tattatttga cctagaaatt
|
||||||
|
gccctccttt tacccttacc atgagcccta caaacaacta atctaccact aatagttacg
|
||||||
|
tcatccctct tattaatcat catcctagcc ctaagtctgg cctatgaatg actacaaaaa
|
||||||
|
ggattagact gagccgaatt ggtatatagt ttaaacaaaa cgaatgattt cgactcatta
|
||||||
|
aattatgata atcatattta ccaaatgccc ctcatttaca taaatattat actagcattt
|
||||||
|
accatctcac ttctgggaat actagtgtat cgctcacacc tcatatcctc cctactatgc
|
||||||
|
ctagaaggaa taatactatc gctgttcatt atagctactc tcataaccct caacacccac
|
||||||
|
tccctcttag ccaatattgt gcctattgcc atactagttt ttgccgcctg cgaagcagcg
|
||||||
|
gtaggcctag ccctactagt ctcaatctcc aacacatatg gcctagacta cgtacataac
|
||||||
|
ctaagcctac tccaatgcta aaactaatcg tcccaacaat tatattacta ccactgacat
|
||||||
|
gactctccaa aaaacacata atttgaatca acacaaccac ccacagccta attattagca
|
||||||
|
tcatccccct actatttttt aaccaaatca acaacaacct atttagctgc tccccaacct
|
||||||
|
tttcctccga ccccctaaca acccccctcc taatactaac tacctgactc ctacccctca
|
||||||
|
caatcatggc aagccaacgc cacttatcca gtgaaccact atcacgaaaa aaactctacc
|
||||||
|
tctctatact aatctcccta caaatctcct taattataac attcacagcc acagaactaa
|
||||||
|
tcatatttta tatcttcttc gaaaccacac ttatccccac cttggctatc atcacccgat
|
||||||
|
gaggcaacca gccagaacgc ctgaacgcag gcacatactt cctattctac accctagtag
|
||||||
|
gctcccttcc cctactcatc gcactaattt acactcacaa caccctaggc tcactaaaca
|
||||||
|
ttctactact cactctcact gcccaagaac tatcaaactc ctgagccaac aacttaatat
|
||||||
|
gactagctta cacaatagct tttatagtaa agatacccct ttacggactc cacttatgac
|
||||||
|
tccctaaagc ccatgtcgaa gcccccatcg ctgggtcaat agtacttgcc gctgtactct
|
||||||
|
taaaactagg cggctatggt ataatacgcc tcacactcat tctcaacccc ctgacaaaac
|
||||||
|
atatagccta ccccttcctt gtactatccc tatggggcat aattataaca agctccatct
|
||||||
|
gcctgcgaca aacagaccta aaatcgctca ttgcatattc ttcaatcagc cacatagccc
|
||||||
|
tcgtagtaac agccattctc atccaaaccc cctgaagctt caccggcgca gtcattctca
|
||||||
|
taatcgccca cggacttaca tcctcattac tattctgcct agcaaactca aactacgaac
|
||||||
|
gcacccacag tcgcatcata atcctctctc aaggacttca aactctactc ccactaatag
|
||||||
|
ctttttgatg acttctagca agcctcgcta acctcgcctt accccccact attaacctac
|
||||||
|
tgggagaact ctctgtgcta gtaaccacat tctcctgatc aaatatcact ctcctactta
|
||||||
|
cagggctcaa catactagtc acagccctat actccctcta catatttacc acaacacaat
|
||||||
|
ggggctcact cacccaccac attaacaaca taaaaccctc attcacacga gaaaacaccc
|
||||||
|
tcatattcat acacctatcc cccattctcc tcctatccct caaccccgac atcattaccg
|
||||||
|
ggttttcctc ttgtaaatat agtttaacca aaacatcaga ttgtgaatct gacaacagag
|
||||||
|
gctcacgacc ccttatttac cgagaaagct cacaagaact gctaactcat gcccccatgt
|
||||||
|
ctaacaacat ggctttctca acttttaaag gataacagct atccattggt cttaggcccc
|
||||||
|
aaaaattttg gtgcaactcc aaataaaagt aataaccatg cacaccacta taaccaccct
|
||||||
|
gaccctgact tccctaattc cccccatcct taccaccctc attaacccta acaaaaaaaa
|
||||||
|
ctcatacccc cattatgtaa aatccattgt cgcatccacc tttattatta gtctcttccc
|
||||||
|
cacaacaata ttcatgtgcc tagaccaaga agttattatc tcgaactgac actgagccac
|
||||||
|
aacccaaaca acccagctct ccctaagctt caaactagac tacttctcca taatattcat
|
||||||
|
ccctgtagca ttgttcgtta catggtccat catagaattc tcactgtgat atataaactc
|
||||||
|
agacccaaac attaatcagt tcttcaaata tctactcatt ttcctaatta ccatactaat
|
||||||
|
cttagttacc gctaacaacc tattccaact gttcatcggc tgagagggcg taggaattat
|
||||||
|
atccttcttg ctcatcagtt gatgatacgc ccgagcagat gccaacacag cagccattca
|
||||||
|
agcaatccta tacaaccgca tcggcgatat cggtttcatc ctcgccttag catgatttat
|
||||||
|
cctacactcc aactcatgag acccacaaca aatagccctt ctaaacgcta atccaagcct
|
||||||
|
caccccacta ctaggcctcc tcctagcagc agcaggcaaa tcagcccaat taggtctcca
|
||||||
|
cccctgactc ccctcagcca tagaaggccc caccccagtc tcagccctac tccactcaag
|
||||||
|
cactatagtc gtagcaggag tcttcttact catccgcttc caccccctag cagaaaatag
|
||||||
|
cccactaatc caaactctaa cactatgctt aggcgctatc accactctat tcgcagcagt
|
||||||
|
ctgcgccctt acacaaaatg acatcaaaaa aatcgtagcc ttctccactt caagtcaact
|
||||||
|
agggctcata gtagttacaa tcggcatcaa ccaaccacac ctagcattcc tgcacatctg
|
||||||
|
tacccacgcc ttcttcaaag ccatactatt tatatgctcc gggtccatca tccacaacct
|
||||||
|
taacaatgaa caagatattc gaaaaatagg aggactactc aaaaccatac ctctcacttc
|
||||||
|
aacctccctc accattggca gcctagcatt agcaggaata cctttcctca caggtttcta
|
||||||
|
ctccaaagac cacatcatcg aaaccgcaaa catatcatac acaaacgcct gagccctatc
|
||||||
|
tattactctc atcgctacct ccctgacaag cgcctatagc actcgaataa ttcttctcac
|
||||||
|
cctaacaggt caacctcgct tccccaccct cactaacatt aacgaaaata accctaccct
|
||||||
|
actaaacccc attaaacgcc tagcagccgg aagcctattc gcaggatttc tcattactaa
|
||||||
|
caacatttcc cccgcatccc ccttccaaac aacaatcccc ctctacctaa aactcgcagc
|
||||||
|
cctcgctgtc actttcctag gacttctaac agccctagac ctcaactacc taaccaacaa
|
||||||
|
acttaaaata aaaaccccac tatacacatt ttatttctcc aacatactcg ggttctaccc
|
||||||
|
tagcatcaca caccgcacaa tcccctatct aggccttctt acgagccaaa acctgcccct
|
||||||
|
actcctccta gacctaacct gactagaaaa gctattacct aaaacaattt cacagcacca
|
||||||
|
aatctccgcc tccatcacca cctcaaccca aaaaggcata attaaacttt acttcctctc
|
||||||
|
tttcttcttc ccactcatcc taaccctact cctaatcata taacctattc ccccgagcaa
|
||||||
|
tctcaattac aacatataca ccaacaaaca atgttcaacc agtaactact actaatcaac
|
||||||
|
gcccataatc atacaaagcc cccgcaccaa taggatcctc ccgaatcaac cctgacccct
|
||||||
|
ctccttcata gattattcag cttcctacac tattaaagtt taccacaacc accaccccat
|
||||||
|
catactcttt cacccacagc accaatccta cctccatcgc taaccccact aaaacactca
|
||||||
|
ccaagacctc aacccctgac ccccatgcct caggatactc ctcaatagcc atcgctgtag
|
||||||
|
tatatccaaa gacaaccatc attcccccta aataaattaa aaaaactatt aaacccatat
|
||||||
|
aacctccccc aaaattcaga ataataacac acccaaccac accgctaaca atcaatacta
|
||||||
|
aacccccata aataggagaa ggcttagaag aaaaccccac aaaccccatt actaaaccca
|
||||||
|
cactcaacag aaacaaagca tacatcatta ttctcgcacg gactacaacc acgaccaatg
|
||||||
|
atatgaaaaa ccatcgttgt atttcaacta caagaacacc aatgacccca atacgcaaaa
|
||||||
|
ttaaccccct aataaaatta attaaccact cattcatcga cctccccacc ccatccaaca
|
||||||
|
tctccgcatg atgaaacttc ggctcactcc ttggcgcctg cctgatcctc caaatcacca
|
||||||
|
caggactatt cctagccatg cactactcac cagacgcctc gaccgccttt tcatcaatcg
|
||||||
|
cccacatcac tcgagacgta aattatggct gaatcatccg ctaccttcac gccaatggcg
|
||||||
|
cctcaatatt ctttatctgc ctcttcctac acatcggacg aggcctatat tacggatcat
|
||||||
|
ttctctactc aaaaacctga aacatcggca ttatcctcct gcttgcaact atagcaacag
|
||||||
|
ccttcatagg ctatgtcctc ccatgaggcc aaatatcatt ctgaggggcc acagtaatta
|
||||||
|
caaacctact atccgccatc ccatacattg ggacagacct ggttcagtga atctgaggag
|
||||||
|
gctactcagt agacagtccc accctcacac gattctttac ctttcacttt atcttaccct
|
||||||
|
tcattattgc agccctagca gcactccacc tcctattctt gcacgaaaca ggatcaaaca
|
||||||
|
accccctagg aatcacctcc cattccgata aaatcacctt ccacccttac tacacaatca
|
||||||
|
aagacgccct cggcttattt ctcttccttc tctccttaat gacattaaca ctactctcac
|
||||||
|
cagacctcct aggcgaccca gacaattata ccctagccaa ccccttaaac acccctcccc
|
||||||
|
acatcaagcc cgaatgatat ttcctattcg cctacacaat tctccgatcc gtccctaaca
|
||||||
|
aactaggagg cgtccttgcc ctactactat ccatcctcat cctggcaata atccccatcc
|
||||||
|
ttcatgtatc caaacaacaa agcataatat ttcgcccact aagccaatca ctttattgac
|
||||||
|
tcctagccgc agacctcctc attctaacct gaatcggagg acaaccagta agctaccctt
|
||||||
|
ttatcatcat tggacaagta gcatccgtac tatacttcac aacaatccta atcctaatac
|
||||||
|
caaccatctc cctaattgaa aacaaaatac tcaaatgggc ctgtccttgt agtataaact
|
||||||
|
aatacaccag tcttgtaaac cggagatgaa aacctttttc caaggacaaa tcagagaaaa
|
||||||
|
agtctttaac tccaccatta gcacccaaag ctaagattct aatttaaact attctctgtt
|
||||||
|
ctttcatggg ggagcagatt tgggtaccac ccaagtattg actcacccat cagcaaccgc
|
||||||
|
tatgtatttc gtacattact gccagccacc atgaatattg tacagtacca taattacttg
|
||||||
|
actacctgca gtacataaaa acctaatcca catcaacccc ccccccccat gcttacaagc
|
||||||
|
aagcacagca atcaaccttc aactgtcata catcaactac aactccaaag acgcccttac
|
||||||
|
acccactagg atatcaacaa acctacccac ccttgacagt acatagcaca taaagtcatt
|
||||||
|
taccgtacat agcacattac agtcaaatcc cttctcgccc ccatggatga cccccctcag
|
||||||
|
ataggggtcc cttgatcacc atcctccgtg aaatcaatat cccgcacaag agtgctactc
|
||||||
|
tcctcgctcc gggcccataa cacttggggg tagctaaagt gaactgtatc cgacatctgg
|
||||||
|
ttcctacttc agggccataa agcctaaata gcccacacgt tccccttaaa taagacatca
|
||||||
|
cgatg
|
||||||
18693
DNA_Alignment/DNA_Alignment/neanderthal.txt_vs_GreatApes.txt.txt
Normal file
18693
DNA_Alignment/DNA_Alignment/neanderthal.txt_vs_GreatApes.txt.txt
Normal file
File diff suppressed because it is too large
Load Diff
16749
DNA_Alignment/DNA_Alignment/neanderthal.txt_vs_protypicalHuman.txt.txt
Normal file
16749
DNA_Alignment/DNA_Alignment/neanderthal.txt_vs_protypicalHuman.txt.txt
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,5 @@
|
|||||||
|
/Users/bradybodily/Repositories/CS5050_Advanced_Algorithms/DNA_Alignment/DNA_Alignment/bin/Debug/DNA_Alignment.exe
|
||||||
|
/Users/bradybodily/Repositories/CS5050_Advanced_Algorithms/DNA_Alignment/DNA_Alignment/bin/Debug/DNA_Alignment.pdb
|
||||||
|
/Users/bradybodily/Repositories/CS5050_Advanced_Algorithms/DNA_Alignment/DNA_Alignment/obj/Debug/DNA_Alignment.csprojAssemblyReference.cache
|
||||||
|
/Users/bradybodily/Repositories/CS5050_Advanced_Algorithms/DNA_Alignment/DNA_Alignment/obj/Debug/DNA_Alignment.exe
|
||||||
|
/Users/bradybodily/Repositories/CS5050_Advanced_Algorithms/DNA_Alignment/DNA_Alignment/obj/Debug/DNA_Alignment.pdb
|
||||||
Binary file not shown.
BIN
DNA_Alignment/DNA_Alignment/obj/Debug/DNA_Alignment.exe
Normal file
BIN
DNA_Alignment/DNA_Alignment/obj/Debug/DNA_Alignment.exe
Normal file
Binary file not shown.
BIN
DNA_Alignment/DNA_Alignment/obj/Debug/DNA_Alignment.pdb
Normal file
BIN
DNA_Alignment/DNA_Alignment/obj/Debug/DNA_Alignment.pdb
Normal file
Binary file not shown.
277
DNA_Alignment/DNA_Alignment/protypicalHuman.txt
Normal file
277
DNA_Alignment/DNA_Alignment/protypicalHuman.txt
Normal file
@@ -0,0 +1,277 @@
|
|||||||
|
gatcacaggt ctatcaccct attaaccact cacgggagct ctccatgcat ttggtatttt
|
||||||
|
cgtctggggg gtatgcacgc gatagcattg cgagacgctg gagccggagc accctatgtc
|
||||||
|
gcagtatctg tctttgattc ctgcctcatc ctattattta tcgcacctac gttcaatatt
|
||||||
|
acaggcgaac atacttacta aagtgtgtta attaattaat gcttgtagga cataataata
|
||||||
|
acaattgaat gtctgcacag ccactttcca cacagacatc ataacaaaaa atttccacca
|
||||||
|
aaccccccct cccccgcttc tggccacagc acttaaacac atctctgcca aaccccaaaa
|
||||||
|
acaaagaacc ctaacaccag cctaaccaga tttcaaattt tatcttttgg cggtatgcac
|
||||||
|
ttttaacagt caccccccaa ctaacacatt attttcccct cccactccca tactactaat
|
||||||
|
ctcatcaata caacccccgc ccatcctacc cagcacacac acaccgctgc taaccccata
|
||||||
|
ccccgaacca accaaacccc aaagacaccc cccacagttt atgtagctta cctcctcaaa
|
||||||
|
gcaatacact gaaaatgttt agacgggctc acatcacccc ataaacaaat aggtttggtc
|
||||||
|
ctagcctttc tattagctct tagtaagatt acacatgcaa gcatccccgt tccagtgagt
|
||||||
|
tcaccctcta aatcaccacg atcaaaagga acaagcatca agcacgcagc aatgcagctc
|
||||||
|
aaaacgctta gcctagccac acccccacgg gaaacagcag tgattaacct ttagcaataa
|
||||||
|
acgaaagttt aactaagcta tactaacccc agggttggtc aatttcgtgc cagccaccgc
|
||||||
|
ggtcacacga ttaacccaag tcaatagaag ccggcgtaaa gagtgtttta gatcaccccc
|
||||||
|
tccccaataa agctaaaact cacctgagtt gtaaaaaact ccagttgaca caaaatagac
|
||||||
|
tacgaaagtg gctttaacat atctgaacac acaatagcta agacccaaac tgggattaga
|
||||||
|
taccccacta tgcttagccc taaacctcaa cagttaaatc aacaaaactg ctcgccagaa
|
||||||
|
cactacgagc cacagcttaa aactcaaagg acctggcggt gcttcatatc cctctagagg
|
||||||
|
agcctgttct gtaatcgata aaccccgatc aacctcacca cctcttgctc agcctatata
|
||||||
|
ccgccatctt cagcaaaccc tgatgaaggc tacaaagtaa gcgcaagtac ccacgtaaag
|
||||||
|
acgttaggtc aaggtgtagc ccatgaggtg gcaagaaatg ggctacattt tctaccccag
|
||||||
|
aaaactacga tagcccttat gaaacttaag ggtcgaaggt ggatttagca gtaaactaag
|
||||||
|
agtagagtgc ttagttgaac agggccctga agcgcgtaca caccgcccgt caccctcctc
|
||||||
|
aagtatactt caaaggacat ttaactaaaa cccctacgca tttatataga ggagacaagt
|
||||||
|
cgtaacatgg taagtgtact ggaaagtgca cttggacgaa ccagagtgta gcttaacaca
|
||||||
|
aagcacccaa cttacactta ggagatttca acttaacttg accgctctga gctaaaccta
|
||||||
|
gccccaaacc cactccacct tactaccaga caaccttagc caaaccattt acccaaataa
|
||||||
|
agtataggcg atagaaattg aaacctggcg caatagatat agtaccgcaa gggaaagatg
|
||||||
|
aaaaattata accaagcata atatagcaag gactaacccc tataccttct gcataatgaa
|
||||||
|
ttaactagaa ataactttgc aaggagagcc aaagctaaga cccccgaaac cagacgagct
|
||||||
|
acctaagaac agctaaaaga gcacacccgt ctatgtagca aaatagtggg aagatttata
|
||||||
|
ggtagaggcg acaaacctac cgagcctggt gatagctggt tgtccaagat agaatcttag
|
||||||
|
ttcaacttta aatttgccca cagaaccctc taaatcccct tgtaaattta actgttagtc
|
||||||
|
caaagaggaa cagctctttg gacactagga aaaaaccttg tagagagagt aaaaaattta
|
||||||
|
acacccatag taggcctaaa agcagccacc aattaagaaa gcgttcaagc tcaacaccca
|
||||||
|
ctacctaaaa aatcccaaac atataactga actcctcaca cccaattgga ccaatctatc
|
||||||
|
accctataga agaactaatg ttagtataag taacatgaaa acattctcct ccgcataagc
|
||||||
|
ctgcgtcaga ttaaaacact gaactgacaa ttaacagccc aatatctaca atcaaccaac
|
||||||
|
aagtcattat taccctcact gtcaacccaa cacaggcatg ctcataagga aaggttaaaa
|
||||||
|
aaagtaaaag gaactcggca aatcttaccc cgcctgttta ccaaaaacat cacctctagc
|
||||||
|
atcaccagta ttagaggcac cgcctgccca gtgacacatg tttaacggcc gcggtaccct
|
||||||
|
aaccgtgcaa aggtagcata atcacttgtt ccttaaatag ggacctgtat gaatggctcc
|
||||||
|
acgagggttc agctgtctct tacttttaac cagtgaaatt gacctgcccg tgaagaggcg
|
||||||
|
ggcataacac agcaagacga gaagacccta tggagcttta atttattaat gcaaacagta
|
||||||
|
cctaacaaac ccacaggtcc taaactacca aacctgcatt aaaaatttcg gttggggcga
|
||||||
|
cctcggagca gaacccaacc tccgagcagt acatgctaag acttcaccag tcaaagcgaa
|
||||||
|
ctactatact caattgatcc aataacttga ccaacggaac aagttaccct agggataaca
|
||||||
|
gcgcaatcct attctagagt ccatatcaac aatagggttt acgacctcga tgttggatca
|
||||||
|
ggacatcccg atggtgcagc cgctattaaa ggttcgtttg ttcaacgatt aaagtcctac
|
||||||
|
gtgatctgag ttcagaccgg agtaatccag gtcggtttct atctacnttc aaattcctcc
|
||||||
|
ctgtacgaaa ggacaagaga aataaggcct acttcacaaa gcgccttccc ccgtaaatga
|
||||||
|
tatcatctca acttagtatt atacccacac ccacccaaga acagggtttg ttaagatggc
|
||||||
|
agagcccggt aatcgcataa aacttaaaac tttacagtca gaggttcaat tcctcttctt
|
||||||
|
aacaacatac ccatggccaa cctcctactc ctcattgtac ccattctaat cgcaatggca
|
||||||
|
ttcctaatgc ttaccgaacg aaaaattcta ggctatatac aactacgcaa aggccccaac
|
||||||
|
gttgtaggcc cctacgggct actacaaccc ttcgctgacg ccataaaact cttcaccaaa
|
||||||
|
gagcccctaa aacccgccac atctaccatc accctctaca tcaccgcccc gaccttagct
|
||||||
|
ctcaccatcg ctcttctact atgaaccccc ctccccatac ccaaccccct ggtcaacctc
|
||||||
|
aacctaggcc tcctatttat tctagccacc tctagcctag ccgtttactc aatcctctga
|
||||||
|
tcagggtgag catcaaactc aaactacgcc ctgatcggcg cactgcgagc agtagcccaa
|
||||||
|
acaatctcat atgaagtcac cctagccatc attctactat caacattact aataagtggc
|
||||||
|
tcctttaacc tctccaccct tatcacaaca caagaacacc tctgattact cctgccatca
|
||||||
|
tgacccttgg ccataatatg atttatctcc acactagcag agaccaaccg aacccccttc
|
||||||
|
gaccttgccg aaggggagtc cgaactagtc tcaggcttca acatcgaata cgccgcaggc
|
||||||
|
cccttcgccc tattcttcat agccgaatac acaaacatta ttataataaa caccctcacc
|
||||||
|
actacaatct tcctaggaac aacatatgac gcactctccc ctgaactcta cacaacatat
|
||||||
|
tttgtcacca agaccctact tctaacctcc ctgttcttat gaattcgaac agcatacccc
|
||||||
|
cgattccgct acgaccaact catacacctc ctatgaaaaa acttcctacc actcacccta
|
||||||
|
gcattactta tatgatatgt ctccataccc attacaatct ccagcattcc ccctcaaacc
|
||||||
|
taagaaatat gtctgataaa agagttactt tgatagagta aataatagga gcttaaaccc
|
||||||
|
ccttatttct aggactatga gaatcgaacc catccctgag aatccaaaat tctccgtgcc
|
||||||
|
acctatcaca ccccatccta aagtaaggtc agctaaataa gctatcgggc ccataccccg
|
||||||
|
aaaatgttgg ttataccctt cccgtactaa ttaatcccct ggcccaaccc gtcatctact
|
||||||
|
ctaccatctt tgcaggcaca ctcatcacag cgctaagctc gcactgattt tttacctgag
|
||||||
|
taggcctaga aataaacatg ctagctttta ttccagttct aaccaaaaaa ataaaccctc
|
||||||
|
gttccacaga agctgccatc aagtatttcc tcacgcaagc aaccgcatcc ataatccttc
|
||||||
|
taatagctat cctcttcaac aatatactct ccggacaatg aaccataacc aatactacca
|
||||||
|
atcaatactc atcattaata atcataatag ctatagcaat aaaactagga atagccccct
|
||||||
|
ttcacttctg agtcccagag gttacccaag gcacccctct gacatccggc ctgcttcttc
|
||||||
|
tcacatgaca aaaactagcc cccatctcaa tcatatacca aatctctccc tcactaaacg
|
||||||
|
taagccttct cctcactctc tcaatcttat ccatcatagc aggcagttga ggtggattaa
|
||||||
|
accaaaccca gctacgcaaa atcttagcat actcctcaat tacccacata ggatgaataa
|
||||||
|
tagcagttct accgtacaac cctaacataa ccattcttaa tttaactatt tatattatcc
|
||||||
|
taactactac cgcattccta ctactcaact taaactccag caccacgacc ctactactat
|
||||||
|
ctcgcacctg aaacaagcta acatgactaa cacccttaat tccatccacc ctcctctccc
|
||||||
|
taggaggcct gcccccgcta accggctttt tgcccaaatg ggccattatc gaagaattca
|
||||||
|
caaaaaacaa tagcctcatc atccccacca tcatagccac catcaccctc cttaacctct
|
||||||
|
acttctacct acgcctaatc tactccacct caatcacact actccccata tctaacaacg
|
||||||
|
taaaaataaa atgacagttt gaacatacaa aacccacccc attcctcccc acactcatcg
|
||||||
|
cccttaccac gctactccta cctatctccc cttttatact aataatctta tagaaattta
|
||||||
|
ggttaaatac agaccaagag ccttcaaagc cctcagtaag ttgcaatact taatttctgt
|
||||||
|
aacagctaag gactgcaaaa ccccactctg catcaactga acgcaaatca gccactttaa
|
||||||
|
ttaagctaag cccttactag accaatggga cttaaaccca caaacactta gttaacagct
|
||||||
|
aagcacccta atcaactggc ttcaatctac ttctcccgcc gccgggaaaa aaggcgggag
|
||||||
|
aagccccggc aggtttgaag ctgcttcttc gaatttgcaa ttcaatatga aaatcacctc
|
||||||
|
ggagctggta aaaagaggcc taacccctgt ctttagattt acagtccaat gcttcactca
|
||||||
|
gccattttac ctcaccccca ctgatgttcg ccgaccgttg actattctct acaaaccaca
|
||||||
|
aagacattgg aacactatac ctattattcg gcgcatgagc tggagtccta ggcacagctc
|
||||||
|
taagcctcct tattcgagcc gagctgggcc agccaggcaa ccttctaggt aacgaccaca
|
||||||
|
tctacaacgt tatcgtcaca gcccatgcat ttgtaataat cttcttcata gtaataccca
|
||||||
|
tcataatcgg aggctttggc aactgactag ttcccctaat aatcggtgcc cccgatatgg
|
||||||
|
cgtttccccg cataaacaac ataagcttct gactcttacc tccctctctc ctactcctgc
|
||||||
|
tcgcatctgc tatagtggag gccggagcag gaacaggttg aacagtctac cctcccttag
|
||||||
|
cagggaacta ctcccaccct ggagcctccg tagacctaac catcttctcc ttacacctag
|
||||||
|
caggtgtctc ctctatctta ggggccatca atttcatcac aacaattatc aatataaaac
|
||||||
|
cccctgccat aacccaatac caaacgcccc tcttcgtctg atccgtccta atcacagcag
|
||||||
|
tcctacttct cctatctctc ccagtcctag ctgctggcat cactatacta ctaacagacc
|
||||||
|
gcaacctcaa caccaccttc ttcgaccccg ccggaggagg agaccccatt ctataccaac
|
||||||
|
acctattctg atttttcggt caccctgaag tttatattct tatcctacca ggcttcggaa
|
||||||
|
taatctccca tattgtaact tactactccg gaaaaaaaga accatttgga tacataggta
|
||||||
|
tggtctgagc tatgatatca attggcttcc tagggtttat cgtgtgagca caccatatat
|
||||||
|
ttacagtagg aatagacgta gacacacgag catatttcac ctccgctacc ataatcatcg
|
||||||
|
ctatccccac cggcgtcaaa gtatttagct gactcgccac actccacgga agcaatatga
|
||||||
|
aatgatctgc tgcagtgctc tgagccctag gattcatctt tcttttcacc gtaggtggcc
|
||||||
|
tgactggcat tgtattagca aactcatcac tagacatcgt actacacgac acgtactacg
|
||||||
|
ttgtagccca cttccactat gtcctatcaa taggagctgt atttgccatc ataggaggct
|
||||||
|
tcattcactg atttccccta ttctcaggct acaccctaga ccaaacctac gccaaaatcc
|
||||||
|
atttcactat catattcatc ggcgtaaatc taactttctt cccacaacac tttctcggcc
|
||||||
|
tatccggaat gccccgacgt tactcggact accccgatgc atacaccaca tgaaacatcc
|
||||||
|
tatcatctgt aggctcattc atttctctaa cagcagtaat attaataatt ttcatgattt
|
||||||
|
gagaagcctt cgcttcgaag cgaaaagtcc taatagtaga agaaccctcc ataaacctgg
|
||||||
|
agtgactata tggatgcccc ccaccctacc acacattcga agaacccgta tacataaaat
|
||||||
|
ctagacaaaa aaggaaggaa tcgaaccccc caaagctggt ttcaagccaa ccccatggcc
|
||||||
|
tccatgactt tttcaaaaag gtattagaaa aaccatttca taactttgtc aaagttaaat
|
||||||
|
tataggctaa atcctatata tcttaatggc acatgcagcg caagtaggtc tacaagacgc
|
||||||
|
tacttcccct atcatagaag agcttatcac ctttcatgat cacgccctca taatcatttt
|
||||||
|
ccttatctgc ttcctagtcc tgtatgccct tttcctaaca ctcacaacaa aactaactaa
|
||||||
|
tactaacatc tcagacgctc aggaaataga aaccgtctga actatcctgc ccgccatcat
|
||||||
|
cctagtcctc atcgccctcc catccctacg catcctttac ataacagacg aggtcaacga
|
||||||
|
tccctccctt accatcaaat caattggcca ccaatggtac tgaacctacg agtacaccga
|
||||||
|
ctacggcgga ctaatcttca actcctacat acttccccca ttattcctag aaccaggcga
|
||||||
|
cctgcgactc cttgacgttg acaatcgagt agtactcccg attgaagccc ccattcgtat
|
||||||
|
aataattaca tcacaagacg tcttgcactc atgagctgtc cccacattag gcttaaaaac
|
||||||
|
agatgcaatt cccggacgtc taaaccaaac cactttcacc gctacacgac cgggggtata
|
||||||
|
ctacggtcaa tgctctgaaa tctgtggagc aaaccacagt ttcatgccca tcgtcctaga
|
||||||
|
attaattccc ctaaaaatct ttgaaatagg gcccgtattt accctatagc accccctcta
|
||||||
|
ccccctctag agcccactgt aaagctaact tagcattaac cttttaagtt aaagattaag
|
||||||
|
agaaccaaca cctctttaca gtgaaatgcc ccaactaaat actaccgtat ggcccaccat
|
||||||
|
aattaccccc atactcctta cactattcct catcacccaa ctaaaaatat taaacacaaa
|
||||||
|
ctaccaccta cctccctcac caaagcccat aaaaataaaa aattataaca aaccctgaga
|
||||||
|
accaaaatga acgaaaatct gttcgcttca ttcattgccc ccacaatcct aggcctaccc
|
||||||
|
gccgcagtac tgatcattct atttccccct ctattgatcc ccacctccaa atatctcatc
|
||||||
|
aacaaccgac taatcaccac ccaacaatga ctaatcaaac taacctcaaa acaaatgata
|
||||||
|
accatacaca acactaaagg acgaacctga tctcttatac tagtatcctt aatcattttt
|
||||||
|
attgccacaa ctaacctcct cggactcctg cctcactcat ttacaccaac cacccaacta
|
||||||
|
tctataaacc tagccatggc catcccctta tgagcgggca cagtgattat aggctttcgc
|
||||||
|
tctaagatta aaaatgccct agcccacttc ttaccacaag gcacacctac accccttatc
|
||||||
|
cccatactag ttattatcga aaccatcagc ctactcattc aaccaatagc cctggccgta
|
||||||
|
cgcctaaccg ctaacattac tgcaggccac ctactcatgc acctaattgg aagcgccacc
|
||||||
|
ctagcaatat caaccattaa ccttccctct acacttatca tcttcacaat tctaattcta
|
||||||
|
ctgactatcc tagaaatcgc tgtcgcctta atccaagcct acgttttcac acttctagta
|
||||||
|
agcctctacc tgcacgacaa cacataatga cccaccaatc acatgcctat catatagtaa
|
||||||
|
aacccagccc atgaccccta acaggggccc tctcagccct cctaatgacc tccggcctag
|
||||||
|
ccatgtgatt tcacttccac tccataacgc tcctcatact aggcctacta accaacacac
|
||||||
|
taaccatata ccaatgatgg cgcgatgtaa cacgagaaag cacataccaa ggccaccaca
|
||||||
|
caccacctgt ccaaaaaggc cttcgatacg ggataatcct atttattacc tcagaagttt
|
||||||
|
ttttcttcgc aggatttttc tgagcctttt accactccag cctagcccct accccccaat
|
||||||
|
taggagggca ctggccccca acaggcatca ccccgctaaa tcccctagaa gtcccactcc
|
||||||
|
taaacacatc cgtattactc gcatcaggag tatcaatcac ctgagctcac catagtctaa
|
||||||
|
tagaaaacaa ccgaaaccaa ataattcaag cactgcttat tacaatttta ctgggtctct
|
||||||
|
attttaccct cctacaagcc tcagagtact tcgagtctcc cttcaccatt tccgacggca
|
||||||
|
tctacggctc aacatttttt gtagccacag gcttccacgg acttcacgtc attattggct
|
||||||
|
caactttcct cactatctgc ttcatccgcc aactaatatt tcactttaca tccaaacatc
|
||||||
|
actttggctt cgaagccgcc gcctgatact ggcattttgt agatgtggtt tgactatttc
|
||||||
|
tgtatgtctc catctattga tgagggtctt actcttttag tataaatagt accgttaact
|
||||||
|
tccaattaac tagttttgac aacattcaaa aaagagtaat aaacttcgcc ttaattttaa
|
||||||
|
taatcaacac cctcctagcc ttactactaa taattattac attttgacta ccacaactca
|
||||||
|
acggctacat agaaaaatcc accccttacg agtgcggctt cgaccctata tcccccgccc
|
||||||
|
gcgtcccttt ctccataaaa ttcttcttag tagctattac cttcttatta tttgatctag
|
||||||
|
aaattgccct ccttttaccc ctaccatgag ccctacaaac aactaacctg ccactaatag
|
||||||
|
ttatgtcatc cctcttatta atcatcatcc tagccctaag tctggcctat gagtgactac
|
||||||
|
aaaaaggatt agactgaacc gaattggtat atagtttaaa caaaacgaat gatttcgact
|
||||||
|
cattaaatta tgataatcat atttaccaaa tgcccctcat ttacataaat attatactag
|
||||||
|
catttaccat ctcacttcta ggaatactag tatatcgctc acacctcata tcctccctac
|
||||||
|
tatgcctaga aggaataata ctatcgctgt tcattatagc tactctcata accctcaaca
|
||||||
|
cccactccct cttagccaat attgtgccta ttgccatact agtctttgcc gcctgcgaag
|
||||||
|
cagcggtggg cctagcccta ctagtctcaa tctccaacac atatggccta gactacgtac
|
||||||
|
ataacctaaa cctactccaa tgctaaaact aatcgtccca acaattatat tactaccact
|
||||||
|
gacatgactt tccaaaaaac acataatttg aatcaacaca accacccaca gcctaattat
|
||||||
|
tagcatcatc cctctactat tttttaacca aatcaacaac aacctattta gctgttcccc
|
||||||
|
aaccttttcc tccgaccccc taacaacccc cctcctaata ctaactacct gactcctacc
|
||||||
|
cctcacaatc atggcaagcc aacgccactt atccagtgaa ccactatcac gaaaaaaact
|
||||||
|
ctacctctct atactaatct ccctacaaat ctccttaatt ataacattca cagccacaga
|
||||||
|
actaatcata ttttatatct tcttcgaaac cacacttatc cccaccttgg ctatcatcac
|
||||||
|
ccgatgaggc aaccagccag aacgcctgaa cgcaggcaca tacttcctat tctacaccct
|
||||||
|
agtaggctcc cttcccctac tcatcgcact aatttacact cacaacaccc taggctcact
|
||||||
|
aaacattcta ctactcactc tcactgccca agaactatca aactcctgag ccaacaactt
|
||||||
|
aatatgacta gcttacacaa tagcttttat agtaaagata cctctttacg gactccactt
|
||||||
|
atgactccct aaagcccatg tcgaagcccc catcgctggg tcaatagtac ttgccgcagt
|
||||||
|
actcttaaaa ctaggcggct atggtataat acgcctcaca ctcattctca accccctgac
|
||||||
|
aaaacacata gcctacccct tccttgtact atccctatga ggcataatta taacaagctc
|
||||||
|
catctgccta cgacaaacag acctaaaatc gctcattgca tactcttcaa tcagccacat
|
||||||
|
agccctcgta gtaacagcca ttctcatcca aaccccctga agcttcaccg gcgcagtcat
|
||||||
|
tctcataatc gcccacgggc ttacatcctc attactattc tgcctagcaa actcaaacta
|
||||||
|
cgaacgcact cacagtcgca tcataatcct ctctcaagga cttcaaactc tactcccact
|
||||||
|
aatagctttt tgatgacttc tagcaagcct cgctaacctc gccttacccc ccactattaa
|
||||||
|
cctactggga gaactctctg tgctagtaac cacgttctcc tgatcaaata tcactctcct
|
||||||
|
acttacagga ctcaacatac tagtcacagc cctatactcc ctctacatat ttaccacaac
|
||||||
|
acaatggggc tcactcaccc accacattaa caacataaaa ccctcattca cacgagaaaa
|
||||||
|
caccctcatg ttcatacacc tatcccccat tctcctccta tccctcaacc ccgacatcat
|
||||||
|
taccgggttt tcctcttgta aatatagttt aaccaaaaca tcagattgtg aatctgacaa
|
||||||
|
cagaggctta cgacccctta tttaccgaga aagctcacaa gaactgctaa ctcatgcccc
|
||||||
|
catgtctaac aacatggctt tctcaacttt taaaggataa cagctatcca ttggtcttag
|
||||||
|
gccccaaaaa ttttggtgca actccaaata aaagtaataa ccatgcacac tactataacc
|
||||||
|
accctaaccc tgacttccct aattcccccc atccttacca ccctcgttaa ccctaacaaa
|
||||||
|
aaaaactcat acccccatta tgtaaaatcc attgtcgcat ccacctttat tatcagtctc
|
||||||
|
ttccccacaa caatattcat gtgcctagac caagaagtta ttatctcgaa ctgacactga
|
||||||
|
gccacaaccc aaacaaccca gctctcccta agcttcaaac tagactactt ctccataata
|
||||||
|
ttcatccctg tagcattgtt cgttacatgg tccatcatag aattctcact gtgatatata
|
||||||
|
aactcagacc caaacattaa tcagttcttc aaatatctac tcatcttcct aattaccata
|
||||||
|
ctaatcttag ttaccgctaa caacctattc caactgttca tcggctgaga gggcgtagga
|
||||||
|
attatatcct tcttgctcat cagttgatga tacgcccgag cagatgccaa cacagcagcc
|
||||||
|
attcaagcaa tcctatacaa ccgtatcggc gatatcggtt tcatcctcgc cttagcatga
|
||||||
|
tttatcctac actccaactc atgagaccca caacaaatag cccttctaaa cgctaatcca
|
||||||
|
agcctcaccc cactactagg cctcctccta gcagcagcag gcaaatcagc ccaattaggt
|
||||||
|
ctccacccct gactcccctc agccatagaa ggccccaccc cagtctcagc cctactccac
|
||||||
|
tcaagcacta tagttgtagc aggaatcttc ttactcatcc gcttccaccc cctagcagaa
|
||||||
|
aatagcccac taatccaaac tctaacacta tgcttaggcg ctatcaccac tctgttcgca
|
||||||
|
gcagtctgcg cccttacaca aaatgacatc aaaaaaatcg tagccttctc cacttcaagt
|
||||||
|
caactaggac tcataatagt tacaatcggc atcaaccaac cacacctagc attcctgcac
|
||||||
|
atctgtaccc acgccttctt caaagccata ctatttatgt gctccgggtc catcatccac
|
||||||
|
aaccttaaca atgaacaaga tattcgaaaa ataggaggac tactcaaaac catacctctc
|
||||||
|
acttcaacct ccctcaccat tggcagccta gcattagcag gaataccttt cctcacaggt
|
||||||
|
ttctactcca aagaccacat catcgaaacc gcaaacatat catacacaaa cgcctgagcc
|
||||||
|
ctatctatta ctctcatcgc tacctccctg acaagcgcct atagcactcg aataattctt
|
||||||
|
ctcaccctaa caggtcaacc tcgcttcccc acccttacta acattaacga aaataacccc
|
||||||
|
accctactaa accccattaa acgcctggca gccggaagcc tattcgcagg atttctcatt
|
||||||
|
actaacaaca tttcccccgc atcccccttc caaacaacaa tccccctcta cctaaaactc
|
||||||
|
acagccctcg ctgtcacttt cctaggactt ctaacagccc tagacctcaa ctacctaacc
|
||||||
|
aacaaactta aaataaaatc cccactatgc acattttatt tctccaacat actcggattc
|
||||||
|
taccctagca tcacacaccg cacaatcccc tatctaggcc ttcttacgag ccaaaacctg
|
||||||
|
cccctactcc tcctagacct aacctgacta gaaaagctat tacctaaaac aatttcacag
|
||||||
|
caccaaatct ccacctccat catcacctca acccaaaaag gcataattaa actttacttc
|
||||||
|
ctctctttct tcttcccact catcctaacc ctactcctaa tcacataacc tattcccccg
|
||||||
|
agcaatctca attacaatat atacaccaac aaacaatgtt caaccagtaa ctactactaa
|
||||||
|
tcaacgccca taatcataca aagcccccgc accaatagga tcctcccgaa tcaaccctga
|
||||||
|
cccctctcct tcataaatta ttcagcttcc tacactatta aagtttacca caaccaccac
|
||||||
|
cccatcatac tctttcaccc acagcaccaa tcctacctcc atcgctaacc ccactaaaac
|
||||||
|
actcaccaag acctcaaccc ctgaccccca tgcctcagga tactcctcaa tagccatcgc
|
||||||
|
tgtagtatat ccaaagacaa ccatcattcc ccctaaataa attaaaaaaa ctattaaacc
|
||||||
|
catataacct cccccaaaat tcagaataat aacacacccg accacaccgc taacaatcaa
|
||||||
|
tactaaaccc ccataaatag gagaaggctt agaagaaaac cccacaaacc ccattactaa
|
||||||
|
acccacactc aacagaaaca aagcatacat cattattctc gcacggacta caaccacgac
|
||||||
|
caatgatatg aaaaaccatc gttgtatttc aactacaaga acaccaatga ccccaatacg
|
||||||
|
caaaactaac cccctaataa aattaattaa ccactcattc atcgacctcc ccaccccatc
|
||||||
|
caacatctcc gcatgatgaa acttcggctc actccttggc gcctgcctga tcctccaaat
|
||||||
|
caccacagga ctattcctag ccatgcacta ctcaccagac gcctcaaccg ccttttcatc
|
||||||
|
aatcgcccac atcactcgag acgtaaatta tggctgaatc atccgctacc ttcacgccaa
|
||||||
|
tggcgcctca atattcttta tctgcctctt cctacacatc gggcgaggcc tatattacgg
|
||||||
|
atcatttctc tactcagaaa cctgaaacat cggcattatc ctcctgcttg caactatagc
|
||||||
|
aacagccttc ataggctatg tcctcccgtg aggccaaata tcattctgag gggccacagt
|
||||||
|
aattacaaac ttactatccg ccatcccata cattgggaca gacctagttc aatgaatctg
|
||||||
|
aggaggctac tcagtagaca gtcccaccct cacacgattc tttacctttc acttcatctt
|
||||||
|
gcccttcatt attgcagccc tagcaacact ccacctccta ttcttgcacg aaacgggatc
|
||||||
|
aaacaacccc ctaggaatca cctcccattc cgataaaatc accttccacc cttactacac
|
||||||
|
aatcaaagac gccctcggct tacttctctt ccttctctcc ttaatgacat taacactatt
|
||||||
|
ctcaccagac ctcctaggcg acccagacaa ttatacccta gccaacccct taaacacccc
|
||||||
|
tccccacatc aagcccgaat gatatttcct attcgcctac acaattctcc gatccgtccc
|
||||||
|
taacaaacta ggaggcgtcc ttgccctatt actatccatc ctcatcctag caataatccc
|
||||||
|
catcctccat atatccaaac aacaaagcat aatatttcgc ccactaagcc aatcacttta
|
||||||
|
ttgactccta gccgcagacc tcctcattct aacctgaatc ggaggacaac cagtaagcta
|
||||||
|
cccttttacc atcattggac aagtagcatc cgtactatac ttcacaacaa tcctaatcct
|
||||||
|
aataccaact atctccctaa ttgaaaacaa aatactcaaa tgggcctgtc cttgtagtat
|
||||||
|
aaactaatac accagtcttg taaaccggag atgaaaacct ttttccaagg acaaatcaga
|
||||||
|
gaaaaagtct ttaactccac cattagcacc caaagctaag attctaattt aaactattct
|
||||||
|
ctgttctttc atggggaagc agatttgggt accacccaag tattgactca cccatcaaca
|
||||||
|
accgctatgt atttcgtaca ttactgccag ccaccatgaa tattgtacgg taccataaat
|
||||||
|
acttgaccac ctgtagtaca taaaaaccca atccacatca aaaccccctc cccatgctta
|
||||||
|
caagcaagta cagcaatcaa ccctcaacta tcacacatca actgcaactc caaagccacc
|
||||||
|
cctcacccac taggatacca acaaacctac ccacccttaa cagtacatag tacataaagc
|
||||||
|
catttaccgt acatagcaca ttacagtcaa atcccttctc gtccccatgg atgacccccc
|
||||||
|
tcagataggg gtcccttgac caccatcctc cgtgaaatca atatcccgca caagagtgct
|
||||||
|
actctcctcg ctccgggccc ataacacttg ggggtagcta aagtgaactg tatccgacat
|
||||||
|
ctggttccta cttcagggtc ataaagccta aatagcccac acgttcccct taaataagac
|
||||||
|
atcacgatg
|
||||||
@@ -0,0 +1,3 @@
|
|||||||
|
This algorithm becomes impracticle at about 25,000 entries due to memory allocation.
|
||||||
|
|
||||||
|
Given larger storage this algorithm is incredibly fast.
|
||||||
53
HW1/.idea/workspace.xml
generated
53
HW1/.idea/workspace.xml
generated
@@ -1,53 +0,0 @@
|
|||||||
<?xml version="1.0" encoding="UTF-8"?>
|
|
||||||
<project version="4">
|
|
||||||
<component name="ChangeListManager">
|
|
||||||
<list default="true" id="19f33c01-5bb2-43f2-8d6d-7eca38041035" name="Default Changelist" comment="" />
|
|
||||||
<option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />
|
|
||||||
<option name="SHOW_DIALOG" value="false" />
|
|
||||||
<option name="HIGHLIGHT_CONFLICTS" value="true" />
|
|
||||||
<option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
|
|
||||||
<option name="LAST_RESOLUTION" value="IGNORE" />
|
|
||||||
</component>
|
|
||||||
<component name="FileTemplateManagerImpl">
|
|
||||||
<option name="RECENT_TEMPLATES">
|
|
||||||
<list>
|
|
||||||
<option value="Python Script" />
|
|
||||||
</list>
|
|
||||||
</option>
|
|
||||||
</component>
|
|
||||||
<component name="ProjectId" id="1WMs8kHEuQFz0MrUaB8LAS4fMg2" />
|
|
||||||
<component name="PropertiesComponent">
|
|
||||||
<property name="WebServerToolWindowFactoryState" value="false" />
|
|
||||||
<property name="settings.editor.selected.configurable" value="com.jetbrains.python.configuration.PyActiveSdkModuleConfigurable" />
|
|
||||||
</component>
|
|
||||||
<component name="RunDashboard">
|
|
||||||
<option name="ruleStates">
|
|
||||||
<list>
|
|
||||||
<RuleState>
|
|
||||||
<option name="name" value="ConfigurationTypeDashboardGroupingRule" />
|
|
||||||
</RuleState>
|
|
||||||
<RuleState>
|
|
||||||
<option name="name" value="StatusDashboardGroupingRule" />
|
|
||||||
</RuleState>
|
|
||||||
</list>
|
|
||||||
</option>
|
|
||||||
</component>
|
|
||||||
<component name="SvnConfiguration">
|
|
||||||
<configuration />
|
|
||||||
</component>
|
|
||||||
<component name="TaskManager">
|
|
||||||
<task active="true" id="Default" summary="Default task">
|
|
||||||
<changelist id="19f33c01-5bb2-43f2-8d6d-7eca38041035" name="Default Changelist" comment="" />
|
|
||||||
<created>1578970640423</created>
|
|
||||||
<option name="number" value="Default" />
|
|
||||||
<option name="presentableId" value="Default" />
|
|
||||||
<updated>1578970640423</updated>
|
|
||||||
<workItem from="1578970648201" duration="1203000" />
|
|
||||||
<workItem from="1578972146851" duration="1094000" />
|
|
||||||
</task>
|
|
||||||
<servers />
|
|
||||||
</component>
|
|
||||||
<component name="TypeScriptGeneratedFilesManager">
|
|
||||||
<option name="version" value="1" />
|
|
||||||
</component>
|
|
||||||
</project>
|
|
||||||
@@ -1,5 +0,0 @@
|
|||||||
import sys
|
|
||||||
|
|
||||||
def main():
|
|
||||||
t = "hello"
|
|
||||||
print(t);
|
|
||||||
12
HW1/env/bin/pip3
vendored
12
HW1/env/bin/pip3
vendored
@@ -1,12 +0,0 @@
|
|||||||
#!/Users/bradybodily/Repositories/CS5050_Advanced_Algorithms/HW1/env/bin/python
|
|
||||||
# EASY-INSTALL-ENTRY-SCRIPT: 'pip==19.0.3','console_scripts','pip3'
|
|
||||||
__requires__ = 'pip==19.0.3'
|
|
||||||
import re
|
|
||||||
import sys
|
|
||||||
from pkg_resources import load_entry_point
|
|
||||||
|
|
||||||
if __name__ == '__main__':
|
|
||||||
sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
|
|
||||||
sys.exit(
|
|
||||||
load_entry_point('pip==19.0.3', 'console_scripts', 'pip3')()
|
|
||||||
)
|
|
||||||
BIN
HW1/env/bin/python3.7
vendored
BIN
HW1/env/bin/python3.7
vendored
Binary file not shown.
