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Issue-356: Support Python 3.13 (#357)
* Issue-356: Support Python 3.13 * Fix deprecated upload/download artifact v3 * Fix deprecated upload/download artifact v3 for python * Fix dup artifact * Fix python test and dotnet artifact * Fix artifact for python again * Fix new dotnet and python issues * Fix download artifact * Fix test upload * Add merge-multiple * Try another fix for the python description * Try again * Revert the password removal
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‎.github/workflows/apps.yml‎

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@@ -53,9 +53,10 @@ jobs:
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- name: Test Artifacts
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run: ls dist/*
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v4
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if: matrix.buildtype == 'Release'
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with:
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name: artifact_${{matrix.os}}
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path: dist/*.*
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publish:
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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steps:
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- uses: actions/download-artifact@v3
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- uses: actions/download-artifact@v4
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with:
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name: artifact
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path: dist
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merge-multiple: true
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- name: Publish Artifacts to Github Releases
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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uses: fnkr/github-action-ghr@v1

‎.github/workflows/dotnet.yml‎

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- name: Configure Windows
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if: matrix.os == 'windows-latest'
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run: cmake ${{github.workspace}} -Ax64 -B${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{matrix.buildtype}} -DPACKAGE_OUTPUT_FILE_PREFIX=${{github.workspace}}/dist -DENABLE_SWIG=ON -DENABLE_PORTABLE=ON -DENABLE_EXAMPLES=OFF -DENABLE_CSHARP=ON -DENABLE_PYTHON=OFF -DCSHARP_TEST_FRAMEWORK=netcoreapp6
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run: cmake ${{github.workspace}} -Ax64 -B${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{matrix.buildtype}} -DPACKAGE_OUTPUT_FILE_PREFIX=${{github.workspace}}/dist -DENABLE_SWIG=ON -DENABLE_PORTABLE=ON -DENABLE_EXAMPLES=OFF -DENABLE_CSHARP=ON -DENABLE_PYTHON=OFF -DCSHARP_TEST_FRAMEWORK=netcoreapp8
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- name: Install Swig
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if: matrix.os == 'macOS-13'
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run: pip install swig==4.0.2 --prefix="$(pwd)/usr"
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- name: Configure OSX
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if: matrix.os == 'macOS-13'
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run: cmake ${{github.workspace}} -B${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{matrix.buildtype}} -DPACKAGE_OUTPUT_FILE_PREFIX=${{github.workspace}}/dist -DENABLE_SWIG=ON -DENABLE_PORTABLE=ON -DENABLE_EXAMPLES=OFF -DENABLE_CSHARP=ON -DENABLE_PYTHON=OFF -DCSHARP_TEST_FRAMEWORK=netcoreapp7 -DSWIG_EXECUTABLE=$(ls $(pwd)/usr/lib/python3.*/site-packages/swig/data/bin/swig) -DSWIG_DIR=$(dirname $(ls $(pwd)/usr/lib/python3.*/site-packages/swig/data/share/swig/4.0.2/swig.swg))
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run: cmake ${{github.workspace}} -B${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{matrix.buildtype}} -DPACKAGE_OUTPUT_FILE_PREFIX=${{github.workspace}}/dist -DENABLE_SWIG=ON -DENABLE_PORTABLE=ON -DENABLE_EXAMPLES=OFF -DENABLE_CSHARP=ON -DENABLE_PYTHON=OFF -DCSHARP_TEST_FRAMEWORK=netcoreapp8 -DSWIG_EXECUTABLE=$(ls $(pwd)/usr/lib/python3.*/site-packages/swig/data/bin/swig) -DSWIG_DIR=$(dirname $(ls $(pwd)/usr/lib/python3.*/site-packages/swig/data/share/swig/4.0.2/swig.swg))
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- name: Build OSX and Windows
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if: matrix.os != 'ubuntu-latest'
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- name: Test Artifacts
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run: ls dist/*
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v4
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if: matrix.buildtype == 'Release'
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with:
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name: artifact_${{matrix.os}}
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path: dist/illumina*.*
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publish:
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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steps:
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- uses: actions/download-artifact@v3
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- uses: actions/download-artifact@v4
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with:
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name: artifact
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path: dist
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merge-multiple: true
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- name: Publish Artifacts to Github Releases
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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uses: fnkr/github-action-ghr@v1