3
HW1/env/pyvenv.cfg
vendored
3
HW1/env/pyvenv.cfg
vendored
@@ -1,3 +0,0 @@
|
|||||||
home = /usr/local/bin
|
|
||||||
include-system-site-packages = false
|
|
||||||
version = 3.7.6
|
|
||||||
@@ -1,76 +0,0 @@
|
|||||||
# This file must be used with "source bin/activate" *from bash*
|
|
||||||
# you cannot run it directly
|
|
||||||
|
|
||||||
deactivate () {
|
|
||||||
# reset old environment variables
|
|
||||||
if [ -n "${_OLD_VIRTUAL_PATH:-}" ] ; then
|
|
||||||
PATH="${_OLD_VIRTUAL_PATH:-}"
|
|
||||||
export PATH
|
|
||||||
unset _OLD_VIRTUAL_PATH
|
|
||||||
fi
|
|
||||||
if [ -n "${_OLD_VIRTUAL_PYTHONHOME:-}" ] ; then
|
|
||||||
PYTHONHOME="${_OLD_VIRTUAL_PYTHONHOME:-}"
|
|
||||||
export PYTHONHOME
|
|
||||||
unset _OLD_VIRTUAL_PYTHONHOME
|
|
||||||
fi
|
|
||||||
|
|
||||||
# This should detect bash and zsh, which have a hash command that must
|
|
||||||
# be called to get it to forget past commands. Without forgetting
|
|
||||||
# past commands the $PATH changes we made may not be respected
|
|
||||||
if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then
|
|
||||||
hash -r
|
|
||||||
fi
|
|
||||||
|
|
||||||
if [ -n "${_OLD_VIRTUAL_PS1:-}" ] ; then
|
|
||||||
PS1="${_OLD_VIRTUAL_PS1:-}"
|
|
||||||
export PS1
|
|
||||||
unset _OLD_VIRTUAL_PS1
|
|
||||||
fi
|
|
||||||
|
|
||||||
unset VIRTUAL_ENV
|
|
||||||
if [ ! "$1" = "nondestructive" ] ; then
|
|
||||||
# Self destruct!
|
|
||||||
unset -f deactivate
|
|
||||||
fi
|
|
||||||
}
|
|
||||||
|
|
||||||
# unset irrelevant variables
|
|
||||||
deactivate nondestructive
|
|
||||||
|
|
||||||
VIRTUAL_ENV="/Users/bradybodily/Repositories/CS5050_Advanced_Algorithms/HW1/venv"
|
|
||||||
export VIRTUAL_ENV
|
|
||||||
|
|
||||||
_OLD_VIRTUAL_PATH="$PATH"
|
|
||||||
PATH="$VIRTUAL_ENV/bin:$PATH"
|
|
||||||
export PATH
|
|
||||||
|
|
||||||
# unset PYTHONHOME if set
|
|
||||||
# this will fail if PYTHONHOME is set to the empty string (which is bad anyway)
|
|
||||||
# could use `if (set -u; : $PYTHONHOME) ;` in bash
|
|
||||||
if [ -n "${PYTHONHOME:-}" ] ; then
|
|
||||||
_OLD_VIRTUAL_PYTHONHOME="${PYTHONHOME:-}"
|
|
||||||
unset PYTHONHOME
|
|
||||||
fi
|
|
||||||
|
|
||||||
if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT:-}" ] ; then
|
|
||||||
_OLD_VIRTUAL_PS1="${PS1:-}"
|
|
||||||
if [ "x(venv) " != x ] ; then
|
|
||||||
PS1="(venv) ${PS1:-}"
|
|
||||||
else
|
|
||||||
if [ "`basename \"$VIRTUAL_ENV\"`" = "__" ] ; then
|
|
||||||
# special case for Aspen magic directories
|
|
||||||
# see http://www.zetadev.com/software/aspen/
|
|
||||||
PS1="[`basename \`dirname \"$VIRTUAL_ENV\"\``] $PS1"
|
|
||||||
else
|
|
||||||
PS1="(`basename \"$VIRTUAL_ENV\"`)$PS1"
|
|
||||||
fi
|
|
||||||
fi
|
|
||||||
export PS1
|
|
||||||
fi
|
|
||||||
|
|
||||||
# This should detect bash and zsh, which have a hash command that must
|
|
||||||
# be called to get it to forget past commands. Without forgetting
|
|
||||||
# past commands the $PATH changes we made may not be respected
|
|
||||||
if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then
|
|
||||||
hash -r
|
|
||||||
fi
|
|
||||||
@@ -1,37 +0,0 @@
|
|||||||
# This file must be used with "source bin/activate.csh" *from csh*.
|
|
||||||
# You cannot run it directly.
|
|
||||||
# Created by Davide Di Blasi <davidedb@gmail.com>.
|
|
||||||
# Ported to Python 3.3 venv by Andrew Svetlov <andrew.svetlov@gmail.com>
|
|
||||||
|
|
||||||
alias deactivate 'test $?_OLD_VIRTUAL_PATH != 0 && setenv PATH "$_OLD_VIRTUAL_PATH" && unset _OLD_VIRTUAL_PATH; rehash; test $?_OLD_VIRTUAL_PROMPT != 0 && set prompt="$_OLD_VIRTUAL_PROMPT" && unset _OLD_VIRTUAL_PROMPT; unsetenv VIRTUAL_ENV; test "\!:*" != "nondestructive" && unalias deactivate'
|
|
||||||
|
|
||||||
# Unset irrelevant variables.
|
|
||||||
deactivate nondestructive
|
|
||||||
|
|
||||||
setenv VIRTUAL_ENV "/Users/bradybodily/Repositories/CS5050_Advanced_Algorithms/HW1/venv"
|
|
||||||
|
|
||||||
set _OLD_VIRTUAL_PATH="$PATH"
|
|
||||||
setenv PATH "$VIRTUAL_ENV/bin:$PATH"
|
|
||||||
|
|
||||||
|
|
||||||
set _OLD_VIRTUAL_PROMPT="$prompt"
|
|
||||||
|
|
||||||
if (! "$?VIRTUAL_ENV_DISABLE_PROMPT") then
|
|
||||||
if ("venv" != "") then
|
|
||||||
set env_name = "venv"
|
|
||||||
else
|
|
||||||
if (`basename "VIRTUAL_ENV"` == "__") then
|
|
||||||
# special case for Aspen magic directories
|
|
||||||
# see http://www.zetadev.com/software/aspen/
|
|
||||||
set env_name = `basename \`dirname "$VIRTUAL_ENV"\``
|
|
||||||
else
|
|
||||||
set env_name = `basename "$VIRTUAL_ENV"`
|
|
||||||
endif
|
|
||||||
endif
|
|
||||||
set prompt = "[$env_name] $prompt"
|
|
||||||
unset env_name
|
|
||||||
endif
|
|
||||||
|
|
||||||
alias pydoc python -m pydoc
|
|
||||||
|
|
||||||
rehash
|
|
||||||
@@ -1,75 +0,0 @@
|
|||||||
# This file must be used with ". bin/activate.fish" *from fish* (http://fishshell.org)
|
|
||||||
# you cannot run it directly
|
|
||||||
|
|
||||||
function deactivate -d "Exit virtualenv and return to normal shell environment"
|
|
||||||
# reset old environment variables
|
|
||||||
if test -n "$_OLD_VIRTUAL_PATH"
|
|
||||||
set -gx PATH $_OLD_VIRTUAL_PATH
|
|
||||||
set -e _OLD_VIRTUAL_PATH
|
|
||||||
end
|
|
||||||
if test -n "$_OLD_VIRTUAL_PYTHONHOME"
|
|
||||||
set -gx PYTHONHOME $_OLD_VIRTUAL_PYTHONHOME
|
|
||||||
set -e _OLD_VIRTUAL_PYTHONHOME
|
|
||||||
end
|
|
||||||
|
|
||||||
if test -n "$_OLD_FISH_PROMPT_OVERRIDE"
|
|
||||||
functions -e fish_prompt
|
|
||||||
set -e _OLD_FISH_PROMPT_OVERRIDE
|
|
||||||
functions -c _old_fish_prompt fish_prompt
|
|
||||||
functions -e _old_fish_prompt
|
|
||||||
end
|
|
||||||
|
|
||||||
set -e VIRTUAL_ENV
|
|
||||||
if test "$argv[1]" != "nondestructive"
|
|
||||||
# Self destruct!
|
|
||||||
functions -e deactivate
|
|
||||||
end
|
|
||||||
end
|
|
||||||
|
|
||||||
# unset irrelevant variables
|
|
||||||
deactivate nondestructive
|
|
||||||
|
|
||||||
set -gx VIRTUAL_ENV "/Users/bradybodily/Repositories/CS5050_Advanced_Algorithms/HW1/venv"
|
|
||||||
|
|
||||||
set -gx _OLD_VIRTUAL_PATH $PATH
|
|
||||||
set -gx PATH "$VIRTUAL_ENV/bin" $PATH
|
|
||||||
|
|
||||||
# unset PYTHONHOME if set
|
|
||||||
if set -q PYTHONHOME
|
|
||||||
set -gx _OLD_VIRTUAL_PYTHONHOME $PYTHONHOME
|
|
||||||
set -e PYTHONHOME
|
|
||||||
end
|
|
||||||
|
|
||||||
if test -z "$VIRTUAL_ENV_DISABLE_PROMPT"
|
|
||||||
# fish uses a function instead of an env var to generate the prompt.
|
|
||||||
|
|
||||||
# save the current fish_prompt function as the function _old_fish_prompt
|
|
||||||
functions -c fish_prompt _old_fish_prompt
|
|
||||||
|
|
||||||
# with the original prompt function renamed, we can override with our own.
|
|
||||||
function fish_prompt
|
|
||||||
# Save the return status of the last command
|
|
||||||
set -l old_status $status
|
|
||||||
|
|
||||||
# Prompt override?
|
|
||||||
if test -n "(venv) "
|
|
||||||
printf "%s%s" "(venv) " (set_color normal)
|
|
||||||
else
|
|
||||||
# ...Otherwise, prepend env
|
|
||||||
set -l _checkbase (basename "$VIRTUAL_ENV")
|
|
||||||
if test $_checkbase = "__"
|
|
||||||
# special case for Aspen magic directories
|
|
||||||
# see http://www.zetadev.com/software/aspen/
|
|
||||||
printf "%s[%s]%s " (set_color -b blue white) (basename (dirname "$VIRTUAL_ENV")) (set_color normal)
|
|
||||||
else
|
|
||||||
printf "%s(%s)%s" (set_color -b blue white) (basename "$VIRTUAL_ENV") (set_color normal)
|
|
||||||
end
|
|
||||||
end
|
|
||||||
|
|
||||||
# Restore the return status of the previous command.
|
|
||||||
echo "exit $old_status" | .
|
|
||||||
_old_fish_prompt
|
|
||||||
end
|
|
||||||
|
|
||||||
set -gx _OLD_FISH_PROMPT_OVERRIDE "$VIRTUAL_ENV"
|
|
||||||
end
|
|
||||||
@@ -1,12 +0,0 @@
|
|||||||
#!/Users/bradybodily/Repositories/CS5050_Advanced_Algorithms/HW1/venv/bin/python
|
|
||||||
# EASY-INSTALL-ENTRY-SCRIPT: 'setuptools==40.8.0','console_scripts','easy_install'
|
|
||||||
__requires__ = 'setuptools==40.8.0'
|
|
||||||
import re
|
|
||||||
import sys
|
|
||||||
from pkg_resources import load_entry_point
|
|
||||||
|
|
||||||
if __name__ == '__main__':
|
|
||||||
sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
|
|
||||||
sys.exit(
|
|
||||||
load_entry_point('setuptools==40.8.0', 'console_scripts', 'easy_install')()
|
|
||||||
)
|
|
||||||
@@ -1,12 +0,0 @@
|
|||||||
#!/Users/bradybodily/Repositories/CS5050_Advanced_Algorithms/HW1/venv/bin/python
|
|
||||||
# EASY-INSTALL-ENTRY-SCRIPT: 'setuptools==40.8.0','console_scripts','easy_install-3.6'
|
|
||||||
__requires__ = 'setuptools==40.8.0'
|
|
||||||
import re
|
|
||||||
import sys
|
|
||||||
from pkg_resources import load_entry_point
|
|
||||||
|
|
||||||
if __name__ == '__main__':
|
|
||||||
sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
|
|
||||||
sys.exit(
|
|
||||||
load_entry_point('setuptools==40.8.0', 'console_scripts', 'easy_install-3.6')()
|
|
||||||
)
|
|
||||||
@@ -1,12 +0,0 @@
|
|||||||
#!/Users/bradybodily/Repositories/CS5050_Advanced_Algorithms/HW1/venv/bin/python
|
|
||||||
# EASY-INSTALL-ENTRY-SCRIPT: 'pip==19.0.3','console_scripts','pip'
|
|
||||||
__requires__ = 'pip==19.0.3'
|
|
||||||
import re
|
|
||||||
import sys
|
|
||||||
from pkg_resources import load_entry_point
|
|
||||||
|
|
||||||
if __name__ == '__main__':
|
|
||||||
sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
|
|
||||||
sys.exit(
|
|
||||||
load_entry_point('pip==19.0.3', 'console_scripts', 'pip')()
|
|
||||||
)
|
|
||||||
@@ -1,12 +0,0 @@
|
|||||||
#!/Users/bradybodily/Repositories/CS5050_Advanced_Algorithms/HW1/venv/bin/python
|
|
||||||
# EASY-INSTALL-ENTRY-SCRIPT: 'pip==19.0.3','console_scripts','pip3.6'
|
|
||||||
__requires__ = 'pip==19.0.3'
|
|
||||||
import re
|
|
||||||
import sys
|
|
||||||
from pkg_resources import load_entry_point
|
|
||||||
|
|
||||||
if __name__ == '__main__':
|
|
||||||
sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
|
|
||||||
sys.exit(
|
|
||||||
load_entry_point('pip==19.0.3', 'console_scripts', 'pip3.6')()
|
|
||||||
)
|
|
||||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
@@ -1,2 +0,0 @@
|
|||||||
./setuptools-40.8.0-py3.6.egg
|
|
||||||
./pip-19.0.3-py3.6.egg
|
|
||||||
@@ -1,73 +0,0 @@
|
|||||||
Metadata-Version: 1.2
|
|
||||||
Name: pip
|
|
||||||
Version: 19.0.3
|
|
||||||
Summary: The PyPA recommended tool for installing Python packages.
|
|
||||||
Home-page: https://pip.pypa.io/
|
|
||||||
Author: The pip developers
|
|
||||||
Author-email: pypa-dev@groups.google.com
|
|
||||||
License: MIT
|
|
||||||
Description: pip - The Python Package Installer
|
|
||||||
==================================
|
|
||||||
|
|
||||||
.. image:: https://img.shields.io/pypi/v/pip.svg
|
|
||||||
:target: https://pypi.org/project/pip/
|
|
||||||
|
|
||||||
.. image:: https://readthedocs.org/projects/pip/badge/?version=latest
|
|
||||||
:target: https://pip.pypa.io/en/latest
|
|
||||||
|
|
||||||
pip is the `package installer`_ for Python. You can use pip to install packages from the `Python Package Index`_ and other indexes.
|
|
||||||
|
|
||||||
Please take a look at our documentation for how to install and use pip:
|
|
||||||
|
|
||||||
* `Installation`_
|
|
||||||
* `Usage`_
|
|
||||||
* `Release notes`_
|
|
||||||
|
|
||||||
If you find bugs, need help, or want to talk to the developers please use our mailing lists or chat rooms:
|
|
||||||
|
|
||||||
* `Issue tracking`_
|
|
||||||
* `Discourse channel`_
|
|
||||||
* `User IRC`_
|
|
||||||
|
|
||||||
If you want to get involved head over to GitHub to get the source code and feel free to jump on the developer mailing lists and chat rooms:
|
|
||||||
|
|
||||||
* `GitHub page`_
|
|
||||||
* `Dev mailing list`_
|
|
||||||
* `Dev IRC`_
|
|
||||||
|
|
||||||
Code of Conduct
|
|
||||||
---------------
|
|
||||||
|
|
||||||
Everyone interacting in the pip project's codebases, issue trackers, chat
|
|
||||||
rooms, and mailing lists is expected to follow the `PyPA Code of Conduct`_.
|
|
||||||
|
|
||||||
.. _package installer: https://packaging.python.org/en/latest/current/
|
|
||||||
.. _Python Package Index: https://pypi.org
|
|
||||||
.. _Installation: https://pip.pypa.io/en/stable/installing.html
|
|
||||||
.. _Usage: https://pip.pypa.io/en/stable/
|
|
||||||
.. _Release notes: https://pip.pypa.io/en/stable/news.html
|
|
||||||
.. _GitHub page: https://github.com/pypa/pip
|
|
||||||
.. _Issue tracking: https://github.com/pypa/pip/issues
|
|
||||||
.. _Discourse channel: https://discuss.python.org/c/packaging
|
|
||||||
.. _Dev mailing list: https://groups.google.com/forum/#!forum/pypa-dev
|
|
||||||
.. _User IRC: https://webchat.freenode.net/?channels=%23pypa
|
|
||||||
.. _Dev IRC: https://webchat.freenode.net/?channels=%23pypa-dev
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.. _PyPA Code of Conduct: https://www.pypa.io/en/latest/code-of-conduct/
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|
||||||
src/pip/_vendor/packaging/requirements.py
|
|
||||||
src/pip/_vendor/packaging/specifiers.py
|
|
||||||
src/pip/_vendor/packaging/utils.py
|
|
||||||
src/pip/_vendor/packaging/version.py
|
|
||||||
src/pip/_vendor/pep517/LICENSE
|
|
||||||
src/pip/_vendor/pep517/__init__.py
|
|
||||||
src/pip/_vendor/pep517/_in_process.py
|
|
||||||
src/pip/_vendor/pep517/build.py
|
|
||||||
src/pip/_vendor/pep517/check.py
|
|
||||||
src/pip/_vendor/pep517/colorlog.py
|
|
||||||
src/pip/_vendor/pep517/compat.py
|
|
||||||
src/pip/_vendor/pep517/envbuild.py
|
|
||||||
src/pip/_vendor/pep517/wrappers.py
|
|
||||||
src/pip/_vendor/pkg_resources/LICENSE
|
|
||||||
src/pip/_vendor/pkg_resources/__init__.py
|
|
||||||
src/pip/_vendor/pkg_resources/py31compat.py
|
|
||||||
src/pip/_vendor/progress/LICENSE
|
|
||||||
src/pip/_vendor/progress/__init__.py
|
|
||||||
src/pip/_vendor/progress/bar.py
|
|
||||||
src/pip/_vendor/progress/counter.py
|
|
||||||
src/pip/_vendor/progress/helpers.py
|
|
||||||
src/pip/_vendor/progress/spinner.py
|
|
||||||
src/pip/_vendor/pytoml/LICENSE
|
|
||||||
src/pip/_vendor/pytoml/__init__.py
|
|
||||||
src/pip/_vendor/pytoml/core.py
|
|
||||||
src/pip/_vendor/pytoml/parser.py
|
|
||||||
src/pip/_vendor/pytoml/test.py
|
|
||||||
src/pip/_vendor/pytoml/utils.py
|
|
||||||
src/pip/_vendor/pytoml/writer.py
|
|
||||||
src/pip/_vendor/requests/LICENSE
|
|
||||||
src/pip/_vendor/requests/__init__.py
|
|
||||||
src/pip/_vendor/requests/__version__.py
|
|
||||||
src/pip/_vendor/requests/_internal_utils.py
|
|
||||||
src/pip/_vendor/requests/adapters.py
|
|
||||||
src/pip/_vendor/requests/api.py
|
|
||||||
src/pip/_vendor/requests/auth.py
|
|
||||||
src/pip/_vendor/requests/certs.py
|
|
||||||
src/pip/_vendor/requests/compat.py
|
|
||||||
src/pip/_vendor/requests/cookies.py
|
|
||||||
src/pip/_vendor/requests/exceptions.py
|
|
||||||
src/pip/_vendor/requests/help.py
|
|
||||||
src/pip/_vendor/requests/hooks.py
|
|
||||||
src/pip/_vendor/requests/models.py
|
|
||||||
src/pip/_vendor/requests/packages.py
|
|
||||||
src/pip/_vendor/requests/sessions.py
|
|
||||||
src/pip/_vendor/requests/status_codes.py
|
|
||||||
src/pip/_vendor/requests/structures.py
|
|
||||||
src/pip/_vendor/requests/utils.py
|
|
||||||
src/pip/_vendor/urllib3/LICENSE.txt
|
|
||||||
src/pip/_vendor/urllib3/__init__.py
|
|
||||||
src/pip/_vendor/urllib3/_collections.py
|
|
||||||
src/pip/_vendor/urllib3/connection.py
|
|
||||||
src/pip/_vendor/urllib3/connectionpool.py
|
|
||||||
src/pip/_vendor/urllib3/exceptions.py
|
|
||||||
src/pip/_vendor/urllib3/fields.py
|
|
||||||
src/pip/_vendor/urllib3/filepost.py
|
|
||||||
src/pip/_vendor/urllib3/poolmanager.py
|
|
||||||
src/pip/_vendor/urllib3/request.py
|
|
||||||
src/pip/_vendor/urllib3/response.py
|
|
||||||
src/pip/_vendor/urllib3/contrib/__init__.py
|
|
||||||
src/pip/_vendor/urllib3/contrib/_appengine_environ.py
|
|
||||||
src/pip/_vendor/urllib3/contrib/appengine.py
|
|
||||||
src/pip/_vendor/urllib3/contrib/ntlmpool.py
|
|
||||||
src/pip/_vendor/urllib3/contrib/pyopenssl.py
|
|
||||||
src/pip/_vendor/urllib3/contrib/securetransport.py
|
|
||||||
src/pip/_vendor/urllib3/contrib/socks.py
|
|
||||||
src/pip/_vendor/urllib3/contrib/_securetransport/__init__.py
|
|
||||||
src/pip/_vendor/urllib3/contrib/_securetransport/bindings.py
|
|
||||||
src/pip/_vendor/urllib3/contrib/_securetransport/low_level.py
|
|
||||||
src/pip/_vendor/urllib3/packages/__init__.py
|
|
||||||
src/pip/_vendor/urllib3/packages/six.py
|
|
||||||
src/pip/_vendor/urllib3/packages/backports/__init__.py
|
|
||||||
src/pip/_vendor/urllib3/packages/backports/makefile.py
|
|
||||||
src/pip/_vendor/urllib3/packages/ssl_match_hostname/__init__.py
|
|
||||||
src/pip/_vendor/urllib3/packages/ssl_match_hostname/_implementation.py
|
|
||||||
src/pip/_vendor/urllib3/util/__init__.py
|
|
||||||
src/pip/_vendor/urllib3/util/connection.py
|
|
||||||
src/pip/_vendor/urllib3/util/queue.py
|
|
||||||
src/pip/_vendor/urllib3/util/request.py
|
|
||||||
src/pip/_vendor/urllib3/util/response.py
|
|
||||||
src/pip/_vendor/urllib3/util/retry.py
|
|
||||||
src/pip/_vendor/urllib3/util/ssl_.py
|
|
||||||
src/pip/_vendor/urllib3/util/timeout.py
|
|
||||||
src/pip/_vendor/urllib3/util/url.py
|
|
||||||
src/pip/_vendor/urllib3/util/wait.py
|
|
||||||
src/pip/_vendor/webencodings/LICENSE
|
|
||||||
src/pip/_vendor/webencodings/__init__.py
|
|
||||||
src/pip/_vendor/webencodings/labels.py
|
|
||||||
src/pip/_vendor/webencodings/mklabels.py
|
|
||||||
src/pip/_vendor/webencodings/tests.py
|
|
||||||
src/pip/_vendor/webencodings/x_user_defined.py
|
|
||||||
@@ -1 +0,0 @@
|
|||||||
|
|
||||||
@@ -1,5 +0,0 @@
|
|||||||
[console_scripts]
|
|
||||||
pip = pip._internal:main
|
|
||||||
pip3 = pip._internal:main
|
|
||||||
pip3.6 = pip._internal:main
|
|
||||||
|
|
||||||
@@ -1 +0,0 @@
|
|||||||
|
|
||||||
@@ -1 +0,0 @@
|
|||||||
pip
|
|
||||||
@@ -1 +0,0 @@
|
|||||||
__version__ = "19.0.3"
|
|
||||||
@@ -1,19 +0,0 @@
|
|||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import os
|
|
||||||
import sys
|
|
||||||
|
|
||||||
# If we are running from a wheel, add the wheel to sys.path
|
|
||||||
# This allows the usage python pip-*.whl/pip install pip-*.whl
|
|
||||||
if __package__ == '':
|
|
||||||
# __file__ is pip-*.whl/pip/__main__.py
|
|
||||||
# first dirname call strips of '/__main__.py', second strips off '/pip'
|
|
||||||
# Resulting path is the name of the wheel itself
|
|
||||||
# Add that to sys.path so we can import pip
|
|
||||||
path = os.path.dirname(os.path.dirname(__file__))
|
|
||||||
sys.path.insert(0, path)
|
|
||||||
|
|
||||||
from pip._internal import main as _main # isort:skip # noqa
|
|
||||||
|
|
||||||
if __name__ == '__main__':
|
|
||||||
sys.exit(_main())
|
|
||||||
@@ -1,78 +0,0 @@
|
|||||||
#!/usr/bin/env python
|
|
||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import locale
|
|
||||||
import logging
|
|
||||||
import os
|
|
||||||
import warnings
|
|
||||||
|
|
||||||
import sys
|
|
||||||
|
|
||||||
# 2016-06-17 barry@debian.org: urllib3 1.14 added optional support for socks,
|
|
||||||
# but if invoked (i.e. imported), it will issue a warning to stderr if socks
|
|
||||||
# isn't available. requests unconditionally imports urllib3's socks contrib
|
|
||||||
# module, triggering this warning. The warning breaks DEP-8 tests (because of
|
|
||||||
# the stderr output) and is just plain annoying in normal usage. I don't want
|
|
||||||
# to add socks as yet another dependency for pip, nor do I want to allow-stder
|
|
||||||
# in the DEP-8 tests, so just suppress the warning. pdb tells me this has to
|
|
||||||
# be done before the import of pip.vcs.
|
|
||||||
from pip._vendor.urllib3.exceptions import DependencyWarning
|
|
||||||
warnings.filterwarnings("ignore", category=DependencyWarning) # noqa
|
|
||||||
|
|
||||||
# We want to inject the use of SecureTransport as early as possible so that any
|
|
||||||
# references or sessions or what have you are ensured to have it, however we
|
|
||||||
# only want to do this in the case that we're running on macOS and the linked
|
|
||||||
# OpenSSL is too old to handle TLSv1.2
|
|
||||||
try:
|
|
||||||
import ssl
|
|
||||||
except ImportError:
|
|
||||||
pass
|
|
||||||
else:
|
|
||||||
# Checks for OpenSSL 1.0.1 on MacOS
|
|
||||||
if sys.platform == "darwin" and ssl.OPENSSL_VERSION_NUMBER < 0x1000100f:
|
|
||||||
try:
|
|
||||||
from pip._vendor.urllib3.contrib import securetransport
|
|
||||||
except (ImportError, OSError):
|
|
||||||
pass
|
|
||||||
else:
|
|
||||||
securetransport.inject_into_urllib3()
|
|
||||||
|
|
||||||
from pip._internal.cli.autocompletion import autocomplete
|
|
||||||
from pip._internal.cli.main_parser import parse_command
|
|
||||||
from pip._internal.commands import commands_dict
|
|
||||||
from pip._internal.exceptions import PipError
|
|
||||||
from pip._internal.utils import deprecation
|
|
||||||
from pip._internal.vcs import git, mercurial, subversion, bazaar # noqa
|
|
||||||
from pip._vendor.urllib3.exceptions import InsecureRequestWarning
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
# Hide the InsecureRequestWarning from urllib3
|
|
||||||
warnings.filterwarnings("ignore", category=InsecureRequestWarning)
|
|
||||||
|
|
||||||
|
|
||||||
def main(args=None):
|
|
||||||
if args is None:
|
|
||||||
args = sys.argv[1:]
|
|
||||||
|
|
||||||
# Configure our deprecation warnings to be sent through loggers
|
|
||||||
deprecation.install_warning_logger()
|
|
||||||
|
|
||||||
autocomplete()
|
|
||||||
|
|
||||||
try:
|
|
||||||
cmd_name, cmd_args = parse_command(args)
|
|
||||||
except PipError as exc:
|
|
||||||
sys.stderr.write("ERROR: %s" % exc)
|
|
||||||
sys.stderr.write(os.linesep)
|
|
||||||
sys.exit(1)
|
|
||||||
|
|
||||||
# Needed for locale.getpreferredencoding(False) to work
|
|
||||||
# in pip._internal.utils.encoding.auto_decode
|
|
||||||
try:
|
|
||||||
locale.setlocale(locale.LC_ALL, '')
|
|
||||||
except locale.Error as e:
|
|
||||||
# setlocale can apparently crash if locale are uninitialized
|
|
||||||
logger.debug("Ignoring error %s when setting locale", e)
|
|
||||||
command = commands_dict[cmd_name](isolated=("--isolated" in cmd_args))
|
|
||||||
return command.main(cmd_args)
|
|
||||||
@@ -1,215 +0,0 @@
|
|||||||
"""Build Environment used for isolation during sdist building
|
|
||||||
"""
|
|
||||||
|
|
||||||
import logging
|
|
||||||
import os
|
|
||||||
import sys
|
|
||||||
import textwrap
|
|
||||||
from collections import OrderedDict
|
|
||||||
from distutils.sysconfig import get_python_lib
|
|
||||||
from sysconfig import get_paths
|
|
||||||
|
|
||||||
from pip._vendor.pkg_resources import Requirement, VersionConflict, WorkingSet
|
|
||||||
|
|
||||||
from pip import __file__ as pip_location
|
|
||||||
from pip._internal.utils.misc import call_subprocess
|
|
||||||
from pip._internal.utils.temp_dir import TempDirectory
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
from pip._internal.utils.ui import open_spinner
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from typing import Tuple, Set, Iterable, Optional, List # noqa: F401
|
|
||||||
from pip._internal.index import PackageFinder # noqa: F401
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class _Prefix:
|
|
||||||
|
|
||||||
def __init__(self, path):
|
|
||||||
# type: (str) -> None
|
|
||||||
self.path = path
|
|
||||||
self.setup = False
|
|
||||||
self.bin_dir = get_paths(
|
|
||||||
'nt' if os.name == 'nt' else 'posix_prefix',
|
|
||||||
vars={'base': path, 'platbase': path}
|
|
||||||
)['scripts']
|
|
||||||
# Note: prefer distutils' sysconfig to get the
|
|
||||||
# library paths so PyPy is correctly supported.
|
|
||||||
purelib = get_python_lib(plat_specific=False, prefix=path)
|
|
||||||
platlib = get_python_lib(plat_specific=True, prefix=path)
|
|
||||||
if purelib == platlib:
|
|
||||||
self.lib_dirs = [purelib]
|
|
||||||
else:
|
|
||||||
self.lib_dirs = [purelib, platlib]
|
|
||||||
|
|
||||||
|
|
||||||
class BuildEnvironment(object):
|
|
||||||
"""Creates and manages an isolated environment to install build deps
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self):
|
|
||||||
# type: () -> None
|
|
||||||
self._temp_dir = TempDirectory(kind="build-env")
|
|
||||||
self._temp_dir.create()
|
|
||||||
|
|
||||||
self._prefixes = OrderedDict((
|
|
||||||
(name, _Prefix(os.path.join(self._temp_dir.path, name)))
|
|
||||||
for name in ('normal', 'overlay')
|
|
||||||
))
|
|
||||||
|
|
||||||
self._bin_dirs = [] # type: List[str]
|
|
||||||
self._lib_dirs = [] # type: List[str]
|
|
||||||
for prefix in reversed(list(self._prefixes.values())):
|
|
||||||
self._bin_dirs.append(prefix.bin_dir)
|
|
||||||
self._lib_dirs.extend(prefix.lib_dirs)
|
|
||||||
|
|
||||||
# Customize site to:
|
|
||||||
# - ensure .pth files are honored
|
|
||||||
# - prevent access to system site packages
|
|
||||||
system_sites = {
|
|
||||||
os.path.normcase(site) for site in (
|
|
||||||
get_python_lib(plat_specific=False),
|
|
||||||
get_python_lib(plat_specific=True),
|
|
||||||
)
|
|
||||||
}
|
|
||||||
self._site_dir = os.path.join(self._temp_dir.path, 'site')
|
|
||||||
if not os.path.exists(self._site_dir):
|
|
||||||
os.mkdir(self._site_dir)
|
|
||||||
with open(os.path.join(self._site_dir, 'sitecustomize.py'), 'w') as fp:
|
|
||||||
fp.write(textwrap.dedent(
|
|
||||||
'''
|
|
||||||
import os, site, sys
|
|
||||||
|
|
||||||
# First, drop system-sites related paths.
|
|
||||||
original_sys_path = sys.path[:]
|
|
||||||
known_paths = set()
|
|
||||||
for path in {system_sites!r}:
|
|
||||||
site.addsitedir(path, known_paths=known_paths)
|
|
||||||
system_paths = set(
|
|
||||||
os.path.normcase(path)
|
|
||||||
for path in sys.path[len(original_sys_path):]
|
|
||||||
)
|
|
||||||
original_sys_path = [
|
|
||||||
path for path in original_sys_path
|
|
||||||
if os.path.normcase(path) not in system_paths
|
|
||||||
]
|
|
||||||
sys.path = original_sys_path
|
|
||||||
|
|
||||||
# Second, add lib directories.
|
|
||||||
# ensuring .pth file are processed.
|
|
||||||
for path in {lib_dirs!r}:
|
|
||||||
assert not path in sys.path
|
|
||||||
site.addsitedir(path)
|
|
||||||
'''
|
|
||||||
).format(system_sites=system_sites, lib_dirs=self._lib_dirs))
|
|
||||||
|
|
||||||
def __enter__(self):
|
|
||||||
self._save_env = {
|
|
||||||
name: os.environ.get(name, None)
|
|
||||||
for name in ('PATH', 'PYTHONNOUSERSITE', 'PYTHONPATH')
|
|
||||||
}
|
|
||||||
|
|
||||||
path = self._bin_dirs[:]
|
|
||||||
old_path = self._save_env['PATH']
|
|
||||||
if old_path:
|
|
||||||
path.extend(old_path.split(os.pathsep))
|
|
||||||
|
|
||||||
pythonpath = [self._site_dir]
|
|
||||||
|
|
||||||
os.environ.update({
|
|
||||||
'PATH': os.pathsep.join(path),
|
|
||||||
'PYTHONNOUSERSITE': '1',
|
|
||||||
'PYTHONPATH': os.pathsep.join(pythonpath),
|
|
||||||
})
|
|
||||||
|
|
||||||
def __exit__(self, exc_type, exc_val, exc_tb):
|
|
||||||
for varname, old_value in self._save_env.items():
|
|
||||||
if old_value is None:
|
|
||||||
os.environ.pop(varname, None)
|
|
||||||
else:
|
|
||||||
os.environ[varname] = old_value
|
|
||||||
|
|
||||||
def cleanup(self):
|
|
||||||
# type: () -> None
|
|
||||||
self._temp_dir.cleanup()
|
|
||||||
|
|
||||||
def check_requirements(self, reqs):
|
|
||||||
# type: (Iterable[str]) -> Tuple[Set[Tuple[str, str]], Set[str]]
|
|
||||||
"""Return 2 sets:
|
|
||||||
- conflicting requirements: set of (installed, wanted) reqs tuples
|
|
||||||
- missing requirements: set of reqs
|
|
||||||
"""
|
|
||||||
missing = set()
|
|
||||||
conflicting = set()
|
|
||||||
if reqs:
|
|
||||||
ws = WorkingSet(self._lib_dirs)
|
|
||||||
for req in reqs:
|
|
||||||
try:
|
|
||||||
if ws.find(Requirement.parse(req)) is None:
|
|
||||||
missing.add(req)
|
|
||||||
except VersionConflict as e:
|
|
||||||
conflicting.add((str(e.args[0].as_requirement()),
|
|
||||||
str(e.args[1])))
|
|
||||||
return conflicting, missing
|
|
||||||
|
|
||||||
def install_requirements(
|
|
||||||
self,
|
|
||||||
finder, # type: PackageFinder
|
|
||||||
requirements, # type: Iterable[str]
|
|
||||||
prefix_as_string, # type: str
|
|
||||||
message # type: Optional[str]
|
|
||||||
):
|
|
||||||
# type: (...) -> None
|
|
||||||
prefix = self._prefixes[prefix_as_string]
|
|
||||||
assert not prefix.setup
|
|
||||||
prefix.setup = True
|
|
||||||
if not requirements:
|
|
||||||
return
|
|
||||||
args = [
|
|
||||||
sys.executable, os.path.dirname(pip_location), 'install',
|
|
||||||
'--ignore-installed', '--no-user', '--prefix', prefix.path,
|
|
||||||
'--no-warn-script-location',
|
|
||||||
] # type: List[str]
|
|
||||||
if logger.getEffectiveLevel() <= logging.DEBUG:
|
|
||||||
args.append('-v')
|
|
||||||
for format_control in ('no_binary', 'only_binary'):
|
|
||||||
formats = getattr(finder.format_control, format_control)
|
|
||||||
args.extend(('--' + format_control.replace('_', '-'),
|
|
||||||
','.join(sorted(formats or {':none:'}))))
|
|
||||||
if finder.index_urls:
|
|
||||||
args.extend(['-i', finder.index_urls[0]])
|
|
||||||
for extra_index in finder.index_urls[1:]:
|
|
||||||
args.extend(['--extra-index-url', extra_index])
|
|
||||||
else:
|
|
||||||
args.append('--no-index')
|
|
||||||
for link in finder.find_links:
|
|
||||||
args.extend(['--find-links', link])
|
|
||||||
for _, host, _ in finder.secure_origins:
|
|
||||||
args.extend(['--trusted-host', host])
|
|
||||||
if finder.allow_all_prereleases:
|
|
||||||
args.append('--pre')
|
|
||||||
args.append('--')
|
|
||||||
args.extend(requirements)
|
|
||||||
with open_spinner(message) as spinner:
|
|
||||||
call_subprocess(args, show_stdout=False, spinner=spinner)
|
|
||||||
|
|
||||||
|
|
||||||
class NoOpBuildEnvironment(BuildEnvironment):
|
|
||||||
"""A no-op drop-in replacement for BuildEnvironment
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self):
|
|
||||||
pass
|
|
||||||
|
|
||||||
def __enter__(self):
|
|
||||||
pass
|
|
||||||
|
|
||||||
def __exit__(self, exc_type, exc_val, exc_tb):
|
|
||||||
pass
|
|
||||||
|
|
||||||
def cleanup(self):
|
|
||||||
pass
|
|
||||||
|
|
||||||
def install_requirements(self, finder, requirements, prefix, message):
|
|
||||||
raise NotImplementedError()
|
|
||||||
@@ -1,224 +0,0 @@
|
|||||||
"""Cache Management
|
|
||||||
"""
|
|
||||||
|
|
||||||
import errno
|
|
||||||
import hashlib
|
|
||||||
import logging
|
|
||||||
import os
|
|
||||||
|
|
||||||
from pip._vendor.packaging.utils import canonicalize_name
|
|
||||||
|
|
||||||
from pip._internal.download import path_to_url
|
|
||||||
from pip._internal.models.link import Link
|
|
||||||
from pip._internal.utils.compat import expanduser
|
|
||||||
from pip._internal.utils.temp_dir import TempDirectory
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
from pip._internal.wheel import InvalidWheelFilename, Wheel
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from typing import Optional, Set, List, Any # noqa: F401
|
|
||||||
from pip._internal.index import FormatControl # noqa: F401
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class Cache(object):
|
|
||||||
"""An abstract class - provides cache directories for data from links
|
|
||||||
|
|
||||||
|
|
||||||
:param cache_dir: The root of the cache.
|
|
||||||
:param format_control: An object of FormatControl class to limit
|
|
||||||
binaries being read from the cache.
|
|
||||||
:param allowed_formats: which formats of files the cache should store.
|
|
||||||
('binary' and 'source' are the only allowed values)
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self, cache_dir, format_control, allowed_formats):
|
|
||||||
# type: (str, FormatControl, Set[str]) -> None
|
|
||||||
super(Cache, self).__init__()
|
|
||||||
self.cache_dir = expanduser(cache_dir) if cache_dir else None
|
|
||||||
self.format_control = format_control
|
|
||||||
self.allowed_formats = allowed_formats
|
|
||||||
|
|
||||||
_valid_formats = {"source", "binary"}
|
|
||||||
assert self.allowed_formats.union(_valid_formats) == _valid_formats
|
|
||||||
|
|
||||||
def _get_cache_path_parts(self, link):
|
|
||||||
# type: (Link) -> List[str]
|
|
||||||
"""Get parts of part that must be os.path.joined with cache_dir
|
|
||||||
"""
|
|
||||||
|
|
||||||
# We want to generate an url to use as our cache key, we don't want to
|
|
||||||
# just re-use the URL because it might have other items in the fragment
|
|
||||||
# and we don't care about those.
|
|
||||||
key_parts = [link.url_without_fragment]
|
|
||||||
if link.hash_name is not None and link.hash is not None:
|
|
||||||
key_parts.append("=".join([link.hash_name, link.hash]))
|
|
||||||
key_url = "#".join(key_parts)
|
|
||||||
|
|
||||||
# Encode our key url with sha224, we'll use this because it has similar
|
|
||||||
# security properties to sha256, but with a shorter total output (and
|
|
||||||
# thus less secure). However the differences don't make a lot of
|
|
||||||
# difference for our use case here.
|
|
||||||
hashed = hashlib.sha224(key_url.encode()).hexdigest()
|
|
||||||
|
|
||||||
# We want to nest the directories some to prevent having a ton of top
|
|
||||||
# level directories where we might run out of sub directories on some
|
|
||||||
# FS.
|
|
||||||
parts = [hashed[:2], hashed[2:4], hashed[4:6], hashed[6:]]
|
|
||||||
|
|
||||||
return parts
|
|
||||||
|
|
||||||
def _get_candidates(self, link, package_name):
|
|
||||||
# type: (Link, Optional[str]) -> List[Any]
|
|
||||||
can_not_cache = (
|
|
||||||
not self.cache_dir or
|
|
||||||
not package_name or
|
|
||||||
not link
|
|
||||||
)
|
|
||||||
if can_not_cache:
|
|
||||||
return []
|
|
||||||
|
|
||||||
canonical_name = canonicalize_name(package_name)
|
|
||||||
formats = self.format_control.get_allowed_formats(
|
|
||||||
canonical_name
|
|
||||||
)
|
|
||||||
if not self.allowed_formats.intersection(formats):
|
|
||||||
return []
|
|
||||||
|
|
||||||
root = self.get_path_for_link(link)
|
|
||||||
try:
|
|
||||||
return os.listdir(root)
|
|
||||||
except OSError as err:
|
|
||||||
if err.errno in {errno.ENOENT, errno.ENOTDIR}:
|
|
||||||
return []
|
|
||||||
raise
|
|
||||||
|
|
||||||
def get_path_for_link(self, link):
|
|
||||||
# type: (Link) -> str
|
|
||||||
"""Return a directory to store cached items in for link.
|
|
||||||
"""
|
|
||||||
raise NotImplementedError()
|
|
||||||
|
|
||||||
def get(self, link, package_name):
|
|
||||||
# type: (Link, Optional[str]) -> Link
|
|
||||||
"""Returns a link to a cached item if it exists, otherwise returns the
|
|
||||||
passed link.
|
|
||||||
"""
|
|
||||||
raise NotImplementedError()
|
|
||||||
|
|
||||||
def _link_for_candidate(self, link, candidate):
|
|
||||||
# type: (Link, str) -> Link
|
|
||||||
root = self.get_path_for_link(link)
|
|
||||||
path = os.path.join(root, candidate)
|
|
||||||
|
|
||||||
return Link(path_to_url(path))
|
|
||||||
|
|
||||||
def cleanup(self):
|
|
||||||
# type: () -> None
|
|
||||||
pass
|
|
||||||
|
|
||||||
|
|
||||||
class SimpleWheelCache(Cache):
|
|
||||||
"""A cache of wheels for future installs.
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self, cache_dir, format_control):
|
|
||||||
# type: (str, FormatControl) -> None
|
|
||||||
super(SimpleWheelCache, self).__init__(
|
|
||||||
cache_dir, format_control, {"binary"}
|
|
||||||
)
|
|
||||||
|
|
||||||
def get_path_for_link(self, link):
|
|
||||||
# type: (Link) -> str
|
|
||||||
"""Return a directory to store cached wheels for link
|
|
||||||
|
|
||||||
Because there are M wheels for any one sdist, we provide a directory
|
|
||||||
to cache them in, and then consult that directory when looking up
|
|
||||||
cache hits.
|
|
||||||
|
|
||||||
We only insert things into the cache if they have plausible version
|
|
||||||
numbers, so that we don't contaminate the cache with things that were
|
|
||||||
not unique. E.g. ./package might have dozens of installs done for it
|
|
||||||
and build a version of 0.0...and if we built and cached a wheel, we'd
|
|
||||||
end up using the same wheel even if the source has been edited.
|
|
||||||
|
|
||||||
:param link: The link of the sdist for which this will cache wheels.
|
|
||||||
"""
|
|
||||||
parts = self._get_cache_path_parts(link)
|
|
||||||
|
|
||||||
# Store wheels within the root cache_dir
|
|
||||||
return os.path.join(self.cache_dir, "wheels", *parts)
|
|
||||||
|
|
||||||
def get(self, link, package_name):
|
|
||||||
# type: (Link, Optional[str]) -> Link
|
|
||||||
candidates = []
|
|
||||||
|
|
||||||
for wheel_name in self._get_candidates(link, package_name):
|
|
||||||
try:
|
|
||||||
wheel = Wheel(wheel_name)
|
|
||||||
except InvalidWheelFilename:
|
|
||||||
continue
|
|
||||||
if not wheel.supported():
|
|
||||||
# Built for a different python/arch/etc
|
|
||||||
continue
|
|
||||||
candidates.append((wheel.support_index_min(), wheel_name))
|
|
||||||
|
|
||||||
if not candidates:
|
|
||||||
return link
|
|
||||||
|
|
||||||
return self._link_for_candidate(link, min(candidates)[1])
|
|
||||||
|
|
||||||
|
|
||||||
class EphemWheelCache(SimpleWheelCache):
|
|
||||||
"""A SimpleWheelCache that creates it's own temporary cache directory
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self, format_control):
|
|
||||||
# type: (FormatControl) -> None
|
|
||||||
self._temp_dir = TempDirectory(kind="ephem-wheel-cache")
|
|
||||||
self._temp_dir.create()
|
|
||||||
|
|
||||||
super(EphemWheelCache, self).__init__(
|
|
||||||
self._temp_dir.path, format_control
|
|
||||||
)
|
|
||||||
|
|
||||||
def cleanup(self):
|
|
||||||
# type: () -> None
|
|
||||||
self._temp_dir.cleanup()
|
|
||||||
|
|
||||||
|
|
||||||
class WheelCache(Cache):
|
|
||||||
"""Wraps EphemWheelCache and SimpleWheelCache into a single Cache
|
|
||||||
|
|
||||||
This Cache allows for gracefully degradation, using the ephem wheel cache
|
|
||||||
when a certain link is not found in the simple wheel cache first.
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self, cache_dir, format_control):
|
|
||||||
# type: (str, FormatControl) -> None
|
|
||||||
super(WheelCache, self).__init__(
|
|
||||||
cache_dir, format_control, {'binary'}
|
|
||||||
)
|
|
||||||
self._wheel_cache = SimpleWheelCache(cache_dir, format_control)
|
|
||||||
self._ephem_cache = EphemWheelCache(format_control)
|
|
||||||
|
|
||||||
def get_path_for_link(self, link):
|
|
||||||
# type: (Link) -> str
|
|
||||||
return self._wheel_cache.get_path_for_link(link)
|
|
||||||
|
|
||||||
def get_ephem_path_for_link(self, link):
|
|
||||||
# type: (Link) -> str
|
|
||||||
return self._ephem_cache.get_path_for_link(link)
|
|
||||||
|
|
||||||
def get(self, link, package_name):
|
|
||||||
# type: (Link, Optional[str]) -> Link
|
|
||||||
retval = self._wheel_cache.get(link, package_name)
|
|
||||||
if retval is link:
|
|
||||||
retval = self._ephem_cache.get(link, package_name)
|
|
||||||
return retval
|
|
||||||
|
|
||||||
def cleanup(self):
|
|
||||||
# type: () -> None
|
|
||||||
self._wheel_cache.cleanup()
|
|
||||||
self._ephem_cache.cleanup()
|
|
||||||
@@ -1,4 +0,0 @@
|
|||||||
"""Subpackage containing all of pip's command line interface related code
|
|
||||||
"""
|
|
||||||
|
|
||||||
# This file intentionally does not import submodules
|
|
||||||
@@ -1,152 +0,0 @@
|
|||||||
"""Logic that powers autocompletion installed by ``pip completion``.
|
|
||||||
"""
|
|
||||||
|
|
||||||
import optparse
|
|
||||||
import os
|
|
||||||
import sys
|
|
||||||
|
|
||||||
from pip._internal.cli.main_parser import create_main_parser
|
|
||||||
from pip._internal.commands import commands_dict, get_summaries
|
|
||||||
from pip._internal.utils.misc import get_installed_distributions
|
|
||||||
|
|
||||||
|
|
||||||
def autocomplete():
|
|
||||||
"""Entry Point for completion of main and subcommand options.
|
|
||||||
"""
|
|
||||||
# Don't complete if user hasn't sourced bash_completion file.
|
|
||||||
if 'PIP_AUTO_COMPLETE' not in os.environ:
|
|
||||||
return
|
|
||||||
cwords = os.environ['COMP_WORDS'].split()[1:]
|
|
||||||
cword = int(os.environ['COMP_CWORD'])
|
|
||||||
try:
|
|
||||||
current = cwords[cword - 1]
|
|
||||||
except IndexError:
|
|
||||||
current = ''
|
|
||||||
|
|
||||||
subcommands = [cmd for cmd, summary in get_summaries()]
|
|
||||||
options = []
|
|
||||||
# subcommand
|
|
||||||
try:
|
|
||||||
subcommand_name = [w for w in cwords if w in subcommands][0]
|
|
||||||
except IndexError:
|
|
||||||
subcommand_name = None
|
|
||||||
|
|
||||||
parser = create_main_parser()
|
|
||||||
# subcommand options
|
|
||||||
if subcommand_name:
|
|
||||||
# special case: 'help' subcommand has no options
|
|
||||||
if subcommand_name == 'help':
|
|
||||||
sys.exit(1)
|
|
||||||
# special case: list locally installed dists for show and uninstall
|
|
||||||
should_list_installed = (
|
|
||||||
subcommand_name in ['show', 'uninstall'] and
|
|
||||||
not current.startswith('-')
|
|
||||||
)
|
|
||||||
if should_list_installed:
|
|
||||||
installed = []
|
|
||||||
lc = current.lower()
|
|
||||||
for dist in get_installed_distributions(local_only=True):
|
|
||||||
if dist.key.startswith(lc) and dist.key not in cwords[1:]:
|
|
||||||
installed.append(dist.key)
|
|
||||||
# if there are no dists installed, fall back to option completion
|
|
||||||
if installed:
|
|
||||||
for dist in installed:
|
|
||||||
print(dist)
|
|
||||||
sys.exit(1)
|
|
||||||
|
|
||||||
subcommand = commands_dict[subcommand_name]()
|
|
||||||
|
|
||||||
for opt in subcommand.parser.option_list_all:
|
|
||||||
if opt.help != optparse.SUPPRESS_HELP:
|
|
||||||
for opt_str in opt._long_opts + opt._short_opts:
|
|
||||||
options.append((opt_str, opt.nargs))
|
|
||||||
|
|
||||||
# filter out previously specified options from available options
|
|
||||||
prev_opts = [x.split('=')[0] for x in cwords[1:cword - 1]]
|
|
||||||
options = [(x, v) for (x, v) in options if x not in prev_opts]
|
|
||||||
# filter options by current input
|
|
||||||
options = [(k, v) for k, v in options if k.startswith(current)]
|
|
||||||
# get completion type given cwords and available subcommand options
|
|
||||||
completion_type = get_path_completion_type(
|
|
||||||
cwords, cword, subcommand.parser.option_list_all,
|
|
||||||
)
|
|
||||||
# get completion files and directories if ``completion_type`` is
|
|
||||||
# ``<file>``, ``<dir>`` or ``<path>``
|
|
||||||
if completion_type:
|
|
||||||
options = auto_complete_paths(current, completion_type)
|
|
||||||
options = ((opt, 0) for opt in options)
|
|
||||||
for option in options:
|
|
||||||
opt_label = option[0]
|
|
||||||
# append '=' to options which require args
|
|
||||||
if option[1] and option[0][:2] == "--":
|
|
||||||
opt_label += '='
|
|
||||||
print(opt_label)
|
|
||||||
else:
|
|
||||||
# show main parser options only when necessary
|
|
||||||
|
|
||||||
opts = [i.option_list for i in parser.option_groups]
|
|
||||||
opts.append(parser.option_list)
|
|
||||||
opts = (o for it in opts for o in it)
|
|
||||||
if current.startswith('-'):
|
|
||||||
for opt in opts:
|
|
||||||
if opt.help != optparse.SUPPRESS_HELP:
|
|
||||||
subcommands += opt._long_opts + opt._short_opts
|
|
||||||
else:
|
|
||||||
# get completion type given cwords and all available options
|
|
||||||
completion_type = get_path_completion_type(cwords, cword, opts)
|
|
||||||
if completion_type:
|
|
||||||
subcommands = auto_complete_paths(current, completion_type)
|
|
||||||
|
|
||||||
print(' '.join([x for x in subcommands if x.startswith(current)]))
|
|
||||||
sys.exit(1)
|
|
||||||
|
|
||||||
|
|
||||||
def get_path_completion_type(cwords, cword, opts):
|
|
||||||
"""Get the type of path completion (``file``, ``dir``, ``path`` or None)
|
|
||||||
|
|
||||||
:param cwords: same as the environmental variable ``COMP_WORDS``
|
|
||||||
:param cword: same as the environmental variable ``COMP_CWORD``
|
|
||||||
:param opts: The available options to check
|
|
||||||
:return: path completion type (``file``, ``dir``, ``path`` or None)
|
|
||||||
"""
|
|
||||||
if cword < 2 or not cwords[cword - 2].startswith('-'):
|
|
||||||
return
|
|
||||||
for opt in opts:
|
|
||||||
if opt.help == optparse.SUPPRESS_HELP:
|
|
||||||
continue
|
|
||||||
for o in str(opt).split('/'):
|
|
||||||
if cwords[cword - 2].split('=')[0] == o:
|
|
||||||
if not opt.metavar or any(
|
|
||||||
x in ('path', 'file', 'dir')
|
|
||||||
for x in opt.metavar.split('/')):
|
|
||||||
return opt.metavar
|
|
||||||
|
|
||||||
|
|
||||||
def auto_complete_paths(current, completion_type):
|
|
||||||
"""If ``completion_type`` is ``file`` or ``path``, list all regular files
|
|
||||||
and directories starting with ``current``; otherwise only list directories
|
|
||||||
starting with ``current``.
|
|
||||||
|
|
||||||
:param current: The word to be completed
|
|
||||||
:param completion_type: path completion type(`file`, `path` or `dir`)i
|
|
||||||
:return: A generator of regular files and/or directories
|
|
||||||
"""
|
|
||||||
directory, filename = os.path.split(current)
|
|
||||||
current_path = os.path.abspath(directory)
|
|
||||||
# Don't complete paths if they can't be accessed
|
|
||||||
if not os.access(current_path, os.R_OK):
|
|
||||||
return
|
|
||||||
filename = os.path.normcase(filename)
|
|
||||||
# list all files that start with ``filename``
|
|
||||||
file_list = (x for x in os.listdir(current_path)
|
|
||||||
if os.path.normcase(x).startswith(filename))
|
|
||||||
for f in file_list:
|
|
||||||
opt = os.path.join(current_path, f)
|
|
||||||
comp_file = os.path.normcase(os.path.join(directory, f))
|
|
||||||
# complete regular files when there is not ``<dir>`` after option
|
|
||||||
# complete directories when there is ``<file>``, ``<path>`` or
|
|
||||||
# ``<dir>``after option
|
|
||||||
if completion_type != 'dir' and os.path.isfile(opt):
|
|
||||||
yield comp_file
|
|
||||||
elif os.path.isdir(opt):
|
|
||||||
yield os.path.join(comp_file, '')
|
|
||||||
@@ -1,341 +0,0 @@
|
|||||||
"""Base Command class, and related routines"""
|
|
||||||
from __future__ import absolute_import, print_function
|
|
||||||
|
|
||||||
import logging
|
|
||||||
import logging.config
|
|
||||||
import optparse
|
|
||||||
import os
|
|
||||||
import platform
|
|
||||||
import sys
|
|
||||||
import traceback
|
|
||||||
|
|
||||||
from pip._internal.cli import cmdoptions
|
|
||||||
from pip._internal.cli.parser import (
|
|
||||||
ConfigOptionParser, UpdatingDefaultsHelpFormatter,
|
|
||||||
)
|
|
||||||
from pip._internal.cli.status_codes import (
|
|
||||||
ERROR, PREVIOUS_BUILD_DIR_ERROR, SUCCESS, UNKNOWN_ERROR,
|
|
||||||
VIRTUALENV_NOT_FOUND,
|
|
||||||
)
|
|
||||||
from pip._internal.download import PipSession
|
|
||||||
from pip._internal.exceptions import (
|
|
||||||
BadCommand, CommandError, InstallationError, PreviousBuildDirError,
|
|
||||||
UninstallationError,
|
|
||||||
)
|
|
||||||
from pip._internal.index import PackageFinder
|
|
||||||
from pip._internal.locations import running_under_virtualenv
|
|
||||||
from pip._internal.req.constructors import (
|
|
||||||
install_req_from_editable, install_req_from_line,
|
|
||||||
)
|
|
||||||
from pip._internal.req.req_file import parse_requirements
|
|
||||||
from pip._internal.utils.deprecation import deprecated
|
|
||||||
from pip._internal.utils.logging import BrokenStdoutLoggingError, setup_logging
|
|
||||||
from pip._internal.utils.misc import (
|
|
||||||
get_prog, normalize_path, redact_password_from_url,
|
|
||||||
)
|
|
||||||
from pip._internal.utils.outdated import pip_version_check
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from typing import Optional, List, Tuple, Any # noqa: F401
|
|
||||||
from optparse import Values # noqa: F401
|
|
||||||
from pip._internal.cache import WheelCache # noqa: F401
|
|
||||||
from pip._internal.req.req_set import RequirementSet # noqa: F401
|
|
||||||
|
|
||||||
__all__ = ['Command']
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class Command(object):
|
|
||||||
name = None # type: Optional[str]
|
|
||||||
usage = None # type: Optional[str]
|
|
||||||
hidden = False # type: bool
|
|
||||||
ignore_require_venv = False # type: bool
|
|
||||||
|
|
||||||
def __init__(self, isolated=False):
|
|
||||||
# type: (bool) -> None
|
|
||||||
parser_kw = {
|
|
||||||
'usage': self.usage,
|
|
||||||
'prog': '%s %s' % (get_prog(), self.name),
|
|
||||||
'formatter': UpdatingDefaultsHelpFormatter(),
|
|
||||||
'add_help_option': False,
|
|
||||||
'name': self.name,
|
|
||||||
'description': self.__doc__,
|
|
||||||
'isolated': isolated,
|
|
||||||
}
|
|
||||||
|
|
||||||
self.parser = ConfigOptionParser(**parser_kw)
|
|
||||||
|
|
||||||
# Commands should add options to this option group
|
|
||||||
optgroup_name = '%s Options' % self.name.capitalize()
|
|
||||||
self.cmd_opts = optparse.OptionGroup(self.parser, optgroup_name)
|
|
||||||
|
|
||||||
# Add the general options
|
|
||||||
gen_opts = cmdoptions.make_option_group(
|
|
||||||
cmdoptions.general_group,
|
|
||||||
self.parser,
|
|
||||||
)
|
|
||||||
self.parser.add_option_group(gen_opts)
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
# type: (Values, List[Any]) -> Any
|
|
||||||
raise NotImplementedError
|
|
||||||
|
|
||||||
def _build_session(self, options, retries=None, timeout=None):
|
|
||||||
# type: (Values, Optional[int], Optional[int]) -> PipSession
|
|
||||||
session = PipSession(
|
|
||||||
cache=(
|
|
||||||
normalize_path(os.path.join(options.cache_dir, "http"))
|
|
||||||
if options.cache_dir else None
|
|
||||||
),
|
|
||||||
retries=retries if retries is not None else options.retries,
|
|
||||||
insecure_hosts=options.trusted_hosts,
|
|
||||||
)
|
|
||||||
|
|
||||||
# Handle custom ca-bundles from the user
|
|
||||||
if options.cert:
|
|
||||||
session.verify = options.cert
|
|
||||||
|
|
||||||
# Handle SSL client certificate
|
|
||||||
if options.client_cert:
|
|
||||||
session.cert = options.client_cert
|
|
||||||
|
|
||||||
# Handle timeouts
|
|
||||||
if options.timeout or timeout:
|
|
||||||
session.timeout = (
|
|
||||||
timeout if timeout is not None else options.timeout
|
|
||||||
)
|
|
||||||
|
|
||||||
# Handle configured proxies
|
|
||||||
if options.proxy:
|
|
||||||
session.proxies = {
|
|
||||||
"http": options.proxy,
|
|
||||||
"https": options.proxy,
|
|
||||||
}
|
|
||||||
|
|
||||||
# Determine if we can prompt the user for authentication or not
|
|
||||||
session.auth.prompting = not options.no_input
|
|
||||||
|
|
||||||
return session
|
|
||||||
|
|
||||||
def parse_args(self, args):
|
|
||||||
# type: (List[str]) -> Tuple
|
|
||||||
# factored out for testability
|
|
||||||
return self.parser.parse_args(args)
|
|
||||||
|
|
||||||
def main(self, args):
|
|
||||||
# type: (List[str]) -> int
|
|
||||||
options, args = self.parse_args(args)
|
|
||||||
|
|
||||||
# Set verbosity so that it can be used elsewhere.
|
|
||||||
self.verbosity = options.verbose - options.quiet
|
|
||||||
|
|
||||||
level_number = setup_logging(
|
|
||||||
verbosity=self.verbosity,
|
|
||||||
no_color=options.no_color,
|
|
||||||
user_log_file=options.log,
|
|
||||||
)
|
|
||||||
|
|
||||||
if sys.version_info[:2] == (3, 4):
|
|
||||||
deprecated(
|
|
||||||
"Python 3.4 support has been deprecated. pip 19.1 will be the "
|
|
||||||
"last one supporting it. Please upgrade your Python as Python "
|
|
||||||
"3.4 won't be maintained after March 2019 (cf PEP 429).",
|
|
||||||
replacement=None,
|
|
||||||
gone_in='19.2',
|
|
||||||
)
|
|
||||||
elif sys.version_info[:2] == (2, 7):
|
|
||||||
message = (
|
|
||||||
"A future version of pip will drop support for Python 2.7."
|
|
||||||
)
|
|
||||||
if platform.python_implementation() == "CPython":
|
|
||||||
message = (
|
|
||||||
"Python 2.7 will reach the end of its life on January "
|
|
||||||
"1st, 2020. Please upgrade your Python as Python 2.7 "
|
|
||||||
"won't be maintained after that date. "
|
|
||||||
) + message
|
|
||||||
deprecated(message, replacement=None, gone_in=None)
|
|
||||||
|
|
||||||
# TODO: Try to get these passing down from the command?
|
|
||||||
# without resorting to os.environ to hold these.
|
|
||||||
# This also affects isolated builds and it should.
|
|
||||||
|
|
||||||
if options.no_input:
|
|
||||||
os.environ['PIP_NO_INPUT'] = '1'
|
|
||||||
|
|
||||||
if options.exists_action:
|
|
||||||
os.environ['PIP_EXISTS_ACTION'] = ' '.join(options.exists_action)
|
|
||||||
|
|
||||||
if options.require_venv and not self.ignore_require_venv:
|
|
||||||
# If a venv is required check if it can really be found
|
|
||||||
if not running_under_virtualenv():
|
|
||||||
logger.critical(
|
|
||||||
'Could not find an activated virtualenv (required).'
|
|
||||||
)
|
|
||||||
sys.exit(VIRTUALENV_NOT_FOUND)
|
|
||||||
|
|
||||||
try:
|
|
||||||
status = self.run(options, args)
|
|
||||||
# FIXME: all commands should return an exit status
|
|
||||||
# and when it is done, isinstance is not needed anymore
|
|
||||||
if isinstance(status, int):
|
|
||||||
return status
|
|
||||||
except PreviousBuildDirError as exc:
|
|
||||||
logger.critical(str(exc))
|
|
||||||
logger.debug('Exception information:', exc_info=True)
|
|
||||||
|
|
||||||
return PREVIOUS_BUILD_DIR_ERROR
|
|
||||||
except (InstallationError, UninstallationError, BadCommand) as exc:
|
|
||||||
logger.critical(str(exc))
|
|
||||||
logger.debug('Exception information:', exc_info=True)
|
|
||||||
|
|
||||||
return ERROR
|
|
||||||
except CommandError as exc:
|
|
||||||
logger.critical('ERROR: %s', exc)
|
|
||||||
logger.debug('Exception information:', exc_info=True)
|
|
||||||
|
|
||||||
return ERROR
|
|
||||||
except BrokenStdoutLoggingError:
|
|
||||||
# Bypass our logger and write any remaining messages to stderr
|
|
||||||
# because stdout no longer works.
|
|
||||||
print('ERROR: Pipe to stdout was broken', file=sys.stderr)
|
|
||||||
if level_number <= logging.DEBUG:
|
|
||||||
traceback.print_exc(file=sys.stderr)
|
|
||||||
|
|
||||||
return ERROR
|
|
||||||
except KeyboardInterrupt:
|
|
||||||
logger.critical('Operation cancelled by user')
|
|
||||||
logger.debug('Exception information:', exc_info=True)
|
|
||||||
|
|
||||||
return ERROR
|
|
||||||
except BaseException:
|
|
||||||
logger.critical('Exception:', exc_info=True)
|
|
||||||
|
|
||||||
return UNKNOWN_ERROR
|
|
||||||
finally:
|
|
||||||
allow_version_check = (
|
|
||||||
# Does this command have the index_group options?
|
|
||||||
hasattr(options, "no_index") and
|
|
||||||
# Is this command allowed to perform this check?
|
|
||||||
not (options.disable_pip_version_check or options.no_index)
|
|
||||||
)
|
|
||||||
# Check if we're using the latest version of pip available
|
|
||||||
if allow_version_check:
|
|
||||||
session = self._build_session(
|
|
||||||
options,
|
|
||||||
retries=0,
|
|
||||||
timeout=min(5, options.timeout)
|
|
||||||
)
|
|
||||||
with session:
|
|
||||||
pip_version_check(session, options)
|
|
||||||
|
|
||||||
# Shutdown the logging module
|
|
||||||
logging.shutdown()
|
|
||||||
|
|
||||||
return SUCCESS
|
|
||||||
|
|
||||||
|
|
||||||
class RequirementCommand(Command):
|
|
||||||
|
|
||||||
@staticmethod
|
|
||||||
def populate_requirement_set(requirement_set, # type: RequirementSet
|
|
||||||
args, # type: List[str]
|
|
||||||
options, # type: Values
|
|
||||||
finder, # type: PackageFinder
|
|
||||||
session, # type: PipSession
|
|
||||||
name, # type: str
|
|
||||||
wheel_cache # type: Optional[WheelCache]
|
|
||||||
):
|
|
||||||
# type: (...) -> None
|
|
||||||
"""
|
|
||||||
Marshal cmd line args into a requirement set.
|
|
||||||
"""
|
|
||||||
# NOTE: As a side-effect, options.require_hashes and
|
|
||||||
# requirement_set.require_hashes may be updated
|
|
||||||
|
|
||||||
for filename in options.constraints:
|
|
||||||
for req_to_add in parse_requirements(
|
|
||||||
filename,
|
|
||||||
constraint=True, finder=finder, options=options,
|
|
||||||
session=session, wheel_cache=wheel_cache):
|
|
||||||
req_to_add.is_direct = True
|
|
||||||
requirement_set.add_requirement(req_to_add)
|
|
||||||
|
|
||||||
for req in args:
|
|
||||||
req_to_add = install_req_from_line(
|
|
||||||
req, None, isolated=options.isolated_mode,
|
|
||||||
use_pep517=options.use_pep517,
|
|
||||||
wheel_cache=wheel_cache
|
|
||||||
)
|
|
||||||
req_to_add.is_direct = True
|
|
||||||
requirement_set.add_requirement(req_to_add)
|
|
||||||
|
|
||||||
for req in options.editables:
|
|
||||||
req_to_add = install_req_from_editable(
|
|
||||||
req,
|
|
||||||
isolated=options.isolated_mode,
|
|
||||||
use_pep517=options.use_pep517,
|
|
||||||
wheel_cache=wheel_cache
|
|
||||||
)
|
|
||||||
req_to_add.is_direct = True
|
|
||||||
requirement_set.add_requirement(req_to_add)
|
|
||||||
|
|
||||||
for filename in options.requirements:
|
|
||||||
for req_to_add in parse_requirements(
|
|
||||||
filename,
|
|
||||||
finder=finder, options=options, session=session,
|
|
||||||
wheel_cache=wheel_cache,
|
|
||||||
use_pep517=options.use_pep517):
|
|
||||||
req_to_add.is_direct = True
|
|
||||||
requirement_set.add_requirement(req_to_add)
|
|
||||||
# If --require-hashes was a line in a requirements file, tell
|
|
||||||
# RequirementSet about it:
|
|
||||||
requirement_set.require_hashes = options.require_hashes
|
|
||||||
|
|
||||||
if not (args or options.editables or options.requirements):
|
|
||||||
opts = {'name': name}
|
|
||||||
if options.find_links:
|
|
||||||
raise CommandError(
|
|
||||||
'You must give at least one requirement to %(name)s '
|
|
||||||
'(maybe you meant "pip %(name)s %(links)s"?)' %
|
|
||||||
dict(opts, links=' '.join(options.find_links)))
|
|
||||||
else:
|
|
||||||
raise CommandError(
|
|
||||||
'You must give at least one requirement to %(name)s '
|
|
||||||
'(see "pip help %(name)s")' % opts)
|
|
||||||
|
|
||||||
def _build_package_finder(
|
|
||||||
self,
|
|
||||||
options, # type: Values
|
|
||||||
session, # type: PipSession
|
|
||||||
platform=None, # type: Optional[str]
|
|
||||||
python_versions=None, # type: Optional[List[str]]
|
|
||||||
abi=None, # type: Optional[str]
|
|
||||||
implementation=None # type: Optional[str]
|
|
||||||
):
|
|
||||||
# type: (...) -> PackageFinder
|
|
||||||
"""
|
|
||||||
Create a package finder appropriate to this requirement command.
|
|
||||||
"""
|
|
||||||
index_urls = [options.index_url] + options.extra_index_urls
|
|
||||||
if options.no_index:
|
|
||||||
logger.debug(
|
|
||||||
'Ignoring indexes: %s',
|
|
||||||
','.join(redact_password_from_url(url) for url in index_urls),
|
|
||||||
)
|
|
||||||
index_urls = []
|
|
||||||
|
|
||||||
return PackageFinder(
|
|
||||||
find_links=options.find_links,
|
|
||||||
format_control=options.format_control,
|
|
||||||
index_urls=index_urls,
|
|
||||||
trusted_hosts=options.trusted_hosts,
|
|
||||||
allow_all_prereleases=options.pre,
|
|
||||||
session=session,
|
|
||||||
platform=platform,
|
|
||||||
versions=python_versions,
|
|
||||||
abi=abi,
|
|
||||||
implementation=implementation,
|
|
||||||
prefer_binary=options.prefer_binary,
|
|
||||||
)
|
|
||||||
@@ -1,809 +0,0 @@
|
|||||||
"""
|
|
||||||
shared options and groups
|
|
||||||
|
|
||||||
The principle here is to define options once, but *not* instantiate them
|
|
||||||
globally. One reason being that options with action='append' can carry state
|
|
||||||
between parses. pip parses general options twice internally, and shouldn't
|
|
||||||
pass on state. To be consistent, all options will follow this design.
|
|
||||||
|
|
||||||
"""
|
|
||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import textwrap
|
|
||||||
import warnings
|
|
||||||
from distutils.util import strtobool
|
|
||||||
from functools import partial
|
|
||||||
from optparse import SUPPRESS_HELP, Option, OptionGroup
|
|
||||||
|
|
||||||
from pip._internal.exceptions import CommandError
|
|
||||||
from pip._internal.locations import USER_CACHE_DIR, src_prefix
|
|
||||||
from pip._internal.models.format_control import FormatControl
|
|
||||||
from pip._internal.models.index import PyPI
|
|
||||||
from pip._internal.utils.hashes import STRONG_HASHES
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
from pip._internal.utils.ui import BAR_TYPES
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from typing import Any, Callable, Dict, List, Optional, Union # noqa: F401
|
|
||||||
from optparse import OptionParser, Values # noqa: F401
|
|
||||||
from pip._internal.cli.parser import ConfigOptionParser # noqa: F401
|
|
||||||
|
|
||||||
|
|
||||||
def raise_option_error(parser, option, msg):
|
|
||||||
"""
|
|
||||||
Raise an option parsing error using parser.error().
|
|
||||||
|
|
||||||
Args:
|
|
||||||
parser: an OptionParser instance.
|
|
||||||
option: an Option instance.
|
|
||||||
msg: the error text.
|
|
||||||
"""
|
|
||||||
msg = '{} error: {}'.format(option, msg)
|
|
||||||
msg = textwrap.fill(' '.join(msg.split()))
|
|
||||||
parser.error(msg)
|
|
||||||
|
|
||||||
|
|
||||||
def make_option_group(group, parser):
|
|
||||||
# type: (Dict[str, Any], ConfigOptionParser) -> OptionGroup
|
|
||||||
"""
|
|
||||||
Return an OptionGroup object
|
|
||||||
group -- assumed to be dict with 'name' and 'options' keys
|
|
||||||
parser -- an optparse Parser
|
|
||||||
"""
|
|
||||||
option_group = OptionGroup(parser, group['name'])
|
|
||||||
for option in group['options']:
|
|
||||||
option_group.add_option(option())
|
|
||||||
return option_group
|
|
||||||
|
|
||||||
|
|
||||||
def check_install_build_global(options, check_options=None):
|
|
||||||
# type: (Values, Optional[Values]) -> None
|
|
||||||
"""Disable wheels if per-setup.py call options are set.
|
|
||||||
|
|
||||||
:param options: The OptionParser options to update.
|
|
||||||
:param check_options: The options to check, if not supplied defaults to
|
|
||||||
options.
|
|
||||||
"""
|
|
||||||
if check_options is None:
|
|
||||||
check_options = options
|
|
||||||
|
|
||||||
def getname(n):
|
|
||||||
return getattr(check_options, n, None)
|
|
||||||
names = ["build_options", "global_options", "install_options"]
|
|
||||||
if any(map(getname, names)):
|
|
||||||
control = options.format_control
|
|
||||||
control.disallow_binaries()
|
|
||||||
warnings.warn(
|
|
||||||
'Disabling all use of wheels due to the use of --build-options '
|
|
||||||
'/ --global-options / --install-options.', stacklevel=2,
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
def check_dist_restriction(options, check_target=False):
|
|
||||||
# type: (Values, bool) -> None
|
|
||||||
"""Function for determining if custom platform options are allowed.
|
|
||||||
|
|
||||||
:param options: The OptionParser options.
|
|
||||||
:param check_target: Whether or not to check if --target is being used.
|
|
||||||
"""
|
|
||||||
dist_restriction_set = any([
|
|
||||||
options.python_version,
|
|
||||||
options.platform,
|
|
||||||
options.abi,
|
|
||||||
options.implementation,
|
|
||||||
])
|
|
||||||
|
|
||||||
binary_only = FormatControl(set(), {':all:'})
|
|
||||||
sdist_dependencies_allowed = (
|
|
||||||
options.format_control != binary_only and
|
|
||||||
not options.ignore_dependencies
|
|
||||||
)
|
|
||||||
|
|
||||||
# Installations or downloads using dist restrictions must not combine
|
|
||||||
# source distributions and dist-specific wheels, as they are not
|
|
||||||
# gauranteed to be locally compatible.
|
|
||||||
if dist_restriction_set and sdist_dependencies_allowed:
|
|
||||||
raise CommandError(
|
|
||||||
"When restricting platform and interpreter constraints using "
|
|
||||||
"--python-version, --platform, --abi, or --implementation, "
|
|
||||||
"either --no-deps must be set, or --only-binary=:all: must be "
|
|
||||||
"set and --no-binary must not be set (or must be set to "
|
|
||||||
":none:)."
|
|
||||||
)
|
|
||||||
|
|
||||||
if check_target:
|
|
||||||
if dist_restriction_set and not options.target_dir:
|
|
||||||
raise CommandError(
|
|
||||||
"Can not use any platform or abi specific options unless "
|
|
||||||
"installing via '--target'"
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
###########
|
|
||||||
# options #
|
|
||||||
###########
|
|
||||||
|
|
||||||
help_ = partial(
|
|
||||||
Option,
|
|
||||||
'-h', '--help',
|
|
||||||
dest='help',
|
|
||||||
action='help',
|
|
||||||
help='Show help.',
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
isolated_mode = partial(
|
|
||||||
Option,
|
|
||||||
"--isolated",
|
|
||||||
dest="isolated_mode",
|
|
||||||
action="store_true",
|
|
||||||
default=False,
|
|
||||||
help=(
|
|
||||||
"Run pip in an isolated mode, ignoring environment variables and user "
|
|
||||||
"configuration."
|
|
||||||
),
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
require_virtualenv = partial(
|
|
||||||
Option,
|
|
||||||
# Run only if inside a virtualenv, bail if not.
|
|
||||||
'--require-virtualenv', '--require-venv',
|
|
||||||
dest='require_venv',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help=SUPPRESS_HELP
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
verbose = partial(
|
|
||||||
Option,
|
|
||||||
'-v', '--verbose',
|
|
||||||
dest='verbose',
|
|
||||||
action='count',
|
|
||||||
default=0,
|
|
||||||
help='Give more output. Option is additive, and can be used up to 3 times.'
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
no_color = partial(
|
|
||||||
Option,
|
|
||||||
'--no-color',
|
|
||||||
dest='no_color',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help="Suppress colored output",
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
version = partial(
|
|
||||||
Option,
|
|
||||||
'-V', '--version',
|
|
||||||
dest='version',
|
|
||||||
action='store_true',
|
|
||||||
help='Show version and exit.',
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
quiet = partial(
|
|
||||||
Option,
|
|
||||||
'-q', '--quiet',
|
|
||||||
dest='quiet',
|
|
||||||
action='count',
|
|
||||||
default=0,
|
|
||||||
help=(
|
|
||||||
'Give less output. Option is additive, and can be used up to 3'
|
|
||||||
' times (corresponding to WARNING, ERROR, and CRITICAL logging'
|
|
||||||
' levels).'
|
|
||||||
),
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
progress_bar = partial(
|
|
||||||
Option,
|
|
||||||
'--progress-bar',
|
|
||||||
dest='progress_bar',
|
|
||||||
type='choice',
|
|
||||||
choices=list(BAR_TYPES.keys()),
|
|
||||||
default='on',
|
|
||||||
help=(
|
|
||||||
'Specify type of progress to be displayed [' +
|
|
||||||
'|'.join(BAR_TYPES.keys()) + '] (default: %default)'
|
|
||||||
),
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
log = partial(
|
|
||||||
Option,
|
|
||||||
"--log", "--log-file", "--local-log",
|
|
||||||
dest="log",
|
|
||||||
metavar="path",
|
|
||||||
help="Path to a verbose appending log."
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
no_input = partial(
|
|
||||||
Option,
|
|
||||||
# Don't ask for input
|
|
||||||
'--no-input',
|
|
||||||
dest='no_input',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help=SUPPRESS_HELP
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
proxy = partial(
|
|
||||||
Option,
|
|
||||||
'--proxy',
|
|
||||||
dest='proxy',
|
|
||||||
type='str',
|
|
||||||
default='',
|
|
||||||
help="Specify a proxy in the form [user:passwd@]proxy.server:port."
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
retries = partial(
|
|
||||||
Option,
|
|
||||||
'--retries',
|
|
||||||
dest='retries',
|
|
||||||
type='int',
|
|
||||||
default=5,
|
|
||||||
help="Maximum number of retries each connection should attempt "
|
|
||||||
"(default %default times).",
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
timeout = partial(
|
|
||||||
Option,
|
|
||||||
'--timeout', '--default-timeout',
|
|
||||||
metavar='sec',
|
|
||||||
dest='timeout',
|
|
||||||
type='float',
|
|
||||||
default=15,
|
|
||||||
help='Set the socket timeout (default %default seconds).',
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
skip_requirements_regex = partial(
|
|
||||||
Option,
|
|
||||||
# A regex to be used to skip requirements
|
|
||||||
'--skip-requirements-regex',
|
|
||||||
dest='skip_requirements_regex',
|
|
||||||
type='str',
|
|
||||||
default='',
|
|
||||||
help=SUPPRESS_HELP,
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
def exists_action():
|
|
||||||
# type: () -> Option
|
|
||||||
return Option(
|
|
||||||
# Option when path already exist
|
|
||||||
'--exists-action',
|
|
||||||
dest='exists_action',
|
|
||||||
type='choice',
|
|
||||||
choices=['s', 'i', 'w', 'b', 'a'],
|
|
||||||
default=[],
|
|
||||||
action='append',
|
|
||||||
metavar='action',
|
|
||||||
help="Default action when a path already exists: "
|
|
||||||
"(s)witch, (i)gnore, (w)ipe, (b)ackup, (a)bort).",
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
cert = partial(
|
|
||||||
Option,
|
|
||||||
'--cert',
|
|
||||||
dest='cert',
|
|
||||||
type='str',
|
|
||||||
metavar='path',
|
|
||||||
help="Path to alternate CA bundle.",
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
client_cert = partial(
|
|
||||||
Option,
|
|
||||||
'--client-cert',
|
|
||||||
dest='client_cert',
|
|
||||||
type='str',
|
|
||||||
default=None,
|
|
||||||
metavar='path',
|
|
||||||
help="Path to SSL client certificate, a single file containing the "
|
|
||||||
"private key and the certificate in PEM format.",
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
index_url = partial(
|
|
||||||
Option,
|
|
||||||
'-i', '--index-url', '--pypi-url',
|
|
||||||
dest='index_url',
|
|
||||||
metavar='URL',
|
|
||||||
default=PyPI.simple_url,
|
|
||||||
help="Base URL of Python Package Index (default %default). "
|
|
||||||
"This should point to a repository compliant with PEP 503 "
|
|
||||||
"(the simple repository API) or a local directory laid out "
|
|
||||||
"in the same format.",
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
def extra_index_url():
|
|
||||||
return Option(
|
|
||||||
'--extra-index-url',
|
|
||||||
dest='extra_index_urls',
|
|
||||||
metavar='URL',
|
|
||||||
action='append',
|
|
||||||
default=[],
|
|
||||||
help="Extra URLs of package indexes to use in addition to "
|
|
||||||
"--index-url. Should follow the same rules as "
|
|
||||||
"--index-url.",
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
no_index = partial(
|
|
||||||
Option,
|
|
||||||
'--no-index',
|
|
||||||
dest='no_index',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help='Ignore package index (only looking at --find-links URLs instead).',
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
def find_links():
|
|
||||||
# type: () -> Option
|
|
||||||
return Option(
|
|
||||||
'-f', '--find-links',
|
|
||||||
dest='find_links',
|
|
||||||
action='append',
|
|
||||||
default=[],
|
|
||||||
metavar='url',
|
|
||||||
help="If a url or path to an html file, then parse for links to "
|
|
||||||
"archives. If a local path or file:// url that's a directory, "
|
|
||||||
"then look for archives in the directory listing.",
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
def trusted_host():
|
|
||||||
# type: () -> Option
|
|
||||||
return Option(
|
|
||||||
"--trusted-host",
|
|
||||||
dest="trusted_hosts",
|
|
||||||
action="append",
|
|
||||||
metavar="HOSTNAME",
|
|
||||||
default=[],
|
|
||||||
help="Mark this host as trusted, even though it does not have valid "
|
|
||||||
"or any HTTPS.",
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
def constraints():
|
|
||||||
# type: () -> Option
|
|
||||||
return Option(
|
|
||||||
'-c', '--constraint',
|
|
||||||
dest='constraints',
|
|
||||||
action='append',
|
|
||||||
default=[],
|
|
||||||
metavar='file',
|
|
||||||
help='Constrain versions using the given constraints file. '
|
|
||||||
'This option can be used multiple times.'
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
def requirements():
|
|
||||||
# type: () -> Option
|
|
||||||
return Option(
|
|
||||||
'-r', '--requirement',
|
|
||||||
dest='requirements',
|
|
||||||
action='append',
|
|
||||||
default=[],
|
|
||||||
metavar='file',
|
|
||||||
help='Install from the given requirements file. '
|
|
||||||
'This option can be used multiple times.'
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
def editable():
|
|
||||||
# type: () -> Option
|
|
||||||
return Option(
|
|
||||||
'-e', '--editable',
|
|
||||||
dest='editables',
|
|
||||||
action='append',
|
|
||||||
default=[],
|
|
||||||
metavar='path/url',
|
|
||||||
help=('Install a project in editable mode (i.e. setuptools '
|
|
||||||
'"develop mode") from a local project path or a VCS url.'),
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
src = partial(
|
|
||||||
Option,
|
|
||||||
'--src', '--source', '--source-dir', '--source-directory',
|
|
||||||
dest='src_dir',
|
|
||||||
metavar='dir',
|
|
||||||
default=src_prefix,
|
|
||||||
help='Directory to check out editable projects into. '
|
|
||||||
'The default in a virtualenv is "<venv path>/src". '
|
|
||||||
'The default for global installs is "<current dir>/src".'
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
def _get_format_control(values, option):
|
|
||||||
# type: (Values, Option) -> Any
|
|
||||||
"""Get a format_control object."""
|
|
||||||
return getattr(values, option.dest)
|
|
||||||
|
|
||||||
|
|
||||||
def _handle_no_binary(option, opt_str, value, parser):
|
|
||||||
# type: (Option, str, str, OptionParser) -> None
|
|
||||||
existing = _get_format_control(parser.values, option)
|
|
||||||
FormatControl.handle_mutual_excludes(
|
|
||||||
value, existing.no_binary, existing.only_binary,
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
def _handle_only_binary(option, opt_str, value, parser):
|
|
||||||
# type: (Option, str, str, OptionParser) -> None
|
|
||||||
existing = _get_format_control(parser.values, option)
|
|
||||||
FormatControl.handle_mutual_excludes(
|
|
||||||
value, existing.only_binary, existing.no_binary,
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
def no_binary():
|
|
||||||
# type: () -> Option
|
|
||||||
format_control = FormatControl(set(), set())
|
|
||||||
return Option(
|
|
||||||
"--no-binary", dest="format_control", action="callback",
|
|
||||||
callback=_handle_no_binary, type="str",
|
|
||||||
default=format_control,
|
|
||||||
help="Do not use binary packages. Can be supplied multiple times, and "
|
|
||||||
"each time adds to the existing value. Accepts either :all: to "
|
|
||||||
"disable all binary packages, :none: to empty the set, or one or "
|
|
||||||
"more package names with commas between them. Note that some "
|
|
||||||
"packages are tricky to compile and may fail to install when "
|
|
||||||
"this option is used on them.",
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
def only_binary():
|
|
||||||
# type: () -> Option
|
|
||||||
format_control = FormatControl(set(), set())
|
|
||||||
return Option(
|
|
||||||
"--only-binary", dest="format_control", action="callback",
|
|
||||||
callback=_handle_only_binary, type="str",
|
|
||||||
default=format_control,
|
|
||||||
help="Do not use source packages. Can be supplied multiple times, and "
|
|
||||||
"each time adds to the existing value. Accepts either :all: to "
|
|
||||||
"disable all source packages, :none: to empty the set, or one or "
|
|
||||||
"more package names with commas between them. Packages without "
|
|
||||||
"binary distributions will fail to install when this option is "
|
|
||||||
"used on them.",
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
platform = partial(
|
|
||||||
Option,
|
|
||||||
'--platform',
|
|
||||||
dest='platform',
|
|
||||||
metavar='platform',
|
|
||||||
default=None,
|
|
||||||
help=("Only use wheels compatible with <platform>. "
|
|
||||||
"Defaults to the platform of the running system."),
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
python_version = partial(
|
|
||||||
Option,
|
|
||||||
'--python-version',
|
|
||||||
dest='python_version',
|
|
||||||
metavar='python_version',
|
|
||||||
default=None,
|
|
||||||
help=("Only use wheels compatible with Python "
|
|
||||||
"interpreter version <version>. If not specified, then the "
|
|
||||||
"current system interpreter minor version is used. A major "
|
|
||||||
"version (e.g. '2') can be specified to match all "
|
|
||||||
"minor revs of that major version. A minor version "
|
|
||||||
"(e.g. '34') can also be specified."),
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
implementation = partial(
|
|
||||||
Option,
|
|
||||||
'--implementation',
|
|
||||||
dest='implementation',
|
|
||||||
metavar='implementation',
|
|
||||||
default=None,
|
|
||||||
help=("Only use wheels compatible with Python "
|
|
||||||
"implementation <implementation>, e.g. 'pp', 'jy', 'cp', "
|
|
||||||
" or 'ip'. If not specified, then the current "
|
|
||||||
"interpreter implementation is used. Use 'py' to force "
|
|
||||||
"implementation-agnostic wheels."),
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
abi = partial(
|
|
||||||
Option,
|
|
||||||
'--abi',
|
|
||||||
dest='abi',
|
|
||||||
metavar='abi',
|
|
||||||
default=None,
|
|
||||||
help=("Only use wheels compatible with Python "
|
|
||||||
"abi <abi>, e.g. 'pypy_41'. If not specified, then the "
|
|
||||||
"current interpreter abi tag is used. Generally "
|
|
||||||
"you will need to specify --implementation, "
|
|
||||||
"--platform, and --python-version when using "
|
|
||||||
"this option."),
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
def prefer_binary():
|
|
||||||
# type: () -> Option
|
|
||||||
return Option(
|
|
||||||
"--prefer-binary",
|
|
||||||
dest="prefer_binary",
|
|
||||||
action="store_true",
|
|
||||||
default=False,
|
|
||||||
help="Prefer older binary packages over newer source packages."
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
cache_dir = partial(
|
|
||||||
Option,
|
|
||||||
"--cache-dir",
|
|
||||||
dest="cache_dir",
|
|
||||||
default=USER_CACHE_DIR,
|
|
||||||
metavar="dir",
|
|
||||||
help="Store the cache data in <dir>."
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
def no_cache_dir_callback(option, opt, value, parser):
|
|
||||||
"""
|
|
||||||
Process a value provided for the --no-cache-dir option.
|
|
||||||
|
|
||||||
This is an optparse.Option callback for the --no-cache-dir option.
|
|
||||||
"""
|
|
||||||
# The value argument will be None if --no-cache-dir is passed via the
|
|
||||||
# command-line, since the option doesn't accept arguments. However,
|
|
||||||
# the value can be non-None if the option is triggered e.g. by an
|
|
||||||
# environment variable, like PIP_NO_CACHE_DIR=true.
|
|
||||||
if value is not None:
|
|
||||||
# Then parse the string value to get argument error-checking.
|
|
||||||
try:
|
|
||||||
strtobool(value)
|
|
||||||
except ValueError as exc:
|
|
||||||
raise_option_error(parser, option=option, msg=str(exc))
|
|
||||||
|
|
||||||
# Originally, setting PIP_NO_CACHE_DIR to a value that strtobool()
|
|
||||||
# converted to 0 (like "false" or "no") caused cache_dir to be disabled
|
|
||||||
# rather than enabled (logic would say the latter). Thus, we disable
|
|
||||||
# the cache directory not just on values that parse to True, but (for
|
|
||||||
# backwards compatibility reasons) also on values that parse to False.
|
|
||||||
# In other words, always set it to False if the option is provided in
|
|
||||||
# some (valid) form.
|
|
||||||
parser.values.cache_dir = False
|
|
||||||
|
|
||||||
|
|
||||||
no_cache = partial(
|
|
||||||
Option,
|
|
||||||
"--no-cache-dir",
|
|
||||||
dest="cache_dir",
|
|
||||||
action="callback",
|
|
||||||
callback=no_cache_dir_callback,
|
|
||||||
help="Disable the cache.",
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
no_deps = partial(
|
|
||||||
Option,
|
|
||||||
'--no-deps', '--no-dependencies',
|
|
||||||
dest='ignore_dependencies',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help="Don't install package dependencies.",
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
build_dir = partial(
|
|
||||||
Option,
|
|
||||||
'-b', '--build', '--build-dir', '--build-directory',
|
|
||||||
dest='build_dir',
|
|
||||||
metavar='dir',
|
|
||||||
help='Directory to unpack packages into and build in. Note that '
|
|
||||||
'an initial build still takes place in a temporary directory. '
|
|
||||||
'The location of temporary directories can be controlled by setting '
|
|
||||||
'the TMPDIR environment variable (TEMP on Windows) appropriately. '
|
|
||||||
'When passed, build directories are not cleaned in case of failures.'
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
ignore_requires_python = partial(
|
|
||||||
Option,
|
|
||||||
'--ignore-requires-python',
|
|
||||||
dest='ignore_requires_python',
|
|
||||||
action='store_true',
|
|
||||||
help='Ignore the Requires-Python information.'
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
no_build_isolation = partial(
|
|
||||||
Option,
|
|
||||||
'--no-build-isolation',
|
|
||||||
dest='build_isolation',
|
|
||||||
action='store_false',
|
|
||||||
default=True,
|
|
||||||
help='Disable isolation when building a modern source distribution. '
|
|
||||||
'Build dependencies specified by PEP 518 must be already installed '
|
|
||||||
'if this option is used.'
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
def no_use_pep517_callback(option, opt, value, parser):
|
|
||||||
"""
|
|
||||||
Process a value provided for the --no-use-pep517 option.
|
|
||||||
|
|
||||||
This is an optparse.Option callback for the no_use_pep517 option.
|
|
||||||
"""
|
|
||||||
# Since --no-use-pep517 doesn't accept arguments, the value argument
|
|
||||||
# will be None if --no-use-pep517 is passed via the command-line.
|
|
||||||
# However, the value can be non-None if the option is triggered e.g.
|
|
||||||
# by an environment variable, for example "PIP_NO_USE_PEP517=true".
|
|
||||||
if value is not None:
|
|
||||||
msg = """A value was passed for --no-use-pep517,
|
|
||||||
probably using either the PIP_NO_USE_PEP517 environment variable
|
|
||||||
or the "no-use-pep517" config file option. Use an appropriate value
|
|
||||||
of the PIP_USE_PEP517 environment variable or the "use-pep517"
|
|
||||||
config file option instead.
|
|
||||||
"""
|
|
||||||
raise_option_error(parser, option=option, msg=msg)
|
|
||||||
|
|
||||||
# Otherwise, --no-use-pep517 was passed via the command-line.
|
|
||||||
parser.values.use_pep517 = False
|
|
||||||
|
|
||||||
|
|
||||||
use_pep517 = partial(
|
|
||||||
Option,
|
|
||||||
'--use-pep517',
|
|
||||||
dest='use_pep517',
|
|
||||||
action='store_true',
|
|
||||||
default=None,
|
|
||||||
help='Use PEP 517 for building source distributions '
|
|
||||||
'(use --no-use-pep517 to force legacy behaviour).'
|
|
||||||
) # type: Any
|
|
||||||
|
|
||||||
no_use_pep517 = partial(
|
|
||||||
Option,
|
|
||||||
'--no-use-pep517',
|
|
||||||
dest='use_pep517',
|
|
||||||
action='callback',
|
|
||||||
callback=no_use_pep517_callback,
|
|
||||||
default=None,
|
|
||||||
help=SUPPRESS_HELP
|
|
||||||
) # type: Any
|
|
||||||
|
|
||||||
install_options = partial(
|
|
||||||
Option,
|
|
||||||
'--install-option',
|
|
||||||
dest='install_options',
|
|
||||||
action='append',
|
|
||||||
metavar='options',
|
|
||||||
help="Extra arguments to be supplied to the setup.py install "
|
|
||||||
"command (use like --install-option=\"--install-scripts=/usr/local/"
|
|
||||||
"bin\"). Use multiple --install-option options to pass multiple "
|
|
||||||
"options to setup.py install. If you are using an option with a "
|
|
||||||
"directory path, be sure to use absolute path.",
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
global_options = partial(
|
|
||||||
Option,
|
|
||||||
'--global-option',
|
|
||||||
dest='global_options',
|
|
||||||
action='append',
|
|
||||||
metavar='options',
|
|
||||||
help="Extra global options to be supplied to the setup.py "
|
|
||||||
"call before the install command.",
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
no_clean = partial(
|
|
||||||
Option,
|
|
||||||
'--no-clean',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help="Don't clean up build directories."