‎.github/workflows/python.yml‎

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strategy:
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matrix:
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os: [ubuntu-latest, windows-2019, macOS-13]
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pyver: ['3.8', '3.9', '3.10', '3.11', '3.12']
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pyver: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
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steps:
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- uses: actions/checkout@v3
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git --version
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- name: Package Python 3.8 and earlier
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if: matrix.os == 'ubuntu-latest' && matrix.pyver != '3.9' && matrix.pyver != '3.10' && matrix.pyver != '3.11' && matrix.pyver != '3.12'
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if: matrix.os == 'ubuntu-latest' && matrix.pyver != '3.9' && matrix.pyver != '3.10' && matrix.pyver != '3.11' && matrix.pyver != '3.12' && matrix.pyver != '3.13'
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run: docker run --rm -v ${{github.workspace}}/:/io ezralanglois/interop sh /io/tools/package.sh /io /io/dist travis OFF
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- name: Package Python 3.9
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if: matrix.os == 'ubuntu-latest' && matrix.pyver == '3.11'
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run: docker run --rm -v ${{github.workspace}}/:/io $DOCKER_IMAGE sh /io/tools/package.sh /io /io/dist travis OFF Release cp311-cp311
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- name: Package Python 3.11
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- name: Package Python 3.12
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if: matrix.os == 'ubuntu-latest' && matrix.pyver == '3.12'
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run: docker run --rm -v ${{github.workspace}}/:/io $DOCKER_IMAGE sh /io/tools/package.sh /io /io/dist travis OFF Release cp312-cp312
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- name: Package Python 3.13
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if: matrix.os == 'ubuntu-latest' && matrix.pyver == '3.13'
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run: docker run --rm -v ${{github.workspace}}/:/io $DOCKER_IMAGE sh /io/tools/package.sh /io /io/dist travis OFF Release cp313-cp313
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- name: Windows Package Python
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if: matrix.os == 'windows-2019'
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shell: cmd
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if: matrix.os == 'macOS-latest' || matrix.os == 'macOS-13'
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run: bash ./tools/package.sh ${{github.workspace}} ${{github.workspace}}/dist travis OFF Release ${{matrix.pyver}}
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v4
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with:
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name: artifact_${{matrix.pyver}}_${{matrix.os}}
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path: dist/*.whl
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publishtest:
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if: startsWith(github.ref, 'refs/tags') != true
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steps:
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- uses: actions/download-artifact@v3
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- uses: actions/download-artifact@v4
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with:
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name: artifact
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path: dist
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merge-multiple: true
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- name: Print dist
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run: ls -lR dist
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- name: Test Publish a Python distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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packages_dir: ./dist
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repository_url: https://test.pypi.org/legacy/
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skip_existing: true
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verbose: true
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publish:
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needs: [build]
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runs-on: ubuntu-latest
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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steps:
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- uses: actions/download-artifact@v3
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- uses: actions/download-artifact@v4
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with:
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name: artifact
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path: dist
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merge-multiple: true
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- name: Publish a Python distribution to PyPI
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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uses: pypa/gh-action-pypi-publish@release/v1

‎README.md‎

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@@ -10,8 +10,8 @@ Illumina sequencers including **NextSeq 1k/2k** and NovaSeqX. These libraries ar
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with one exception: GA systems have been excluded.
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***
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> We now support an interface to 3.8-3.12
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> Note that 3.10-3.12 are CentOS 7 or later while earlier versions support Centos 5 or later
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> We now support an interface to 3.8-3.13
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> Note that 3.10-3.13 are CentOS 7 or later while earlier versions support Centos 5 or later
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> Note: dumptext has been deprecated in favor of imaging_table and will be removed in the next version
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***
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### Python
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Supported versions for binary distribution: 3.5-3.10.
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Supported versions for binary distribution: 3.8-3.13.
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** Python 2.7 support has been removed **
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** Python 2.7, 3.5, 3.6, 3.7 support has been removed **
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You should have NumPy already installed.
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‎docs/src/changes.md‎

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# Changes {#changes}
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## v1.4.0
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| Date | Description |
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|------------|--------------------------------|
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| 2025-03-13 | Issue-356: Support Python 3.13 |
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## v1.3.2
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| Date | Description |

‎docs/src/index.md‎

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the original data (collapsed quality scores).
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***
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> We now support an interface to Python 3.6 to 3.11 (see contents below)
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> We now support an interface to Python 3.8 to 3.13 (see contents below)
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***
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Compatibility

‎docs/src/install.md‎

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Note, we only distribute from GitHub currently, and not PyPi or NuGet.org. These should
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be compatible with most Linux Versions, Mac OSX and Windows. We support
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Python 3.8 to 3.12.
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Python 3.8 to 3.13.
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### Binary Archive (C++, C#, Python, Java)
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$ pip install interop
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~~~~~~~~~~~~~
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Supported versions for binary distribution: 3.8 to 3.12.
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Supported versions for binary distribution: 3.8 to 3.13.
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Test the installation
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‎docs/src/python_binding.md‎

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$ pip install -f https://github.com/Illumina/interop/releases/tag/v1.1.2 interop
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$ pip install -f https://github.com/Illumina/interop/releases/latest interop
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Note, only Python versions 3.8 to 3.12 are currently
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Note, only Python versions 3.8 to 3.13 are currently
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supported as binary builds. Other Python versions must be built
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from source.
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‎src/ext/python/__main__.py.in‎

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parser.set_defaults(test=False)
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param = parser.parse_args()
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if param.test:
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testsuite = unittest.makeSuite(CoreTests)
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testsuite = unittest.defaultTestLoader.loadTestsFromTestCase(CoreTests)
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unittest.TextTestRunner(verbosity=1).run(testsuite)
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interop.core._run_doctests()
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‎src/ext/python/setup.py.in‎

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setup(
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name='interop',
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version='@INTEROP_VERSION@',
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description="""The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files
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produced by Illumina sequencers. These libraries are backwards compatible and capable of supporting
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prior releases of the software, with one exception: GA systems have been excluded.""",
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description="The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files.",
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long_description="""The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files
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produced by Illumina sequencers. These libraries are backwards compatible and capable of supporting
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prior releases of the software, with one exception: GA systems have been excluded.""",

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