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
pre = partial(
|
|
||||||
Option,
|
|
||||||
'--pre',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help="Include pre-release and development versions. By default, "
|
|
||||||
"pip only finds stable versions.",
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
disable_pip_version_check = partial(
|
|
||||||
Option,
|
|
||||||
"--disable-pip-version-check",
|
|
||||||
dest="disable_pip_version_check",
|
|
||||||
action="store_true",
|
|
||||||
default=False,
|
|
||||||
help="Don't periodically check PyPI to determine whether a new version "
|
|
||||||
"of pip is available for download. Implied with --no-index.",
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
# Deprecated, Remove later
|
|
||||||
always_unzip = partial(
|
|
||||||
Option,
|
|
||||||
'-Z', '--always-unzip',
|
|
||||||
dest='always_unzip',
|
|
||||||
action='store_true',
|
|
||||||
help=SUPPRESS_HELP,
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
def _merge_hash(option, opt_str, value, parser):
|
|
||||||
# type: (Option, str, str, OptionParser) -> None
|
|
||||||
"""Given a value spelled "algo:digest", append the digest to a list
|
|
||||||
pointed to in a dict by the algo name."""
|
|
||||||
if not parser.values.hashes:
|
|
||||||
parser.values.hashes = {} # type: ignore
|
|
||||||
try:
|
|
||||||
algo, digest = value.split(':', 1)
|
|
||||||
except ValueError:
|
|
||||||
parser.error('Arguments to %s must be a hash name '
|
|
||||||
'followed by a value, like --hash=sha256:abcde...' %
|
|
||||||
opt_str)
|
|
||||||
if algo not in STRONG_HASHES:
|
|
||||||
parser.error('Allowed hash algorithms for %s are %s.' %
|
|
||||||
(opt_str, ', '.join(STRONG_HASHES)))
|
|
||||||
parser.values.hashes.setdefault(algo, []).append(digest)
|
|
||||||
|
|
||||||
|
|
||||||
hash = partial(
|
|
||||||
Option,
|
|
||||||
'--hash',
|
|
||||||
# Hash values eventually end up in InstallRequirement.hashes due to
|
|
||||||
# __dict__ copying in process_line().
|
|
||||||
dest='hashes',
|
|
||||||
action='callback',
|
|
||||||
callback=_merge_hash,
|
|
||||||
type='string',
|
|
||||||
help="Verify that the package's archive matches this "
|
|
||||||
'hash before installing. Example: --hash=sha256:abcdef...',
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
require_hashes = partial(
|
|
||||||
Option,
|
|
||||||
'--require-hashes',
|
|
||||||
dest='require_hashes',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help='Require a hash to check each requirement against, for '
|
|
||||||
'repeatable installs. This option is implied when any package in a '
|
|
||||||
'requirements file has a --hash option.',
|
|
||||||
) # type: Callable[..., Option]
|
|
||||||
|
|
||||||
|
|
||||||
##########
|
|
||||||
# groups #
|
|
||||||
##########
|
|
||||||
|
|
||||||
general_group = {
|
|
||||||
'name': 'General Options',
|
|
||||||
'options': [
|
|
||||||
help_,
|
|
||||||
isolated_mode,
|
|
||||||
require_virtualenv,
|
|
||||||
verbose,
|
|
||||||
version,
|
|
||||||
quiet,
|
|
||||||
log,
|
|
||||||
no_input,
|
|
||||||
proxy,
|
|
||||||
retries,
|
|
||||||
timeout,
|
|
||||||
skip_requirements_regex,
|
|
||||||
exists_action,
|
|
||||||
trusted_host,
|
|
||||||
cert,
|
|
||||||
client_cert,
|
|
||||||
cache_dir,
|
|
||||||
no_cache,
|
|
||||||
disable_pip_version_check,
|
|
||||||
no_color,
|
|
||||||
]
|
|
||||||
} # type: Dict[str, Any]
|
|
||||||
|
|
||||||
index_group = {
|
|
||||||
'name': 'Package Index Options',
|
|
||||||
'options': [
|
|
||||||
index_url,
|
|
||||||
extra_index_url,
|
|
||||||
no_index,
|
|
||||||
find_links,
|
|
||||||
]
|
|
||||||
} # type: Dict[str, Any]
|
|
||||||
@@ -1,104 +0,0 @@
|
|||||||
"""A single place for constructing and exposing the main parser
|
|
||||||
"""
|
|
||||||
|
|
||||||
import os
|
|
||||||
import sys
|
|
||||||
|
|
||||||
from pip import __version__
|
|
||||||
from pip._internal.cli import cmdoptions
|
|
||||||
from pip._internal.cli.parser import (
|
|
||||||
ConfigOptionParser, UpdatingDefaultsHelpFormatter,
|
|
||||||
)
|
|
||||||
from pip._internal.commands import (
|
|
||||||
commands_dict, get_similar_commands, get_summaries,
|
|
||||||
)
|
|
||||||
from pip._internal.exceptions import CommandError
|
|
||||||
from pip._internal.utils.misc import get_prog
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from typing import Tuple, List # noqa: F401
|
|
||||||
|
|
||||||
|
|
||||||
__all__ = ["create_main_parser", "parse_command"]
|
|
||||||
|
|
||||||
|
|
||||||
def create_main_parser():
|
|
||||||
# type: () -> ConfigOptionParser
|
|
||||||
"""Creates and returns the main parser for pip's CLI
|
|
||||||
"""
|
|
||||||
|
|
||||||
parser_kw = {
|
|
||||||
'usage': '\n%prog <command> [options]',
|
|
||||||
'add_help_option': False,
|
|
||||||
'formatter': UpdatingDefaultsHelpFormatter(),
|
|
||||||
'name': 'global',
|
|
||||||
'prog': get_prog(),
|
|
||||||
}
|
|
||||||
|
|
||||||
parser = ConfigOptionParser(**parser_kw)
|
|
||||||
parser.disable_interspersed_args()
|
|
||||||
|
|
||||||
pip_pkg_dir = os.path.abspath(os.path.join(
|
|
||||||
os.path.dirname(__file__), "..", "..",
|
|
||||||
))
|
|
||||||
parser.version = 'pip %s from %s (python %s)' % (
|
|
||||||
__version__, pip_pkg_dir, sys.version[:3],
|
|
||||||
)
|
|
||||||
|
|
||||||
# add the general options
|
|
||||||
gen_opts = cmdoptions.make_option_group(cmdoptions.general_group, parser)
|
|
||||||
parser.add_option_group(gen_opts)
|
|
||||||
|
|
||||||
# so the help formatter knows
|
|
||||||
parser.main = True # type: ignore
|
|
||||||
|
|
||||||
# create command listing for description
|
|
||||||
command_summaries = get_summaries()
|
|
||||||
description = [''] + ['%-27s %s' % (i, j) for i, j in command_summaries]
|
|
||||||
parser.description = '\n'.join(description)
|
|
||||||
|
|
||||||
return parser
|
|
||||||
|
|
||||||
|
|
||||||
def parse_command(args):
|
|
||||||
# type: (List[str]) -> Tuple[str, List[str]]
|
|
||||||
parser = create_main_parser()
|
|
||||||
|
|
||||||
# Note: parser calls disable_interspersed_args(), so the result of this
|
|
||||||
# call is to split the initial args into the general options before the
|
|
||||||
# subcommand and everything else.
|
|
||||||
# For example:
|
|
||||||
# args: ['--timeout=5', 'install', '--user', 'INITools']
|
|
||||||
# general_options: ['--timeout==5']
|
|
||||||
# args_else: ['install', '--user', 'INITools']
|
|
||||||
general_options, args_else = parser.parse_args(args)
|
|
||||||
|
|
||||||
# --version
|
|
||||||
if general_options.version:
|
|
||||||
sys.stdout.write(parser.version) # type: ignore
|
|
||||||
sys.stdout.write(os.linesep)
|
|
||||||
sys.exit()
|
|
||||||
|
|
||||||
# pip || pip help -> print_help()
|
|
||||||
if not args_else or (args_else[0] == 'help' and len(args_else) == 1):
|
|
||||||
parser.print_help()
|
|
||||||
sys.exit()
|
|
||||||
|
|
||||||
# the subcommand name
|
|
||||||
cmd_name = args_else[0]
|
|
||||||
|
|
||||||
if cmd_name not in commands_dict:
|
|
||||||
guess = get_similar_commands(cmd_name)
|
|
||||||
|
|
||||||
msg = ['unknown command "%s"' % cmd_name]
|
|
||||||
if guess:
|
|
||||||
msg.append('maybe you meant "%s"' % guess)
|
|
||||||
|
|
||||||
raise CommandError(' - '.join(msg))
|
|
||||||
|
|
||||||
# all the args without the subcommand
|
|
||||||
cmd_args = args[:]
|
|
||||||
cmd_args.remove(cmd_name)
|
|
||||||
|
|
||||||
return cmd_name, cmd_args
|
|
||||||
@@ -1,261 +0,0 @@
|
|||||||
"""Base option parser setup"""
|
|
||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import logging
|
|
||||||
import optparse
|
|
||||||
import sys
|
|
||||||
import textwrap
|
|
||||||
from distutils.util import strtobool
|
|
||||||
|
|
||||||
from pip._vendor.six import string_types
|
|
||||||
|
|
||||||
from pip._internal.cli.status_codes import UNKNOWN_ERROR
|
|
||||||
from pip._internal.configuration import Configuration, ConfigurationError
|
|
||||||
from pip._internal.utils.compat import get_terminal_size
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class PrettyHelpFormatter(optparse.IndentedHelpFormatter):
|
|
||||||
"""A prettier/less verbose help formatter for optparse."""
|
|
||||||
|
|
||||||
def __init__(self, *args, **kwargs):
|
|
||||||
# help position must be aligned with __init__.parseopts.description
|
|
||||||
kwargs['max_help_position'] = 30
|
|
||||||
kwargs['indent_increment'] = 1
|
|
||||||
kwargs['width'] = get_terminal_size()[0] - 2
|
|
||||||
optparse.IndentedHelpFormatter.__init__(self, *args, **kwargs)
|
|
||||||
|
|
||||||
def format_option_strings(self, option):
|
|
||||||
return self._format_option_strings(option, ' <%s>', ', ')
|
|
||||||
|
|
||||||
def _format_option_strings(self, option, mvarfmt=' <%s>', optsep=', '):
|
|
||||||
"""
|
|
||||||
Return a comma-separated list of option strings and metavars.
|
|
||||||
|
|
||||||
:param option: tuple of (short opt, long opt), e.g: ('-f', '--format')
|
|
||||||
:param mvarfmt: metavar format string - evaluated as mvarfmt % metavar
|
|
||||||
:param optsep: separator
|
|
||||||
"""
|
|
||||||
opts = []
|
|
||||||
|
|
||||||
if option._short_opts:
|
|
||||||
opts.append(option._short_opts[0])
|
|
||||||
if option._long_opts:
|
|
||||||
opts.append(option._long_opts[0])
|
|
||||||
if len(opts) > 1:
|
|
||||||
opts.insert(1, optsep)
|
|
||||||
|
|
||||||
if option.takes_value():
|
|
||||||
metavar = option.metavar or option.dest.lower()
|
|
||||||
opts.append(mvarfmt % metavar.lower())
|
|
||||||
|
|
||||||
return ''.join(opts)
|
|
||||||
|
|
||||||
def format_heading(self, heading):
|
|
||||||
if heading == 'Options':
|
|
||||||
return ''
|
|
||||||
return heading + ':\n'
|
|
||||||
|
|
||||||
def format_usage(self, usage):
|
|
||||||
"""
|
|
||||||
Ensure there is only one newline between usage and the first heading
|
|
||||||
if there is no description.
|
|
||||||
"""
|
|
||||||
msg = '\nUsage: %s\n' % self.indent_lines(textwrap.dedent(usage), " ")
|
|
||||||
return msg
|
|
||||||
|
|
||||||
def format_description(self, description):
|
|
||||||
# leave full control over description to us
|
|
||||||
if description:
|
|
||||||
if hasattr(self.parser, 'main'):
|
|
||||||
label = 'Commands'
|
|
||||||
else:
|
|
||||||
label = 'Description'
|
|
||||||
# some doc strings have initial newlines, some don't
|
|
||||||
description = description.lstrip('\n')
|
|
||||||
# some doc strings have final newlines and spaces, some don't
|
|
||||||
description = description.rstrip()
|
|
||||||
# dedent, then reindent
|
|
||||||
description = self.indent_lines(textwrap.dedent(description), " ")
|
|
||||||
description = '%s:\n%s\n' % (label, description)
|
|
||||||
return description
|
|
||||||
else:
|
|
||||||
return ''
|
|
||||||
|
|
||||||
def format_epilog(self, epilog):
|
|
||||||
# leave full control over epilog to us
|
|
||||||
if epilog:
|
|
||||||
return epilog
|
|
||||||
else:
|
|
||||||
return ''
|
|
||||||
|
|
||||||
def indent_lines(self, text, indent):
|
|
||||||
new_lines = [indent + line for line in text.split('\n')]
|
|
||||||
return "\n".join(new_lines)
|
|
||||||
|
|
||||||
|
|
||||||
class UpdatingDefaultsHelpFormatter(PrettyHelpFormatter):
|
|
||||||
"""Custom help formatter for use in ConfigOptionParser.
|
|
||||||
|
|
||||||
This is updates the defaults before expanding them, allowing
|
|
||||||
them to show up correctly in the help listing.
|
|
||||||
"""
|
|
||||||
|
|
||||||
def expand_default(self, option):
|
|
||||||
if self.parser is not None:
|
|
||||||
self.parser._update_defaults(self.parser.defaults)
|
|
||||||
return optparse.IndentedHelpFormatter.expand_default(self, option)
|
|
||||||
|
|
||||||
|
|
||||||
class CustomOptionParser(optparse.OptionParser):
|
|
||||||
|
|
||||||
def insert_option_group(self, idx, *args, **kwargs):
|
|
||||||
"""Insert an OptionGroup at a given position."""
|
|
||||||
group = self.add_option_group(*args, **kwargs)
|
|
||||||
|
|
||||||
self.option_groups.pop()
|
|
||||||
self.option_groups.insert(idx, group)
|
|
||||||
|
|
||||||
return group
|
|
||||||
|
|
||||||
@property
|
|
||||||
def option_list_all(self):
|
|
||||||
"""Get a list of all options, including those in option groups."""
|
|
||||||
res = self.option_list[:]
|
|
||||||
for i in self.option_groups:
|
|
||||||
res.extend(i.option_list)
|
|
||||||
|
|
||||||
return res
|
|
||||||
|
|
||||||
|
|
||||||
class ConfigOptionParser(CustomOptionParser):
|
|
||||||
"""Custom option parser which updates its defaults by checking the
|
|
||||||
configuration files and environmental variables"""
|
|
||||||
|
|
||||||
def __init__(self, *args, **kwargs):
|
|
||||||
self.name = kwargs.pop('name')
|
|
||||||
|
|
||||||
isolated = kwargs.pop("isolated", False)
|
|
||||||
self.config = Configuration(isolated)
|
|
||||||
|
|
||||||
assert self.name
|
|
||||||
optparse.OptionParser.__init__(self, *args, **kwargs)
|
|
||||||
|
|
||||||
def check_default(self, option, key, val):
|
|
||||||
try:
|
|
||||||
return option.check_value(key, val)
|
|
||||||
except optparse.OptionValueError as exc:
|
|
||||||
print("An error occurred during configuration: %s" % exc)
|
|
||||||
sys.exit(3)
|
|
||||||
|
|
||||||
def _get_ordered_configuration_items(self):
|
|
||||||
# Configuration gives keys in an unordered manner. Order them.
|
|
||||||
override_order = ["global", self.name, ":env:"]
|
|
||||||
|
|
||||||
# Pool the options into different groups
|
|
||||||
section_items = {name: [] for name in override_order}
|
|
||||||
for section_key, val in self.config.items():
|
|
||||||
# ignore empty values
|
|
||||||
if not val:
|
|
||||||
logger.debug(
|
|
||||||
"Ignoring configuration key '%s' as it's value is empty.",
|
|
||||||
section_key
|
|
||||||
)
|
|
||||||
continue
|
|
||||||
|
|
||||||
section, key = section_key.split(".", 1)
|
|
||||||
if section in override_order:
|
|
||||||
section_items[section].append((key, val))
|
|
||||||
|
|
||||||
# Yield each group in their override order
|
|
||||||
for section in override_order:
|
|
||||||
for key, val in section_items[section]:
|
|
||||||
yield key, val
|
|
||||||
|
|
||||||
def _update_defaults(self, defaults):
|
|
||||||
"""Updates the given defaults with values from the config files and
|
|
||||||
the environ. Does a little special handling for certain types of
|
|
||||||
options (lists)."""
|
|
||||||
|
|
||||||
# Accumulate complex default state.
|
|
||||||
self.values = optparse.Values(self.defaults)
|
|
||||||
late_eval = set()
|
|
||||||
# Then set the options with those values
|
|
||||||
for key, val in self._get_ordered_configuration_items():
|
|
||||||
# '--' because configuration supports only long names
|
|
||||||
option = self.get_option('--' + key)
|
|
||||||
|
|
||||||
# Ignore options not present in this parser. E.g. non-globals put
|
|
||||||
# in [global] by users that want them to apply to all applicable
|
|
||||||
# commands.
|
|
||||||
if option is None:
|
|
||||||
continue
|
|
||||||
|
|
||||||
if option.action in ('store_true', 'store_false', 'count'):
|
|
||||||
try:
|
|
||||||
val = strtobool(val)
|
|
||||||
except ValueError:
|
|
||||||
error_msg = invalid_config_error_message(
|
|
||||||
option.action, key, val
|
|
||||||
)
|
|
||||||
self.error(error_msg)
|
|
||||||
|
|
||||||
elif option.action == 'append':
|
|
||||||
val = val.split()
|
|
||||||
val = [self.check_default(option, key, v) for v in val]
|
|
||||||
elif option.action == 'callback':
|
|
||||||
late_eval.add(option.dest)
|
|
||||||
opt_str = option.get_opt_string()
|
|
||||||
val = option.convert_value(opt_str, val)
|
|
||||||
# From take_action
|
|
||||||
args = option.callback_args or ()
|
|
||||||
kwargs = option.callback_kwargs or {}
|
|
||||||
option.callback(option, opt_str, val, self, *args, **kwargs)
|
|
||||||
else:
|
|
||||||
val = self.check_default(option, key, val)
|
|
||||||
|
|
||||||
defaults[option.dest] = val
|
|
||||||
|
|
||||||
for key in late_eval:
|
|
||||||
defaults[key] = getattr(self.values, key)
|
|
||||||
self.values = None
|
|
||||||
return defaults
|
|
||||||
|
|
||||||
def get_default_values(self):
|
|
||||||
"""Overriding to make updating the defaults after instantiation of
|
|
||||||
the option parser possible, _update_defaults() does the dirty work."""
|
|
||||||
if not self.process_default_values:
|
|
||||||
# Old, pre-Optik 1.5 behaviour.
|
|
||||||
return optparse.Values(self.defaults)
|
|
||||||
|
|
||||||
# Load the configuration, or error out in case of an error
|
|
||||||
try:
|
|
||||||
self.config.load()
|
|
||||||
except ConfigurationError as err:
|
|
||||||
self.exit(UNKNOWN_ERROR, str(err))
|
|
||||||
|
|
||||||
defaults = self._update_defaults(self.defaults.copy()) # ours
|
|
||||||
for option in self._get_all_options():
|
|
||||||
default = defaults.get(option.dest)
|
|
||||||
if isinstance(default, string_types):
|
|
||||||
opt_str = option.get_opt_string()
|
|
||||||
defaults[option.dest] = option.check_value(opt_str, default)
|
|
||||||
return optparse.Values(defaults)
|
|
||||||
|
|
||||||
def error(self, msg):
|
|
||||||
self.print_usage(sys.stderr)
|
|
||||||
self.exit(UNKNOWN_ERROR, "%s\n" % msg)
|
|
||||||
|
|
||||||
|
|
||||||
def invalid_config_error_message(action, key, val):
|
|
||||||
"""Returns a better error message when invalid configuration option
|
|
||||||
is provided."""
|
|
||||||
if action in ('store_true', 'store_false'):
|
|
||||||
return ("{0} is not a valid value for {1} option, "
|
|
||||||
"please specify a boolean value like yes/no, "
|
|
||||||
"true/false or 1/0 instead.").format(val, key)
|
|
||||||
|
|
||||||
return ("{0} is not a valid value for {1} option, "
|
|
||||||
"please specify a numerical value like 1/0 "
|
|
||||||
"instead.").format(val, key)
|
|
||||||
@@ -1,8 +0,0 @@
|
|||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
SUCCESS = 0
|
|
||||||
ERROR = 1
|
|
||||||
UNKNOWN_ERROR = 2
|
|
||||||
VIRTUALENV_NOT_FOUND = 3
|
|
||||||
PREVIOUS_BUILD_DIR_ERROR = 4
|
|
||||||
NO_MATCHES_FOUND = 23
|
|
||||||
@@ -1,79 +0,0 @@
|
|||||||
"""
|
|
||||||
Package containing all pip commands
|
|
||||||
"""
|
|
||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
from pip._internal.commands.completion import CompletionCommand
|
|
||||||
from pip._internal.commands.configuration import ConfigurationCommand
|
|
||||||
from pip._internal.commands.download import DownloadCommand
|
|
||||||
from pip._internal.commands.freeze import FreezeCommand
|
|
||||||
from pip._internal.commands.hash import HashCommand
|
|
||||||
from pip._internal.commands.help import HelpCommand
|
|
||||||
from pip._internal.commands.list import ListCommand
|
|
||||||
from pip._internal.commands.check import CheckCommand
|
|
||||||
from pip._internal.commands.search import SearchCommand
|
|
||||||
from pip._internal.commands.show import ShowCommand
|
|
||||||
from pip._internal.commands.install import InstallCommand
|
|
||||||
from pip._internal.commands.uninstall import UninstallCommand
|
|
||||||
from pip._internal.commands.wheel import WheelCommand
|
|
||||||
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from typing import List, Type # noqa: F401
|
|
||||||
from pip._internal.cli.base_command import Command # noqa: F401
|
|
||||||
|
|
||||||
commands_order = [
|
|
||||||
InstallCommand,
|
|
||||||
DownloadCommand,
|
|
||||||
UninstallCommand,
|
|
||||||
FreezeCommand,
|
|
||||||
ListCommand,
|
|
||||||
ShowCommand,
|
|
||||||
CheckCommand,
|
|
||||||
ConfigurationCommand,
|
|
||||||
SearchCommand,
|
|
||||||
WheelCommand,
|
|
||||||
HashCommand,
|
|
||||||
CompletionCommand,
|
|
||||||
HelpCommand,
|
|
||||||
] # type: List[Type[Command]]
|
|
||||||
|
|
||||||
commands_dict = {c.name: c for c in commands_order}
|
|
||||||
|
|
||||||
|
|
||||||
def get_summaries(ordered=True):
|
|
||||||
"""Yields sorted (command name, command summary) tuples."""
|
|
||||||
|
|
||||||
if ordered:
|
|
||||||
cmditems = _sort_commands(commands_dict, commands_order)
|
|
||||||
else:
|
|
||||||
cmditems = commands_dict.items()
|
|
||||||
|
|
||||||
for name, command_class in cmditems:
|
|
||||||
yield (name, command_class.summary)
|
|
||||||
|
|
||||||
|
|
||||||
def get_similar_commands(name):
|
|
||||||
"""Command name auto-correct."""
|
|
||||||
from difflib import get_close_matches
|
|
||||||
|
|
||||||
name = name.lower()
|
|
||||||
|
|
||||||
close_commands = get_close_matches(name, commands_dict.keys())
|
|
||||||
|
|
||||||
if close_commands:
|
|
||||||
return close_commands[0]
|
|
||||||
else:
|
|
||||||
return False
|
|
||||||
|
|
||||||
|
|
||||||
def _sort_commands(cmddict, order):
|
|
||||||
def keyfn(key):
|
|
||||||
try:
|
|
||||||
return order.index(key[1])
|
|
||||||
except ValueError:
|
|
||||||
# unordered items should come last
|
|
||||||
return 0xff
|
|
||||||
|
|
||||||
return sorted(cmddict.items(), key=keyfn)
|
|
||||||
@@ -1,41 +0,0 @@
|
|||||||
import logging
|
|
||||||
|
|
||||||
from pip._internal.cli.base_command import Command
|
|
||||||
from pip._internal.operations.check import (
|
|
||||||
check_package_set, create_package_set_from_installed,
|
|
||||||
)
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class CheckCommand(Command):
|
|
||||||
"""Verify installed packages have compatible dependencies."""
|
|
||||||
name = 'check'
|
|
||||||
usage = """
|
|
||||||
%prog [options]"""
|
|
||||||
summary = 'Verify installed packages have compatible dependencies.'
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
package_set, parsing_probs = create_package_set_from_installed()
|
|
||||||
missing, conflicting = check_package_set(package_set)
|
|
||||||
|
|
||||||
for project_name in missing:
|
|
||||||
version = package_set[project_name].version
|
|
||||||
for dependency in missing[project_name]:
|
|
||||||
logger.info(
|
|
||||||
"%s %s requires %s, which is not installed.",
|
|
||||||
project_name, version, dependency[0],
|
|
||||||
)
|
|
||||||
|
|
||||||
for project_name in conflicting:
|
|
||||||
version = package_set[project_name].version
|
|
||||||
for dep_name, dep_version, req in conflicting[project_name]:
|
|
||||||
logger.info(
|
|
||||||
"%s %s has requirement %s, but you have %s %s.",
|
|
||||||
project_name, version, req, dep_name, dep_version,
|
|
||||||
)
|
|
||||||
|
|
||||||
if missing or conflicting or parsing_probs:
|
|
||||||
return 1
|
|
||||||
else:
|
|
||||||
logger.info("No broken requirements found.")
|
|
||||||
@@ -1,94 +0,0 @@
|
|||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import sys
|
|
||||||
import textwrap
|
|
||||||
|
|
||||||
from pip._internal.cli.base_command import Command
|
|
||||||
from pip._internal.utils.misc import get_prog
|
|
||||||
|
|
||||||
BASE_COMPLETION = """
|
|
||||||
# pip %(shell)s completion start%(script)s# pip %(shell)s completion end
|
|
||||||
"""
|
|
||||||
|
|
||||||
COMPLETION_SCRIPTS = {
|
|
||||||
'bash': """
|
|
||||||
_pip_completion()
|
|
||||||
{
|
|
||||||
COMPREPLY=( $( COMP_WORDS="${COMP_WORDS[*]}" \\
|
|
||||||
COMP_CWORD=$COMP_CWORD \\
|
|
||||||
PIP_AUTO_COMPLETE=1 $1 ) )
|
|
||||||
}
|
|
||||||
complete -o default -F _pip_completion %(prog)s
|
|
||||||
""",
|
|
||||||
'zsh': """
|
|
||||||
function _pip_completion {
|
|
||||||
local words cword
|
|
||||||
read -Ac words
|
|
||||||
read -cn cword
|
|
||||||
reply=( $( COMP_WORDS="$words[*]" \\
|
|
||||||
COMP_CWORD=$(( cword-1 )) \\
|
|
||||||
PIP_AUTO_COMPLETE=1 $words[1] ) )
|
|
||||||
}
|
|
||||||
compctl -K _pip_completion %(prog)s
|
|
||||||
""",
|
|
||||||
'fish': """
|
|
||||||
function __fish_complete_pip
|
|
||||||
set -lx COMP_WORDS (commandline -o) ""
|
|
||||||
set -lx COMP_CWORD ( \\
|
|
||||||
math (contains -i -- (commandline -t) $COMP_WORDS)-1 \\
|
|
||||||
)
|
|
||||||
set -lx PIP_AUTO_COMPLETE 1
|
|
||||||
string split \\ -- (eval $COMP_WORDS[1])
|
|
||||||
end
|
|
||||||
complete -fa "(__fish_complete_pip)" -c %(prog)s
|
|
||||||
""",
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
class CompletionCommand(Command):
|
|
||||||
"""A helper command to be used for command completion."""
|
|
||||||
name = 'completion'
|
|
||||||
summary = 'A helper command used for command completion.'
|
|
||||||
ignore_require_venv = True
|
|
||||||
|
|
||||||
def __init__(self, *args, **kw):
|
|
||||||
super(CompletionCommand, self).__init__(*args, **kw)
|
|
||||||
|
|
||||||
cmd_opts = self.cmd_opts
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--bash', '-b',
|
|
||||||
action='store_const',
|
|
||||||
const='bash',
|
|
||||||
dest='shell',
|
|
||||||
help='Emit completion code for bash')
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--zsh', '-z',
|
|
||||||
action='store_const',
|
|
||||||
const='zsh',
|
|
||||||
dest='shell',
|
|
||||||
help='Emit completion code for zsh')
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--fish', '-f',
|
|
||||||
action='store_const',
|
|
||||||
const='fish',
|
|
||||||
dest='shell',
|
|
||||||
help='Emit completion code for fish')
|
|
||||||
|
|
||||||
self.parser.insert_option_group(0, cmd_opts)
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
"""Prints the completion code of the given shell"""
|
|
||||||
shells = COMPLETION_SCRIPTS.keys()
|
|
||||||
shell_options = ['--' + shell for shell in sorted(shells)]
|
|
||||||
if options.shell in shells:
|
|
||||||
script = textwrap.dedent(
|
|
||||||
COMPLETION_SCRIPTS.get(options.shell, '') % {
|
|
||||||
'prog': get_prog(),
|
|
||||||
}
|
|
||||||
)
|
|
||||||
print(BASE_COMPLETION % {'script': script, 'shell': options.shell})
|
|
||||||
else:
|
|
||||||
sys.stderr.write(
|
|
||||||
'ERROR: You must pass %s\n' % ' or '.join(shell_options)
|
|
||||||
)
|
|
||||||
@@ -1,227 +0,0 @@
|
|||||||
import logging
|
|
||||||
import os
|
|
||||||
import subprocess
|
|
||||||
|
|
||||||
from pip._internal.cli.base_command import Command
|
|
||||||
from pip._internal.cli.status_codes import ERROR, SUCCESS
|
|
||||||
from pip._internal.configuration import Configuration, kinds
|
|
||||||
from pip._internal.exceptions import PipError
|
|
||||||
from pip._internal.locations import venv_config_file
|
|
||||||
from pip._internal.utils.misc import get_prog
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class ConfigurationCommand(Command):
|
|
||||||
"""Manage local and global configuration.
|
|
||||||
|
|
||||||
Subcommands:
|
|
||||||
|
|
||||||
list: List the active configuration (or from the file specified)
|
|
||||||
edit: Edit the configuration file in an editor
|
|
||||||
get: Get the value associated with name
|
|
||||||
set: Set the name=value
|
|
||||||
unset: Unset the value associated with name
|
|
||||||
|
|
||||||
If none of --user, --global and --venv are passed, a virtual
|
|
||||||
environment configuration file is used if one is active and the file
|
|
||||||
exists. Otherwise, all modifications happen on the to the user file by
|
|
||||||
default.
|
|
||||||
"""
|
|
||||||
|
|
||||||
name = 'config'
|
|
||||||
usage = """
|
|
||||||
%prog [<file-option>] list
|
|
||||||
%prog [<file-option>] [--editor <editor-path>] edit
|
|
||||||
|
|
||||||
%prog [<file-option>] get name
|
|
||||||
%prog [<file-option>] set name value
|
|
||||||
%prog [<file-option>] unset name
|
|
||||||
"""
|
|
||||||
|
|
||||||
summary = "Manage local and global configuration."
|
|
||||||
|
|
||||||
def __init__(self, *args, **kwargs):
|
|
||||||
super(ConfigurationCommand, self).__init__(*args, **kwargs)
|
|
||||||
|
|
||||||
self.configuration = None
|
|
||||||
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'--editor',
|
|
||||||
dest='editor',
|
|
||||||
action='store',
|
|
||||||
default=None,
|
|
||||||
help=(
|
|
||||||
'Editor to use to edit the file. Uses VISUAL or EDITOR '
|
|
||||||
'environment variables if not provided.'
|
|
||||||
)
|
|
||||||
)
|
|
||||||
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'--global',
|
|
||||||
dest='global_file',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help='Use the system-wide configuration file only'
|
|
||||||
)
|
|
||||||
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'--user',
|
|
||||||
dest='user_file',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help='Use the user configuration file only'
|
|
||||||
)
|
|
||||||
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'--venv',
|
|
||||||
dest='venv_file',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help='Use the virtualenv configuration file only'
|
|
||||||
)
|
|
||||||
|
|
||||||
self.parser.insert_option_group(0, self.cmd_opts)
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
handlers = {
|
|
||||||
"list": self.list_values,
|
|
||||||
"edit": self.open_in_editor,
|
|
||||||
"get": self.get_name,
|
|
||||||
"set": self.set_name_value,
|
|
||||||
"unset": self.unset_name
|
|
||||||
}
|
|
||||||
|
|
||||||
# Determine action
|
|
||||||
if not args or args[0] not in handlers:
|
|
||||||
logger.error("Need an action ({}) to perform.".format(
|
|
||||||
", ".join(sorted(handlers)))
|
|
||||||
)
|
|
||||||
return ERROR
|
|
||||||
|
|
||||||
action = args[0]
|
|
||||||
|
|
||||||
# Determine which configuration files are to be loaded
|
|
||||||
# Depends on whether the command is modifying.
|
|
||||||
try:
|
|
||||||
load_only = self._determine_file(
|
|
||||||
options, need_value=(action in ["get", "set", "unset", "edit"])
|
|
||||||
)
|
|
||||||
except PipError as e:
|
|
||||||
logger.error(e.args[0])
|
|
||||||
return ERROR
|
|
||||||
|
|
||||||
# Load a new configuration
|
|
||||||
self.configuration = Configuration(
|
|
||||||
isolated=options.isolated_mode, load_only=load_only
|
|
||||||
)
|
|
||||||
self.configuration.load()
|
|
||||||
|
|
||||||
# Error handling happens here, not in the action-handlers.
|
|
||||||
try:
|
|
||||||
handlers[action](options, args[1:])
|
|
||||||
except PipError as e:
|
|
||||||
logger.error(e.args[0])
|
|
||||||
return ERROR
|
|
||||||
|
|
||||||
return SUCCESS
|
|
||||||
|
|
||||||
def _determine_file(self, options, need_value):
|
|
||||||
file_options = {
|
|
||||||
kinds.USER: options.user_file,
|
|
||||||
kinds.GLOBAL: options.global_file,
|
|
||||||
kinds.VENV: options.venv_file
|
|
||||||
}
|
|
||||||
|
|
||||||
if sum(file_options.values()) == 0:
|
|
||||||
if not need_value:
|
|
||||||
return None
|
|
||||||
# Default to user, unless there's a virtualenv file.
|
|
||||||
elif os.path.exists(venv_config_file):
|
|
||||||
return kinds.VENV
|
|
||||||
else:
|
|
||||||
return kinds.USER
|
|
||||||
elif sum(file_options.values()) == 1:
|
|
||||||
# There's probably a better expression for this.
|
|
||||||
return [key for key in file_options if file_options[key]][0]
|
|
||||||
|
|
||||||
raise PipError(
|
|
||||||
"Need exactly one file to operate upon "
|
|
||||||
"(--user, --venv, --global) to perform."
|
|
||||||
)
|
|
||||||
|
|
||||||
def list_values(self, options, args):
|
|
||||||
self._get_n_args(args, "list", n=0)
|
|
||||||
|
|
||||||
for key, value in sorted(self.configuration.items()):
|
|
||||||
logger.info("%s=%r", key, value)
|
|
||||||
|
|
||||||
def get_name(self, options, args):
|
|
||||||
key = self._get_n_args(args, "get [name]", n=1)
|
|
||||||
value = self.configuration.get_value(key)
|
|
||||||
|
|
||||||
logger.info("%s", value)
|
|
||||||
|
|
||||||
def set_name_value(self, options, args):
|
|
||||||
key, value = self._get_n_args(args, "set [name] [value]", n=2)
|
|
||||||
self.configuration.set_value(key, value)
|
|
||||||
|
|
||||||
self._save_configuration()
|
|
||||||
|
|
||||||
def unset_name(self, options, args):
|
|
||||||
key = self._get_n_args(args, "unset [name]", n=1)
|
|
||||||
self.configuration.unset_value(key)
|
|
||||||
|
|
||||||
self._save_configuration()
|
|
||||||
|
|
||||||
def open_in_editor(self, options, args):
|
|
||||||
editor = self._determine_editor(options)
|
|
||||||
|
|
||||||
fname = self.configuration.get_file_to_edit()
|
|
||||||
if fname is None:
|
|
||||||
raise PipError("Could not determine appropriate file.")
|
|
||||||
|
|
||||||
try:
|
|
||||||
subprocess.check_call([editor, fname])
|
|
||||||
except subprocess.CalledProcessError as e:
|
|
||||||
raise PipError(
|
|
||||||
"Editor Subprocess exited with exit code {}"
|
|
||||||
.format(e.returncode)
|
|
||||||
)
|
|
||||||
|
|
||||||
def _get_n_args(self, args, example, n):
|
|
||||||
"""Helper to make sure the command got the right number of arguments
|
|
||||||
"""
|
|
||||||
if len(args) != n:
|
|
||||||
msg = (
|
|
||||||
'Got unexpected number of arguments, expected {}. '
|
|
||||||
'(example: "{} config {}")'
|
|
||||||
).format(n, get_prog(), example)
|
|
||||||
raise PipError(msg)
|
|
||||||
|
|
||||||
if n == 1:
|
|
||||||
return args[0]
|
|
||||||
else:
|
|
||||||
return args
|
|
||||||
|
|
||||||
def _save_configuration(self):
|
|
||||||
# We successfully ran a modifying command. Need to save the
|
|
||||||
# configuration.
|
|
||||||
try:
|
|
||||||
self.configuration.save()
|
|
||||||
except Exception:
|
|
||||||
logger.error(
|
|
||||||
"Unable to save configuration. Please report this as a bug.",
|
|
||||||
exc_info=1
|
|
||||||
)
|
|
||||||
raise PipError("Internal Error.")
|
|
||||||
|
|
||||||
def _determine_editor(self, options):
|
|
||||||
if options.editor is not None:
|
|
||||||
return options.editor
|
|
||||||
elif "VISUAL" in os.environ:
|
|
||||||
return os.environ["VISUAL"]
|
|
||||||
elif "EDITOR" in os.environ:
|
|
||||||
return os.environ["EDITOR"]
|
|
||||||
else:
|
|
||||||
raise PipError("Could not determine editor to use.")
|
|
||||||
@@ -1,176 +0,0 @@
|
|||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import logging
|
|
||||||
import os
|
|
||||||
|
|
||||||
from pip._internal.cli import cmdoptions
|
|
||||||
from pip._internal.cli.base_command import RequirementCommand
|
|
||||||
from pip._internal.operations.prepare import RequirementPreparer
|
|
||||||
from pip._internal.req import RequirementSet
|
|
||||||
from pip._internal.req.req_tracker import RequirementTracker
|
|
||||||
from pip._internal.resolve import Resolver
|
|
||||||
from pip._internal.utils.filesystem import check_path_owner
|
|
||||||
from pip._internal.utils.misc import ensure_dir, normalize_path
|
|
||||||
from pip._internal.utils.temp_dir import TempDirectory
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class DownloadCommand(RequirementCommand):
|
|
||||||
"""
|
|
||||||
Download packages from:
|
|
||||||
|
|
||||||
- PyPI (and other indexes) using requirement specifiers.
|
|
||||||
- VCS project urls.
|
|
||||||
- Local project directories.
|
|
||||||
- Local or remote source archives.
|
|
||||||
|
|
||||||
pip also supports downloading from "requirements files", which provide
|
|
||||||
an easy way to specify a whole environment to be downloaded.
|
|
||||||
"""
|
|
||||||
name = 'download'
|
|
||||||
|
|
||||||
usage = """
|
|
||||||
%prog [options] <requirement specifier> [package-index-options] ...
|
|
||||||
%prog [options] -r <requirements file> [package-index-options] ...
|
|
||||||
%prog [options] <vcs project url> ...
|
|
||||||
%prog [options] <local project path> ...
|
|
||||||
%prog [options] <archive url/path> ..."""
|
|
||||||
|
|
||||||
summary = 'Download packages.'
|
|
||||||
|
|
||||||
def __init__(self, *args, **kw):
|
|
||||||
super(DownloadCommand, self).__init__(*args, **kw)
|
|
||||||
|
|
||||||
cmd_opts = self.cmd_opts
|
|
||||||
|
|
||||||
cmd_opts.add_option(cmdoptions.constraints())
|
|
||||||
cmd_opts.add_option(cmdoptions.requirements())
|
|
||||||
cmd_opts.add_option(cmdoptions.build_dir())
|
|
||||||
cmd_opts.add_option(cmdoptions.no_deps())
|
|
||||||
cmd_opts.add_option(cmdoptions.global_options())
|
|
||||||
cmd_opts.add_option(cmdoptions.no_binary())
|
|
||||||
cmd_opts.add_option(cmdoptions.only_binary())
|
|
||||||
cmd_opts.add_option(cmdoptions.prefer_binary())
|
|
||||||
cmd_opts.add_option(cmdoptions.src())
|
|
||||||
cmd_opts.add_option(cmdoptions.pre())
|
|
||||||
cmd_opts.add_option(cmdoptions.no_clean())
|
|
||||||
cmd_opts.add_option(cmdoptions.require_hashes())
|
|
||||||
cmd_opts.add_option(cmdoptions.progress_bar())
|
|
||||||
cmd_opts.add_option(cmdoptions.no_build_isolation())
|
|
||||||
cmd_opts.add_option(cmdoptions.use_pep517())
|
|
||||||
cmd_opts.add_option(cmdoptions.no_use_pep517())
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'-d', '--dest', '--destination-dir', '--destination-directory',
|
|
||||||
dest='download_dir',
|
|
||||||
metavar='dir',
|
|
||||||
default=os.curdir,
|
|
||||||
help=("Download packages into <dir>."),
|
|
||||||
)
|
|
||||||
|
|
||||||
cmd_opts.add_option(cmdoptions.platform())
|
|
||||||
cmd_opts.add_option(cmdoptions.python_version())
|
|
||||||
cmd_opts.add_option(cmdoptions.implementation())
|
|
||||||
cmd_opts.add_option(cmdoptions.abi())
|
|
||||||
|
|
||||||
index_opts = cmdoptions.make_option_group(
|
|
||||||
cmdoptions.index_group,
|
|
||||||
self.parser,
|
|
||||||
)
|
|
||||||
|
|
||||||
self.parser.insert_option_group(0, index_opts)
|
|
||||||
self.parser.insert_option_group(0, cmd_opts)
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
options.ignore_installed = True
|
|
||||||
# editable doesn't really make sense for `pip download`, but the bowels
|
|
||||||
# of the RequirementSet code require that property.
|
|
||||||
options.editables = []
|
|
||||||
|
|
||||||
if options.python_version:
|
|
||||||
python_versions = [options.python_version]
|
|
||||||
else:
|
|
||||||
python_versions = None
|
|
||||||
|
|
||||||
cmdoptions.check_dist_restriction(options)
|
|
||||||
|
|
||||||
options.src_dir = os.path.abspath(options.src_dir)
|
|
||||||
options.download_dir = normalize_path(options.download_dir)
|
|
||||||
|
|
||||||
ensure_dir(options.download_dir)
|
|
||||||
|
|
||||||
with self._build_session(options) as session:
|
|
||||||
finder = self._build_package_finder(
|
|
||||||
options=options,
|
|
||||||
session=session,
|
|
||||||
platform=options.platform,
|
|
||||||
python_versions=python_versions,
|
|
||||||
abi=options.abi,
|
|
||||||
implementation=options.implementation,
|
|
||||||
)
|
|
||||||
build_delete = (not (options.no_clean or options.build_dir))
|
|
||||||
if options.cache_dir and not check_path_owner(options.cache_dir):
|
|
||||||
logger.warning(
|
|
||||||
"The directory '%s' or its parent directory is not owned "
|
|
||||||
"by the current user and caching wheels has been "
|
|
||||||
"disabled. check the permissions and owner of that "
|
|
||||||
"directory. If executing pip with sudo, you may want "
|
|
||||||
"sudo's -H flag.",
|
|
||||||
options.cache_dir,
|
|
||||||
)
|
|
||||||
options.cache_dir = None
|
|
||||||
|
|
||||||
with RequirementTracker() as req_tracker, TempDirectory(
|
|
||||||
options.build_dir, delete=build_delete, kind="download"
|
|
||||||
) as directory:
|
|
||||||
|
|
||||||
requirement_set = RequirementSet(
|
|
||||||
require_hashes=options.require_hashes,
|
|
||||||
)
|
|
||||||
self.populate_requirement_set(
|
|
||||||
requirement_set,
|
|
||||||
args,
|
|
||||||
options,
|
|
||||||
finder,
|
|
||||||
session,
|
|
||||||
self.name,
|
|
||||||
None
|
|
||||||
)
|
|
||||||
|
|
||||||
preparer = RequirementPreparer(
|
|
||||||
build_dir=directory.path,
|
|
||||||
src_dir=options.src_dir,
|
|
||||||
download_dir=options.download_dir,
|
|
||||||
wheel_download_dir=None,
|
|
||||||
progress_bar=options.progress_bar,
|
|
||||||
build_isolation=options.build_isolation,
|
|
||||||
req_tracker=req_tracker,
|
|
||||||
)
|
|
||||||
|
|
||||||
resolver = Resolver(
|
|
||||||
preparer=preparer,
|
|
||||||
finder=finder,
|
|
||||||
session=session,
|
|
||||||
wheel_cache=None,
|
|
||||||
use_user_site=False,
|
|
||||||
upgrade_strategy="to-satisfy-only",
|
|
||||||
force_reinstall=False,
|
|
||||||
ignore_dependencies=options.ignore_dependencies,
|
|
||||||
ignore_requires_python=False,
|
|
||||||
ignore_installed=True,
|
|
||||||
isolated=options.isolated_mode,
|
|
||||||
)
|
|
||||||
resolver.resolve(requirement_set)
|
|
||||||
|
|
||||||
downloaded = ' '.join([
|
|
||||||
req.name for req in requirement_set.successfully_downloaded
|
|
||||||
])
|
|
||||||
if downloaded:
|
|
||||||
logger.info('Successfully downloaded %s', downloaded)
|
|
||||||
|
|
||||||
# Clean up
|
|
||||||
if not options.no_clean:
|
|
||||||
requirement_set.cleanup_files()
|
|
||||||
|
|
||||||
return requirement_set
|
|
||||||
@@ -1,96 +0,0 @@
|
|||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import sys
|
|
||||||
|
|
||||||
from pip._internal.cache import WheelCache
|
|
||||||
from pip._internal.cli.base_command import Command
|
|
||||||
from pip._internal.models.format_control import FormatControl
|
|
||||||
from pip._internal.operations.freeze import freeze
|
|
||||||
from pip._internal.utils.compat import stdlib_pkgs
|
|
||||||
|
|
||||||
DEV_PKGS = {'pip', 'setuptools', 'distribute', 'wheel'}
|
|
||||||
|
|
||||||
|
|
||||||
class FreezeCommand(Command):
|
|
||||||
"""
|
|
||||||
Output installed packages in requirements format.
|
|
||||||
|
|
||||||
packages are listed in a case-insensitive sorted order.
|
|
||||||
"""
|
|
||||||
name = 'freeze'
|
|
||||||
usage = """
|
|
||||||
%prog [options]"""
|
|
||||||
summary = 'Output installed packages in requirements format.'
|
|
||||||
log_streams = ("ext://sys.stderr", "ext://sys.stderr")
|
|
||||||
|
|
||||||
def __init__(self, *args, **kw):
|
|
||||||
super(FreezeCommand, self).__init__(*args, **kw)
|
|
||||||
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'-r', '--requirement',
|
|
||||||
dest='requirements',
|
|
||||||
action='append',
|
|
||||||
default=[],
|
|
||||||
metavar='file',
|
|
||||||
help="Use the order in the given requirements file and its "
|
|
||||||
"comments when generating output. This option can be "
|
|
||||||
"used multiple times.")
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'-f', '--find-links',
|
|
||||||
dest='find_links',
|
|
||||||
action='append',
|
|
||||||
default=[],
|
|
||||||
metavar='URL',
|
|
||||||
help='URL for finding packages, which will be added to the '
|
|
||||||
'output.')
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'-l', '--local',
|
|
||||||
dest='local',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help='If in a virtualenv that has global access, do not output '
|
|
||||||
'globally-installed packages.')
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'--user',
|
|
||||||
dest='user',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help='Only output packages installed in user-site.')
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'--all',
|
|
||||||
dest='freeze_all',
|
|
||||||
action='store_true',
|
|
||||||
help='Do not skip these packages in the output:'
|
|
||||||
' %s' % ', '.join(DEV_PKGS))
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'--exclude-editable',
|
|
||||||
dest='exclude_editable',
|
|
||||||
action='store_true',
|
|
||||||
help='Exclude editable package from output.')
|
|
||||||
|
|
||||||
self.parser.insert_option_group(0, self.cmd_opts)
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
format_control = FormatControl(set(), set())
|
|
||||||
wheel_cache = WheelCache(options.cache_dir, format_control)
|
|
||||||
skip = set(stdlib_pkgs)
|
|
||||||
if not options.freeze_all:
|
|
||||||
skip.update(DEV_PKGS)
|
|
||||||
|
|
||||||
freeze_kwargs = dict(
|
|
||||||
requirement=options.requirements,
|
|
||||||
find_links=options.find_links,
|
|
||||||
local_only=options.local,
|
|
||||||
user_only=options.user,
|
|
||||||
skip_regex=options.skip_requirements_regex,
|
|
||||||
isolated=options.isolated_mode,
|
|
||||||
wheel_cache=wheel_cache,
|
|
||||||
skip=skip,
|
|
||||||
exclude_editable=options.exclude_editable,
|
|
||||||
)
|
|
||||||
|
|
||||||
try:
|
|
||||||
for line in freeze(**freeze_kwargs):
|
|
||||||
sys.stdout.write(line + '\n')
|
|
||||||
finally:
|
|
||||||
wheel_cache.cleanup()
|
|
||||||
@@ -1,57 +0,0 @@
|
|||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import hashlib
|
|
||||||
import logging
|
|
||||||
import sys
|
|
||||||
|
|
||||||
from pip._internal.cli.base_command import Command
|
|
||||||
from pip._internal.cli.status_codes import ERROR
|
|
||||||
from pip._internal.utils.hashes import FAVORITE_HASH, STRONG_HASHES
|
|
||||||
from pip._internal.utils.misc import read_chunks
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class HashCommand(Command):
|
|
||||||
"""
|
|
||||||
Compute a hash of a local package archive.
|
|
||||||
|
|
||||||
These can be used with --hash in a requirements file to do repeatable
|
|
||||||
installs.
|
|
||||||
|
|
||||||
"""
|
|
||||||
name = 'hash'
|
|
||||||
usage = '%prog [options] <file> ...'
|
|
||||||
summary = 'Compute hashes of package archives.'
|
|
||||||
ignore_require_venv = True
|
|
||||||
|
|
||||||
def __init__(self, *args, **kw):
|
|
||||||
super(HashCommand, self).__init__(*args, **kw)
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'-a', '--algorithm',
|
|
||||||
dest='algorithm',
|
|
||||||
choices=STRONG_HASHES,
|
|
||||||
action='store',
|
|
||||||
default=FAVORITE_HASH,
|
|
||||||
help='The hash algorithm to use: one of %s' %
|
|
||||||
', '.join(STRONG_HASHES))
|
|
||||||
self.parser.insert_option_group(0, self.cmd_opts)
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
if not args:
|
|
||||||
self.parser.print_usage(sys.stderr)
|
|
||||||
return ERROR
|
|
||||||
|
|
||||||
algorithm = options.algorithm
|
|
||||||
for path in args:
|
|
||||||
logger.info('%s:\n--hash=%s:%s',
|
|
||||||
path, algorithm, _hash_of_file(path, algorithm))
|
|
||||||
|
|
||||||
|
|
||||||
def _hash_of_file(path, algorithm):
|
|
||||||
"""Return the hash digest of a file."""
|
|
||||||
with open(path, 'rb') as archive:
|
|
||||||
hash = hashlib.new(algorithm)
|
|
||||||
for chunk in read_chunks(archive):
|
|
||||||
hash.update(chunk)
|
|
||||||
return hash.hexdigest()
|
|
||||||
@@ -1,37 +0,0 @@
|
|||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
from pip._internal.cli.base_command import Command
|
|
||||||
from pip._internal.cli.status_codes import SUCCESS
|
|
||||||
from pip._internal.exceptions import CommandError
|
|
||||||
|
|
||||||
|
|
||||||
class HelpCommand(Command):
|
|
||||||
"""Show help for commands"""
|
|
||||||
name = 'help'
|
|
||||||
usage = """
|
|
||||||
%prog <command>"""
|
|
||||||
summary = 'Show help for commands.'
|
|
||||||
ignore_require_venv = True
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
from pip._internal.commands import commands_dict, get_similar_commands
|
|
||||||
|
|
||||||
try:
|
|
||||||
# 'pip help' with no args is handled by pip.__init__.parseopt()
|
|
||||||
cmd_name = args[0] # the command we need help for
|
|
||||||
except IndexError:
|
|
||||||
return SUCCESS
|
|
||||||
|
|
||||||
if cmd_name not in commands_dict:
|
|
||||||
guess = get_similar_commands(cmd_name)
|
|
||||||
|
|
||||||
msg = ['unknown command "%s"' % cmd_name]
|
|
||||||
if guess:
|
|
||||||
msg.append('maybe you meant "%s"' % guess)
|
|
||||||
|
|
||||||
raise CommandError(' - '.join(msg))
|
|
||||||
|
|
||||||
command = commands_dict[cmd_name]()
|
|
||||||
command.parser.print_help()
|
|
||||||
|
|
||||||
return SUCCESS
|
|
||||||
@@ -1,566 +0,0 @@
|
|||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import errno
|
|
||||||
import logging
|
|
||||||
import operator
|
|
||||||
import os
|
|
||||||
import shutil
|
|
||||||
from optparse import SUPPRESS_HELP
|
|
||||||
|
|
||||||
from pip._vendor import pkg_resources
|
|
||||||
|
|
||||||
from pip._internal.cache import WheelCache
|
|
||||||
from pip._internal.cli import cmdoptions
|
|
||||||
from pip._internal.cli.base_command import RequirementCommand
|
|
||||||
from pip._internal.cli.status_codes import ERROR
|
|
||||||
from pip._internal.exceptions import (
|
|
||||||
CommandError, InstallationError, PreviousBuildDirError,
|
|
||||||
)
|
|
||||||
from pip._internal.locations import distutils_scheme, virtualenv_no_global
|
|
||||||
from pip._internal.operations.check import check_install_conflicts
|
|
||||||
from pip._internal.operations.prepare import RequirementPreparer
|
|
||||||
from pip._internal.req import RequirementSet, install_given_reqs
|
|
||||||
from pip._internal.req.req_tracker import RequirementTracker
|
|
||||||
from pip._internal.resolve import Resolver
|
|
||||||
from pip._internal.utils.filesystem import check_path_owner
|
|
||||||
from pip._internal.utils.misc import (
|
|
||||||
ensure_dir, get_installed_version,
|
|
||||||
protect_pip_from_modification_on_windows,
|
|
||||||
)
|
|
||||||
from pip._internal.utils.temp_dir import TempDirectory
|
|
||||||
from pip._internal.wheel import WheelBuilder
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class InstallCommand(RequirementCommand):
|
|
||||||
"""
|
|
||||||
Install packages from:
|
|
||||||
|
|
||||||
- PyPI (and other indexes) using requirement specifiers.
|
|
||||||
- VCS project urls.
|
|
||||||
- Local project directories.
|
|
||||||
- Local or remote source archives.
|
|
||||||
|
|
||||||
pip also supports installing from "requirements files", which provide
|
|
||||||
an easy way to specify a whole environment to be installed.
|
|
||||||
"""
|
|
||||||
name = 'install'
|
|
||||||
|
|
||||||
usage = """
|
|
||||||
%prog [options] <requirement specifier> [package-index-options] ...
|
|
||||||
%prog [options] -r <requirements file> [package-index-options] ...
|
|
||||||
%prog [options] [-e] <vcs project url> ...
|
|
||||||
%prog [options] [-e] <local project path> ...
|
|
||||||
%prog [options] <archive url/path> ..."""
|
|
||||||
|
|
||||||
summary = 'Install packages.'
|
|
||||||
|
|
||||||
def __init__(self, *args, **kw):
|
|
||||||
super(InstallCommand, self).__init__(*args, **kw)
|
|
||||||
|
|
||||||
cmd_opts = self.cmd_opts
|
|
||||||
|
|
||||||
cmd_opts.add_option(cmdoptions.requirements())
|
|
||||||
cmd_opts.add_option(cmdoptions.constraints())
|
|
||||||
cmd_opts.add_option(cmdoptions.no_deps())
|
|
||||||
cmd_opts.add_option(cmdoptions.pre())
|
|
||||||
|
|
||||||
cmd_opts.add_option(cmdoptions.editable())
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'-t', '--target',
|
|
||||||
dest='target_dir',
|
|
||||||
metavar='dir',
|
|
||||||
default=None,
|
|
||||||
help='Install packages into <dir>. '
|
|
||||||
'By default this will not replace existing files/folders in '
|
|
||||||
'<dir>. Use --upgrade to replace existing packages in <dir> '
|
|
||||||
'with new versions.'
|
|
||||||
)
|
|
||||||
cmd_opts.add_option(cmdoptions.platform())
|
|
||||||
cmd_opts.add_option(cmdoptions.python_version())
|
|
||||||
cmd_opts.add_option(cmdoptions.implementation())
|
|
||||||
cmd_opts.add_option(cmdoptions.abi())
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--user',
|
|
||||||
dest='use_user_site',
|
|
||||||
action='store_true',
|
|
||||||
help="Install to the Python user install directory for your "
|
|
||||||
"platform. Typically ~/.local/, or %APPDATA%\\Python on "
|
|
||||||
"Windows. (See the Python documentation for site.USER_BASE "
|
|
||||||
"for full details.)")
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--no-user',
|
|
||||||
dest='use_user_site',
|
|
||||||
action='store_false',
|
|
||||||
help=SUPPRESS_HELP)
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--root',
|
|
||||||
dest='root_path',
|
|
||||||
metavar='dir',
|
|
||||||
default=None,
|
|
||||||
help="Install everything relative to this alternate root "
|
|
||||||
"directory.")
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--prefix',
|
|
||||||
dest='prefix_path',
|
|
||||||
metavar='dir',
|
|
||||||
default=None,
|
|
||||||
help="Installation prefix where lib, bin and other top-level "
|
|
||||||
"folders are placed")
|
|
||||||
|
|
||||||
cmd_opts.add_option(cmdoptions.build_dir())
|
|
||||||
|
|
||||||
cmd_opts.add_option(cmdoptions.src())
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'-U', '--upgrade',
|
|
||||||
dest='upgrade',
|
|
||||||
action='store_true',
|
|
||||||
help='Upgrade all specified packages to the newest available '
|
|
||||||
'version. The handling of dependencies depends on the '
|
|
||||||
'upgrade-strategy used.'
|
|
||||||
)
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--upgrade-strategy',
|
|
||||||
dest='upgrade_strategy',
|
|
||||||
default='only-if-needed',
|
|
||||||
choices=['only-if-needed', 'eager'],
|
|
||||||
help='Determines how dependency upgrading should be handled '
|
|
||||||
'[default: %default]. '
|
|
||||||
'"eager" - dependencies are upgraded regardless of '
|
|
||||||
'whether the currently installed version satisfies the '
|
|
||||||
'requirements of the upgraded package(s). '
|
|
||||||
'"only-if-needed" - are upgraded only when they do not '
|
|
||||||
'satisfy the requirements of the upgraded package(s).'
|
|
||||||
)
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--force-reinstall',
|
|
||||||
dest='force_reinstall',
|
|
||||||
action='store_true',
|
|
||||||
help='Reinstall all packages even if they are already '
|
|
||||||
'up-to-date.')
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'-I', '--ignore-installed',
|
|
||||||
dest='ignore_installed',
|
|
||||||
action='store_true',
|
|
||||||
help='Ignore the installed packages (reinstalling instead).')
|
|
||||||
|
|
||||||
cmd_opts.add_option(cmdoptions.ignore_requires_python())
|
|
||||||
cmd_opts.add_option(cmdoptions.no_build_isolation())
|
|
||||||
cmd_opts.add_option(cmdoptions.use_pep517())
|
|
||||||
cmd_opts.add_option(cmdoptions.no_use_pep517())
|
|
||||||
|
|
||||||
cmd_opts.add_option(cmdoptions.install_options())
|
|
||||||
cmd_opts.add_option(cmdoptions.global_options())
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
"--compile",
|
|
||||||
action="store_true",
|
|
||||||
dest="compile",
|
|
||||||
default=True,
|
|
||||||
help="Compile Python source files to bytecode",
|
|
||||||
)
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
"--no-compile",
|
|
||||||
action="store_false",
|
|
||||||
dest="compile",
|
|
||||||
help="Do not compile Python source files to bytecode",
|
|
||||||
)
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
"--no-warn-script-location",
|
|
||||||
action="store_false",
|
|
||||||
dest="warn_script_location",
|
|
||||||
default=True,
|
|
||||||
help="Do not warn when installing scripts outside PATH",
|
|
||||||
)
|
|
||||||
cmd_opts.add_option(
|
|
||||||
"--no-warn-conflicts",
|
|
||||||
action="store_false",
|
|
||||||
dest="warn_about_conflicts",
|
|
||||||
default=True,
|
|
||||||
help="Do not warn about broken dependencies",
|
|
||||||
)
|
|
||||||
|
|
||||||
cmd_opts.add_option(cmdoptions.no_binary())
|
|
||||||
cmd_opts.add_option(cmdoptions.only_binary())
|
|
||||||
cmd_opts.add_option(cmdoptions.prefer_binary())
|
|
||||||
cmd_opts.add_option(cmdoptions.no_clean())
|
|
||||||
cmd_opts.add_option(cmdoptions.require_hashes())
|
|
||||||
cmd_opts.add_option(cmdoptions.progress_bar())
|
|
||||||
|
|
||||||
index_opts = cmdoptions.make_option_group(
|
|
||||||
cmdoptions.index_group,
|
|
||||||
self.parser,
|
|
||||||
)
|
|
||||||
|
|
||||||
self.parser.insert_option_group(0, index_opts)
|
|
||||||
self.parser.insert_option_group(0, cmd_opts)
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
cmdoptions.check_install_build_global(options)
|
|
||||||
upgrade_strategy = "to-satisfy-only"
|
|
||||||
if options.upgrade:
|
|
||||||
upgrade_strategy = options.upgrade_strategy
|
|
||||||
|
|
||||||
if options.build_dir:
|
|
||||||
options.build_dir = os.path.abspath(options.build_dir)
|
|
||||||
|
|
||||||
cmdoptions.check_dist_restriction(options, check_target=True)
|
|
||||||
|
|
||||||
if options.python_version:
|
|
||||||
python_versions = [options.python_version]
|
|
||||||
else:
|
|
||||||
python_versions = None
|
|
||||||
|
|
||||||
options.src_dir = os.path.abspath(options.src_dir)
|
|
||||||
install_options = options.install_options or []
|
|
||||||
if options.use_user_site:
|
|
||||||
if options.prefix_path:
|
|
||||||
raise CommandError(
|
|
||||||
"Can not combine '--user' and '--prefix' as they imply "
|
|
||||||
"different installation locations"
|
|
||||||
)
|
|
||||||
if virtualenv_no_global():
|
|
||||||
raise InstallationError(
|
|
||||||
"Can not perform a '--user' install. User site-packages "
|
|
||||||
"are not visible in this virtualenv."
|
|
||||||
)
|
|
||||||
install_options.append('--user')
|
|
||||||
install_options.append('--prefix=')
|
|
||||||
|
|
||||||
target_temp_dir = TempDirectory(kind="target")
|
|
||||||
if options.target_dir:
|
|
||||||
options.ignore_installed = True
|
|
||||||
options.target_dir = os.path.abspath(options.target_dir)
|
|
||||||
if (os.path.exists(options.target_dir) and not
|
|
||||||
os.path.isdir(options.target_dir)):
|
|
||||||
raise CommandError(
|
|
||||||
"Target path exists but is not a directory, will not "
|
|
||||||
"continue."
|
|
||||||
)
|
|
||||||
|
|
||||||
# Create a target directory for using with the target option
|
|
||||||
target_temp_dir.create()
|
|
||||||
install_options.append('--home=' + target_temp_dir.path)
|
|
||||||
|
|
||||||
global_options = options.global_options or []
|
|
||||||
|
|
||||||
with self._build_session(options) as session:
|
|
||||||
finder = self._build_package_finder(
|
|
||||||
options=options,
|
|
||||||
session=session,
|
|
||||||
platform=options.platform,
|
|
||||||
python_versions=python_versions,
|
|
||||||
abi=options.abi,
|
|
||||||
implementation=options.implementation,
|
|
||||||
)
|
|
||||||
build_delete = (not (options.no_clean or options.build_dir))
|
|
||||||
wheel_cache = WheelCache(options.cache_dir, options.format_control)
|
|
||||||
|
|
||||||
if options.cache_dir and not check_path_owner(options.cache_dir):
|
|
||||||
logger.warning(
|
|
||||||
"The directory '%s' or its parent directory is not owned "
|
|
||||||
"by the current user and caching wheels has been "
|
|
||||||
"disabled. check the permissions and owner of that "
|
|
||||||
"directory. If executing pip with sudo, you may want "
|
|
||||||
"sudo's -H flag.",
|
|
||||||
options.cache_dir,
|
|
||||||
)
|
|
||||||
options.cache_dir = None
|
|
||||||
|
|
||||||
with RequirementTracker() as req_tracker, TempDirectory(
|
|
||||||
options.build_dir, delete=build_delete, kind="install"
|
|
||||||
) as directory:
|
|
||||||
requirement_set = RequirementSet(
|
|
||||||
require_hashes=options.require_hashes,
|
|
||||||
check_supported_wheels=not options.target_dir,
|
|
||||||
)
|
|
||||||
|
|
||||||
try:
|
|
||||||
self.populate_requirement_set(
|
|
||||||
requirement_set, args, options, finder, session,
|
|
||||||
self.name, wheel_cache
|
|
||||||
)
|
|
||||||
preparer = RequirementPreparer(
|
|
||||||
build_dir=directory.path,
|
|
||||||
src_dir=options.src_dir,
|
|
||||||
download_dir=None,
|
|
||||||
wheel_download_dir=None,
|
|
||||||
progress_bar=options.progress_bar,
|
|
||||||
build_isolation=options.build_isolation,
|
|
||||||
req_tracker=req_tracker,
|
|
||||||
)
|
|
||||||
|
|
||||||
resolver = Resolver(
|
|
||||||
preparer=preparer,
|
|
||||||
finder=finder,
|
|
||||||
session=session,
|
|
||||||
wheel_cache=wheel_cache,
|
|
||||||
use_user_site=options.use_user_site,
|
|
||||||
upgrade_strategy=upgrade_strategy,
|
|
||||||
force_reinstall=options.force_reinstall,
|
|
||||||
ignore_dependencies=options.ignore_dependencies,
|
|
||||||
ignore_requires_python=options.ignore_requires_python,
|
|
||||||
ignore_installed=options.ignore_installed,
|
|
||||||
isolated=options.isolated_mode,
|
|
||||||
use_pep517=options.use_pep517
|
|
||||||
)
|
|
||||||
resolver.resolve(requirement_set)
|
|
||||||
|
|
||||||
protect_pip_from_modification_on_windows(
|
|
||||||
modifying_pip=requirement_set.has_requirement("pip")
|
|
||||||
)
|
|
||||||
|
|
||||||
# Consider legacy and PEP517-using requirements separately
|
|
||||||
legacy_requirements = []
|
|
||||||
pep517_requirements = []
|
|
||||||
for req in requirement_set.requirements.values():
|
|
||||||
if req.use_pep517:
|
|
||||||
pep517_requirements.append(req)
|
|
||||||
else:
|
|
||||||
legacy_requirements.append(req)
|
|
||||||
|
|
||||||
# We don't build wheels for legacy requirements if we
|
|
||||||
# don't have wheel installed or we don't have a cache dir
|
|
||||||
try:
|
|
||||||
import wheel # noqa: F401
|
|
||||||
build_legacy = bool(options.cache_dir)
|
|
||||||
except ImportError:
|
|
||||||
build_legacy = False
|
|
||||||
|
|
||||||
wb = WheelBuilder(
|
|
||||||
finder, preparer, wheel_cache,
|
|
||||||
build_options=[], global_options=[],
|
|
||||||
)
|
|
||||||
|
|
||||||
# Always build PEP 517 requirements
|
|
||||||
build_failures = wb.build(
|
|
||||||
pep517_requirements,
|
|
||||||
session=session, autobuilding=True
|
|
||||||
)
|
|
||||||
|
|
||||||
if build_legacy:
|
|
||||||
# We don't care about failures building legacy
|
|
||||||
# requirements, as we'll fall through to a direct
|
|
||||||
# install for those.
|
|
||||||
wb.build(
|
|
||||||
legacy_requirements,
|
|
||||||
session=session, autobuilding=True
|
|
||||||
)
|
|
||||||
|
|
||||||
# If we're using PEP 517, we cannot do a direct install
|
|
||||||
# so we fail here.
|
|
||||||
if build_failures:
|
|
||||||
raise InstallationError(
|
|
||||||
"Could not build wheels for {} which use"
|
|
||||||
" PEP 517 and cannot be installed directly".format(
|
|
||||||
", ".join(r.name for r in build_failures)))
|
|
||||||
|
|
||||||
to_install = resolver.get_installation_order(
|
|
||||||
requirement_set
|
|
||||||
)
|
|
||||||
|
|
||||||
# Consistency Checking of the package set we're installing.
|
|
||||||
should_warn_about_conflicts = (
|
|
||||||
not options.ignore_dependencies and
|
|
||||||
options.warn_about_conflicts
|
|
||||||
)
|
|
||||||
if should_warn_about_conflicts:
|
|
||||||
self._warn_about_conflicts(to_install)
|
|
||||||
|
|
||||||
# Don't warn about script install locations if
|
|
||||||
# --target has been specified
|
|
||||||
warn_script_location = options.warn_script_location
|
|
||||||
if options.target_dir:
|
|
||||||
warn_script_location = False
|
|
||||||
|
|
||||||
installed = install_given_reqs(
|
|
||||||
to_install,
|
|
||||||
install_options,
|
|
||||||
global_options,
|
|
||||||
root=options.root_path,
|
|
||||||
home=target_temp_dir.path,
|
|
||||||
prefix=options.prefix_path,
|
|
||||||
pycompile=options.compile,
|
|
||||||
warn_script_location=warn_script_location,
|
|
||||||
use_user_site=options.use_user_site,
|
|
||||||
)
|
|
||||||
|
|
||||||
lib_locations = get_lib_location_guesses(
|
|
||||||
user=options.use_user_site,
|
|
||||||
home=target_temp_dir.path,
|
|
||||||
root=options.root_path,
|
|
||||||
prefix=options.prefix_path,
|
|
||||||
isolated=options.isolated_mode,
|
|
||||||
)
|
|
||||||
working_set = pkg_resources.WorkingSet(lib_locations)
|
|
||||||
|
|
||||||
reqs = sorted(installed, key=operator.attrgetter('name'))
|
|
||||||
items = []
|
|
||||||
for req in reqs:
|
|
||||||
item = req.name
|
|
||||||
try:
|
|
||||||
installed_version = get_installed_version(
|
|
||||||
req.name, working_set=working_set
|
|
||||||
)
|
|
||||||
if installed_version:
|
|
||||||
item += '-' + installed_version
|
|
||||||
except Exception:
|
|
||||||
pass
|
|
||||||
items.append(item)
|
|
||||||
installed = ' '.join(items)
|
|
||||||
if installed:
|
|
||||||
logger.info('Successfully installed %s', installed)
|
|
||||||
except EnvironmentError as error:
|
|
||||||
show_traceback = (self.verbosity >= 1)
|
|
||||||
|
|
||||||
message = create_env_error_message(
|
|
||||||
error, show_traceback, options.use_user_site,
|
|
||||||
)
|
|
||||||
logger.error(message, exc_info=show_traceback)
|
|
||||||
|
|
||||||
return ERROR
|
|
||||||
except PreviousBuildDirError:
|
|
||||||
options.no_clean = True
|
|
||||||
raise
|
|
||||||
finally:
|
|
||||||
# Clean up
|
|
||||||
if not options.no_clean:
|
|
||||||
requirement_set.cleanup_files()
|
|
||||||
wheel_cache.cleanup()
|
|
||||||
|
|
||||||
if options.target_dir:
|
|
||||||
self._handle_target_dir(
|
|
||||||
options.target_dir, target_temp_dir, options.upgrade
|
|
||||||
)
|
|
||||||
return requirement_set
|
|
||||||
|
|
||||||
def _handle_target_dir(self, target_dir, target_temp_dir, upgrade):
|
|
||||||
ensure_dir(target_dir)
|
|
||||||
|
|
||||||
# Checking both purelib and platlib directories for installed
|
|
||||||
# packages to be moved to target directory
|
|
||||||
lib_dir_list = []
|
|
||||||
|
|
||||||
with target_temp_dir:
|
|
||||||
# Checking both purelib and platlib directories for installed
|
|
||||||
# packages to be moved to target directory
|
|
||||||
scheme = distutils_scheme('', home=target_temp_dir.path)
|
|
||||||
purelib_dir = scheme['purelib']
|
|
||||||
platlib_dir = scheme['platlib']
|
|
||||||
data_dir = scheme['data']
|
|
||||||
|
|
||||||
if os.path.exists(purelib_dir):
|
|
||||||
lib_dir_list.append(purelib_dir)
|
|
||||||
if os.path.exists(platlib_dir) and platlib_dir != purelib_dir:
|
|
||||||
lib_dir_list.append(platlib_dir)
|
|
||||||
if os.path.exists(data_dir):
|
|
||||||
lib_dir_list.append(data_dir)
|
|
||||||
|
|
||||||
for lib_dir in lib_dir_list:
|
|
||||||
for item in os.listdir(lib_dir):
|
|
||||||
if lib_dir == data_dir:
|
|
||||||
ddir = os.path.join(data_dir, item)
|
|
||||||
if any(s.startswith(ddir) for s in lib_dir_list[:-1]):
|
|
||||||
continue
|
|
||||||
target_item_dir = os.path.join(target_dir, item)
|
|
||||||
if os.path.exists(target_item_dir):
|
|
||||||
if not upgrade:
|
|
||||||
logger.warning(
|
|
||||||
'Target directory %s already exists. Specify '
|
|
||||||
'--upgrade to force replacement.',
|
|
||||||
target_item_dir
|
|
||||||
)
|
|
||||||
continue
|
|
||||||
if os.path.islink(target_item_dir):
|
|
||||||
logger.warning(
|
|
||||||
'Target directory %s already exists and is '
|
|
||||||
'a link. Pip will not automatically replace '
|
|
||||||
'links, please remove if replacement is '
|
|
||||||
'desired.',
|
|
||||||
target_item_dir
|
|
||||||
)
|
|
||||||
continue
|
|
||||||
if os.path.isdir(target_item_dir):
|
|
||||||
shutil.rmtree(target_item_dir)
|
|
||||||
else:
|
|
||||||
os.remove(target_item_dir)
|
|
||||||
|
|
||||||
shutil.move(
|
|
||||||
os.path.join(lib_dir, item),
|
|
||||||
target_item_dir
|
|
||||||
)
|
|
||||||
|
|
||||||
def _warn_about_conflicts(self, to_install):
|
|
||||||
try:
|
|
||||||
package_set, _dep_info = check_install_conflicts(to_install)
|
|
||||||
except Exception:
|
|
||||||
logger.error("Error checking for conflicts.", exc_info=True)
|
|
||||||
return
|
|
||||||
missing, conflicting = _dep_info
|
|
||||||
|
|
||||||
# NOTE: There is some duplication here from pip check
|
|
||||||
for project_name in missing:
|
|
||||||
version = package_set[project_name][0]
|
|
||||||
for dependency in missing[project_name]:
|
|
||||||
logger.critical(
|
|
||||||
"%s %s requires %s, which is not installed.",
|
|
||||||
project_name, version, dependency[1],
|
|
||||||
)
|
|
||||||
|
|
||||||
for project_name in conflicting:
|
|
||||||
version = package_set[project_name][0]
|
|
||||||
for dep_name, dep_version, req in conflicting[project_name]:
|
|
||||||
logger.critical(
|
|
||||||
"%s %s has requirement %s, but you'll have %s %s which is "
|
|
||||||
"incompatible.",
|
|
||||||
project_name, version, req, dep_name, dep_version,
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
def get_lib_location_guesses(*args, **kwargs):
|
|
||||||
scheme = distutils_scheme('', *args, **kwargs)
|
|
||||||
return [scheme['purelib'], scheme['platlib']]
|
|
||||||
|
|
||||||
|
|
||||||
def create_env_error_message(error, show_traceback, using_user_site):
|
|
||||||
"""Format an error message for an EnvironmentError
|
|
||||||
|
|
||||||
It may occur anytime during the execution of the install command.
|
|
||||||
"""
|
|
||||||
parts = []
|
|
||||||
|
|
||||||
# Mention the error if we are not going to show a traceback
|
|
||||||
parts.append("Could not install packages due to an EnvironmentError")
|
|
||||||
if not show_traceback:
|
|
||||||
parts.append(": ")
|
|
||||||
parts.append(str(error))
|
|
||||||
else:
|
|
||||||
parts.append(".")
|
|
||||||
|
|
||||||
# Spilt the error indication from a helper message (if any)
|
|
||||||
parts[-1] += "\n"
|
|
||||||
|
|
||||||
# Suggest useful actions to the user:
|
|
||||||
# (1) using user site-packages or (2) verifying the permissions
|
|
||||||
if error.errno == errno.EACCES:
|
|
||||||
user_option_part = "Consider using the `--user` option"
|
|
||||||
permissions_part = "Check the permissions"
|
|
||||||
|
|
||||||
if not using_user_site:
|
|
||||||
parts.extend([
|
|
||||||
user_option_part, " or ",
|
|
||||||
permissions_part.lower(),
|
|
||||||
])
|
|
||||||
else:
|
|
||||||
parts.append(permissions_part)
|
|
||||||
parts.append(".\n")
|
|
||||||
|
|
||||||
return "".join(parts).strip() + "\n"
|
|
||||||
@@ -1,301 +0,0 @@
|
|||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import json
|
|
||||||
import logging
|
|
||||||
|
|
||||||
from pip._vendor import six
|
|
||||||
from pip._vendor.six.moves import zip_longest
|
|
||||||
|
|
||||||
from pip._internal.cli import cmdoptions
|
|
||||||
from pip._internal.cli.base_command import Command
|
|
||||||
from pip._internal.exceptions import CommandError
|
|
||||||
from pip._internal.index import PackageFinder
|
|
||||||
from pip._internal.utils.misc import (
|
|
||||||
dist_is_editable, get_installed_distributions,
|
|
||||||
)
|
|
||||||
from pip._internal.utils.packaging import get_installer
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class ListCommand(Command):
|
|
||||||
"""
|
|
||||||
List installed packages, including editables.
|
|
||||||
|
|
||||||
Packages are listed in a case-insensitive sorted order.
|
|
||||||
"""
|
|
||||||
name = 'list'
|
|
||||||
usage = """
|
|
||||||
%prog [options]"""
|
|
||||||
summary = 'List installed packages.'
|
|
||||||
|
|
||||||
def __init__(self, *args, **kw):
|
|
||||||
super(ListCommand, self).__init__(*args, **kw)
|
|
||||||
|
|
||||||
cmd_opts = self.cmd_opts
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'-o', '--outdated',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help='List outdated packages')
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'-u', '--uptodate',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help='List uptodate packages')
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'-e', '--editable',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help='List editable projects.')
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'-l', '--local',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help=('If in a virtualenv that has global access, do not list '
|
|
||||||
'globally-installed packages.'),
|
|
||||||
)
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'--user',
|
|
||||||
dest='user',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help='Only output packages installed in user-site.')
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--pre',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help=("Include pre-release and development versions. By default, "
|
|
||||||
"pip only finds stable versions."),
|
|
||||||
)
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--format',
|
|
||||||
action='store',
|
|
||||||
dest='list_format',
|
|
||||||
default="columns",
|
|
||||||
choices=('columns', 'freeze', 'json'),
|
|
||||||
help="Select the output format among: columns (default), freeze, "
|
|
||||||
"or json",
|
|
||||||
)
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--not-required',
|
|
||||||
action='store_true',
|
|
||||||
dest='not_required',
|
|
||||||
help="List packages that are not dependencies of "
|
|
||||||
"installed packages.",
|
|
||||||
)
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--exclude-editable',
|
|
||||||
action='store_false',
|
|
||||||
dest='include_editable',
|
|
||||||
help='Exclude editable package from output.',
|
|
||||||
)
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--include-editable',
|
|
||||||
action='store_true',
|
|
||||||
dest='include_editable',
|
|
||||||
help='Include editable package from output.',
|
|
||||||
default=True,
|
|
||||||
)
|
|
||||||
index_opts = cmdoptions.make_option_group(
|
|
||||||
cmdoptions.index_group, self.parser
|
|
||||||
)
|
|
||||||
|
|
||||||
self.parser.insert_option_group(0, index_opts)
|
|
||||||
self.parser.insert_option_group(0, cmd_opts)
|
|
||||||
|
|
||||||
def _build_package_finder(self, options, index_urls, session):
|
|
||||||
"""
|
|
||||||
Create a package finder appropriate to this list command.
|
|
||||||
"""
|
|
||||||
return PackageFinder(
|
|
||||||
find_links=options.find_links,
|
|
||||||
index_urls=index_urls,
|
|
||||||
allow_all_prereleases=options.pre,
|
|
||||||
trusted_hosts=options.trusted_hosts,
|
|
||||||
session=session,
|
|
||||||
)
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
if options.outdated and options.uptodate:
|
|
||||||
raise CommandError(
|
|
||||||
"Options --outdated and --uptodate cannot be combined.")
|
|
||||||
|
|
||||||
packages = get_installed_distributions(
|
|
||||||
local_only=options.local,
|
|
||||||
user_only=options.user,
|
|
||||||
editables_only=options.editable,
|
|
||||||
include_editables=options.include_editable,
|
|
||||||
)
|
|
||||||
|
|
||||||
# get_not_required must be called firstly in order to find and
|
|
||||||
# filter out all dependencies correctly. Otherwise a package
|
|
||||||
# can't be identified as requirement because some parent packages
|
|
||||||
# could be filtered out before.
|
|
||||||
if options.not_required:
|
|
||||||
packages = self.get_not_required(packages, options)
|
|
||||||
|
|
||||||
if options.outdated:
|
|
||||||
packages = self.get_outdated(packages, options)
|
|
||||||
elif options.uptodate:
|
|
||||||
packages = self.get_uptodate(packages, options)
|
|
||||||
|
|
||||||
self.output_package_listing(packages, options)
|
|
||||||
|
|
||||||
def get_outdated(self, packages, options):
|
|
||||||
return [
|
|
||||||
dist for dist in self.iter_packages_latest_infos(packages, options)
|
|
||||||
if dist.latest_version > dist.parsed_version
|
|
||||||
]
|
|
||||||
|
|
||||||
def get_uptodate(self, packages, options):
|
|
||||||
return [
|
|
||||||
dist for dist in self.iter_packages_latest_infos(packages, options)
|
|
||||||
if dist.latest_version == dist.parsed_version
|
|
||||||
]
|
|
||||||
|
|
||||||
def get_not_required(self, packages, options):
|
|
||||||
dep_keys = set()
|
|
||||||
for dist in packages:
|
|
||||||
dep_keys.update(requirement.key for requirement in dist.requires())
|
|
||||||
return {pkg for pkg in packages if pkg.key not in dep_keys}
|
|
||||||
|
|
||||||
def iter_packages_latest_infos(self, packages, options):
|
|
||||||
index_urls = [options.index_url] + options.extra_index_urls
|
|
||||||
if options.no_index:
|
|
||||||
logger.debug('Ignoring indexes: %s', ','.join(index_urls))
|
|
||||||
index_urls = []
|
|
||||||
|
|
||||||
with self._build_session(options) as session:
|
|
||||||
finder = self._build_package_finder(options, index_urls, session)
|
|
||||||
|
|
||||||
for dist in packages:
|
|
||||||
typ = 'unknown'
|
|
||||||
all_candidates = finder.find_all_candidates(dist.key)
|
|
||||||
if not options.pre:
|
|
||||||
# Remove prereleases
|
|
||||||
all_candidates = [candidate for candidate in all_candidates
|
|
||||||
if not candidate.version.is_prerelease]
|
|
||||||
|
|
||||||
if not all_candidates:
|
|
||||||
continue
|
|
||||||
best_candidate = max(all_candidates,
|
|
||||||
key=finder._candidate_sort_key)
|
|
||||||
remote_version = best_candidate.version
|
|
||||||
if best_candidate.location.is_wheel:
|
|
||||||
typ = 'wheel'
|
|
||||||
else:
|
|
||||||
typ = 'sdist'
|
|
||||||
# This is dirty but makes the rest of the code much cleaner
|
|
||||||
dist.latest_version = remote_version
|
|
||||||
dist.latest_filetype = typ
|
|
||||||
yield dist
|
|
||||||
|
|
||||||
def output_package_listing(self, packages, options):
|
|
||||||
packages = sorted(
|
|
||||||
packages,
|
|
||||||
key=lambda dist: dist.project_name.lower(),
|
|
||||||
)
|
|
||||||
if options.list_format == 'columns' and packages:
|
|
||||||
data, header = format_for_columns(packages, options)
|
|
||||||
self.output_package_listing_columns(data, header)
|
|
||||||
elif options.list_format == 'freeze':
|
|
||||||
for dist in packages:
|
|
||||||
if options.verbose >= 1:
|
|
||||||
logger.info("%s==%s (%s)", dist.project_name,
|
|
||||||
dist.version, dist.location)
|
|
||||||
else:
|
|
||||||
logger.info("%s==%s", dist.project_name, dist.version)
|
|
||||||
elif options.list_format == 'json':
|
|
||||||
logger.info(format_for_json(packages, options))
|
|
||||||
|
|
||||||
def output_package_listing_columns(self, data, header):
|
|
||||||
# insert the header first: we need to know the size of column names
|
|
||||||
if len(data) > 0:
|
|
||||||
data.insert(0, header)
|
|
||||||
|
|
||||||
pkg_strings, sizes = tabulate(data)
|
|
||||||
|
|
||||||
# Create and add a separator.
|
|
||||||
if len(data) > 0:
|
|
||||||
pkg_strings.insert(1, " ".join(map(lambda x: '-' * x, sizes)))
|
|
||||||
|
|
||||||
for val in pkg_strings:
|
|
||||||
logger.info(val)
|
|
||||||
|
|
||||||
|
|
||||||
def tabulate(vals):
|
|
||||||
# From pfmoore on GitHub:
|
|
||||||
# https://github.com/pypa/pip/issues/3651#issuecomment-216932564
|
|
||||||
assert len(vals) > 0
|
|
||||||
|
|
||||||
sizes = [0] * max(len(x) for x in vals)
|
|
||||||
for row in vals:
|
|
||||||
sizes = [max(s, len(str(c))) for s, c in zip_longest(sizes, row)]
|
|
||||||
|
|
||||||
result = []
|
|
||||||
for row in vals:
|
|
||||||
display = " ".join([str(c).ljust(s) if c is not None else ''
|
|
||||||
for s, c in zip_longest(sizes, row)])
|
|
||||||
result.append(display)
|
|
||||||
|
|
||||||
return result, sizes
|
|
||||||
|
|
||||||
|
|
||||||
def format_for_columns(pkgs, options):
|
|
||||||
"""
|
|
||||||
Convert the package data into something usable
|
|
||||||
by output_package_listing_columns.
|
|
||||||
"""
|
|
||||||
running_outdated = options.outdated
|
|
||||||
# Adjust the header for the `pip list --outdated` case.
|
|
||||||
if running_outdated:
|
|
||||||
header = ["Package", "Version", "Latest", "Type"]
|
|
||||||
else:
|
|
||||||
header = ["Package", "Version"]
|
|
||||||
|
|
||||||
data = []
|
|
||||||
if options.verbose >= 1 or any(dist_is_editable(x) for x in pkgs):
|
|
||||||
header.append("Location")
|
|
||||||
if options.verbose >= 1:
|
|
||||||
header.append("Installer")
|
|
||||||
|
|
||||||
for proj in pkgs:
|
|
||||||
# if we're working on the 'outdated' list, separate out the
|
|
||||||
# latest_version and type
|
|
||||||
row = [proj.project_name, proj.version]
|
|
||||||
|
|
||||||
if running_outdated:
|
|
||||||
row.append(proj.latest_version)
|
|
||||||
row.append(proj.latest_filetype)
|
|
||||||
|
|
||||||
if options.verbose >= 1 or dist_is_editable(proj):
|
|
||||||
row.append(proj.location)
|
|
||||||
if options.verbose >= 1:
|
|
||||||
row.append(get_installer(proj))
|
|
||||||
|
|
||||||
data.append(row)
|
|
||||||
|
|
||||||
return data, header
|
|
||||||
|
|
||||||
|
|
||||||
def format_for_json(packages, options):
|
|
||||||
data = []
|
|
||||||
for dist in packages:
|
|
||||||
info = {
|
|
||||||
'name': dist.project_name,
|
|
||||||
'version': six.text_type(dist.version),
|
|
||||||
}
|
|
||||||
if options.verbose >= 1:
|
|
||||||
info['location'] = dist.location
|
|
||||||
info['installer'] = get_installer(dist)
|
|
||||||
if options.outdated:
|
|
||||||
info['latest_version'] = six.text_type(dist.latest_version)
|
|
||||||
info['latest_filetype'] = dist.latest_filetype
|
|
||||||
data.append(info)
|
|
||||||
return json.dumps(data)
|
|
||||||
@@ -1,135 +0,0 @@
|
|||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import logging
|
|
||||||
import sys
|
|
||||||
import textwrap
|
|
||||||
from collections import OrderedDict
|
|
||||||
|
|
||||||
from pip._vendor import pkg_resources
|
|
||||||
from pip._vendor.packaging.version import parse as parse_version
|
|
||||||
# NOTE: XMLRPC Client is not annotated in typeshed as on 2017-07-17, which is
|
|
||||||
# why we ignore the type on this import
|
|
||||||
from pip._vendor.six.moves import xmlrpc_client # type: ignore
|
|
||||||
|
|
||||||
from pip._internal.cli.base_command import Command
|
|
||||||
from pip._internal.cli.status_codes import NO_MATCHES_FOUND, SUCCESS
|
|
||||||
from pip._internal.download import PipXmlrpcTransport
|
|
||||||
from pip._internal.exceptions import CommandError
|
|
||||||
from pip._internal.models.index import PyPI
|
|
||||||
from pip._internal.utils.compat import get_terminal_size
|
|
||||||
from pip._internal.utils.logging import indent_log
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class SearchCommand(Command):
|
|
||||||
"""Search for PyPI packages whose name or summary contains <query>."""
|
|
||||||
name = 'search'
|
|
||||||
usage = """
|
|
||||||
%prog [options] <query>"""
|
|
||||||
summary = 'Search PyPI for packages.'
|
|
||||||
ignore_require_venv = True
|
|
||||||
|
|
||||||
def __init__(self, *args, **kw):
|
|
||||||
super(SearchCommand, self).__init__(*args, **kw)
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'-i', '--index',
|
|
||||||
dest='index',
|
|
||||||
metavar='URL',
|
|
||||||
default=PyPI.pypi_url,
|
|
||||||
help='Base URL of Python Package Index (default %default)')
|
|
||||||
|
|
||||||
self.parser.insert_option_group(0, self.cmd_opts)
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
if not args:
|
|
||||||
raise CommandError('Missing required argument (search query).')
|
|
||||||
query = args
|
|
||||||
pypi_hits = self.search(query, options)
|
|
||||||
hits = transform_hits(pypi_hits)
|
|
||||||
|
|
||||||
terminal_width = None
|
|
||||||
if sys.stdout.isatty():
|
|
||||||
terminal_width = get_terminal_size()[0]
|
|
||||||
|
|
||||||
print_results(hits, terminal_width=terminal_width)
|
|
||||||
if pypi_hits:
|
|
||||||
return SUCCESS
|
|
||||||
return NO_MATCHES_FOUND
|
|
||||||
|
|
||||||
def search(self, query, options):
|
|
||||||
index_url = options.index
|
|
||||||
with self._build_session(options) as session:
|
|
||||||
transport = PipXmlrpcTransport(index_url, session)
|
|
||||||
pypi = xmlrpc_client.ServerProxy(index_url, transport)
|
|
||||||
hits = pypi.search({'name': query, 'summary': query}, 'or')
|
|
||||||
return hits
|
|
||||||
|
|
||||||
|
|
||||||
def transform_hits(hits):
|
|
||||||
"""
|
|
||||||
The list from pypi is really a list of versions. We want a list of
|
|
||||||
packages with the list of versions stored inline. This converts the
|
|
||||||
list from pypi into one we can use.
|
|
||||||
"""
|
|
||||||
packages = OrderedDict()
|
|
||||||
for hit in hits:
|
|
||||||
name = hit['name']
|
|
||||||
summary = hit['summary']
|
|
||||||
version = hit['version']
|
|
||||||
|
|
||||||
if name not in packages.keys():
|
|
||||||
packages[name] = {
|
|
||||||
'name': name,
|
|
||||||
'summary': summary,
|
|
||||||
'versions': [version],
|
|
||||||
}
|
|
||||||
else:
|
|
||||||
packages[name]['versions'].append(version)
|
|
||||||
|
|
||||||
# if this is the highest version, replace summary and score
|
|
||||||
if version == highest_version(packages[name]['versions']):
|
|
||||||
packages[name]['summary'] = summary
|
|
||||||
|
|
||||||
return list(packages.values())
|
|
||||||
|
|
||||||
|
|
||||||
def print_results(hits, name_column_width=None, terminal_width=None):
|
|
||||||
if not hits:
|
|
||||||
return
|
|
||||||
if name_column_width is None:
|
|
||||||
name_column_width = max([
|
|
||||||
len(hit['name']) + len(highest_version(hit.get('versions', ['-'])))
|
|
||||||
for hit in hits
|
|
||||||
]) + 4
|
|
||||||
|
|
||||||
installed_packages = [p.project_name for p in pkg_resources.working_set]
|
|
||||||
for hit in hits:
|
|
||||||
name = hit['name']
|
|
||||||
summary = hit['summary'] or ''
|
|
||||||
latest = highest_version(hit.get('versions', ['-']))
|
|
||||||
if terminal_width is not None:
|
|
||||||
target_width = terminal_width - name_column_width - 5
|
|
||||||
if target_width > 10:
|
|
||||||
# wrap and indent summary to fit terminal
|
|
||||||
summary = textwrap.wrap(summary, target_width)
|
|
||||||
summary = ('\n' + ' ' * (name_column_width + 3)).join(summary)
|
|
||||||
|
|
||||||
line = '%-*s - %s' % (name_column_width,
|
|
||||||
'%s (%s)' % (name, latest), summary)
|
|
||||||
try:
|
|
||||||
logger.info(line)
|
|
||||||
if name in installed_packages:
|
|
||||||
dist = pkg_resources.get_distribution(name)
|
|
||||||
with indent_log():
|
|
||||||
if dist.version == latest:
|
|
||||||
logger.info('INSTALLED: %s (latest)', dist.version)
|
|
||||||
else:
|
|
||||||
logger.info('INSTALLED: %s', dist.version)
|
|
||||||
logger.info('LATEST: %s', latest)
|
|
||||||
except UnicodeEncodeError:
|
|
||||||
pass
|
|
||||||
|
|
||||||
|
|
||||||
def highest_version(versions):
|
|
||||||
return max(versions, key=parse_version)
|
|
||||||
@@ -1,168 +0,0 @@
|
|||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import logging
|
|
||||||
import os
|
|
||||||
from email.parser import FeedParser # type: ignore
|
|
||||||
|
|
||||||
from pip._vendor import pkg_resources
|
|
||||||
from pip._vendor.packaging.utils import canonicalize_name
|
|
||||||
|
|
||||||
from pip._internal.cli.base_command import Command
|
|
||||||
from pip._internal.cli.status_codes import ERROR, SUCCESS
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class ShowCommand(Command):
|
|
||||||
"""
|
|
||||||
Show information about one or more installed packages.
|
|
||||||
|
|
||||||
The output is in RFC-compliant mail header format.
|
|
||||||
"""
|
|
||||||
name = 'show'
|
|
||||||
usage = """
|
|
||||||
%prog [options] <package> ..."""
|
|
||||||
summary = 'Show information about installed packages.'
|
|
||||||
ignore_require_venv = True
|
|
||||||
|
|
||||||
def __init__(self, *args, **kw):
|
|
||||||
super(ShowCommand, self).__init__(*args, **kw)
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'-f', '--files',
|
|
||||||
dest='files',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help='Show the full list of installed files for each package.')
|
|
||||||
|
|
||||||
self.parser.insert_option_group(0, self.cmd_opts)
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
if not args:
|
|
||||||
logger.warning('ERROR: Please provide a package name or names.')
|
|
||||||
return ERROR
|
|
||||||
query = args
|
|
||||||
|
|
||||||
results = search_packages_info(query)
|
|
||||||
if not print_results(
|
|
||||||
results, list_files=options.files, verbose=options.verbose):
|
|
||||||
return ERROR
|
|
||||||
return SUCCESS
|
|
||||||
|
|
||||||
|
|
||||||
def search_packages_info(query):
|
|
||||||
"""
|
|
||||||
Gather details from installed distributions. Print distribution name,
|
|
||||||
version, location, and installed files. Installed files requires a
|
|
||||||
pip generated 'installed-files.txt' in the distributions '.egg-info'
|
|
||||||
directory.
|
|
||||||
"""
|
|
||||||
installed = {}
|
|
||||||
for p in pkg_resources.working_set:
|
|
||||||
installed[canonicalize_name(p.project_name)] = p
|
|
||||||
|
|
||||||
query_names = [canonicalize_name(name) for name in query]
|
|
||||||
|
|
||||||
for dist in [installed[pkg] for pkg in query_names if pkg in installed]:
|
|
||||||
package = {
|
|
||||||
'name': dist.project_name,
|
|
||||||
'version': dist.version,
|
|
||||||
'location': dist.location,
|
|
||||||
'requires': [dep.project_name for dep in dist.requires()],
|
|
||||||
}
|
|
||||||
file_list = None
|
|
||||||
metadata = None
|
|
||||||
if isinstance(dist, pkg_resources.DistInfoDistribution):
|
|
||||||
# RECORDs should be part of .dist-info metadatas
|
|
||||||
if dist.has_metadata('RECORD'):
|
|
||||||
lines = dist.get_metadata_lines('RECORD')
|
|
||||||
paths = [l.split(',')[0] for l in lines]
|
|
||||||
paths = [os.path.join(dist.location, p) for p in paths]
|
|
||||||
file_list = [os.path.relpath(p, dist.location) for p in paths]
|
|
||||||
|
|
||||||
if dist.has_metadata('METADATA'):
|
|
||||||
metadata = dist.get_metadata('METADATA')
|
|
||||||
else:
|
|
||||||
# Otherwise use pip's log for .egg-info's
|
|
||||||
if dist.has_metadata('installed-files.txt'):
|
|
||||||
paths = dist.get_metadata_lines('installed-files.txt')
|
|
||||||
paths = [os.path.join(dist.egg_info, p) for p in paths]
|
|
||||||
file_list = [os.path.relpath(p, dist.location) for p in paths]
|
|
||||||
|
|
||||||
if dist.has_metadata('PKG-INFO'):
|
|
||||||
metadata = dist.get_metadata('PKG-INFO')
|
|
||||||
|
|
||||||
if dist.has_metadata('entry_points.txt'):
|
|
||||||
entry_points = dist.get_metadata_lines('entry_points.txt')
|
|
||||||
package['entry_points'] = entry_points
|
|
||||||
|
|
||||||
if dist.has_metadata('INSTALLER'):
|
|
||||||
for line in dist.get_metadata_lines('INSTALLER'):
|
|
||||||
if line.strip():
|
|
||||||
package['installer'] = line.strip()
|
|
||||||
break
|
|
||||||
|
|
||||||
# @todo: Should pkg_resources.Distribution have a
|
|
||||||
# `get_pkg_info` method?
|
|
||||||
feed_parser = FeedParser()
|
|
||||||
feed_parser.feed(metadata)
|
|
||||||
pkg_info_dict = feed_parser.close()
|
|
||||||
for key in ('metadata-version', 'summary',
|
|
||||||
'home-page', 'author', 'author-email', 'license'):
|
|
||||||
package[key] = pkg_info_dict.get(key)
|
|
||||||
|
|
||||||
# It looks like FeedParser cannot deal with repeated headers
|
|
||||||
classifiers = []
|
|
||||||
for line in metadata.splitlines():
|
|
||||||
if line.startswith('Classifier: '):
|
|
||||||
classifiers.append(line[len('Classifier: '):])
|
|
||||||
package['classifiers'] = classifiers
|
|
||||||
|
|
||||||
if file_list:
|
|
||||||
package['files'] = sorted(file_list)
|
|
||||||
yield package
|
|
||||||
|
|
||||||
|
|
||||||
def print_results(distributions, list_files=False, verbose=False):
|
|
||||||
"""
|
|
||||||
Print the informations from installed distributions found.
|
|
||||||
"""
|
|
||||||
results_printed = False
|
|
||||||
for i, dist in enumerate(distributions):
|
|
||||||
results_printed = True
|
|
||||||
if i > 0:
|
|
||||||
logger.info("---")
|
|
||||||
|
|
||||||
name = dist.get('name', '')
|
|
||||||
required_by = [
|
|
||||||
pkg.project_name for pkg in pkg_resources.working_set
|
|
||||||
if name in [required.name for required in pkg.requires()]
|
|
||||||
]
|
|
||||||
|
|
||||||
logger.info("Name: %s", name)
|
|
||||||
logger.info("Version: %s", dist.get('version', ''))
|
|
||||||
logger.info("Summary: %s", dist.get('summary', ''))
|
|
||||||
logger.info("Home-page: %s", dist.get('home-page', ''))
|
|
||||||
logger.info("Author: %s", dist.get('author', ''))
|
|
||||||
logger.info("Author-email: %s", dist.get('author-email', ''))
|
|
||||||
logger.info("License: %s", dist.get('license', ''))
|
|
||||||
logger.info("Location: %s", dist.get('location', ''))
|
|
||||||
logger.info("Requires: %s", ', '.join(dist.get('requires', [])))
|
|
||||||
logger.info("Required-by: %s", ', '.join(required_by))
|
|
||||||
|
|
||||||
if verbose:
|
|
||||||
logger.info("Metadata-Version: %s",
|
|
||||||
dist.get('metadata-version', ''))
|
|
||||||
logger.info("Installer: %s", dist.get('installer', ''))
|
|
||||||
logger.info("Classifiers:")
|
|
||||||
for classifier in dist.get('classifiers', []):
|
|
||||||
logger.info(" %s", classifier)
|
|
||||||
logger.info("Entry-points:")
|
|
||||||
for entry in dist.get('entry_points', []):
|
|
||||||
logger.info(" %s", entry.strip())
|
|
||||||
if list_files:
|
|
||||||
logger.info("Files:")
|
|
||||||
for line in dist.get('files', []):
|
|
||||||
logger.info(" %s", line.strip())
|
|
||||||
if "files" not in dist:
|
|
||||||
logger.info("Cannot locate installed-files.txt")
|
|
||||||
return results_printed
|
|
||||||
@@ -1,78 +0,0 @@
|
|||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
from pip._vendor.packaging.utils import canonicalize_name
|
|
||||||
|
|
||||||
from pip._internal.cli.base_command import Command
|
|
||||||
from pip._internal.exceptions import InstallationError
|
|
||||||
from pip._internal.req import parse_requirements
|
|
||||||
from pip._internal.req.constructors import install_req_from_line
|
|
||||||
from pip._internal.utils.misc import protect_pip_from_modification_on_windows
|
|
||||||
|
|
||||||
|
|
||||||
class UninstallCommand(Command):
|
|
||||||
"""
|
|
||||||
Uninstall packages.
|
|
||||||
|
|
||||||
pip is able to uninstall most installed packages. Known exceptions are:
|
|
||||||
|
|
||||||
- Pure distutils packages installed with ``python setup.py install``, which
|
|
||||||
leave behind no metadata to determine what files were installed.
|
|
||||||
- Script wrappers installed by ``python setup.py develop``.
|
|
||||||
"""
|
|
||||||
name = 'uninstall'
|
|
||||||
usage = """
|
|
||||||
%prog [options] <package> ...
|
|
||||||
%prog [options] -r <requirements file> ..."""
|
|
||||||
summary = 'Uninstall packages.'
|
|
||||||
|
|
||||||
def __init__(self, *args, **kw):
|
|
||||||
super(UninstallCommand, self).__init__(*args, **kw)
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'-r', '--requirement',
|
|
||||||
dest='requirements',
|
|
||||||
action='append',
|
|
||||||
default=[],
|
|
||||||
metavar='file',
|
|
||||||
help='Uninstall all the packages listed in the given requirements '
|
|
||||||
'file. This option can be used multiple times.',
|
|
||||||
)
|
|
||||||
self.cmd_opts.add_option(
|
|
||||||
'-y', '--yes',
|
|
||||||
dest='yes',
|
|
||||||
action='store_true',
|
|
||||||
help="Don't ask for confirmation of uninstall deletions.")
|
|
||||||
|
|
||||||
self.parser.insert_option_group(0, self.cmd_opts)
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
with self._build_session(options) as session:
|
|
||||||
reqs_to_uninstall = {}
|
|
||||||
for name in args:
|
|
||||||
req = install_req_from_line(
|
|
||||||
name, isolated=options.isolated_mode,
|
|
||||||
)
|
|
||||||
if req.name:
|
|
||||||
reqs_to_uninstall[canonicalize_name(req.name)] = req
|
|
||||||
for filename in options.requirements:
|
|
||||||
for req in parse_requirements(
|
|
||||||
filename,
|
|
||||||
options=options,
|
|
||||||
session=session):
|
|
||||||
if req.name:
|
|
||||||
reqs_to_uninstall[canonicalize_name(req.name)] = req
|
|
||||||
if not reqs_to_uninstall:
|
|
||||||
raise InstallationError(
|
|
||||||
'You must give at least one requirement to %(name)s (see '
|
|
||||||
'"pip help %(name)s")' % dict(name=self.name)
|
|
||||||
)
|
|
||||||
|
|
||||||
protect_pip_from_modification_on_windows(
|
|
||||||
modifying_pip="pip" in reqs_to_uninstall
|
|
||||||
)
|
|
||||||
|
|
||||||
for req in reqs_to_uninstall.values():
|
|
||||||
uninstall_pathset = req.uninstall(
|
|
||||||
auto_confirm=options.yes, verbose=self.verbosity > 0,
|
|
||||||
)
|
|
||||||
if uninstall_pathset:
|
|
||||||
uninstall_pathset.commit()
|
|
||||||
@@ -1,186 +0,0 @@
|
|||||||
# -*- coding: utf-8 -*-
|
|
||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import logging
|
|
||||||
import os
|
|
||||||
|
|
||||||
from pip._internal.cache import WheelCache
|
|
||||||
from pip._internal.cli import cmdoptions
|
|
||||||
from pip._internal.cli.base_command import RequirementCommand
|
|
||||||
from pip._internal.exceptions import CommandError, PreviousBuildDirError
|
|
||||||
from pip._internal.operations.prepare import RequirementPreparer
|
|
||||||
from pip._internal.req import RequirementSet
|
|
||||||
from pip._internal.req.req_tracker import RequirementTracker
|
|
||||||
from pip._internal.resolve import Resolver
|
|
||||||
from pip._internal.utils.temp_dir import TempDirectory
|
|
||||||
from pip._internal.wheel import WheelBuilder
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
class WheelCommand(RequirementCommand):
|
|
||||||
"""
|
|
||||||
Build Wheel archives for your requirements and dependencies.
|
|
||||||
|
|
||||||
Wheel is a built-package format, and offers the advantage of not
|
|
||||||
recompiling your software during every install. For more details, see the
|
|
||||||
wheel docs: https://wheel.readthedocs.io/en/latest/
|
|
||||||
|
|
||||||
Requirements: setuptools>=0.8, and wheel.
|
|
||||||
|
|
||||||
'pip wheel' uses the bdist_wheel setuptools extension from the wheel
|
|
||||||
package to build individual wheels.
|
|
||||||
|
|
||||||
"""
|
|
||||||
|
|
||||||
name = 'wheel'
|
|
||||||
usage = """
|
|
||||||
%prog [options] <requirement specifier> ...
|
|
||||||
%prog [options] -r <requirements file> ...
|
|
||||||
%prog [options] [-e] <vcs project url> ...
|
|
||||||
%prog [options] [-e] <local project path> ...
|
|
||||||
%prog [options] <archive url/path> ..."""
|
|
||||||
|
|
||||||
summary = 'Build wheels from your requirements.'
|
|
||||||
|
|
||||||
def __init__(self, *args, **kw):
|
|
||||||
super(WheelCommand, self).__init__(*args, **kw)
|
|
||||||
|
|
||||||
cmd_opts = self.cmd_opts
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'-w', '--wheel-dir',
|
|
||||||
dest='wheel_dir',
|
|
||||||
metavar='dir',
|
|
||||||
default=os.curdir,
|
|
||||||
help=("Build wheels into <dir>, where the default is the "
|
|
||||||
"current working directory."),
|
|
||||||
)
|
|
||||||
cmd_opts.add_option(cmdoptions.no_binary())
|
|
||||||
cmd_opts.add_option(cmdoptions.only_binary())
|
|
||||||
cmd_opts.add_option(cmdoptions.prefer_binary())
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--build-option',
|
|
||||||
dest='build_options',
|
|
||||||
metavar='options',
|
|
||||||
action='append',
|
|
||||||
help="Extra arguments to be supplied to 'setup.py bdist_wheel'.",
|
|
||||||
)
|
|
||||||
cmd_opts.add_option(cmdoptions.no_build_isolation())
|
|
||||||
cmd_opts.add_option(cmdoptions.use_pep517())
|
|
||||||
cmd_opts.add_option(cmdoptions.no_use_pep517())
|
|
||||||
cmd_opts.add_option(cmdoptions.constraints())
|
|
||||||
cmd_opts.add_option(cmdoptions.editable())
|
|
||||||
cmd_opts.add_option(cmdoptions.requirements())
|
|
||||||
cmd_opts.add_option(cmdoptions.src())
|
|
||||||
cmd_opts.add_option(cmdoptions.ignore_requires_python())
|
|
||||||
cmd_opts.add_option(cmdoptions.no_deps())
|
|
||||||
cmd_opts.add_option(cmdoptions.build_dir())
|
|
||||||
cmd_opts.add_option(cmdoptions.progress_bar())
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--global-option',
|
|
||||||
dest='global_options',
|
|
||||||
action='append',
|
|
||||||
metavar='options',
|
|
||||||
help="Extra global options to be supplied to the setup.py "
|
|
||||||
"call before the 'bdist_wheel' command.")
|
|
||||||
|
|
||||||
cmd_opts.add_option(
|
|
||||||
'--pre',
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help=("Include pre-release and development versions. By default, "
|
|
||||||
"pip only finds stable versions."),
|
|
||||||
)
|
|
||||||
|
|
||||||
cmd_opts.add_option(cmdoptions.no_clean())
|
|
||||||
cmd_opts.add_option(cmdoptions.require_hashes())
|
|
||||||
|
|
||||||
index_opts = cmdoptions.make_option_group(
|
|
||||||
cmdoptions.index_group,
|
|
||||||
self.parser,
|
|
||||||
)
|
|
||||||
|
|
||||||
self.parser.insert_option_group(0, index_opts)
|
|
||||||
self.parser.insert_option_group(0, cmd_opts)
|
|
||||||
|
|
||||||
def run(self, options, args):
|
|
||||||
cmdoptions.check_install_build_global(options)
|
|
||||||
|
|
||||||
index_urls = [options.index_url] + options.extra_index_urls
|
|
||||||
if options.no_index:
|
|
||||||
logger.debug('Ignoring indexes: %s', ','.join(index_urls))
|
|
||||||
index_urls = []
|
|
||||||
|
|
||||||
if options.build_dir:
|
|
||||||
options.build_dir = os.path.abspath(options.build_dir)
|
|
||||||
|
|
||||||
options.src_dir = os.path.abspath(options.src_dir)
|
|
||||||
|
|
||||||
with self._build_session(options) as session:
|
|
||||||
finder = self._build_package_finder(options, session)
|
|
||||||
build_delete = (not (options.no_clean or options.build_dir))
|
|
||||||
wheel_cache = WheelCache(options.cache_dir, options.format_control)
|
|
||||||
|
|
||||||
with RequirementTracker() as req_tracker, TempDirectory(
|
|
||||||
options.build_dir, delete=build_delete, kind="wheel"
|
|
||||||
) as directory:
|
|
||||||
|
|
||||||
requirement_set = RequirementSet(
|
|
||||||
require_hashes=options.require_hashes,
|
|
||||||
)
|
|
||||||
|
|
||||||
try:
|
|
||||||
self.populate_requirement_set(
|
|
||||||
requirement_set, args, options, finder, session,
|
|
||||||
self.name, wheel_cache
|
|
||||||
)
|
|
||||||
|
|
||||||
preparer = RequirementPreparer(
|
|
||||||
build_dir=directory.path,
|
|
||||||
src_dir=options.src_dir,
|
|
||||||
download_dir=None,
|
|
||||||
wheel_download_dir=options.wheel_dir,
|
|
||||||
progress_bar=options.progress_bar,
|
|
||||||
build_isolation=options.build_isolation,
|
|
||||||
req_tracker=req_tracker,
|
|
||||||
)
|
|
||||||
|
|
||||||
resolver = Resolver(
|
|
||||||
preparer=preparer,
|
|
||||||
finder=finder,
|
|
||||||
session=session,
|
|
||||||
wheel_cache=wheel_cache,
|
|
||||||
use_user_site=False,
|
|
||||||
upgrade_strategy="to-satisfy-only",
|
|
||||||
force_reinstall=False,
|
|
||||||
ignore_dependencies=options.ignore_dependencies,
|
|
||||||
ignore_requires_python=options.ignore_requires_python,
|
|
||||||
ignore_installed=True,
|
|
||||||
isolated=options.isolated_mode,
|
|
||||||
use_pep517=options.use_pep517
|
|
||||||
)
|
|
||||||
resolver.resolve(requirement_set)
|
|
||||||
|
|
||||||
# build wheels
|
|
||||||
wb = WheelBuilder(
|
|
||||||
finder, preparer, wheel_cache,
|
|
||||||
build_options=options.build_options or [],
|
|
||||||
global_options=options.global_options or [],
|
|
||||||
no_clean=options.no_clean,
|
|
||||||
)
|
|
||||||
build_failures = wb.build(
|
|
||||||
requirement_set.requirements.values(), session=session,
|
|
||||||
)
|
|
||||||
if len(build_failures) != 0:
|
|
||||||
raise CommandError(
|
|
||||||
"Failed to build one or more wheels"
|
|
||||||
)
|
|
||||||
except PreviousBuildDirError:
|
|
||||||
options.no_clean = True
|
|
||||||
raise
|
|
||||||
finally:
|
|
||||||
if not options.no_clean:
|
|
||||||
requirement_set.cleanup_files()
|
|
||||||
wheel_cache.cleanup()
|
|
||||||
@@ -1,387 +0,0 @@
|
|||||||
"""Configuration management setup
|
|
||||||
|
|
||||||
Some terminology:
|
|
||||||
- name
|
|
||||||
As written in config files.
|
|
||||||
- value
|
|
||||||
Value associated with a name
|
|
||||||
- key
|
|
||||||
Name combined with it's section (section.name)
|
|
||||||
- variant
|
|
||||||
A single word describing where the configuration key-value pair came from
|
|
||||||
"""
|
|
||||||
|
|
||||||
import locale
|
|
||||||
import logging
|
|
||||||
import os
|
|
||||||
|
|
||||||
from pip._vendor import six
|
|
||||||
from pip._vendor.six.moves import configparser
|
|
||||||
|
|
||||||
from pip._internal.exceptions import (
|
|
||||||
ConfigurationError, ConfigurationFileCouldNotBeLoaded,
|
|
||||||
)
|
|
||||||
from pip._internal.locations import (
|
|
||||||
legacy_config_file, new_config_file, running_under_virtualenv,
|
|
||||||
site_config_files, venv_config_file,
|
|
||||||
)
|
|
||||||
from pip._internal.utils.misc import ensure_dir, enum
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from typing import ( # noqa: F401
|
|
||||||
Any, Dict, Iterable, List, NewType, Optional, Tuple
|
|
||||||
)
|
|
||||||
|
|
||||||
RawConfigParser = configparser.RawConfigParser # Shorthand
|
|
||||||
Kind = NewType("Kind", str)
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
# NOTE: Maybe use the optionx attribute to normalize keynames.
|
|
||||||
def _normalize_name(name):
|
|
||||||
# type: (str) -> str
|
|
||||||
"""Make a name consistent regardless of source (environment or file)
|
|
||||||
"""
|
|
||||||
name = name.lower().replace('_', '-')
|
|
||||||
if name.startswith('--'):
|
|
||||||
name = name[2:] # only prefer long opts
|
|
||||||
return name
|
|
||||||
|
|
||||||
|
|
||||||
def _disassemble_key(name):
|
|
||||||
# type: (str) -> List[str]
|
|
||||||
return name.split(".", 1)
|
|
||||||
|
|
||||||
|
|
||||||
# The kinds of configurations there are.
|
|
||||||
kinds = enum(
|
|
||||||
USER="user", # User Specific
|
|
||||||
GLOBAL="global", # System Wide
|
|
||||||
VENV="venv", # Virtual Environment Specific
|
|
||||||
ENV="env", # from PIP_CONFIG_FILE
|
|
||||||
ENV_VAR="env-var", # from Environment Variables
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
class Configuration(object):
|
|
||||||
"""Handles management of configuration.
|
|
||||||
|
|
||||||
Provides an interface to accessing and managing configuration files.
|
|
||||||
|
|
||||||
This class converts provides an API that takes "section.key-name" style
|
|
||||||
keys and stores the value associated with it as "key-name" under the
|
|
||||||
section "section".
|
|
||||||
|
|
||||||
This allows for a clean interface wherein the both the section and the
|
|
||||||
key-name are preserved in an easy to manage form in the configuration files
|
|
||||||
and the data stored is also nice.
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self, isolated, load_only=None):
|
|
||||||
# type: (bool, Kind) -> None
|
|
||||||
super(Configuration, self).__init__()
|
|
||||||
|
|
||||||
_valid_load_only = [kinds.USER, kinds.GLOBAL, kinds.VENV, None]
|
|
||||||
if load_only not in _valid_load_only:
|
|
||||||
raise ConfigurationError(
|
|
||||||
"Got invalid value for load_only - should be one of {}".format(
|
|
||||||
", ".join(map(repr, _valid_load_only[:-1]))
|
|
||||||
)
|
|
||||||
)
|
|
||||||
self.isolated = isolated # type: bool
|
|
||||||
self.load_only = load_only # type: Optional[Kind]
|
|
||||||
|
|
||||||
# The order here determines the override order.
|
|
||||||
self._override_order = [
|
|
||||||
kinds.GLOBAL, kinds.USER, kinds.VENV, kinds.ENV, kinds.ENV_VAR
|
|
||||||
]
|
|
||||||
|
|
||||||
self._ignore_env_names = ["version", "help"]
|
|
||||||
|
|
||||||
# Because we keep track of where we got the data from
|
|
||||||
self._parsers = {
|
|
||||||
variant: [] for variant in self._override_order
|
|
||||||
} # type: Dict[Kind, List[Tuple[str, RawConfigParser]]]
|
|
||||||
self._config = {
|
|
||||||
variant: {} for variant in self._override_order
|
|
||||||
} # type: Dict[Kind, Dict[str, Any]]
|
|
||||||
self._modified_parsers = [] # type: List[Tuple[str, RawConfigParser]]
|
|
||||||
|
|
||||||
def load(self):
|
|
||||||
# type: () -> None
|
|
||||||
"""Loads configuration from configuration files and environment
|
|
||||||
"""
|
|
||||||
self._load_config_files()
|
|
||||||
if not self.isolated:
|
|
||||||
self._load_environment_vars()
|
|
||||||
|
|
||||||
def get_file_to_edit(self):
|
|
||||||
# type: () -> Optional[str]
|
|
||||||
"""Returns the file with highest priority in configuration
|
|
||||||
"""
|
|
||||||
assert self.load_only is not None, \
|
|
||||||
"Need to be specified a file to be editing"
|
|
||||||
|
|
||||||
try:
|
|
||||||
return self._get_parser_to_modify()[0]
|
|
||||||
except IndexError:
|
|
||||||
return None
|
|
||||||
|
|
||||||
def items(self):
|
|
||||||
# type: () -> Iterable[Tuple[str, Any]]
|
|
||||||
"""Returns key-value pairs like dict.items() representing the loaded
|
|
||||||
configuration
|
|
||||||
"""
|
|
||||||
return self._dictionary.items()
|
|
||||||
|
|
||||||
def get_value(self, key):
|
|
||||||
# type: (str) -> Any
|
|
||||||
"""Get a value from the configuration.
|
|
||||||
"""
|
|
||||||
try:
|
|
||||||
return self._dictionary[key]
|
|
||||||
except KeyError:
|
|
||||||
raise ConfigurationError("No such key - {}".format(key))
|
|
||||||
|
|
||||||
def set_value(self, key, value):
|
|
||||||
# type: (str, Any) -> None
|
|
||||||
"""Modify a value in the configuration.
|
|
||||||
"""
|
|
||||||
self._ensure_have_load_only()
|
|
||||||
|
|
||||||
fname, parser = self._get_parser_to_modify()
|
|
||||||
|
|
||||||
if parser is not None:
|
|
||||||
section, name = _disassemble_key(key)
|
|
||||||
|
|
||||||
# Modify the parser and the configuration
|
|
||||||
if not parser.has_section(section):
|
|
||||||
parser.add_section(section)
|
|
||||||
parser.set(section, name, value)
|
|
||||||
|
|
||||||
self._config[self.load_only][key] = value
|
|
||||||
self._mark_as_modified(fname, parser)
|
|
||||||
|
|
||||||
def unset_value(self, key):
|
|
||||||
# type: (str) -> None
|
|
||||||
"""Unset a value in the configuration.
|
|
||||||
"""
|
|
||||||
self._ensure_have_load_only()
|
|
||||||
|
|
||||||
if key not in self._config[self.load_only]:
|
|
||||||
raise ConfigurationError("No such key - {}".format(key))
|
|
||||||
|
|
||||||
fname, parser = self._get_parser_to_modify()
|
|
||||||
|
|
||||||
if parser is not None:
|
|
||||||
section, name = _disassemble_key(key)
|
|
||||||
|
|
||||||
# Remove the key in the parser
|
|
||||||
modified_something = False
|
|
||||||
if parser.has_section(section):
|
|
||||||
# Returns whether the option was removed or not
|
|
||||||
modified_something = parser.remove_option(section, name)
|
|
||||||
|
|
||||||
if modified_something:
|
|
||||||
# name removed from parser, section may now be empty
|
|
||||||
section_iter = iter(parser.items(section))
|
|
||||||
try:
|
|
||||||
val = six.next(section_iter)
|
|
||||||
except StopIteration:
|
|
||||||
val = None
|
|
||||||
|
|
||||||
if val is None:
|
|
||||||
parser.remove_section(section)
|
|
||||||
|
|
||||||
self._mark_as_modified(fname, parser)
|
|
||||||
else:
|
|
||||||
raise ConfigurationError(
|
|
||||||
"Fatal Internal error [id=1]. Please report as a bug."
|
|
||||||
)
|
|
||||||
|
|
||||||
del self._config[self.load_only][key]
|
|
||||||
|
|
||||||
def save(self):
|
|
||||||
# type: () -> None
|
|
||||||
"""Save the currentin-memory state.
|
|
||||||
"""
|
|
||||||
self._ensure_have_load_only()
|
|
||||||
|
|
||||||
for fname, parser in self._modified_parsers:
|
|
||||||
logger.info("Writing to %s", fname)
|
|
||||||
|
|
||||||
# Ensure directory exists.
|
|
||||||
ensure_dir(os.path.dirname(fname))
|
|
||||||
|
|
||||||
with open(fname, "w") as f:
|
|
||||||
parser.write(f) # type: ignore
|
|
||||||
|
|
||||||
#
|
|
||||||
# Private routines
|
|
||||||
#
|
|
||||||
|
|
||||||
def _ensure_have_load_only(self):
|
|
||||||
# type: () -> None
|
|
||||||
if self.load_only is None:
|
|
||||||
raise ConfigurationError("Needed a specific file to be modifying.")
|
|
||||||
logger.debug("Will be working with %s variant only", self.load_only)
|
|
||||||
|
|
||||||
@property
|
|
||||||
def _dictionary(self):
|
|
||||||
# type: () -> Dict[str, Any]
|
|
||||||
"""A dictionary representing the loaded configuration.
|
|
||||||
"""
|
|
||||||
# NOTE: Dictionaries are not populated if not loaded. So, conditionals
|
|
||||||
# are not needed here.
|
|
||||||
retval = {}
|
|
||||||
|
|
||||||
for variant in self._override_order:
|
|
||||||
retval.update(self._config[variant])
|
|
||||||
|
|
||||||
return retval
|
|
||||||
|
|
||||||
def _load_config_files(self):
|
|
||||||
# type: () -> None
|
|
||||||
"""Loads configuration from configuration files
|
|
||||||
"""
|
|
||||||
config_files = dict(self._iter_config_files())
|
|
||||||
if config_files[kinds.ENV][0:1] == [os.devnull]:
|
|
||||||
logger.debug(
|
|
||||||
"Skipping loading configuration files due to "
|
|
||||||
"environment's PIP_CONFIG_FILE being os.devnull"
|
|
||||||
)
|
|
||||||
return
|
|
||||||
|
|
||||||
for variant, files in config_files.items():
|
|
||||||
for fname in files:
|
|
||||||
# If there's specific variant set in `load_only`, load only
|
|
||||||
# that variant, not the others.
|
|
||||||
if self.load_only is not None and variant != self.load_only:
|
|
||||||
logger.debug(
|
|
||||||
"Skipping file '%s' (variant: %s)", fname, variant
|
|
||||||
)
|
|
||||||
continue
|
|
||||||
|
|
||||||
parser = self._load_file(variant, fname)
|
|
||||||
|
|
||||||
# Keeping track of the parsers used
|
|
||||||
self._parsers[variant].append((fname, parser))
|
|
||||||
|
|
||||||
def _load_file(self, variant, fname):
|
|
||||||
# type: (Kind, str) -> RawConfigParser
|
|
||||||
logger.debug("For variant '%s', will try loading '%s'", variant, fname)
|
|
||||||
parser = self._construct_parser(fname)
|
|
||||||
|
|
||||||
for section in parser.sections():
|
|
||||||
items = parser.items(section)
|
|
||||||
self._config[variant].update(self._normalized_keys(section, items))
|
|
||||||
|
|
||||||
return parser
|
|
||||||
|
|
||||||
def _construct_parser(self, fname):
|
|
||||||
# type: (str) -> RawConfigParser
|
|
||||||
parser = configparser.RawConfigParser()
|
|
||||||
# If there is no such file, don't bother reading it but create the
|
|
||||||
# parser anyway, to hold the data.
|
|
||||||
# Doing this is useful when modifying and saving files, where we don't
|
|
||||||
# need to construct a parser.
|
|
||||||
if os.path.exists(fname):
|
|
||||||
try:
|
|
||||||
parser.read(fname)
|
|
||||||
except UnicodeDecodeError:
|
|
||||||
# See https://github.com/pypa/pip/issues/4963
|
|
||||||
raise ConfigurationFileCouldNotBeLoaded(
|
|
||||||
reason="contains invalid {} characters".format(
|
|
||||||
locale.getpreferredencoding(False)
|
|
||||||
),
|
|
||||||
fname=fname,
|
|
||||||
)
|
|
||||||
except configparser.Error as error:
|
|
||||||
# See https://github.com/pypa/pip/issues/4893
|
|
||||||
raise ConfigurationFileCouldNotBeLoaded(error=error)
|
|
||||||
return parser
|
|
||||||
|
|
||||||
def _load_environment_vars(self):
|
|
||||||
# type: () -> None
|
|
||||||
"""Loads configuration from environment variables
|
|
||||||
"""
|
|
||||||
self._config[kinds.ENV_VAR].update(
|
|
||||||
self._normalized_keys(":env:", self._get_environ_vars())
|
|
||||||
)
|
|
||||||
|
|
||||||
def _normalized_keys(self, section, items):
|
|
||||||
# type: (str, Iterable[Tuple[str, Any]]) -> Dict[str, Any]
|
|
||||||
"""Normalizes items to construct a dictionary with normalized keys.
|
|
||||||
|
|
||||||
This routine is where the names become keys and are made the same
|
|
||||||
regardless of source - configuration files or environment.
|
|
||||||
"""
|
|
||||||
normalized = {}
|
|
||||||
for name, val in items:
|
|
||||||
key = section + "." + _normalize_name(name)
|
|
||||||
normalized[key] = val
|
|
||||||
return normalized
|
|
||||||
|
|
||||||
def _get_environ_vars(self):
|
|
||||||
# type: () -> Iterable[Tuple[str, str]]
|
|
||||||
"""Returns a generator with all environmental vars with prefix PIP_"""
|
|
||||||
for key, val in os.environ.items():
|
|
||||||
should_be_yielded = (
|
|
||||||
key.startswith("PIP_") and
|
|
||||||
key[4:].lower() not in self._ignore_env_names
|
|
||||||
)
|
|
||||||
if should_be_yielded:
|
|
||||||
yield key[4:].lower(), val
|
|
||||||
|
|
||||||
# XXX: This is patched in the tests.
|
|
||||||
def _iter_config_files(self):
|
|
||||||
# type: () -> Iterable[Tuple[Kind, List[str]]]
|
|
||||||
"""Yields variant and configuration files associated with it.
|
|
||||||
|
|
||||||
This should be treated like items of a dictionary.
|
|
||||||
"""
|
|
||||||
# SMELL: Move the conditions out of this function
|
|
||||||
|
|
||||||
# environment variables have the lowest priority
|
|
||||||
config_file = os.environ.get('PIP_CONFIG_FILE', None)
|
|
||||||
if config_file is not None:
|
|
||||||
yield kinds.ENV, [config_file]
|
|
||||||
else:
|
|
||||||
yield kinds.ENV, []
|
|
||||||
|
|
||||||
# at the base we have any global configuration
|
|
||||||
yield kinds.GLOBAL, list(site_config_files)
|
|
||||||
|
|
||||||
# per-user configuration next
|
|
||||||
should_load_user_config = not self.isolated and not (
|
|
||||||
config_file and os.path.exists(config_file)
|
|
||||||
)
|
|
||||||
if should_load_user_config:
|
|
||||||
# The legacy config file is overridden by the new config file
|
|
||||||
yield kinds.USER, [legacy_config_file, new_config_file]
|
|
||||||
|
|
||||||
# finally virtualenv configuration first trumping others
|
|
||||||
if running_under_virtualenv():
|
|
||||||
yield kinds.VENV, [venv_config_file]
|
|
||||||
|
|
||||||
def _get_parser_to_modify(self):
|
|
||||||
# type: () -> Tuple[str, RawConfigParser]
|
|
||||||
# Determine which parser to modify
|
|
||||||
parsers = self._parsers[self.load_only]
|
|
||||||
if not parsers:
|
|
||||||
# This should not happen if everything works correctly.
|
|
||||||
raise ConfigurationError(
|
|
||||||
"Fatal Internal error [id=2]. Please report as a bug."
|
|
||||||
)
|
|
||||||
|
|
||||||
# Use the highest priority parser.
|
|
||||||
return parsers[-1]
|
|
||||||
|
|
||||||
# XXX: This is patched in the tests.
|
|
||||||
def _mark_as_modified(self, fname, parser):
|
|
||||||
# type: (str, RawConfigParser) -> None
|
|
||||||
file_parser_tuple = (fname, parser)
|
|
||||||
if file_parser_tuple not in self._modified_parsers:
|
|
||||||
self._modified_parsers.append(file_parser_tuple)
|
|
||||||
@@ -1,971 +0,0 @@
|
|||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import cgi
|
|
||||||
import email.utils
|
|
||||||
import getpass
|
|
||||||
import json
|
|
||||||
import logging
|
|
||||||
import mimetypes
|
|
||||||
import os
|
|
||||||
import platform
|
|
||||||
import re
|
|
||||||
import shutil
|
|
||||||
import sys
|
|
||||||
|
|
||||||
from pip._vendor import requests, six, urllib3
|
|
||||||
from pip._vendor.cachecontrol import CacheControlAdapter
|
|
||||||
from pip._vendor.cachecontrol.caches import FileCache
|
|
||||||
from pip._vendor.lockfile import LockError
|
|
||||||
from pip._vendor.requests.adapters import BaseAdapter, HTTPAdapter
|
|
||||||
from pip._vendor.requests.auth import AuthBase, HTTPBasicAuth
|
|
||||||
from pip._vendor.requests.models import CONTENT_CHUNK_SIZE, Response
|
|
||||||
from pip._vendor.requests.structures import CaseInsensitiveDict
|
|
||||||
from pip._vendor.requests.utils import get_netrc_auth
|
|
||||||
# NOTE: XMLRPC Client is not annotated in typeshed as on 2017-07-17, which is
|
|
||||||
# why we ignore the type on this import
|
|
||||||
from pip._vendor.six.moves import xmlrpc_client # type: ignore
|
|
||||||
from pip._vendor.six.moves.urllib import parse as urllib_parse
|
|
||||||
from pip._vendor.six.moves.urllib import request as urllib_request
|
|
||||||
from pip._vendor.urllib3.util import IS_PYOPENSSL
|
|
||||||
|
|
||||||
import pip
|
|
||||||
from pip._internal.exceptions import HashMismatch, InstallationError
|
|
||||||
from pip._internal.locations import write_delete_marker_file
|
|
||||||
from pip._internal.models.index import PyPI
|
|
||||||
from pip._internal.utils.encoding import auto_decode
|
|
||||||
from pip._internal.utils.filesystem import check_path_owner
|
|
||||||
from pip._internal.utils.glibc import libc_ver
|
|
||||||
from pip._internal.utils.logging import indent_log
|
|
||||||
from pip._internal.utils.misc import (
|
|
||||||
ARCHIVE_EXTENSIONS, ask_path_exists, backup_dir, call_subprocess, consume,
|
|
||||||
display_path, format_size, get_installed_version, rmtree,
|
|
||||||
split_auth_from_netloc, splitext, unpack_file,
|
|
||||||
)
|
|
||||||
from pip._internal.utils.setuptools_build import SETUPTOOLS_SHIM
|
|
||||||
from pip._internal.utils.temp_dir import TempDirectory
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
from pip._internal.utils.ui import DownloadProgressProvider
|
|
||||||
from pip._internal.vcs import vcs
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from typing import ( # noqa: F401
|
|
||||||
Optional, Tuple, Dict, IO, Text, Union
|
|
||||||
)
|
|
||||||
from pip._internal.models.link import Link # noqa: F401
|
|
||||||
from pip._internal.utils.hashes import Hashes # noqa: F401
|
|
||||||
from pip._internal.vcs import AuthInfo # noqa: F401
|
|
||||||
|
|
||||||
try:
|
|
||||||
import ssl # noqa
|
|
||||||
except ImportError:
|
|
||||||
ssl = None
|
|
||||||
|
|
||||||
HAS_TLS = (ssl is not None) or IS_PYOPENSSL
|
|
||||||
|
|
||||||
__all__ = ['get_file_content',
|
|
||||||
'is_url', 'url_to_path', 'path_to_url',
|
|
||||||
'is_archive_file', 'unpack_vcs_link',
|
|
||||||
'unpack_file_url', 'is_vcs_url', 'is_file_url',
|
|
||||||
'unpack_http_url', 'unpack_url']
|
|
||||||
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
def user_agent():
|
|
||||||
"""
|
|
||||||
Return a string representing the user agent.
|
|
||||||
"""
|
|
||||||
data = {
|
|
||||||
"installer": {"name": "pip", "version": pip.__version__},
|
|
||||||
"python": platform.python_version(),
|
|
||||||
"implementation": {
|
|
||||||
"name": platform.python_implementation(),
|
|
||||||
},
|
|
||||||
}
|
|
||||||
|
|
||||||
if data["implementation"]["name"] == 'CPython':
|
|
||||||
data["implementation"]["version"] = platform.python_version()
|
|
||||||
elif data["implementation"]["name"] == 'PyPy':
|
|
||||||
if sys.pypy_version_info.releaselevel == 'final':
|
|
||||||
pypy_version_info = sys.pypy_version_info[:3]
|
|
||||||
else:
|
|
||||||
pypy_version_info = sys.pypy_version_info
|
|
||||||
data["implementation"]["version"] = ".".join(
|
|
||||||
[str(x) for x in pypy_version_info]
|
|
||||||
)
|
|
||||||
elif data["implementation"]["name"] == 'Jython':
|
|
||||||
# Complete Guess
|
|
||||||
data["implementation"]["version"] = platform.python_version()
|
|
||||||
elif data["implementation"]["name"] == 'IronPython':
|
|
||||||
# Complete Guess
|
|
||||||
data["implementation"]["version"] = platform.python_version()
|
|
||||||
|
|
||||||
if sys.platform.startswith("linux"):
|
|
||||||
from pip._vendor import distro
|
|
||||||
distro_infos = dict(filter(
|
|
||||||
lambda x: x[1],
|
|
||||||
zip(["name", "version", "id"], distro.linux_distribution()),
|
|
||||||
))
|
|
||||||
libc = dict(filter(
|
|
||||||
lambda x: x[1],
|
|
||||||
zip(["lib", "version"], libc_ver()),
|
|
||||||
))
|
|
||||||
if libc:
|
|
||||||
distro_infos["libc"] = libc
|
|
||||||
if distro_infos:
|
|
||||||
data["distro"] = distro_infos
|
|
||||||
|
|
||||||
if sys.platform.startswith("darwin") and platform.mac_ver()[0]:
|
|
||||||
data["distro"] = {"name": "macOS", "version": platform.mac_ver()[0]}
|
|
||||||
|
|
||||||
if platform.system():
|
|
||||||
data.setdefault("system", {})["name"] = platform.system()
|
|
||||||
|
|
||||||
if platform.release():
|
|
||||||
data.setdefault("system", {})["release"] = platform.release()
|
|
||||||
|
|
||||||
if platform.machine():
|
|
||||||
data["cpu"] = platform.machine()
|
|
||||||
|
|
||||||
if HAS_TLS:
|
|
||||||
data["openssl_version"] = ssl.OPENSSL_VERSION
|
|
||||||
|
|
||||||
setuptools_version = get_installed_version("setuptools")
|
|
||||||
if setuptools_version is not None:
|
|
||||||
data["setuptools_version"] = setuptools_version
|
|
||||||
|
|
||||||
return "{data[installer][name]}/{data[installer][version]} {json}".format(
|
|
||||||
data=data,
|
|
||||||
json=json.dumps(data, separators=(",", ":"), sort_keys=True),
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
class MultiDomainBasicAuth(AuthBase):
|
|
||||||
|
|
||||||
def __init__(self, prompting=True):
|
|
||||||
# type: (bool) -> None
|
|
||||||
self.prompting = prompting
|
|
||||||
self.passwords = {} # type: Dict[str, AuthInfo]
|
|
||||||
|
|
||||||
def __call__(self, req):
|
|
||||||
parsed = urllib_parse.urlparse(req.url)
|
|
||||||
|
|
||||||
# Split the credentials from the netloc.
|
|
||||||
netloc, url_user_password = split_auth_from_netloc(parsed.netloc)
|
|
||||||
|
|
||||||
# Set the url of the request to the url without any credentials
|
|
||||||
req.url = urllib_parse.urlunparse(parsed[:1] + (netloc,) + parsed[2:])
|
|
||||||
|
|
||||||
# Use any stored credentials that we have for this netloc
|
|
||||||
username, password = self.passwords.get(netloc, (None, None))
|
|
||||||
|
|
||||||
# Use the credentials embedded in the url if we have none stored
|
|
||||||
if username is None:
|
|
||||||
username, password = url_user_password
|
|
||||||
|
|
||||||
# Get creds from netrc if we still don't have them
|
|
||||||
if username is None and password is None:
|
|
||||||
netrc_auth = get_netrc_auth(req.url)
|
|
||||||
username, password = netrc_auth if netrc_auth else (None, None)
|
|
||||||
|
|
||||||
if username or password:
|
|
||||||
# Store the username and password
|
|
||||||
self.passwords[netloc] = (username, password)
|
|
||||||
|
|
||||||
# Send the basic auth with this request
|
|
||||||
req = HTTPBasicAuth(username or "", password or "")(req)
|
|
||||||
|
|
||||||
# Attach a hook to handle 401 responses
|
|
||||||
req.register_hook("response", self.handle_401)
|
|
||||||
|
|
||||||
return req
|
|
||||||
|
|
||||||
def handle_401(self, resp, **kwargs):
|
|
||||||
# We only care about 401 responses, anything else we want to just
|
|
||||||
# pass through the actual response
|
|
||||||
if resp.status_code != 401:
|
|
||||||
return resp
|
|
||||||
|
|
||||||
# We are not able to prompt the user so simply return the response
|
|
||||||
if not self.prompting:
|
|
||||||
return resp
|
|
||||||
|
|
||||||
parsed = urllib_parse.urlparse(resp.url)
|
|
||||||
|
|
||||||
# Prompt the user for a new username and password
|
|
||||||
username = six.moves.input("User for %s: " % parsed.netloc)
|
|
||||||
password = getpass.getpass("Password: ")
|
|
||||||
|
|
||||||
# Store the new username and password to use for future requests
|
|
||||||
if username or password:
|
|
||||||
self.passwords[parsed.netloc] = (username, password)
|
|
||||||
|
|
||||||
# Consume content and release the original connection to allow our new
|
|
||||||
# request to reuse the same one.
|
|
||||||
resp.content
|
|
||||||
resp.raw.release_conn()
|
|
||||||
|
|
||||||
# Add our new username and password to the request
|
|
||||||
req = HTTPBasicAuth(username or "", password or "")(resp.request)
|
|
||||||
req.register_hook("response", self.warn_on_401)
|
|
||||||
|
|
||||||
# Send our new request
|
|
||||||
new_resp = resp.connection.send(req, **kwargs)
|
|
||||||
new_resp.history.append(resp)
|
|
||||||
|
|
||||||
return new_resp
|
|
||||||
|
|
||||||
def warn_on_401(self, resp, **kwargs):
|
|
||||||
# warn user that they provided incorrect credentials
|
|
||||||
if resp.status_code == 401:
|
|
||||||
logger.warning('401 Error, Credentials not correct for %s',
|
|
||||||
resp.request.url)
|
|
||||||
|
|
||||||
|
|
||||||
class LocalFSAdapter(BaseAdapter):
|
|
||||||
|
|
||||||
def send(self, request, stream=None, timeout=None, verify=None, cert=None,
|
|
||||||
proxies=None):
|
|
||||||
pathname = url_to_path(request.url)
|
|
||||||
|
|
||||||
resp = Response()
|
|
||||||
resp.status_code = 200
|
|
||||||
resp.url = request.url
|
|
||||||
|
|
||||||
try:
|
|
||||||
stats = os.stat(pathname)
|
|
||||||
except OSError as exc:
|
|
||||||
resp.status_code = 404
|
|
||||||
resp.raw = exc
|
|
||||||
else:
|
|
||||||
modified = email.utils.formatdate(stats.st_mtime, usegmt=True)
|
|
||||||
content_type = mimetypes.guess_type(pathname)[0] or "text/plain"
|
|
||||||
resp.headers = CaseInsensitiveDict({
|
|
||||||
"Content-Type": content_type,
|
|
||||||
"Content-Length": stats.st_size,
|
|
||||||
"Last-Modified": modified,
|
|
||||||
})
|
|
||||||
|
|
||||||
resp.raw = open(pathname, "rb")
|
|
||||||
resp.close = resp.raw.close
|
|
||||||
|
|
||||||
return resp
|
|
||||||
|
|
||||||
def close(self):
|
|
||||||
pass
|
|
||||||
|
|
||||||
|
|
||||||
class SafeFileCache(FileCache):
|
|
||||||
"""
|
|
||||||
A file based cache which is safe to use even when the target directory may
|
|
||||||
not be accessible or writable.
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self, *args, **kwargs):
|
|
||||||
super(SafeFileCache, self).__init__(*args, **kwargs)
|
|
||||||
|
|
||||||
# Check to ensure that the directory containing our cache directory
|
|
||||||
# is owned by the user current executing pip. If it does not exist
|
|
||||||
# we will check the parent directory until we find one that does exist.
|
|
||||||
# If it is not owned by the user executing pip then we will disable
|
|
||||||
# the cache and log a warning.
|
|
||||||
if not check_path_owner(self.directory):
|
|
||||||
logger.warning(
|
|
||||||
"The directory '%s' or its parent directory is not owned by "
|
|
||||||
"the current user and the cache has been disabled. Please "
|
|
||||||
"check the permissions and owner of that directory. If "
|
|
||||||
"executing pip with sudo, you may want sudo's -H flag.",
|
|
||||||
self.directory,
|
|
||||||
)
|
|
||||||
|
|
||||||
# Set our directory to None to disable the Cache
|
|
||||||
self.directory = None
|
|
||||||
|
|
||||||
def get(self, *args, **kwargs):
|
|
||||||
# If we don't have a directory, then the cache should be a no-op.
|
|
||||||
if self.directory is None:
|
|
||||||
return
|
|
||||||
|
|
||||||
try:
|
|
||||||
return super(SafeFileCache, self).get(*args, **kwargs)
|
|
||||||
except (LockError, OSError, IOError):
|
|
||||||
# We intentionally silence this error, if we can't access the cache
|
|
||||||
# then we can just skip caching and process the request as if
|
|
||||||
# caching wasn't enabled.
|
|
||||||
pass
|
|
||||||
|
|
||||||
def set(self, *args, **kwargs):
|
|
||||||
# If we don't have a directory, then the cache should be a no-op.
|
|
||||||
if self.directory is None:
|
|
||||||
return
|
|
||||||
|
|
||||||
try:
|
|
||||||
return super(SafeFileCache, self).set(*args, **kwargs)
|
|
||||||
except (LockError, OSError, IOError):
|
|
||||||
# We intentionally silence this error, if we can't access the cache
|
|
||||||
# then we can just skip caching and process the request as if
|
|
||||||
# caching wasn't enabled.
|
|
||||||
pass
|
|
||||||
|
|
||||||
def delete(self, *args, **kwargs):
|
|
||||||
# If we don't have a directory, then the cache should be a no-op.
|
|
||||||
if self.directory is None:
|
|
||||||
return
|
|
||||||
|
|
||||||
try:
|
|
||||||
return super(SafeFileCache, self).delete(*args, **kwargs)
|
|
||||||
except (LockError, OSError, IOError):
|
|
||||||
# We intentionally silence this error, if we can't access the cache
|
|
||||||
# then we can just skip caching and process the request as if
|
|
||||||
# caching wasn't enabled.
|
|
||||||
pass
|
|
||||||
|
|
||||||
|
|
||||||
class InsecureHTTPAdapter(HTTPAdapter):
|
|
||||||
|
|
||||||
def cert_verify(self, conn, url, verify, cert):
|
|
||||||
conn.cert_reqs = 'CERT_NONE'
|
|
||||||
conn.ca_certs = None
|
|
||||||
|
|
||||||
|
|
||||||
class PipSession(requests.Session):
|
|
||||||
|
|
||||||
timeout = None # type: Optional[int]
|
|
||||||
|
|
||||||
def __init__(self, *args, **kwargs):
|
|
||||||
retries = kwargs.pop("retries", 0)
|
|
||||||
cache = kwargs.pop("cache", None)
|
|
||||||
insecure_hosts = kwargs.pop("insecure_hosts", [])
|
|
||||||
|
|
||||||
super(PipSession, self).__init__(*args, **kwargs)
|
|
||||||
|
|
||||||
# Attach our User Agent to the request
|
|
||||||
self.headers["User-Agent"] = user_agent()
|
|
||||||
|
|
||||||
# Attach our Authentication handler to the session
|
|
||||||
self.auth = MultiDomainBasicAuth()
|
|
||||||
|
|
||||||
# Create our urllib3.Retry instance which will allow us to customize
|
|
||||||
# how we handle retries.
|
|
||||||
retries = urllib3.Retry(
|
|
||||||
# Set the total number of retries that a particular request can
|
|
||||||
# have.
|
|
||||||
total=retries,
|
|
||||||
|
|
||||||
# A 503 error from PyPI typically means that the Fastly -> Origin
|
|
||||||
# connection got interrupted in some way. A 503 error in general
|
|
||||||
# is typically considered a transient error so we'll go ahead and
|
|
||||||
# retry it.
|
|
||||||
# A 500 may indicate transient error in Amazon S3
|
|
||||||
# A 520 or 527 - may indicate transient error in CloudFlare
|
|
||||||
status_forcelist=[500, 503, 520, 527],
|
|
||||||
|
|
||||||
# Add a small amount of back off between failed requests in
|
|
||||||
# order to prevent hammering the service.
|
|
||||||
backoff_factor=0.25,
|
|
||||||
)
|
|
||||||
|
|
||||||
# We want to _only_ cache responses on securely fetched origins. We do
|
|
||||||
# this because we can't validate the response of an insecurely fetched
|
|
||||||
# origin, and we don't want someone to be able to poison the cache and
|
|
||||||
# require manual eviction from the cache to fix it.
|
|
||||||
if cache:
|
|
||||||
secure_adapter = CacheControlAdapter(
|
|
||||||
cache=SafeFileCache(cache, use_dir_lock=True),
|
|
||||||
max_retries=retries,
|
|
||||||
)
|
|
||||||
else:
|
|
||||||
secure_adapter = HTTPAdapter(max_retries=retries)
|
|
||||||
|
|
||||||
# Our Insecure HTTPAdapter disables HTTPS validation. It does not
|
|
||||||
# support caching (see above) so we'll use it for all http:// URLs as
|
|
||||||
# well as any https:// host that we've marked as ignoring TLS errors
|
|
||||||
# for.
|
|
||||||
insecure_adapter = InsecureHTTPAdapter(max_retries=retries)
|
|
||||||
|
|
||||||
self.mount("https://", secure_adapter)
|
|
||||||
self.mount("http://", insecure_adapter)
|
|
||||||
|
|
||||||
# Enable file:// urls
|
|
||||||
self.mount("file://", LocalFSAdapter())
|
|
||||||
|
|
||||||
# We want to use a non-validating adapter for any requests which are
|
|
||||||
# deemed insecure.
|
|
||||||
for host in insecure_hosts:
|
|
||||||
self.mount("https://{}/".format(host), insecure_adapter)
|
|
||||||
|
|
||||||
def request(self, method, url, *args, **kwargs):
|
|
||||||
# Allow setting a default timeout on a session
|
|
||||||
kwargs.setdefault("timeout", self.timeout)
|
|
||||||
|
|
||||||
# Dispatch the actual request
|
|
||||||
return super(PipSession, self).request(method, url, *args, **kwargs)
|
|
||||||
|
|
||||||
|
|
||||||
def get_file_content(url, comes_from=None, session=None):
|
|
||||||
# type: (str, Optional[str], Optional[PipSession]) -> Tuple[str, Text]
|
|
||||||
"""Gets the content of a file; it may be a filename, file: URL, or
|
|
||||||
http: URL. Returns (location, content). Content is unicode.
|
|
||||||
|
|
||||||
:param url: File path or url.
|
|
||||||
:param comes_from: Origin description of requirements.
|
|
||||||
:param session: Instance of pip.download.PipSession.
|
|
||||||
"""
|
|
||||||
if session is None:
|
|
||||||
raise TypeError(
|
|
||||||
"get_file_content() missing 1 required keyword argument: 'session'"
|
|
||||||
)
|
|
||||||
|
|
||||||
match = _scheme_re.search(url)
|
|
||||||
if match:
|
|
||||||
scheme = match.group(1).lower()
|
|
||||||
if (scheme == 'file' and comes_from and
|
|
||||||
comes_from.startswith('http')):
|
|
||||||
raise InstallationError(
|
|
||||||
'Requirements file %s references URL %s, which is local'
|
|
||||||
% (comes_from, url))
|
|
||||||
if scheme == 'file':
|
|
||||||
path = url.split(':', 1)[1]
|
|
||||||
path = path.replace('\\', '/')
|
|
||||||
match = _url_slash_drive_re.match(path)
|
|
||||||
if match:
|
|
||||||
path = match.group(1) + ':' + path.split('|', 1)[1]
|
|
||||||
path = urllib_parse.unquote(path)
|
|
||||||
if path.startswith('/'):
|
|
||||||
path = '/' + path.lstrip('/')
|
|
||||||
url = path
|
|
||||||
else:
|
|
||||||
# FIXME: catch some errors
|
|
||||||
resp = session.get(url)
|
|
||||||
resp.raise_for_status()
|
|
||||||
return resp.url, resp.text
|
|
||||||
try:
|
|
||||||
with open(url, 'rb') as f:
|
|
||||||
content = auto_decode(f.read())
|
|
||||||
except IOError as exc:
|
|
||||||
raise InstallationError(
|
|
||||||
'Could not open requirements file: %s' % str(exc)
|
|
||||||
)
|
|
||||||
return url, content
|
|
||||||
|
|
||||||
|
|
||||||
_scheme_re = re.compile(r'^(http|https|file):', re.I)
|
|
||||||
_url_slash_drive_re = re.compile(r'/*([a-z])\|', re.I)
|
|
||||||
|
|
||||||
|
|
||||||
def is_url(name):
|
|
||||||
# type: (Union[str, Text]) -> bool
|
|
||||||
"""Returns true if the name looks like a URL"""
|
|
||||||
if ':' not in name:
|
|
||||||
return False
|
|
||||||
scheme = name.split(':', 1)[0].lower()
|
|
||||||
return scheme in ['http', 'https', 'file', 'ftp'] + vcs.all_schemes
|
|
||||||
|
|
||||||
|
|
||||||
def url_to_path(url):
|
|
||||||
# type: (str) -> str
|
|
||||||
"""
|
|
||||||
Convert a file: URL to a path.
|
|
||||||
"""
|
|
||||||
assert url.startswith('file:'), (
|
|
||||||
"You can only turn file: urls into filenames (not %r)" % url)
|
|
||||||
|
|
||||||
_, netloc, path, _, _ = urllib_parse.urlsplit(url)
|
|
||||||
|
|
||||||
# if we have a UNC path, prepend UNC share notation
|
|
||||||
if netloc:
|
|
||||||
netloc = '\\\\' + netloc
|
|
||||||
|
|
||||||
path = urllib_request.url2pathname(netloc + path)
|
|
||||||
return path
|
|
||||||
|
|
||||||
|
|
||||||
def path_to_url(path):
|
|
||||||
# type: (Union[str, Text]) -> str
|
|
||||||
"""
|
|
||||||
Convert a path to a file: URL. The path will be made absolute and have
|
|
||||||
quoted path parts.
|
|
||||||
"""
|
|
||||||
path = os.path.normpath(os.path.abspath(path))
|
|
||||||
url = urllib_parse.urljoin('file:', urllib_request.pathname2url(path))
|
|
||||||
return url
|
|
||||||
|
|
||||||
|
|
||||||
def is_archive_file(name):
|
|
||||||
# type: (str) -> bool
|
|
||||||
"""Return True if `name` is a considered as an archive file."""
|
|
||||||
ext = splitext(name)[1].lower()
|
|
||||||
if ext in ARCHIVE_EXTENSIONS:
|
|
||||||
return True
|
|
||||||
return False
|
|
||||||
|
|
||||||
|
|
||||||
def unpack_vcs_link(link, location):
|
|
||||||
vcs_backend = _get_used_vcs_backend(link)
|
|
||||||
vcs_backend.unpack(location)
|
|
||||||
|
|
||||||
|
|
||||||
def _get_used_vcs_backend(link):
|
|
||||||
for backend in vcs.backends:
|
|
||||||
if link.scheme in backend.schemes:
|
|
||||||
vcs_backend = backend(link.url)
|
|
||||||
return vcs_backend
|
|
||||||
|
|
||||||
|
|
||||||
def is_vcs_url(link):
|
|
||||||
# type: (Link) -> bool
|
|
||||||
return bool(_get_used_vcs_backend(link))
|
|
||||||
|
|
||||||
|
|
||||||
def is_file_url(link):
|
|
||||||
# type: (Link) -> bool
|
|
||||||
return link.url.lower().startswith('file:')
|
|
||||||
|
|
||||||
|
|
||||||
def is_dir_url(link):
|
|
||||||
# type: (Link) -> bool
|
|
||||||
"""Return whether a file:// Link points to a directory.
|
|
||||||
|
|
||||||
``link`` must not have any other scheme but file://. Call is_file_url()
|
|
||||||
first.
|
|
||||||
|
|
||||||
"""
|
|
||||||
link_path = url_to_path(link.url_without_fragment)
|
|
||||||
return os.path.isdir(link_path)
|
|
||||||
|
|
||||||
|
|
||||||
def _progress_indicator(iterable, *args, **kwargs):
|
|
||||||
return iterable
|
|
||||||
|
|
||||||
|
|
||||||
def _download_url(
|
|
||||||
resp, # type: Response
|
|
||||||
link, # type: Link
|
|
||||||
content_file, # type: IO
|
|
||||||
hashes, # type: Hashes
|
|
||||||
progress_bar # type: str
|
|
||||||
):
|
|
||||||
# type: (...) -> None
|
|
||||||
try:
|
|
||||||
total_length = int(resp.headers['content-length'])
|
|
||||||
except (ValueError, KeyError, TypeError):
|
|
||||||
total_length = 0
|
|
||||||
|
|
||||||
cached_resp = getattr(resp, "from_cache", False)
|
|
||||||
if logger.getEffectiveLevel() > logging.INFO:
|
|
||||||
show_progress = False
|
|
||||||
elif cached_resp:
|
|
||||||
show_progress = False
|
|
||||||
elif total_length > (40 * 1000):
|
|
||||||
show_progress = True
|
|
||||||
elif not total_length:
|
|
||||||
show_progress = True
|
|
||||||
else:
|
|
||||||
show_progress = False
|
|
||||||
|
|
||||||
show_url = link.show_url
|
|
||||||
|
|
||||||
def resp_read(chunk_size):
|
|
||||||
try:
|
|
||||||
# Special case for urllib3.
|
|
||||||
for chunk in resp.raw.stream(
|
|
||||||
chunk_size,
|
|
||||||
# We use decode_content=False here because we don't
|
|
||||||
# want urllib3 to mess with the raw bytes we get
|
|
||||||
# from the server. If we decompress inside of
|
|
||||||
# urllib3 then we cannot verify the checksum
|
|
||||||
# because the checksum will be of the compressed
|
|
||||||
# file. This breakage will only occur if the
|
|
||||||
# server adds a Content-Encoding header, which
|
|
||||||
# depends on how the server was configured:
|
|
||||||
# - Some servers will notice that the file isn't a
|
|
||||||
# compressible file and will leave the file alone
|
|
||||||
# and with an empty Content-Encoding
|
|
||||||
# - Some servers will notice that the file is
|
|
||||||
# already compressed and will leave the file
|
|
||||||
# alone and will add a Content-Encoding: gzip
|
|
||||||
# header
|
|
||||||
# - Some servers won't notice anything at all and
|
|
||||||
# will take a file that's already been compressed
|
|
||||||
# and compress it again and set the
|
|
||||||
# Content-Encoding: gzip header
|
|
||||||
#
|
|
||||||
# By setting this not to decode automatically we
|
|
||||||
# hope to eliminate problems with the second case.
|
|
||||||
decode_content=False):
|
|
||||||
yield chunk
|
|
||||||
except AttributeError:
|
|
||||||
# Standard file-like object.
|
|
||||||
while True:
|
|
||||||
chunk = resp.raw.read(chunk_size)
|
|
||||||
if not chunk:
|
|
||||||
break
|
|
||||||
yield chunk
|
|
||||||
|
|
||||||
def written_chunks(chunks):
|
|
||||||
for chunk in chunks:
|
|
||||||
content_file.write(chunk)
|
|
||||||
yield chunk
|
|
||||||
|
|
||||||
progress_indicator = _progress_indicator
|
|
||||||
|
|
||||||
if link.netloc == PyPI.netloc:
|
|
||||||
url = show_url
|
|
||||||
else:
|
|
||||||
url = link.url_without_fragment
|
|
||||||
|
|
||||||
if show_progress: # We don't show progress on cached responses
|
|
||||||
progress_indicator = DownloadProgressProvider(progress_bar,
|
|
||||||
max=total_length)
|
|
||||||
if total_length:
|
|
||||||
logger.info("Downloading %s (%s)", url, format_size(total_length))
|
|
||||||
else:
|
|
||||||
logger.info("Downloading %s", url)
|
|
||||||
elif cached_resp:
|
|
||||||
logger.info("Using cached %s", url)
|
|
||||||
else:
|
|
||||||
logger.info("Downloading %s", url)
|
|
||||||
|
|
||||||
logger.debug('Downloading from URL %s', link)
|
|
||||||
|
|
||||||
downloaded_chunks = written_chunks(
|
|
||||||
progress_indicator(
|
|
||||||
resp_read(CONTENT_CHUNK_SIZE),
|
|
||||||
CONTENT_CHUNK_SIZE
|
|
||||||
)
|
|
||||||
)
|
|
||||||
if hashes:
|
|
||||||
hashes.check_against_chunks(downloaded_chunks)
|
|
||||||
else:
|
|
||||||
consume(downloaded_chunks)
|
|
||||||
|
|
||||||
|
|
||||||
def _copy_file(filename, location, link):
|
|
||||||
copy = True
|
|
||||||
download_location = os.path.join(location, link.filename)
|
|
||||||
if os.path.exists(download_location):
|
|
||||||
response = ask_path_exists(
|
|
||||||
'The file %s exists. (i)gnore, (w)ipe, (b)ackup, (a)abort' %
|
|
||||||
display_path(download_location), ('i', 'w', 'b', 'a'))
|
|
||||||
if response == 'i':
|
|
||||||
copy = False
|
|
||||||
elif response == 'w':
|
|
||||||
logger.warning('Deleting %s', display_path(download_location))
|
|
||||||
os.remove(download_location)
|
|
||||||
elif response == 'b':
|
|
||||||
dest_file = backup_dir(download_location)
|
|
||||||
logger.warning(
|
|
||||||
'Backing up %s to %s',
|
|
||||||
display_path(download_location),
|
|
||||||
display_path(dest_file),
|
|
||||||
)
|
|
||||||
shutil.move(download_location, dest_file)
|
|
||||||
elif response == 'a':
|
|
||||||
sys.exit(-1)
|
|
||||||
if copy:
|
|
||||||
shutil.copy(filename, download_location)
|
|
||||||
logger.info('Saved %s', display_path(download_location))
|
|
||||||
|
|
||||||
|
|
||||||
def unpack_http_url(
|
|
||||||
link, # type: Link
|
|
||||||
location, # type: str
|
|
||||||
download_dir=None, # type: Optional[str]
|
|
||||||
session=None, # type: Optional[PipSession]
|
|
||||||
hashes=None, # type: Optional[Hashes]
|
|
||||||
progress_bar="on" # type: str
|
|
||||||
):
|
|
||||||
# type: (...) -> None
|
|
||||||
if session is None:
|
|
||||||
raise TypeError(
|
|
||||||
"unpack_http_url() missing 1 required keyword argument: 'session'"
|
|
||||||
)
|
|
||||||
|
|
||||||
with TempDirectory(kind="unpack") as temp_dir:
|
|
||||||
# If a download dir is specified, is the file already downloaded there?
|
|
||||||
already_downloaded_path = None
|
|
||||||
if download_dir:
|
|
||||||
already_downloaded_path = _check_download_dir(link,
|
|
||||||
download_dir,
|
|
||||||
hashes)
|
|
||||||
|
|
||||||
if already_downloaded_path:
|
|
||||||
from_path = already_downloaded_path
|
|
||||||
content_type = mimetypes.guess_type(from_path)[0]
|
|
||||||
else:
|
|
||||||
# let's download to a tmp dir
|
|
||||||
from_path, content_type = _download_http_url(link,
|
|
||||||
session,
|
|
||||||
temp_dir.path,
|
|
||||||
hashes,
|
|
||||||
progress_bar)
|
|
||||||
|
|
||||||
# unpack the archive to the build dir location. even when only
|
|
||||||
# downloading archives, they have to be unpacked to parse dependencies
|
|
||||||
unpack_file(from_path, location, content_type, link)
|
|
||||||
|
|
||||||
# a download dir is specified; let's copy the archive there
|
|
||||||
if download_dir and not already_downloaded_path:
|
|
||||||
_copy_file(from_path, download_dir, link)
|
|
||||||
|
|
||||||
if not already_downloaded_path:
|
|
||||||
os.unlink(from_path)
|
|
||||||
|
|
||||||
|
|
||||||
def unpack_file_url(
|
|
||||||
link, # type: Link
|
|
||||||
location, # type: str
|
|
||||||
download_dir=None, # type: Optional[str]
|
|
||||||
hashes=None # type: Optional[Hashes]
|
|
||||||
):
|
|
||||||
# type: (...) -> None
|
|
||||||
"""Unpack link into location.
|
|
||||||
|
|
||||||
If download_dir is provided and link points to a file, make a copy
|
|
||||||
of the link file inside download_dir.
|
|
||||||
"""
|
|
||||||
link_path = url_to_path(link.url_without_fragment)
|
|
||||||
|
|
||||||
# If it's a url to a local directory
|
|
||||||
if is_dir_url(link):
|
|
||||||
if os.path.isdir(location):
|
|
||||||
rmtree(location)
|
|
||||||
shutil.copytree(link_path, location, symlinks=True)
|
|
||||||
if download_dir:
|
|
||||||
logger.info('Link is a directory, ignoring download_dir')
|
|
||||||
return
|
|
||||||
|
|
||||||
# If --require-hashes is off, `hashes` is either empty, the
|
|
||||||
# link's embedded hash, or MissingHashes; it is required to
|
|
||||||
# match. If --require-hashes is on, we are satisfied by any
|
|
||||||
# hash in `hashes` matching: a URL-based or an option-based
|
|
||||||
# one; no internet-sourced hash will be in `hashes`.
|
|
||||||
if hashes:
|
|
||||||
hashes.check_against_path(link_path)
|
|
||||||
|
|
||||||
# If a download dir is specified, is the file already there and valid?
|
|
||||||
already_downloaded_path = None
|
|
||||||
if download_dir:
|
|
||||||
already_downloaded_path = _check_download_dir(link,
|
|
||||||
download_dir,
|
|
||||||
hashes)
|
|
||||||
|
|
||||||
if already_downloaded_path:
|
|
||||||
from_path = already_downloaded_path
|
|
||||||
else:
|
|
||||||
from_path = link_path
|
|
||||||
|
|
||||||
content_type = mimetypes.guess_type(from_path)[0]
|
|
||||||
|
|
||||||
# unpack the archive to the build dir location. even when only downloading
|
|
||||||
# archives, they have to be unpacked to parse dependencies
|
|
||||||
unpack_file(from_path, location, content_type, link)
|
|
||||||
|
|
||||||
# a download dir is specified and not already downloaded
|
|
||||||
if download_dir and not already_downloaded_path:
|
|
||||||
_copy_file(from_path, download_dir, link)
|
|
||||||
|
|
||||||
|
|
||||||
def _copy_dist_from_dir(link_path, location):
|
|
||||||
"""Copy distribution files in `link_path` to `location`.
|
|
||||||
|
|
||||||
Invoked when user requests to install a local directory. E.g.:
|
|
||||||
|
|
||||||
pip install .
|
|
||||||
pip install ~/dev/git-repos/python-prompt-toolkit
|
|
||||||
|
|
||||||
"""
|
|
||||||
|
|
||||||
# Note: This is currently VERY SLOW if you have a lot of data in the
|
|
||||||
# directory, because it copies everything with `shutil.copytree`.
|
|
||||||
# What it should really do is build an sdist and install that.
|
|
||||||
# See https://github.com/pypa/pip/issues/2195
|
|
||||||
|
|
||||||
if os.path.isdir(location):
|
|
||||||
rmtree(location)
|
|
||||||
|
|
||||||
# build an sdist
|
|
||||||
setup_py = 'setup.py'
|
|
||||||
sdist_args = [sys.executable]
|
|
||||||
sdist_args.append('-c')
|
|
||||||
sdist_args.append(SETUPTOOLS_SHIM % setup_py)
|
|
||||||
sdist_args.append('sdist')
|
|
||||||
sdist_args += ['--dist-dir', location]
|
|
||||||
logger.info('Running setup.py sdist for %s', link_path)
|
|
||||||
|
|
||||||
with indent_log():
|
|
||||||
call_subprocess(sdist_args, cwd=link_path, show_stdout=False)
|
|
||||||
|
|
||||||
# unpack sdist into `location`
|
|
||||||
sdist = os.path.join(location, os.listdir(location)[0])
|
|
||||||
logger.info('Unpacking sdist %s into %s', sdist, location)
|
|
||||||
unpack_file(sdist, location, content_type=None, link=None)
|
|
||||||
|
|
||||||
|
|
||||||
class PipXmlrpcTransport(xmlrpc_client.Transport):
|
|
||||||
"""Provide a `xmlrpclib.Transport` implementation via a `PipSession`
|
|
||||||
object.
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self, index_url, session, use_datetime=False):
|
|
||||||
xmlrpc_client.Transport.__init__(self, use_datetime)
|
|
||||||
index_parts = urllib_parse.urlparse(index_url)
|
|
||||||
self._scheme = index_parts.scheme
|
|
||||||
self._session = session
|
|
||||||
|
|
||||||
def request(self, host, handler, request_body, verbose=False):
|
|
||||||
parts = (self._scheme, host, handler, None, None, None)
|
|
||||||
url = urllib_parse.urlunparse(parts)
|
|
||||||
try:
|
|
||||||
headers = {'Content-Type': 'text/xml'}
|
|
||||||
response = self._session.post(url, data=request_body,
|
|
||||||
headers=headers, stream=True)
|
|
||||||
response.raise_for_status()
|
|
||||||
self.verbose = verbose
|
|
||||||
return self.parse_response(response.raw)
|
|
||||||
except requests.HTTPError as exc:
|
|
||||||
logger.critical(
|
|
||||||
"HTTP error %s while getting %s",
|
|
||||||
exc.response.status_code, url,
|
|
||||||
)
|
|
||||||
raise
|
|
||||||
|
|
||||||
|
|
||||||
def unpack_url(
|
|
||||||
link, # type: Optional[Link]
|
|
||||||
location, # type: Optional[str]
|
|
||||||
download_dir=None, # type: Optional[str]
|
|
||||||
only_download=False, # type: bool
|
|
||||||
session=None, # type: Optional[PipSession]
|
|
||||||
hashes=None, # type: Optional[Hashes]
|
|
||||||
progress_bar="on" # type: str
|
|
||||||
):
|
|
||||||
# type: (...) -> None
|
|
||||||
"""Unpack link.
|
|
||||||
If link is a VCS link:
|
|
||||||
if only_download, export into download_dir and ignore location
|
|
||||||
else unpack into location
|
|
||||||
for other types of link:
|
|
||||||
- unpack into location
|
|
||||||
- if download_dir, copy the file into download_dir
|
|
||||||
- if only_download, mark location for deletion
|
|
||||||
|
|
||||||
:param hashes: A Hashes object, one of whose embedded hashes must match,
|
|
||||||
or HashMismatch will be raised. If the Hashes is empty, no matches are
|
|
||||||
required, and unhashable types of requirements (like VCS ones, which
|
|
||||||
would ordinarily raise HashUnsupported) are allowed.
|
|
||||||
"""
|
|
||||||
# non-editable vcs urls
|
|
||||||
if is_vcs_url(link):
|
|
||||||
unpack_vcs_link(link, location)
|
|
||||||
|
|
||||||
# file urls
|
|
||||||
elif is_file_url(link):
|
|
||||||
unpack_file_url(link, location, download_dir, hashes=hashes)
|
|
||||||
|
|
||||||
# http urls
|
|
||||||
else:
|
|
||||||
if session is None:
|
|
||||||
session = PipSession()
|
|
||||||
|
|
||||||
unpack_http_url(
|
|
||||||
link,
|
|
||||||
location,
|
|
||||||
download_dir,
|
|
||||||
session,
|
|
||||||
hashes=hashes,
|
|
||||||
progress_bar=progress_bar
|
|
||||||
)
|
|
||||||
if only_download:
|
|
||||||
write_delete_marker_file(location)
|
|
||||||
|
|
||||||
|
|
||||||
def _download_http_url(
|
|
||||||
link, # type: Link
|
|
||||||
session, # type: PipSession
|
|
||||||
temp_dir, # type: str
|
|
||||||
hashes, # type: Hashes
|
|
||||||
progress_bar # type: str
|
|
||||||
):
|
|
||||||
# type: (...) -> Tuple[str, str]
|
|
||||||
"""Download link url into temp_dir using provided session"""
|
|
||||||
target_url = link.url.split('#', 1)[0]
|
|
||||||
try:
|
|
||||||
resp = session.get(
|
|
||||||
target_url,
|
|
||||||
# We use Accept-Encoding: identity here because requests
|
|
||||||
# defaults to accepting compressed responses. This breaks in
|
|
||||||
# a variety of ways depending on how the server is configured.
|
|
||||||
# - Some servers will notice that the file isn't a compressible
|
|
||||||
# file and will leave the file alone and with an empty
|
|
||||||
# Content-Encoding
|
|
||||||
# - Some servers will notice that the file is already
|
|
||||||
# compressed and will leave the file alone and will add a
|
|
||||||
# Content-Encoding: gzip header
|
|
||||||
# - Some servers won't notice anything at all and will take
|
|
||||||
# a file that's already been compressed and compress it again
|
|
||||||
# and set the Content-Encoding: gzip header
|
|
||||||
# By setting this to request only the identity encoding We're
|
|
||||||
# hoping to eliminate the third case. Hopefully there does not
|
|
||||||
# exist a server which when given a file will notice it is
|
|
||||||
# already compressed and that you're not asking for a
|
|
||||||
# compressed file and will then decompress it before sending
|
|
||||||
# because if that's the case I don't think it'll ever be
|
|
||||||
# possible to make this work.
|
|
||||||
headers={"Accept-Encoding": "identity"},
|
|
||||||
stream=True,
|
|
||||||
)
|
|
||||||
resp.raise_for_status()
|
|
||||||
except requests.HTTPError as exc:
|
|
||||||
logger.critical(
|
|
||||||
"HTTP error %s while getting %s", exc.response.status_code, link,
|
|
||||||
)
|
|
||||||
raise
|
|
||||||
|
|
||||||
content_type = resp.headers.get('content-type', '')
|
|
||||||
filename = link.filename # fallback
|
|
||||||
# Have a look at the Content-Disposition header for a better guess
|
|
||||||
content_disposition = resp.headers.get('content-disposition')
|
|
||||||
if content_disposition:
|
|
||||||
type, params = cgi.parse_header(content_disposition)
|
|
||||||
# We use ``or`` here because we don't want to use an "empty" value
|
|
||||||
# from the filename param.
|
|
||||||
filename = params.get('filename') or filename
|
|
||||||
ext = splitext(filename)[1]
|
|
||||||
if not ext:
|
|
||||||
ext = mimetypes.guess_extension(content_type)
|
|
||||||
if ext:
|
|
||||||
filename += ext
|
|
||||||
if not ext and link.url != resp.url:
|
|
||||||
ext = os.path.splitext(resp.url)[1]
|
|
||||||
if ext:
|
|
||||||
filename += ext
|
|
||||||
file_path = os.path.join(temp_dir, filename)
|
|
||||||
with open(file_path, 'wb') as content_file:
|
|
||||||
_download_url(resp, link, content_file, hashes, progress_bar)
|
|
||||||
return file_path, content_type
|
|
||||||
|
|
||||||
|
|
||||||
def _check_download_dir(link, download_dir, hashes):
|
|
||||||
# type: (Link, str, Hashes) -> Optional[str]
|
|
||||||
""" Check download_dir for previously downloaded file with correct hash
|
|
||||||
If a correct file is found return its path else None
|
|
||||||
"""
|
|
||||||
download_path = os.path.join(download_dir, link.filename)
|
|
||||||
if os.path.exists(download_path):
|
|
||||||
# If already downloaded, does its hash match?
|
|
||||||
logger.info('File was already downloaded %s', download_path)
|
|
||||||
if hashes:
|
|
||||||
try:
|
|
||||||
hashes.check_against_path(download_path)
|
|
||||||
except HashMismatch:
|
|
||||||
logger.warning(
|
|
||||||
'Previously-downloaded file %s has bad hash. '
|
|
||||||
'Re-downloading.',
|
|
||||||
download_path
|
|
||||||
)
|
|
||||||
os.unlink(download_path)
|
|
||||||
return None
|
|
||||||
return download_path
|
|
||||||
return None
|
|
||||||
@@ -1,274 +0,0 @@
|
|||||||
"""Exceptions used throughout package"""
|
|
||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
from itertools import chain, groupby, repeat
|
|
||||||
|
|
||||||
from pip._vendor.six import iteritems
|
|
||||||
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from typing import Optional # noqa: F401
|
|
||||||
from pip._internal.req.req_install import InstallRequirement # noqa: F401
|
|
||||||
|
|
||||||
|
|
||||||
class PipError(Exception):
|
|
||||||
"""Base pip exception"""
|
|
||||||
|
|
||||||
|
|
||||||
class ConfigurationError(PipError):
|
|
||||||
"""General exception in configuration"""
|
|
||||||
|
|
||||||
|
|
||||||
class InstallationError(PipError):
|
|
||||||
"""General exception during installation"""
|
|
||||||
|
|
||||||
|
|
||||||
class UninstallationError(PipError):
|
|
||||||
"""General exception during uninstallation"""
|
|
||||||
|
|
||||||
|
|
||||||
class DistributionNotFound(InstallationError):
|
|
||||||
"""Raised when a distribution cannot be found to satisfy a requirement"""
|
|
||||||
|
|
||||||
|
|
||||||
class RequirementsFileParseError(InstallationError):
|
|
||||||
"""Raised when a general error occurs parsing a requirements file line."""
|
|
||||||
|
|
||||||
|
|
||||||
class BestVersionAlreadyInstalled(PipError):
|
|
||||||
"""Raised when the most up-to-date version of a package is already
|
|
||||||
installed."""
|
|
||||||
|
|
||||||
|
|
||||||
class BadCommand(PipError):
|
|
||||||
"""Raised when virtualenv or a command is not found"""
|
|
||||||
|
|
||||||
|
|
||||||
class CommandError(PipError):
|
|
||||||
"""Raised when there is an error in command-line arguments"""
|
|
||||||
|
|
||||||
|
|
||||||
class PreviousBuildDirError(PipError):
|
|
||||||
"""Raised when there's a previous conflicting build directory"""
|
|
||||||
|
|
||||||
|
|
||||||
class InvalidWheelFilename(InstallationError):
|
|
||||||
"""Invalid wheel filename."""
|
|
||||||
|
|
||||||
|
|
||||||
class UnsupportedWheel(InstallationError):
|
|
||||||
"""Unsupported wheel."""
|
|
||||||
|
|
||||||
|
|
||||||
class HashErrors(InstallationError):
|
|
||||||
"""Multiple HashError instances rolled into one for reporting"""
|
|
||||||
|
|
||||||
def __init__(self):
|
|
||||||
self.errors = []
|
|
||||||
|
|
||||||
def append(self, error):
|
|
||||||
self.errors.append(error)
|
|
||||||
|
|
||||||
def __str__(self):
|
|
||||||
lines = []
|
|
||||||
self.errors.sort(key=lambda e: e.order)
|
|
||||||
for cls, errors_of_cls in groupby(self.errors, lambda e: e.__class__):
|
|
||||||
lines.append(cls.head)
|
|
||||||
lines.extend(e.body() for e in errors_of_cls)
|
|
||||||
if lines:
|
|
||||||
return '\n'.join(lines)
|
|
||||||
|
|
||||||
def __nonzero__(self):
|
|
||||||
return bool(self.errors)
|
|
||||||
|
|
||||||
def __bool__(self):
|
|
||||||
return self.__nonzero__()
|
|
||||||
|
|
||||||
|
|
||||||
class HashError(InstallationError):
|
|
||||||
"""
|
|
||||||
A failure to verify a package against known-good hashes
|
|
||||||
|
|
||||||
:cvar order: An int sorting hash exception classes by difficulty of
|
|
||||||
recovery (lower being harder), so the user doesn't bother fretting
|
|
||||||
about unpinned packages when he has deeper issues, like VCS
|
|
||||||
dependencies, to deal with. Also keeps error reports in a
|
|
||||||
deterministic order.
|
|
||||||
:cvar head: A section heading for display above potentially many
|
|
||||||
exceptions of this kind
|
|
||||||
:ivar req: The InstallRequirement that triggered this error. This is
|
|
||||||
pasted on after the exception is instantiated, because it's not
|
|
||||||
typically available earlier.
|
|
||||||
|
|
||||||
"""
|
|
||||||
req = None # type: Optional[InstallRequirement]
|
|
||||||
head = ''
|
|
||||||
|
|
||||||
def body(self):
|
|
||||||
"""Return a summary of me for display under the heading.
|
|
||||||
|
|
||||||
This default implementation simply prints a description of the
|
|
||||||
triggering requirement.
|
|
||||||
|
|
||||||
:param req: The InstallRequirement that provoked this error, with
|
|
||||||
populate_link() having already been called
|
|
||||||
|
|
||||||
"""
|
|
||||||
return ' %s' % self._requirement_name()
|
|
||||||
|
|
||||||
def __str__(self):
|
|
||||||
return '%s\n%s' % (self.head, self.body())
|
|
||||||
|
|
||||||
def _requirement_name(self):
|
|
||||||
"""Return a description of the requirement that triggered me.
|
|
||||||
|
|
||||||
This default implementation returns long description of the req, with
|
|
||||||
line numbers
|
|
||||||
|
|
||||||
"""
|
|
||||||
return str(self.req) if self.req else 'unknown package'
|
|
||||||
|
|
||||||
|
|
||||||
class VcsHashUnsupported(HashError):
|
|
||||||
"""A hash was provided for a version-control-system-based requirement, but
|
|
||||||
we don't have a method for hashing those."""
|
|
||||||
|
|
||||||
order = 0
|
|
||||||
head = ("Can't verify hashes for these requirements because we don't "
|
|
||||||
"have a way to hash version control repositories:")
|
|
||||||
|
|
||||||
|
|
||||||
class DirectoryUrlHashUnsupported(HashError):
|
|
||||||
"""A hash was provided for a version-control-system-based requirement, but
|
|
||||||
we don't have a method for hashing those."""
|
|
||||||
|
|
||||||
order = 1
|
|
||||||
head = ("Can't verify hashes for these file:// requirements because they "
|
|
||||||
"point to directories:")
|
|
||||||
|
|
||||||
|
|
||||||
class HashMissing(HashError):
|
|
||||||
"""A hash was needed for a requirement but is absent."""
|
|
||||||
|
|
||||||
order = 2
|
|
||||||
head = ('Hashes are required in --require-hashes mode, but they are '
|
|
||||||
'missing from some requirements. Here is a list of those '
|
|
||||||
'requirements along with the hashes their downloaded archives '
|
|
||||||
'actually had. Add lines like these to your requirements files to '
|
|
||||||
'prevent tampering. (If you did not enable --require-hashes '
|
|
||||||
'manually, note that it turns on automatically when any package '
|
|
||||||
'has a hash.)')
|
|
||||||
|
|
||||||
def __init__(self, gotten_hash):
|
|
||||||
"""
|
|
||||||
:param gotten_hash: The hash of the (possibly malicious) archive we
|
|
||||||
just downloaded
|
|
||||||
"""
|
|
||||||
self.gotten_hash = gotten_hash
|
|
||||||
|
|
||||||
def body(self):
|
|
||||||
# Dodge circular import.
|
|
||||||
from pip._internal.utils.hashes import FAVORITE_HASH
|
|
||||||
|
|
||||||
package = None
|
|
||||||
if self.req:
|
|
||||||
# In the case of URL-based requirements, display the original URL
|
|
||||||
# seen in the requirements file rather than the package name,
|
|
||||||
# so the output can be directly copied into the requirements file.
|
|
||||||
package = (self.req.original_link if self.req.original_link
|
|
||||||
# In case someone feeds something downright stupid
|
|
||||||
# to InstallRequirement's constructor.
|
|
||||||
else getattr(self.req, 'req', None))
|
|
||||||
return ' %s --hash=%s:%s' % (package or 'unknown package',
|
|
||||||
FAVORITE_HASH,
|
|
||||||
self.gotten_hash)
|
|
||||||
|
|
||||||
|
|
||||||
class HashUnpinned(HashError):
|
|
||||||
"""A requirement had a hash specified but was not pinned to a specific
|
|
||||||
version."""
|
|
||||||
|
|
||||||
order = 3
|
|
||||||
head = ('In --require-hashes mode, all requirements must have their '
|
|
||||||
'versions pinned with ==. These do not:')
|
|
||||||
|
|
||||||
|
|
||||||
class HashMismatch(HashError):
|
|
||||||
"""
|
|
||||||
Distribution file hash values don't match.
|
|
||||||
|
|
||||||
:ivar package_name: The name of the package that triggered the hash
|
|
||||||
mismatch. Feel free to write to this after the exception is raise to
|
|
||||||
improve its error message.
|
|
||||||
|
|
||||||
"""
|
|
||||||
order = 4
|
|
||||||
head = ('THESE PACKAGES DO NOT MATCH THE HASHES FROM THE REQUIREMENTS '
|
|
||||||
'FILE. If you have updated the package versions, please update '
|
|
||||||
'the hashes. Otherwise, examine the package contents carefully; '
|
|
||||||
'someone may have tampered with them.')
|
|
||||||
|
|
||||||
def __init__(self, allowed, gots):
|
|
||||||
"""
|
|
||||||
:param allowed: A dict of algorithm names pointing to lists of allowed
|
|
||||||
hex digests
|
|
||||||
:param gots: A dict of algorithm names pointing to hashes we
|
|
||||||
actually got from the files under suspicion
|
|
||||||
"""
|
|
||||||
self.allowed = allowed
|
|
||||||
self.gots = gots
|
|
||||||
|
|
||||||
def body(self):
|
|
||||||
return ' %s:\n%s' % (self._requirement_name(),
|
|
||||||
self._hash_comparison())
|
|
||||||
|
|
||||||
def _hash_comparison(self):
|
|
||||||
"""
|
|
||||||
Return a comparison of actual and expected hash values.
|
|
||||||
|
|
||||||
Example::
|
|
||||||
|
|
||||||
Expected sha256 abcdeabcdeabcdeabcdeabcdeabcdeabcdeabcdeabcde
|
|
||||||
or 123451234512345123451234512345123451234512345
|
|
||||||
Got bcdefbcdefbcdefbcdefbcdefbcdefbcdefbcdefbcdef
|
|
||||||
|
|
||||||
"""
|
|
||||||
def hash_then_or(hash_name):
|
|
||||||
# For now, all the decent hashes have 6-char names, so we can get
|
|
||||||
# away with hard-coding space literals.
|
|
||||||
return chain([hash_name], repeat(' or'))
|
|
||||||
|
|
||||||
lines = []
|
|
||||||
for hash_name, expecteds in iteritems(self.allowed):
|
|
||||||
prefix = hash_then_or(hash_name)
|
|
||||||
lines.extend((' Expected %s %s' % (next(prefix), e))
|
|
||||||
for e in expecteds)
|
|
||||||
lines.append(' Got %s\n' %
|
|
||||||
self.gots[hash_name].hexdigest())
|
|
||||||
prefix = ' or'
|
|
||||||
return '\n'.join(lines)
|
|
||||||
|
|
||||||
|
|
||||||
class UnsupportedPythonVersion(InstallationError):
|
|
||||||
"""Unsupported python version according to Requires-Python package
|
|
||||||
metadata."""
|
|
||||||
|
|
||||||
|
|
||||||
class ConfigurationFileCouldNotBeLoaded(ConfigurationError):
|
|
||||||
"""When there are errors while loading a configuration file
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self, reason="could not be loaded", fname=None, error=None):
|
|
||||||
super(ConfigurationFileCouldNotBeLoaded, self).__init__(error)
|
|
||||||
self.reason = reason
|
|
||||||
self.fname = fname
|
|
||||||
self.error = error
|
|
||||||
|
|
||||||
def __str__(self):
|
|
||||||
if self.fname is not None:
|
|
||||||
message_part = " in {}.".format(self.fname)
|
|
||||||
else:
|
|
||||||
assert self.error is not None
|
|
||||||
message_part = ".\n{}\n".format(self.error.message)
|
|
||||||
return "Configuration file {}{}".format(self.reason, message_part)
|
|
||||||
@@ -1,990 +0,0 @@
|
|||||||
"""Routines related to PyPI, indexes"""
|
|
||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import cgi
|
|
||||||
import itertools
|
|
||||||
import logging
|
|
||||||
import mimetypes
|
|
||||||
import os
|
|
||||||
import posixpath
|
|
||||||
import re
|
|
||||||
import sys
|
|
||||||
from collections import namedtuple
|
|
||||||
|
|
||||||
from pip._vendor import html5lib, requests, six
|
|
||||||
from pip._vendor.distlib.compat import unescape
|
|
||||||
from pip._vendor.packaging import specifiers
|
|
||||||
from pip._vendor.packaging.utils import canonicalize_name
|
|
||||||
from pip._vendor.packaging.version import parse as parse_version
|
|
||||||
from pip._vendor.requests.exceptions import RetryError, SSLError
|
|
||||||
from pip._vendor.six.moves.urllib import parse as urllib_parse
|
|
||||||
from pip._vendor.six.moves.urllib import request as urllib_request
|
|
||||||
|
|
||||||
from pip._internal.download import HAS_TLS, is_url, path_to_url, url_to_path
|
|
||||||
from pip._internal.exceptions import (
|
|
||||||
BestVersionAlreadyInstalled, DistributionNotFound, InvalidWheelFilename,
|
|
||||||
UnsupportedWheel,
|
|
||||||
)
|
|
||||||
from pip._internal.models.candidate import InstallationCandidate
|
|
||||||
from pip._internal.models.format_control import FormatControl
|
|
||||||
from pip._internal.models.index import PyPI
|
|
||||||
from pip._internal.models.link import Link
|
|
||||||
from pip._internal.pep425tags import get_supported
|
|
||||||
from pip._internal.utils.compat import ipaddress
|
|
||||||
from pip._internal.utils.logging import indent_log
|
|
||||||
from pip._internal.utils.misc import (
|
|
||||||
ARCHIVE_EXTENSIONS, SUPPORTED_EXTENSIONS, WHEEL_EXTENSION, normalize_path,
|
|
||||||
redact_password_from_url,
|
|
||||||
)
|
|
||||||
from pip._internal.utils.packaging import check_requires_python
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
from pip._internal.wheel import Wheel
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from logging import Logger # noqa: F401
|
|
||||||
from typing import ( # noqa: F401
|
|
||||||
Tuple, Optional, Any, List, Union, Callable, Set, Sequence,
|
|
||||||
Iterable, MutableMapping
|
|
||||||
)
|
|
||||||
from pip._vendor.packaging.version import _BaseVersion # noqa: F401
|
|
||||||
from pip._vendor.requests import Response # noqa: F401
|
|
||||||
from pip._internal.req import InstallRequirement # noqa: F401
|
|
||||||
from pip._internal.download import PipSession # noqa: F401
|
|
||||||
|
|
||||||
SecureOrigin = Tuple[str, str, Optional[str]]
|
|
||||||
BuildTag = Tuple[Any, ...] # either emply tuple or Tuple[int, str]
|
|
||||||
CandidateSortingKey = Tuple[int, _BaseVersion, BuildTag, Optional[int]]
|
|
||||||
|
|
||||||
__all__ = ['FormatControl', 'PackageFinder']
|
|
||||||
|
|
||||||
|
|
||||||
SECURE_ORIGINS = [
|
|
||||||
# protocol, hostname, port
|
|
||||||
# Taken from Chrome's list of secure origins (See: http://bit.ly/1qrySKC)
|
|
||||||
("https", "*", "*"),
|
|
||||||
("*", "localhost", "*"),
|
|
||||||
("*", "127.0.0.0/8", "*"),
|
|
||||||
("*", "::1/128", "*"),
|
|
||||||
("file", "*", None),
|
|
||||||
# ssh is always secure.
|
|
||||||
("ssh", "*", "*"),
|
|
||||||
] # type: List[SecureOrigin]
|
|
||||||
|
|
||||||
|
|
||||||
logger = logging.getLogger(__name__)
|
|
||||||
|
|
||||||
|
|
||||||
def _match_vcs_scheme(url):
|
|
||||||
# type: (str) -> Optional[str]
|
|
||||||
"""Look for VCS schemes in the URL.
|
|
||||||
|
|
||||||
Returns the matched VCS scheme, or None if there's no match.
|
|
||||||
"""
|
|
||||||
from pip._internal.vcs import VcsSupport
|
|
||||||
for scheme in VcsSupport.schemes:
|
|
||||||
if url.lower().startswith(scheme) and url[len(scheme)] in '+:':
|
|
||||||
return scheme
|
|
||||||
return None
|
|
||||||
|
|
||||||
|
|
||||||
def _is_url_like_archive(url):
|
|
||||||
# type: (str) -> bool
|
|
||||||
"""Return whether the URL looks like an archive.
|
|
||||||
"""
|
|
||||||
filename = Link(url).filename
|
|
||||||
for bad_ext in ARCHIVE_EXTENSIONS:
|
|
||||||
if filename.endswith(bad_ext):
|
|
||||||
return True
|
|
||||||
return False
|
|
||||||
|
|
||||||
|
|
||||||
class _NotHTML(Exception):
|
|
||||||
def __init__(self, content_type, request_desc):
|
|
||||||
# type: (str, str) -> None
|
|
||||||
super(_NotHTML, self).__init__(content_type, request_desc)
|
|
||||||
self.content_type = content_type
|
|
||||||
self.request_desc = request_desc
|
|
||||||
|
|
||||||
|
|
||||||
def _ensure_html_header(response):
|
|
||||||
# type: (Response) -> None
|
|
||||||
"""Check the Content-Type header to ensure the response contains HTML.
|
|
||||||
|
|
||||||
Raises `_NotHTML` if the content type is not text/html.
|
|
||||||
"""
|
|
||||||
content_type = response.headers.get("Content-Type", "")
|
|
||||||
if not content_type.lower().startswith("text/html"):
|
|
||||||
raise _NotHTML(content_type, response.request.method)
|
|
||||||
|
|
||||||
|
|
||||||
class _NotHTTP(Exception):
|
|
||||||
pass
|
|
||||||
|
|
||||||
|
|
||||||
def _ensure_html_response(url, session):
|
|
||||||
# type: (str, PipSession) -> None
|
|
||||||
"""Send a HEAD request to the URL, and ensure the response contains HTML.
|
|
||||||
|
|
||||||
Raises `_NotHTTP` if the URL is not available for a HEAD request, or
|
|
||||||
`_NotHTML` if the content type is not text/html.
|
|
||||||
"""
|
|
||||||
scheme, netloc, path, query, fragment = urllib_parse.urlsplit(url)
|
|
||||||
if scheme not in {'http', 'https'}:
|
|
||||||
raise _NotHTTP()
|
|
||||||
|
|
||||||
resp = session.head(url, allow_redirects=True)
|
|
||||||
resp.raise_for_status()
|
|
||||||
|
|
||||||
_ensure_html_header(resp)
|
|
||||||
|
|
||||||
|
|
||||||
def _get_html_response(url, session):
|
|
||||||
# type: (str, PipSession) -> Response
|
|
||||||
"""Access an HTML page with GET, and return the response.
|
|
||||||
|
|
||||||
This consists of three parts:
|
|
||||||
|
|
||||||
1. If the URL looks suspiciously like an archive, send a HEAD first to
|
|
||||||
check the Content-Type is HTML, to avoid downloading a large file.
|
|
||||||
Raise `_NotHTTP` if the content type cannot be determined, or
|
|
||||||
`_NotHTML` if it is not HTML.
|
|
||||||
2. Actually perform the request. Raise HTTP exceptions on network failures.
|
|
||||||
3. Check the Content-Type header to make sure we got HTML, and raise
|
|
||||||
`_NotHTML` otherwise.
|
|
||||||
"""
|
|
||||||
if _is_url_like_archive(url):
|
|
||||||
_ensure_html_response(url, session=session)
|
|
||||||
|
|
||||||
logger.debug('Getting page %s', url)
|
|
||||||
|
|
||||||
resp = session.get(
|
|
||||||
url,
|
|
||||||
headers={
|
|
||||||
"Accept": "text/html",
|
|
||||||
# We don't want to blindly returned cached data for
|
|
||||||
# /simple/, because authors generally expecting that
|
|
||||||
# twine upload && pip install will function, but if
|
|
||||||
# they've done a pip install in the last ~10 minutes
|
|
||||||
# it won't. Thus by setting this to zero we will not
|
|
||||||
# blindly use any cached data, however the benefit of
|
|
||||||
# using max-age=0 instead of no-cache, is that we will
|
|
||||||
# still support conditional requests, so we will still
|
|
||||||
# minimize traffic sent in cases where the page hasn't
|
|
||||||
# changed at all, we will just always incur the round
|
|
||||||
# trip for the conditional GET now instead of only
|
|
||||||
# once per 10 minutes.
|
|
||||||
# For more information, please see pypa/pip#5670.
|
|
||||||
"Cache-Control": "max-age=0",
|
|
||||||
},
|
|
||||||
)
|
|
||||||
resp.raise_for_status()
|
|
||||||
|
|
||||||
# The check for archives above only works if the url ends with
|
|
||||||
# something that looks like an archive. However that is not a
|
|
||||||
# requirement of an url. Unless we issue a HEAD request on every
|
|
||||||
# url we cannot know ahead of time for sure if something is HTML
|
|
||||||
# or not. However we can check after we've downloaded it.
|
|
||||||
_ensure_html_header(resp)
|
|
||||||
|
|
||||||
return resp
|
|
||||||
|
|
||||||
|
|
||||||
def _handle_get_page_fail(
|
|
||||||
link, # type: Link
|
|
||||||
reason, # type: Union[str, Exception]
|
|
||||||
meth=None # type: Optional[Callable[..., None]]
|
|
||||||
):
|
|
||||||
# type: (...) -> None
|
|
||||||
if meth is None:
|
|
||||||
meth = logger.debug
|
|
||||||
meth("Could not fetch URL %s: %s - skipping", link, reason)
|
|
||||||
|
|
||||||
|
|
||||||
def _get_html_page(link, session=None):
|
|
||||||
# type: (Link, Optional[PipSession]) -> Optional[HTMLPage]
|
|
||||||
if session is None:
|
|
||||||
raise TypeError(
|
|
||||||
"_get_html_page() missing 1 required keyword argument: 'session'"
|
|
||||||
)
|
|
||||||
|
|
||||||
url = link.url.split('#', 1)[0]
|
|
||||||
|
|
||||||
# Check for VCS schemes that do not support lookup as web pages.
|
|
||||||
vcs_scheme = _match_vcs_scheme(url)
|
|
||||||
if vcs_scheme:
|
|
||||||
logger.debug('Cannot look at %s URL %s', vcs_scheme, link)
|
|
||||||
return None
|
|
||||||
|
|
||||||
# Tack index.html onto file:// URLs that point to directories
|
|
||||||
scheme, _, path, _, _, _ = urllib_parse.urlparse(url)
|
|
||||||
if (scheme == 'file' and os.path.isdir(urllib_request.url2pathname(path))):
|
|
||||||
# add trailing slash if not present so urljoin doesn't trim
|
|
||||||
# final segment
|
|
||||||
if not url.endswith('/'):
|
|
||||||
url += '/'
|
|
||||||
url = urllib_parse.urljoin(url, 'index.html')
|
|
||||||
logger.debug(' file: URL is directory, getting %s', url)
|
|
||||||
|
|
||||||
try:
|
|
||||||
resp = _get_html_response(url, session=session)
|
|
||||||
except _NotHTTP as exc:
|
|
||||||
logger.debug(
|
|
||||||
'Skipping page %s because it looks like an archive, and cannot '
|
|
||||||
'be checked by HEAD.', link,
|
|
||||||
)
|
|
||||||
except _NotHTML as exc:
|
|
||||||
logger.debug(
|
|
||||||
'Skipping page %s because the %s request got Content-Type: %s',
|
|
||||||
link, exc.request_desc, exc.content_type,
|
|
||||||
)
|
|
||||||
except requests.HTTPError as exc:
|
|
||||||
_handle_get_page_fail(link, exc)
|
|
||||||
except RetryError as exc:
|
|
||||||
_handle_get_page_fail(link, exc)
|
|
||||||
except SSLError as exc:
|
|
||||||
reason = "There was a problem confirming the ssl certificate: "
|
|
||||||
reason += str(exc)
|
|
||||||
_handle_get_page_fail(link, reason, meth=logger.info)
|
|
||||||
except requests.ConnectionError as exc:
|
|
||||||
_handle_get_page_fail(link, "connection error: %s" % exc)
|
|
||||||
except requests.Timeout:
|
|
||||||
_handle_get_page_fail(link, "timed out")
|
|
||||||
else:
|
|
||||||
return HTMLPage(resp.content, resp.url, resp.headers)
|
|
||||||
return None
|
|
||||||
|
|
||||||
|
|
||||||
class PackageFinder(object):
|
|
||||||
"""This finds packages.
|
|
||||||
|
|
||||||
This is meant to match easy_install's technique for looking for
|
|
||||||
packages, by reading pages and looking for appropriate links.
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(
|
|
||||||
self,
|
|
||||||
find_links, # type: List[str]
|
|
||||||
index_urls, # type: List[str]
|
|
||||||
allow_all_prereleases=False, # type: bool
|
|
||||||
trusted_hosts=None, # type: Optional[Iterable[str]]
|
|
||||||
session=None, # type: Optional[PipSession]
|
|
||||||
format_control=None, # type: Optional[FormatControl]
|
|
||||||
platform=None, # type: Optional[str]
|
|
||||||
versions=None, # type: Optional[List[str]]
|
|
||||||
abi=None, # type: Optional[str]
|
|
||||||
implementation=None, # type: Optional[str]
|
|
||||||
prefer_binary=False # type: bool
|
|
||||||
):
|
|
||||||
# type: (...) -> None
|
|
||||||
"""Create a PackageFinder.
|
|
||||||
|
|
||||||
:param format_control: A FormatControl object or None. Used to control
|
|
||||||
the selection of source packages / binary packages when consulting
|
|
||||||
the index and links.
|
|
||||||
:param platform: A string or None. If None, searches for packages
|
|
||||||
that are supported by the current system. Otherwise, will find
|
|
||||||
packages that can be built on the platform passed in. These
|
|
||||||
packages will only be downloaded for distribution: they will
|
|
||||||
not be built locally.
|
|
||||||
:param versions: A list of strings or None. This is passed directly
|
|
||||||
to pep425tags.py in the get_supported() method.
|
|
||||||
:param abi: A string or None. This is passed directly
|
|
||||||
to pep425tags.py in the get_supported() method.
|
|
||||||
:param implementation: A string or None. This is passed directly
|
|
||||||
to pep425tags.py in the get_supported() method.
|
|
||||||
"""
|
|
||||||
if session is None:
|
|
||||||
raise TypeError(
|
|
||||||
"PackageFinder() missing 1 required keyword argument: "
|
|
||||||
"'session'"
|
|
||||||
)
|
|
||||||
|
|
||||||
# Build find_links. If an argument starts with ~, it may be
|
|
||||||
# a local file relative to a home directory. So try normalizing
|
|
||||||
# it and if it exists, use the normalized version.
|
|
||||||
# This is deliberately conservative - it might be fine just to
|
|
||||||
# blindly normalize anything starting with a ~...
|
|
||||||
self.find_links = [] # type: List[str]
|
|
||||||
for link in find_links:
|
|
||||||
if link.startswith('~'):
|
|
||||||
new_link = normalize_path(link)
|
|
||||||
if os.path.exists(new_link):
|
|
||||||
link = new_link
|
|
||||||
self.find_links.append(link)
|
|
||||||
|
|
||||||
self.index_urls = index_urls
|
|
||||||
|
|
||||||
# These are boring links that have already been logged somehow:
|
|
||||||
self.logged_links = set() # type: Set[Link]
|
|
||||||
|
|
||||||
self.format_control = format_control or FormatControl(set(), set())
|
|
||||||
|
|
||||||
# Domains that we won't emit warnings for when not using HTTPS
|
|
||||||
self.secure_origins = [
|
|
||||||
("*", host, "*")
|
|
||||||
for host in (trusted_hosts if trusted_hosts else [])
|
|
||||||
] # type: List[SecureOrigin]
|
|
||||||
|
|
||||||
# Do we want to allow _all_ pre-releases?
|
|
||||||
self.allow_all_prereleases = allow_all_prereleases
|
|
||||||
|
|
||||||
# The Session we'll use to make requests
|
|
||||||
self.session = session
|
|
||||||
|
|
||||||
# The valid tags to check potential found wheel candidates against
|
|
||||||
self.valid_tags = get_supported(
|
|
||||||
versions=versions,
|
|
||||||
platform=platform,
|
|
||||||
abi=abi,
|
|
||||||
impl=implementation,
|
|
||||||
)
|
|
||||||
|
|
||||||
# Do we prefer old, but valid, binary dist over new source dist
|
|
||||||
self.prefer_binary = prefer_binary
|
|
||||||
|
|
||||||
# If we don't have TLS enabled, then WARN if anyplace we're looking
|
|
||||||
# relies on TLS.
|
|
||||||
if not HAS_TLS:
|
|
||||||
for link in itertools.chain(self.index_urls, self.find_links):
|
|
||||||
parsed = urllib_parse.urlparse(link)
|
|
||||||
if parsed.scheme == "https":
|
|
||||||
logger.warning(
|
|
||||||
"pip is configured with locations that require "
|
|
||||||
"TLS/SSL, however the ssl module in Python is not "
|
|
||||||
"available."
|
|
||||||
)
|
|
||||||
break
|
|
||||||
|
|
||||||
def get_formatted_locations(self):
|
|
||||||
# type: () -> str
|
|
||||||
lines = []
|
|
||||||
if self.index_urls and self.index_urls != [PyPI.simple_url]:
|
|
||||||
lines.append(
|
|
||||||
"Looking in indexes: {}".format(", ".join(
|
|
||||||
redact_password_from_url(url) for url in self.index_urls))
|
|
||||||
)
|
|
||||||
if self.find_links:
|
|
||||||
lines.append(
|
|
||||||
"Looking in links: {}".format(", ".join(self.find_links))
|
|
||||||
)
|
|
||||||
return "\n".join(lines)
|
|
||||||
|
|
||||||
@staticmethod
|
|
||||||
def _sort_locations(locations, expand_dir=False):
|
|
||||||
# type: (Sequence[str], bool) -> Tuple[List[str], List[str]]
|
|
||||||
"""
|
|
||||||
Sort locations into "files" (archives) and "urls", and return
|
|
||||||
a pair of lists (files,urls)
|
|
||||||
"""
|
|
||||||
files = []
|
|
||||||
urls = []
|
|
||||||
|
|
||||||
# puts the url for the given file path into the appropriate list
|
|
||||||
def sort_path(path):
|
|
||||||
url = path_to_url(path)
|
|
||||||
if mimetypes.guess_type(url, strict=False)[0] == 'text/html':
|
|
||||||
urls.append(url)
|
|
||||||
else:
|
|
||||||
files.append(url)
|
|
||||||
|
|
||||||
for url in locations:
|
|
||||||
|
|
||||||
is_local_path = os.path.exists(url)
|
|
||||||
is_file_url = url.startswith('file:')
|
|
||||||
|
|
||||||
if is_local_path or is_file_url:
|
|
||||||
if is_local_path:
|
|
||||||
path = url
|
|
||||||
else:
|
|
||||||
path = url_to_path(url)
|
|
||||||
if os.path.isdir(path):
|
|
||||||
if expand_dir:
|
|
||||||
path = os.path.realpath(path)
|
|
||||||
for item in os.listdir(path):
|
|
||||||
sort_path(os.path.join(path, item))
|
|
||||||
elif is_file_url:
|
|
||||||
urls.append(url)
|
|
||||||
else:
|
|
||||||
logger.warning(
|
|
||||||
"Path '{0}' is ignored: "
|
|
||||||
"it is a directory.".format(path),
|
|
||||||
)
|
|
||||||
elif os.path.isfile(path):
|
|
||||||
sort_path(path)
|
|
||||||
else:
|
|
||||||
logger.warning(
|
|
||||||
"Url '%s' is ignored: it is neither a file "
|
|
||||||
"nor a directory.", url,
|
|
||||||
)
|
|
||||||
elif is_url(url):
|
|
||||||
# Only add url with clear scheme
|
|
||||||
urls.append(url)
|
|
||||||
else:
|
|
||||||
logger.warning(
|
|
||||||
"Url '%s' is ignored. It is either a non-existing "
|
|
||||||
"path or lacks a specific scheme.", url,
|
|
||||||
)
|
|
||||||
|
|
||||||
return files, urls
|
|
||||||
|
|
||||||
def _candidate_sort_key(self, candidate):
|
|
||||||
# type: (InstallationCandidate) -> CandidateSortingKey
|
|
||||||
"""
|
|
||||||
Function used to generate link sort key for link tuples.
|
|
||||||
The greater the return value, the more preferred it is.
|
|
||||||
If not finding wheels, then sorted by version only.
|
|
||||||
If finding wheels, then the sort order is by version, then:
|
|
||||||
1. existing installs
|
|
||||||
2. wheels ordered via Wheel.support_index_min(self.valid_tags)
|
|
||||||
3. source archives
|
|
||||||
If prefer_binary was set, then all wheels are sorted above sources.
|
|
||||||
Note: it was considered to embed this logic into the Link
|
|
||||||
comparison operators, but then different sdist links
|
|
||||||
with the same version, would have to be considered equal
|
|
||||||
"""
|
|
||||||
support_num = len(self.valid_tags)
|
|
||||||
build_tag = tuple() # type: BuildTag
|
|
||||||
binary_preference = 0
|
|
||||||
if candidate.location.is_wheel:
|
|
||||||
# can raise InvalidWheelFilename
|
|
||||||
wheel = Wheel(candidate.location.filename)
|
|
||||||
if not wheel.supported(self.valid_tags):
|
|
||||||
raise UnsupportedWheel(
|
|
||||||
"%s is not a supported wheel for this platform. It "
|
|
||||||
"can't be sorted." % wheel.filename
|
|
||||||
)
|
|
||||||
if self.prefer_binary:
|
|
||||||
binary_preference = 1
|
|
||||||
pri = -(wheel.support_index_min(self.valid_tags))
|
|
||||||
if wheel.build_tag is not None:
|
|
||||||
match = re.match(r'^(\d+)(.*)$', wheel.build_tag)
|
|
||||||
build_tag_groups = match.groups()
|
|
||||||
build_tag = (int(build_tag_groups[0]), build_tag_groups[1])
|
|
||||||
else: # sdist
|
|
||||||
pri = -(support_num)
|
|
||||||
return (binary_preference, candidate.version, build_tag, pri)
|
|
||||||
|
|
||||||
def _validate_secure_origin(self, logger, location):
|
|
||||||
# type: (Logger, Link) -> bool
|
|
||||||
# Determine if this url used a secure transport mechanism
|
|
||||||
parsed = urllib_parse.urlparse(str(location))
|
|
||||||
origin = (parsed.scheme, parsed.hostname, parsed.port)
|
|
||||||
|
|
||||||
# The protocol to use to see if the protocol matches.
|
|
||||||
# Don't count the repository type as part of the protocol: in
|
|
||||||
# cases such as "git+ssh", only use "ssh". (I.e., Only verify against
|
|
||||||
# the last scheme.)
|
|
||||||
protocol = origin[0].rsplit('+', 1)[-1]
|
|
||||||
|
|
||||||
# Determine if our origin is a secure origin by looking through our
|
|
||||||
# hardcoded list of secure origins, as well as any additional ones
|
|
||||||
# configured on this PackageFinder instance.
|
|
||||||
for secure_origin in (SECURE_ORIGINS + self.secure_origins):
|
|
||||||
if protocol != secure_origin[0] and secure_origin[0] != "*":
|
|
||||||
continue
|
|
||||||
|
|
||||||
try:
|
|
||||||
# We need to do this decode dance to ensure that we have a
|
|
||||||
# unicode object, even on Python 2.x.
|
|
||||||
addr = ipaddress.ip_address(
|
|
||||||
origin[1]
|
|
||||||
if (
|
|
||||||
isinstance(origin[1], six.text_type) or
|
|
||||||
origin[1] is None
|
|
||||||
)
|
|
||||||
else origin[1].decode("utf8")
|
|
||||||
)
|
|
||||||
network = ipaddress.ip_network(
|
|
||||||
secure_origin[1]
|
|
||||||
if isinstance(secure_origin[1], six.text_type)
|
|
||||||
# setting secure_origin[1] to proper Union[bytes, str]
|
|
||||||
# creates problems in other places
|
|
||||||
else secure_origin[1].decode("utf8") # type: ignore
|
|
||||||
)
|
|
||||||
except ValueError:
|
|
||||||
# We don't have both a valid address or a valid network, so
|
|
||||||
# we'll check this origin against hostnames.
|
|
||||||
if (origin[1] and
|
|
||||||
origin[1].lower() != secure_origin[1].lower() and
|
|
||||||
secure_origin[1] != "*"):
|
|
||||||
continue
|
|
||||||
else:
|
|
||||||
# We have a valid address and network, so see if the address
|
|
||||||
# is contained within the network.
|
|
||||||
if addr not in network:
|
|
||||||
continue
|
|
||||||
|
|
||||||
# Check to see if the port patches
|
|
||||||
if (origin[2] != secure_origin[2] and
|
|
||||||
secure_origin[2] != "*" and
|
|
||||||
secure_origin[2] is not None):
|
|
||||||
continue
|
|
||||||
|
|
||||||
# If we've gotten here, then this origin matches the current
|
|
||||||
# secure origin and we should return True
|
|
||||||
return True
|
|
||||||
|
|
||||||
# If we've gotten to this point, then the origin isn't secure and we
|
|
||||||
# will not accept it as a valid location to search. We will however
|
|
||||||
# log a warning that we are ignoring it.
|
|
||||||
logger.warning(
|
|
||||||
"The repository located at %s is not a trusted or secure host and "
|
|
||||||
"is being ignored. If this repository is available via HTTPS we "
|
|
||||||
"recommend you use HTTPS instead, otherwise you may silence "
|
|
||||||
"this warning and allow it anyway with '--trusted-host %s'.",
|
|
||||||
parsed.hostname,
|
|
||||||
parsed.hostname,
|
|
||||||
)
|
|
||||||
|
|
||||||
return False
|
|
||||||
|
|
||||||
def _get_index_urls_locations(self, project_name):
|
|
||||||
# type: (str) -> List[str]
|
|
||||||
"""Returns the locations found via self.index_urls
|
|
||||||
|
|
||||||
Checks the url_name on the main (first in the list) index and
|
|
||||||
use this url_name to produce all locations
|
|
||||||
"""
|
|
||||||
|
|
||||||
def mkurl_pypi_url(url):
|
|
||||||
loc = posixpath.join(
|
|
||||||
url,
|
|
||||||
urllib_parse.quote(canonicalize_name(project_name)))
|
|
||||||
# For maximum compatibility with easy_install, ensure the path
|
|
||||||
# ends in a trailing slash. Although this isn't in the spec
|
|
||||||
# (and PyPI can handle it without the slash) some other index
|
|
||||||
# implementations might break if they relied on easy_install's
|
|
||||||
# behavior.
|
|
||||||
if not loc.endswith('/'):
|
|
||||||
loc = loc + '/'
|
|
||||||
return loc
|
|
||||||
|
|
||||||
return [mkurl_pypi_url(url) for url in self.index_urls]
|
|
||||||
|
|
||||||
def find_all_candidates(self, project_name):
|
|
||||||
# type: (str) -> List[Optional[InstallationCandidate]]
|
|
||||||
"""Find all available InstallationCandidate for project_name
|
|
||||||
|
|
||||||
This checks index_urls and find_links.
|
|
||||||
All versions found are returned as an InstallationCandidate list.
|
|
||||||
|
|
||||||
See _link_package_versions for details on which files are accepted
|
|
||||||
"""
|
|
||||||
index_locations = self._get_index_urls_locations(project_name)
|
|
||||||
index_file_loc, index_url_loc = self._sort_locations(index_locations)
|
|
||||||
fl_file_loc, fl_url_loc = self._sort_locations(
|
|
||||||
self.find_links, expand_dir=True,
|
|
||||||
)
|
|
||||||
|
|
||||||
file_locations = (Link(url) for url in itertools.chain(
|
|
||||||
index_file_loc, fl_file_loc,
|
|
||||||
))
|
|
||||||
|
|
||||||
# We trust every url that the user has given us whether it was given
|
|
||||||
# via --index-url or --find-links.
|
|
||||||
# We want to filter out any thing which does not have a secure origin.
|
|
||||||
url_locations = [
|
|
||||||
link for link in itertools.chain(
|
|
||||||
(Link(url) for url in index_url_loc),
|
|
||||||
(Link(url) for url in fl_url_loc),
|
|
||||||
)
|
|
||||||
if self._validate_secure_origin(logger, link)
|
|
||||||
]
|
|
||||||
|
|
||||||
logger.debug('%d location(s) to search for versions of %s:',
|
|
||||||
len(url_locations), project_name)
|
|
||||||
|
|
||||||
for location in url_locations:
|
|
||||||
logger.debug('* %s', location)
|
|
||||||
|
|
||||||
canonical_name = canonicalize_name(project_name)
|
|
||||||
formats = self.format_control.get_allowed_formats(canonical_name)
|
|
||||||
search = Search(project_name, canonical_name, formats)
|
|
||||||
find_links_versions = self._package_versions(
|
|
||||||
# We trust every directly linked archive in find_links
|
|
||||||
(Link(url, '-f') for url in self.find_links),
|
|
||||||
search
|
|
||||||
)
|
|
||||||
|
|
||||||
page_versions = []
|
|
||||||
for page in self._get_pages(url_locations, project_name):
|
|
||||||
logger.debug('Analyzing links from page %s', page.url)
|
|
||||||
with indent_log():
|
|
||||||
page_versions.extend(
|
|
||||||
self._package_versions(page.iter_links(), search)
|
|
||||||
)
|
|
||||||
|
|
||||||
file_versions = self._package_versions(file_locations, search)
|
|
||||||
if file_versions:
|
|
||||||
file_versions.sort(reverse=True)
|
|
||||||
logger.debug(
|
|
||||||
'Local files found: %s',
|
|
||||||
', '.join([
|
|
||||||
url_to_path(candidate.location.url)
|
|
||||||
for candidate in file_versions
|
|
||||||
])
|
|
||||||
)
|
|
||||||
|
|
||||||
# This is an intentional priority ordering
|
|
||||||
return file_versions + find_links_versions + page_versions
|
|
||||||
|
|
||||||
def find_requirement(self, req, upgrade):
|
|
||||||
# type: (InstallRequirement, bool) -> Optional[Link]
|
|
||||||
"""Try to find a Link matching req
|
|
||||||
|
|
||||||
Expects req, an InstallRequirement and upgrade, a boolean
|
|
||||||
Returns a Link if found,
|
|
||||||
Raises DistributionNotFound or BestVersionAlreadyInstalled otherwise
|
|
||||||
"""
|
|
||||||
all_candidates = self.find_all_candidates(req.name)
|
|
||||||
|
|
||||||
# Filter out anything which doesn't match our specifier
|
|
||||||
compatible_versions = set(
|
|
||||||
req.specifier.filter(
|
|
||||||
# We turn the version object into a str here because otherwise
|
|
||||||
# when we're debundled but setuptools isn't, Python will see
|
|
||||||
# packaging.version.Version and
|
|
||||||
# pkg_resources._vendor.packaging.version.Version as different
|
|
||||||
# types. This way we'll use a str as a common data interchange
|
|
||||||
# format. If we stop using the pkg_resources provided specifier
|
|
||||||
# and start using our own, we can drop the cast to str().
|
|
||||||
[str(c.version) for c in all_candidates],
|
|
||||||
prereleases=(
|
|
||||||
self.allow_all_prereleases
|
|
||||||
if self.allow_all_prereleases else None
|
|
||||||
),
|
|
||||||
)
|
|
||||||
)
|
|
||||||
applicable_candidates = [
|
|
||||||
# Again, converting to str to deal with debundling.
|
|
||||||
c for c in all_candidates if str(c.version) in compatible_versions
|
|
||||||
]
|
|
||||||
|
|
||||||
if applicable_candidates:
|
|
||||||
best_candidate = max(applicable_candidates,
|
|
||||||
key=self._candidate_sort_key)
|
|
||||||
else:
|
|
||||||
best_candidate = None
|
|
||||||
|
|
||||||
if req.satisfied_by is not None:
|
|
||||||
installed_version = parse_version(req.satisfied_by.version)
|
|
||||||
else:
|
|
||||||
installed_version = None
|
|
||||||
|
|
||||||
if installed_version is None and best_candidate is None:
|
|
||||||
logger.critical(
|
|
||||||
'Could not find a version that satisfies the requirement %s '
|
|
||||||
'(from versions: %s)',
|
|
||||||
req,
|
|
||||||
', '.join(
|
|
||||||
sorted(
|
|
||||||
{str(c.version) for c in all_candidates},
|
|
||||||
key=parse_version,
|
|
||||||
)
|
|
||||||
)
|
|
||||||
)
|
|
||||||
|
|
||||||
raise DistributionNotFound(
|
|
||||||
'No matching distribution found for %s' % req
|
|
||||||
)
|
|
||||||
|
|
||||||
best_installed = False
|
|
||||||
if installed_version and (
|
|
||||||
best_candidate is None or
|
|
||||||
best_candidate.version <= installed_version):
|
|
||||||
best_installed = True
|
|
||||||
|
|
||||||
if not upgrade and installed_version is not None:
|
|
||||||
if best_installed:
|
|
||||||
logger.debug(
|
|
||||||
'Existing installed version (%s) is most up-to-date and '
|
|
||||||
'satisfies requirement',
|
|
||||||
installed_version,
|
|
||||||
)
|
|
||||||
else:
|
|
||||||
logger.debug(
|
|
||||||
'Existing installed version (%s) satisfies requirement '
|
|
||||||
'(most up-to-date version is %s)',
|
|
||||||
installed_version,
|
|
||||||
best_candidate.version,
|
|
||||||
)
|
|
||||||
return None
|
|
||||||
|
|
||||||
if best_installed:
|
|
||||||
# We have an existing version, and its the best version
|
|
||||||
logger.debug(
|
|
||||||
'Installed version (%s) is most up-to-date (past versions: '
|
|
||||||
'%s)',
|
|
||||||
installed_version,
|
|
||||||
', '.join(sorted(compatible_versions, key=parse_version)) or
|
|
||||||
"none",
|
|
||||||
)
|
|
||||||
raise BestVersionAlreadyInstalled
|
|
||||||
|
|
||||||
logger.debug(
|
|
||||||
'Using version %s (newest of versions: %s)',
|
|
||||||
best_candidate.version,
|
|
||||||
', '.join(sorted(compatible_versions, key=parse_version))
|
|
||||||
)
|
|
||||||
return best_candidate.location
|
|
||||||
|
|
||||||
def _get_pages(self, locations, project_name):
|
|
||||||
# type: (Iterable[Link], str) -> Iterable[HTMLPage]
|
|
||||||
"""
|
|
||||||
Yields (page, page_url) from the given locations, skipping
|
|
||||||
locations that have errors.
|
|
||||||
"""
|
|
||||||
seen = set() # type: Set[Link]
|
|
||||||
for location in locations:
|
|
||||||
if location in seen:
|
|
||||||
continue
|
|
||||||
seen.add(location)
|
|
||||||
|
|
||||||
page = _get_html_page(location, session=self.session)
|
|
||||||
if page is None:
|
|
||||||
continue
|
|
||||||
|
|
||||||
yield page
|
|
||||||
|
|
||||||
_py_version_re = re.compile(r'-py([123]\.?[0-9]?)$')
|
|
||||||
|
|
||||||
def _sort_links(self, links):
|
|
||||||
# type: (Iterable[Link]) -> List[Link]
|
|
||||||
"""
|
|
||||||
Returns elements of links in order, non-egg links first, egg links
|
|
||||||
second, while eliminating duplicates
|
|
||||||
"""
|
|
||||||
eggs, no_eggs = [], []
|
|
||||||
seen = set() # type: Set[Link]
|
|
||||||
for link in links:
|
|
||||||
if link not in seen:
|
|
||||||
seen.add(link)
|
|
||||||
if link.egg_fragment:
|
|
||||||
eggs.append(link)
|
|
||||||
else:
|
|
||||||
no_eggs.append(link)
|
|
||||||
return no_eggs + eggs
|
|
||||||
|
|
||||||
def _package_versions(
|
|
||||||
self,
|
|
||||||
links, # type: Iterable[Link]
|
|
||||||
search # type: Search
|
|
||||||
):
|
|
||||||
# type: (...) -> List[Optional[InstallationCandidate]]
|
|
||||||
result = []
|
|
||||||
for link in self._sort_links(links):
|
|
||||||
v = self._link_package_versions(link, search)
|
|
||||||
if v is not None:
|
|
||||||
result.append(v)
|
|
||||||
return result
|
|
||||||
|
|
||||||
def _log_skipped_link(self, link, reason):
|
|
||||||
# type: (Link, str) -> None
|
|
||||||
if link not in self.logged_links:
|
|
||||||
logger.debug('Skipping link %s; %s', link, reason)
|
|
||||||
self.logged_links.add(link)
|
|
||||||
|
|
||||||
def _link_package_versions(self, link, search):
|
|
||||||
# type: (Link, Search) -> Optional[InstallationCandidate]
|
|
||||||
"""Return an InstallationCandidate or None"""
|
|
||||||
version = None
|
|
||||||
if link.egg_fragment:
|
|
||||||
egg_info = link.egg_fragment
|
|
||||||
ext = link.ext
|
|
||||||
else:
|
|
||||||
egg_info, ext = link.splitext()
|
|
||||||
if not ext:
|
|
||||||
self._log_skipped_link(link, 'not a file')
|
|
||||||
return None
|
|
||||||
if ext not in SUPPORTED_EXTENSIONS:
|
|
||||||
self._log_skipped_link(
|
|
||||||
link, 'unsupported archive format: %s' % ext,
|
|
||||||
)
|
|
||||||
return None
|
|
||||||
if "binary" not in search.formats and ext == WHEEL_EXTENSION:
|
|
||||||
self._log_skipped_link(
|
|
||||||
link, 'No binaries permitted for %s' % search.supplied,
|
|
||||||
)
|
|
||||||
return None
|
|
||||||
if "macosx10" in link.path and ext == '.zip':
|
|
||||||
self._log_skipped_link(link, 'macosx10 one')
|
|
||||||
return None
|
|
||||||
if ext == WHEEL_EXTENSION:
|
|
||||||
try:
|
|
||||||
wheel = Wheel(link.filename)
|
|
||||||
except InvalidWheelFilename:
|
|
||||||
self._log_skipped_link(link, 'invalid wheel filename')
|
|
||||||
return None
|
|
||||||
if canonicalize_name(wheel.name) != search.canonical:
|
|
||||||
self._log_skipped_link(
|
|
||||||
link, 'wrong project name (not %s)' % search.supplied)
|
|
||||||
return None
|
|
||||||
|
|
||||||
if not wheel.supported(self.valid_tags):
|
|
||||||
self._log_skipped_link(
|
|
||||||
link, 'it is not compatible with this Python')
|
|
||||||
return None
|
|
||||||
|
|
||||||
version = wheel.version
|
|
||||||
|
|
||||||
# This should be up by the search.ok_binary check, but see issue 2700.
|
|
||||||
if "source" not in search.formats and ext != WHEEL_EXTENSION:
|
|
||||||
self._log_skipped_link(
|
|
||||||
link, 'No sources permitted for %s' % search.supplied,
|
|
||||||
)
|
|
||||||
return None
|
|
||||||
|
|
||||||
if not version:
|
|
||||||
version = _egg_info_matches(egg_info, search.canonical)
|
|
||||||
if not version:
|
|
||||||
self._log_skipped_link(
|
|
||||||
link, 'Missing project version for %s' % search.supplied)
|
|
||||||
return None
|
|
||||||
|
|
||||||
match = self._py_version_re.search(version)
|
|
||||||
if match:
|
|
||||||
version = version[:match.start()]
|
|
||||||
py_version = match.group(1)
|
|
||||||
if py_version != sys.version[:3]:
|
|
||||||
self._log_skipped_link(
|
|
||||||
link, 'Python version is incorrect')
|
|
||||||
return None
|
|
||||||
try:
|
|
||||||
support_this_python = check_requires_python(link.requires_python)
|
|
||||||
except specifiers.InvalidSpecifier:
|
|
||||||
logger.debug("Package %s has an invalid Requires-Python entry: %s",
|
|
||||||
link.filename, link.requires_python)
|
|
||||||
support_this_python = True
|
|
||||||
|
|
||||||
if not support_this_python:
|
|
||||||
logger.debug("The package %s is incompatible with the python "
|
|
||||||
"version in use. Acceptable python versions are: %s",
|
|
||||||
link, link.requires_python)
|
|
||||||
return None
|
|
||||||
logger.debug('Found link %s, version: %s', link, version)
|
|
||||||
|
|
||||||
return InstallationCandidate(search.supplied, version, link)
|
|
||||||
|
|
||||||
|
|
||||||
def _find_name_version_sep(egg_info, canonical_name):
|
|
||||||
# type: (str, str) -> int
|
|
||||||
"""Find the separator's index based on the package's canonical name.
|
|
||||||
|
|
||||||
`egg_info` must be an egg info string for the given package, and
|
|
||||||
`canonical_name` must be the package's canonical name.
|
|
||||||
|
|
||||||
This function is needed since the canonicalized name does not necessarily
|
|
||||||
have the same length as the egg info's name part. An example::
|
|
||||||
|
|
||||||
>>> egg_info = 'foo__bar-1.0'
|
|
||||||
>>> canonical_name = 'foo-bar'
|
|
||||||
>>> _find_name_version_sep(egg_info, canonical_name)
|
|
||||||
8
|
|
||||||
"""
|
|
||||||
# Project name and version must be separated by one single dash. Find all
|
|
||||||
# occurrences of dashes; if the string in front of it matches the canonical
|
|
||||||
# name, this is the one separating the name and version parts.
|
|
||||||
for i, c in enumerate(egg_info):
|
|
||||||
if c != "-":
|
|
||||||
continue
|
|
||||||
if canonicalize_name(egg_info[:i]) == canonical_name:
|
|
||||||
return i
|
|
||||||
raise ValueError("{} does not match {}".format(egg_info, canonical_name))
|
|
||||||
|
|
||||||
|
|
||||||
def _egg_info_matches(egg_info, canonical_name):
|
|
||||||
# type: (str, str) -> Optional[str]
|
|
||||||
"""Pull the version part out of a string.
|
|
||||||
|
|
||||||
:param egg_info: The string to parse. E.g. foo-2.1
|
|
||||||
:param canonical_name: The canonicalized name of the package this
|
|
||||||
belongs to.
|
|
||||||
"""
|
|
||||||
try:
|
|
||||||
version_start = _find_name_version_sep(egg_info, canonical_name) + 1
|
|
||||||
except ValueError:
|
|
||||||
return None
|
|
||||||
version = egg_info[version_start:]
|
|
||||||
if not version:
|
|
||||||
return None
|
|
||||||
return version
|
|
||||||
|
|
||||||
|
|
||||||
def _determine_base_url(document, page_url):
|
|
||||||
"""Determine the HTML document's base URL.
|
|
||||||
|
|
||||||
This looks for a ``<base>`` tag in the HTML document. If present, its href
|
|
||||||
attribute denotes the base URL of anchor tags in the document. If there is
|
|
||||||
no such tag (or if it does not have a valid href attribute), the HTML
|
|
||||||
file's URL is used as the base URL.
|
|
||||||
|
|
||||||
:param document: An HTML document representation. The current
|
|
||||||
implementation expects the result of ``html5lib.parse()``.
|
|
||||||
:param page_url: The URL of the HTML document.
|
|
||||||
"""
|
|
||||||
for base in document.findall(".//base"):
|
|
||||||
href = base.get("href")
|
|
||||||
if href is not None:
|
|
||||||
return href
|
|
||||||
return page_url
|
|
||||||
|
|
||||||
|
|
||||||
def _get_encoding_from_headers(headers):
|
|
||||||
"""Determine if we have any encoding information in our headers.
|
|
||||||
"""
|
|
||||||
if headers and "Content-Type" in headers:
|
|
||||||
content_type, params = cgi.parse_header(headers["Content-Type"])
|
|
||||||
if "charset" in params:
|
|
||||||
return params['charset']
|
|
||||||
return None
|
|
||||||
|
|
||||||
|
|
||||||
_CLEAN_LINK_RE = re.compile(r'[^a-z0-9$&+,/:;=?@.#%_\\|-]', re.I)
|
|
||||||
|
|
||||||
|
|
||||||
def _clean_link(url):
|
|
||||||
# type: (str) -> str
|
|
||||||
"""Makes sure a link is fully encoded. That is, if a ' ' shows up in
|
|
||||||
the link, it will be rewritten to %20 (while not over-quoting
|
|
||||||
% or other characters)."""
|
|
||||||
return _CLEAN_LINK_RE.sub(lambda match: '%%%2x' % ord(match.group(0)), url)
|
|
||||||
|
|
||||||
|
|
||||||
class HTMLPage(object):
|
|
||||||
"""Represents one page, along with its URL"""
|
|
||||||
|
|
||||||
def __init__(self, content, url, headers=None):
|
|
||||||
# type: (bytes, str, MutableMapping[str, str]) -> None
|
|
||||||
self.content = content
|
|
||||||
self.url = url
|
|
||||||
self.headers = headers
|
|
||||||
|
|
||||||
def __str__(self):
|
|
||||||
return redact_password_from_url(self.url)
|
|
||||||
|
|
||||||
def iter_links(self):
|
|
||||||
# type: () -> Iterable[Link]
|
|
||||||
"""Yields all links in the page"""
|
|
||||||
document = html5lib.parse(
|
|
||||||
self.content,
|
|
||||||
transport_encoding=_get_encoding_from_headers(self.headers),
|
|
||||||
namespaceHTMLElements=False,
|
|
||||||
)
|
|
||||||
base_url = _determine_base_url(document, self.url)
|
|
||||||
for anchor in document.findall(".//a"):
|
|
||||||
if anchor.get("href"):
|
|
||||||
href = anchor.get("href")
|
|
||||||
url = _clean_link(urllib_parse.urljoin(base_url, href))
|
|
||||||
pyrequire = anchor.get('data-requires-python')
|
|
||||||
pyrequire = unescape(pyrequire) if pyrequire else None
|
|
||||||
yield Link(url, self.url, requires_python=pyrequire)
|
|
||||||
|
|
||||||
|
|
||||||
Search = namedtuple('Search', 'supplied canonical formats')
|
|
||||||
"""Capture key aspects of a search.
|
|
||||||
|
|
||||||
:attribute supplied: The user supplied package.
|
|
||||||
:attribute canonical: The canonical package name.
|
|
||||||
:attribute formats: The formats allowed for this package. Should be a set
|
|
||||||
with 'binary' or 'source' or both in it.
|
|
||||||
"""
|
|
||||||
@@ -1,211 +0,0 @@
|
|||||||
"""Locations where we look for configs, install stuff, etc"""
|
|
||||||
from __future__ import absolute_import
|
|
||||||
|
|
||||||
import os
|
|
||||||
import os.path
|
|
||||||
import platform
|
|
||||||
import site
|
|
||||||
import sys
|
|
||||||
import sysconfig
|
|
||||||
from distutils import sysconfig as distutils_sysconfig
|
|
||||||
from distutils.command.install import SCHEME_KEYS # type: ignore
|
|
||||||
|
|
||||||
from pip._internal.utils import appdirs
|
|
||||||
from pip._internal.utils.compat import WINDOWS, expanduser
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from typing import Any, Union, Dict, List, Optional # noqa: F401
|
|
||||||
|
|
||||||
|
|
||||||
# Application Directories
|
|
||||||
USER_CACHE_DIR = appdirs.user_cache_dir("pip")
|
|
||||||
|
|
||||||
|
|
||||||
DELETE_MARKER_MESSAGE = '''\
|
|
||||||
This file is placed here by pip to indicate the source was put
|
|
||||||
here by pip.
|
|
||||||
|
|
||||||
Once this package is successfully installed this source code will be
|
|
||||||
deleted (unless you remove this file).
|
|
||||||
'''
|
|
||||||
PIP_DELETE_MARKER_FILENAME = 'pip-delete-this-directory.txt'
|
|
||||||
|
|
||||||
|
|
||||||
def write_delete_marker_file(directory):
|
|
||||||
# type: (str) -> None
|
|
||||||
"""
|
|
||||||
Write the pip delete marker file into this directory.
|
|
||||||
"""
|
|
||||||
filepath = os.path.join(directory, PIP_DELETE_MARKER_FILENAME)
|
|
||||||
with open(filepath, 'w') as marker_fp:
|
|
||||||
marker_fp.write(DELETE_MARKER_MESSAGE)
|
|
||||||
|
|
||||||
|
|
||||||
def running_under_virtualenv():
|
|
||||||
# type: () -> bool
|
|
||||||
"""
|
|
||||||
Return True if we're running inside a virtualenv, False otherwise.
|
|
||||||
|
|
||||||
"""
|
|
||||||
if hasattr(sys, 'real_prefix'):
|
|
||||||
return True
|
|
||||||
elif sys.prefix != getattr(sys, "base_prefix", sys.prefix):
|
|
||||||
return True
|
|
||||||
|
|
||||||
return False
|
|
||||||
|
|
||||||
|
|
||||||
def virtualenv_no_global():
|
|
||||||
# type: () -> bool
|
|
||||||
"""
|
|
||||||
Return True if in a venv and no system site packages.
|
|
||||||
"""
|
|
||||||
# this mirrors the logic in virtualenv.py for locating the
|
|
||||||
# no-global-site-packages.txt file
|
|
||||||
site_mod_dir = os.path.dirname(os.path.abspath(site.__file__))
|
|
||||||
no_global_file = os.path.join(site_mod_dir, 'no-global-site-packages.txt')
|
|
||||||
if running_under_virtualenv() and os.path.isfile(no_global_file):
|
|
||||||
return True
|
|
||||||
else:
|
|
||||||
return False
|
|
||||||
|
|
||||||
|
|
||||||
if running_under_virtualenv():
|
|
||||||
src_prefix = os.path.join(sys.prefix, 'src')
|
|
||||||
else:
|
|
||||||
# FIXME: keep src in cwd for now (it is not a temporary folder)
|
|
||||||
try:
|
|
||||||
src_prefix = os.path.join(os.getcwd(), 'src')
|
|
||||||
except OSError:
|
|
||||||
# In case the current working directory has been renamed or deleted
|
|
||||||
sys.exit(
|
|
||||||
"The folder you are executing pip from can no longer be found."
|
|
||||||
)
|
|
||||||
|
|
||||||
# under macOS + virtualenv sys.prefix is not properly resolved
|
|
||||||
# it is something like /path/to/python/bin/..
|
|
||||||
# Note: using realpath due to tmp dirs on OSX being symlinks
|
|
||||||
src_prefix = os.path.abspath(src_prefix)
|
|
||||||
|
|
||||||
# FIXME doesn't account for venv linked to global site-packages
|
|
||||||
|
|
||||||
site_packages = sysconfig.get_path("purelib") # type: Optional[str]
|
|
||||||
|
|
||||||
# This is because of a bug in PyPy's sysconfig module, see
|
|
||||||
# https://bitbucket.org/pypy/pypy/issues/2506/sysconfig-returns-incorrect-paths
|
|
||||||
# for more information.
|
|
||||||
if platform.python_implementation().lower() == "pypy":
|
|
||||||
site_packages = distutils_sysconfig.get_python_lib()
|
|
||||||
try:
|
|
||||||
# Use getusersitepackages if this is present, as it ensures that the
|
|
||||||
# value is initialised properly.
|
|
||||||
user_site = site.getusersitepackages()
|
|
||||||
except AttributeError:
|
|
||||||
user_site = site.USER_SITE
|
|
||||||
user_dir = expanduser('~')
|
|
||||||
if WINDOWS:
|
|
||||||
bin_py = os.path.join(sys.prefix, 'Scripts')
|
|
||||||
bin_user = os.path.join(user_site, 'Scripts')
|
|
||||||
# buildout uses 'bin' on Windows too?
|
|
||||||
if not os.path.exists(bin_py):
|
|
||||||
bin_py = os.path.join(sys.prefix, 'bin')
|
|
||||||
bin_user = os.path.join(user_site, 'bin')
|
|
||||||
|
|
||||||
config_basename = 'pip.ini'
|
|
||||||
|
|
||||||
legacy_storage_dir = os.path.join(user_dir, 'pip')
|
|
||||||
legacy_config_file = os.path.join(
|
|
||||||
legacy_storage_dir,
|
|
||||||
config_basename,
|
|
||||||
)
|
|
||||||
else:
|
|
||||||
bin_py = os.path.join(sys.prefix, 'bin')
|
|
||||||
bin_user = os.path.join(user_site, 'bin')
|
|
||||||
|
|
||||||
config_basename = 'pip.conf'
|
|
||||||
|
|
||||||
legacy_storage_dir = os.path.join(user_dir, '.pip')
|
|
||||||
legacy_config_file = os.path.join(
|
|
||||||
legacy_storage_dir,
|
|
||||||
config_basename,
|
|
||||||
)
|
|
||||||
# Forcing to use /usr/local/bin for standard macOS framework installs
|
|
||||||
# Also log to ~/Library/Logs/ for use with the Console.app log viewer
|
|
||||||
if sys.platform[:6] == 'darwin' and sys.prefix[:16] == '/System/Library/':
|
|
||||||
bin_py = '/usr/local/bin'
|
|
||||||
|
|
||||||
site_config_files = [
|
|
||||||
os.path.join(path, config_basename)
|
|
||||||
for path in appdirs.site_config_dirs('pip')
|
|
||||||
]
|
|
||||||
|
|
||||||
venv_config_file = os.path.join(sys.prefix, config_basename)
|
|
||||||
new_config_file = os.path.join(appdirs.user_config_dir("pip"), config_basename)
|
|
||||||
|
|
||||||
|
|
||||||
def distutils_scheme(dist_name, user=False, home=None, root=None,
|
|
||||||
isolated=False, prefix=None):
|
|
||||||
# type:(str, bool, str, str, bool, str) -> dict
|
|
||||||
"""
|
|
||||||
Return a distutils install scheme
|
|
||||||
"""
|
|
||||||
from distutils.dist import Distribution
|
|
||||||
|
|
||||||
scheme = {}
|
|
||||||
|
|
||||||
if isolated:
|
|
||||||
extra_dist_args = {"script_args": ["--no-user-cfg"]}
|
|
||||||
else:
|
|
||||||
extra_dist_args = {}
|
|
||||||
dist_args = {'name': dist_name} # type: Dict[str, Union[str, List[str]]]
|
|
||||||
dist_args.update(extra_dist_args)
|
|
||||||
|
|
||||||
d = Distribution(dist_args)
|
|
||||||
# Ignoring, typeshed issue reported python/typeshed/issues/2567
|
|
||||||
d.parse_config_files()
|
|
||||||
# NOTE: Ignoring type since mypy can't find attributes on 'Command'
|
|
||||||
i = d.get_command_obj('install', create=True) # type: Any
|
|
||||||
assert i is not None
|
|
||||||
# NOTE: setting user or home has the side-effect of creating the home dir
|
|
||||||
# or user base for installations during finalize_options()
|
|
||||||
# ideally, we'd prefer a scheme class that has no side-effects.
|
|
||||||
assert not (user and prefix), "user={} prefix={}".format(user, prefix)
|
|
||||||
i.user = user or i.user
|
|
||||||
if user:
|
|
||||||
i.prefix = ""
|
|
||||||
i.prefix = prefix or i.prefix
|
|
||||||
i.home = home or i.home
|
|
||||||
i.root = root or i.root
|
|
||||||
i.finalize_options()
|
|
||||||
for key in SCHEME_KEYS:
|
|
||||||
scheme[key] = getattr(i, 'install_' + key)
|
|
||||||
|
|
||||||
# install_lib specified in setup.cfg should install *everything*
|
|
||||||
# into there (i.e. it takes precedence over both purelib and
|
|
||||||
# platlib). Note, i.install_lib is *always* set after
|
|
||||||
# finalize_options(); we only want to override here if the user
|
|
||||||
# has explicitly requested it hence going back to the config
|
|
||||||
|
|
||||||
# Ignoring, typeshed issue reported python/typeshed/issues/2567
|
|
||||||
if 'install_lib' in d.get_option_dict('install'): # type: ignore
|
|
||||||
scheme.update(dict(purelib=i.install_lib, platlib=i.install_lib))
|
|
||||||
|
|
||||||
if running_under_virtualenv():
|
|
||||||
scheme['headers'] = os.path.join(
|
|
||||||
sys.prefix,
|
|
||||||
'include',
|
|
||||||
'site',
|
|
||||||
'python' + sys.version[:3],
|
|
||||||
dist_name,
|
|
||||||
)
|
|
||||||
|
|
||||||
if root is not None:
|
|
||||||
path_no_drive = os.path.splitdrive(
|
|
||||||
os.path.abspath(scheme["headers"]))[1]
|
|
||||||
scheme["headers"] = os.path.join(
|
|
||||||
root,
|
|
||||||
path_no_drive[1:],
|
|
||||||
)
|
|
||||||
|
|
||||||
return scheme
|
|
||||||
@@ -1,2 +0,0 @@
|
|||||||
"""A package that contains models that represent entities.
|
|
||||||
"""
|
|
||||||
@@ -1,31 +0,0 @@
|
|||||||
from pip._vendor.packaging.version import parse as parse_version
|
|
||||||
|
|
||||||
from pip._internal.utils.models import KeyBasedCompareMixin
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from pip._vendor.packaging.version import _BaseVersion # noqa: F401
|
|
||||||
from pip._internal.models.link import Link # noqa: F401
|
|
||||||
from typing import Any, Union # noqa: F401
|
|
||||||
|
|
||||||
|
|
||||||
class InstallationCandidate(KeyBasedCompareMixin):
|
|
||||||
"""Represents a potential "candidate" for installation.
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self, project, version, location):
|
|
||||||
# type: (Any, str, Link) -> None
|
|
||||||
self.project = project
|
|
||||||
self.version = parse_version(version) # type: _BaseVersion
|
|
||||||
self.location = location
|
|
||||||
|
|
||||||
super(InstallationCandidate, self).__init__(
|
|
||||||
key=(self.project, self.version, self.location),
|
|
||||||
defining_class=InstallationCandidate
|
|
||||||
)
|
|
||||||
|
|
||||||
def __repr__(self):
|
|
||||||
# type: () -> str
|
|
||||||
return "<InstallationCandidate({!r}, {!r}, {!r})>".format(
|
|
||||||
self.project, self.version, self.location,
|
|
||||||
)
|
|
||||||
@@ -1,73 +0,0 @@
|
|||||||
from pip._vendor.packaging.utils import canonicalize_name
|
|
||||||
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from typing import Optional, Set, FrozenSet # noqa: F401
|
|
||||||
|
|
||||||
|
|
||||||
class FormatControl(object):
|
|
||||||
"""Helper for managing formats from which a package can be installed.
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self, no_binary=None, only_binary=None):
|
|
||||||
# type: (Optional[Set], Optional[Set]) -> None
|
|
||||||
if no_binary is None:
|
|
||||||
no_binary = set()
|
|
||||||
if only_binary is None:
|
|
||||||
only_binary = set()
|
|
||||||
|
|
||||||
self.no_binary = no_binary
|
|
||||||
self.only_binary = only_binary
|
|
||||||
|
|
||||||
def __eq__(self, other):
|
|
||||||
return self.__dict__ == other.__dict__
|
|
||||||
|
|
||||||
def __ne__(self, other):
|
|
||||||
return not self.__eq__(other)
|
|
||||||
|
|
||||||
def __repr__(self):
|
|
||||||
return "{}({}, {})".format(
|
|
||||||
self.__class__.__name__,
|
|
||||||
self.no_binary,
|
|
||||||
self.only_binary
|
|
||||||
)
|
|
||||||
|
|
||||||
@staticmethod
|
|
||||||
def handle_mutual_excludes(value, target, other):
|
|
||||||
# type: (str, Optional[Set], Optional[Set]) -> None
|
|
||||||
new = value.split(',')
|
|
||||||
while ':all:' in new:
|
|
||||||
other.clear()
|
|
||||||
target.clear()
|
|
||||||
target.add(':all:')
|
|
||||||
del new[:new.index(':all:') + 1]
|
|
||||||
# Without a none, we want to discard everything as :all: covers it
|
|
||||||
if ':none:' not in new:
|
|
||||||
return
|
|
||||||
for name in new:
|
|
||||||
if name == ':none:':
|
|
||||||
target.clear()
|
|
||||||
continue
|
|
||||||
name = canonicalize_name(name)
|
|
||||||
other.discard(name)
|
|
||||||
target.add(name)
|
|
||||||
|
|
||||||
def get_allowed_formats(self, canonical_name):
|
|
||||||
# type: (str) -> FrozenSet
|
|
||||||
result = {"binary", "source"}
|
|
||||||
if canonical_name in self.only_binary:
|
|
||||||
result.discard('source')
|
|
||||||
elif canonical_name in self.no_binary:
|
|
||||||
result.discard('binary')
|
|
||||||
elif ':all:' in self.only_binary:
|
|
||||||
result.discard('source')
|
|
||||||
elif ':all:' in self.no_binary:
|
|
||||||
result.discard('binary')
|
|
||||||
return frozenset(result)
|
|
||||||
|
|
||||||
def disallow_binaries(self):
|
|
||||||
# type: () -> None
|
|
||||||
self.handle_mutual_excludes(
|
|
||||||
':all:', self.no_binary, self.only_binary,
|
|
||||||
)
|
|
||||||
@@ -1,31 +0,0 @@
|
|||||||
from pip._vendor.six.moves.urllib import parse as urllib_parse
|
|
||||||
|
|
||||||
|
|
||||||
class PackageIndex(object):
|
|
||||||
"""Represents a Package Index and provides easier access to endpoints
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self, url, file_storage_domain):
|
|
||||||
# type: (str, str) -> None
|
|
||||||
super(PackageIndex, self).__init__()
|
|
||||||
self.url = url
|
|
||||||
self.netloc = urllib_parse.urlsplit(url).netloc
|
|
||||||
self.simple_url = self._url_for_path('simple')
|
|
||||||
self.pypi_url = self._url_for_path('pypi')
|
|
||||||
|
|
||||||
# This is part of a temporary hack used to block installs of PyPI
|
|
||||||
# packages which depend on external urls only necessary until PyPI can
|
|
||||||
# block such packages themselves
|
|
||||||
self.file_storage_domain = file_storage_domain
|
|
||||||
|
|
||||||
def _url_for_path(self, path):
|
|
||||||
# type: (str) -> str
|
|
||||||
return urllib_parse.urljoin(self.url, path)
|
|
||||||
|
|
||||||
|
|
||||||
PyPI = PackageIndex(
|
|
||||||
'https://pypi.org/', file_storage_domain='files.pythonhosted.org'
|
|
||||||
)
|
|
||||||
TestPyPI = PackageIndex(
|
|
||||||
'https://test.pypi.org/', file_storage_domain='test-files.pythonhosted.org'
|
|
||||||
)
|
|
||||||
@@ -1,163 +0,0 @@
|
|||||||
import posixpath
|
|
||||||
import re
|
|
||||||
|
|
||||||
from pip._vendor.six.moves.urllib import parse as urllib_parse
|
|
||||||
|
|
||||||
from pip._internal.download import path_to_url
|
|
||||||
from pip._internal.utils.misc import (
|
|
||||||
WHEEL_EXTENSION, redact_password_from_url, splitext,
|
|
||||||
)
|
|
||||||
from pip._internal.utils.models import KeyBasedCompareMixin
|
|
||||||
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
|
|
||||||
|
|
||||||
if MYPY_CHECK_RUNNING:
|
|
||||||
from typing import Optional, Tuple, Union, Text # noqa: F401
|
|
||||||
from pip._internal.index import HTMLPage # noqa: F401
|
|
||||||
|
|
||||||
|
|
||||||
class Link(KeyBasedCompareMixin):
|
|
||||||
"""Represents a parsed link from a Package Index's simple URL
|
|
||||||
"""
|
|
||||||
|
|
||||||
def __init__(self, url, comes_from=None, requires_python=None):
|
|
||||||
# type: (str, Optional[Union[str, HTMLPage]], Optional[str]) -> None
|
|
||||||
"""
|
|
||||||
url:
|
|
||||||
url of the resource pointed to (href of the link)
|
|
||||||
comes_from:
|
|
||||||
instance of HTMLPage where the link was found, or string.
|
|
||||||
requires_python:
|
|
||||||
String containing the `Requires-Python` metadata field, specified
|
|
||||||
in PEP 345. This may be specified by a data-requires-python
|
|
||||||
attribute in the HTML link tag, as described in PEP 503.
|
|
||||||
"""
|
|
||||||
|
|
||||||
# url can be a UNC windows share
|
|
||||||
if url.startswith('\\\\'):
|
|
||||||
url = path_to_url(url)
|
|
||||||
|
|
||||||
self.url = url
|
|
||||||
self.comes_from = comes_from
|
|
||||||
self.requires_python = requires_python if requires_python else None
|
|
||||||
|
|
||||||
super(Link, self).__init__(
|
|
||||||
key=(self.url),
|
|
||||||
defining_class=Link
|
|
||||||
)
|
|
||||||
|
|
||||||
def __str__(self):
|
|
||||||
if self.requires_python:
|
|
||||||
rp = ' (requires-python:%s)' % self.requires_python
|
|
||||||
else:
|
|
||||||
rp = ''
|
|
||||||
if self.comes_from:
|
|
||||||
return '%s (from %s)%s' % (redact_password_from_url(self.url),
|
|
||||||
self.comes_from, rp)
|
|
||||||
else:
|
|
||||||
return redact_password_from_url(str(self.url))
|
|
||||||
|
|
||||||
def __repr__(self):
|
|
||||||
return '<Link %s>' % self
|
|
||||||
|
|
||||||
@property
|
|
||||||
def filename(self):
|
|
||||||
# type: () -> str
|
|
||||||
_, netloc, path, _, _ = urllib_parse.urlsplit(self.url)
|
|
||||||
name = posixpath.basename(path.rstrip('/')) or netloc
|
|
||||||
name = urllib_parse.unquote(name)
|
|
||||||
assert name, ('URL %r produced no filename' % self.url)
|
|
||||||
return name
|
|
||||||
|
|
||||||
@property
|
|
||||||
def scheme(self):
|
|
||||||
# type: () -> str
|
|
||||||
return urllib_parse.urlsplit(self.url)[0]
|
|
||||||
|
|
||||||
@property
|
|
||||||
def netloc(self):
|
|
||||||
# type: () -> str
|
|
||||||
return urllib_parse.urlsplit(self.url)[1]
|
|
||||||
|
|
||||||
@property
|
|
||||||
def path(self):
|
|
||||||
# type: () -> str
|
|
||||||
return urllib_parse.unquote(urllib_parse.urlsplit(self.url)[2])
|
|
||||||
|
|
||||||
def splitext(self):
|
|
||||||
# type: () -> Tuple[str, str]
|
|
||||||
return splitext(posixpath.basename(self.path.rstrip('/')))
|
|
||||||
|
|
||||||
@property
|
|
||||||
def ext(self):
|
|
||||||
# type: () -> str
|
|
||||||
return self.splitext()[1]
|
|
||||||
|
|
||||||
@property
|
|
||||||
def url_without_fragment(self):
|
|
||||||
# type: () -> str
|
|
||||||
scheme, netloc, path, query, fragment = urllib_parse.urlsplit(self.url)
|
|
||||||
return urllib_parse.urlunsplit((scheme, netloc, path, query, None))
|
|
||||||
|
|
||||||
_egg_fragment_re = re.compile(r'[#&]egg=([^&]*)')
|
|
||||||
|
|
||||||
@property
|
|
||||||
def egg_fragment(self):
|
|
||||||
# type: () -> Optional[str]
|
|
||||||
match = self._egg_fragment_re.search(self.url)
|
|
||||||
if not match:
|
|
||||||
return None
|
|
||||||
return match.group(1)
|
|
||||||
|
|
||||||
_subdirectory_fragment_re = re.compile(r'[#&]subdirectory=([^&]*)')
|
|
||||||
|
|
||||||
@property
|
|
||||||
def subdirectory_fragment(self):
|
|
||||||
# type: () -> Optional[str]
|
|
||||||
match = self._subdirectory_fragment_re.search(self.url)
|
|
||||||
if not match:
|
|
||||||
return None
|
|
||||||
return match.group(1)
|
|
||||||
|
|
||||||
_hash_re = re.compile(
|
|
||||||
r'(sha1|sha224|sha384|sha256|sha512|md5)=([a-f0-9]+)'
|
|
||||||
)
|
|
||||||
|
|
||||||
@property
|
|
||||||
def hash(self):
|
|
||||||
# type: () -> Optional[str]
|
|
||||||
match = self._hash_re.search(self.url)
|
|
||||||
if match:
|
|
||||||
return match.group(2)
|
|
||||||
return None
|
|
||||||
|
|
||||||
@property
|
|
||||||
def hash_name(self):
|
|
||||||
# type: () -> Optional[str]
|
|
||||||
match = self._hash_re.search(self.url)
|
|
||||||
if match:
|
|
||||||
return match.group(1)
|
|
||||||
return None
|
|
||||||
|
|
||||||
@property
|
|
||||||
def show_url(self):
|
|
||||||
# type: () -> Optional[str]
|
|
||||||
return posixpath.basename(self.url.split('#', 1)[0].split('?', 1)[0])
|
|
||||||
|
|
||||||
@property
|
|
||||||
def is_wheel(self):
|
|
||||||
# type: () -> bool
|
|
||||||
return self.ext == WHEEL_EXTENSION
|
|
||||||
|
|
||||||
@property
|
|
||||||
def is_artifact(self):
|
|
||||||
# type: () -> bool
|
|
||||||
"""
|
|
||||||
Determines if this points to an actual artifact (e.g. a tarball) or if
|
|
||||||
it points to an "abstract" thing like a path or a VCS location.
|
|
||||||
"""
|
|
||||||
from pip._internal.vcs import vcs
|
|
||||||
|
|
||||||
if self.scheme in vcs.all_schemes:
|
|
||||||
return False
|
|
||||||
|
|
||||||
return True
|
|
||||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user