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update Python and workflows
- NEP: removed 3.9, 3.10, added 3.13, 3.14 - update actions versions - updated deployment workflow - based on gridData - removed MDAnalysis deployment action - use trusted publishing (as before) - bump python to 3.14 for workflow steps - do not run online tests for deployment workflow - renamed deploy.yaml -> deploy.yml and setup trusted publishers - improved debugging - verbose output for testpypi deployment to aid debugging - allow testpypi deployment to pass when file already uploaded (testing only)
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‎.github/workflows/deploy.yaml‎

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‎.github/workflows/deploy.yml‎

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name: PyPi Package Deployment
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on:
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push:
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tags:
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- "*"
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release:
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types:
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- published
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concurrency:
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group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}"
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cancel-in-progress: false
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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build:
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name: Build package
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v6
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: "3.14"
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- name: Install build dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build twine
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- name: Build package (binary wheel and source distribution package)
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run: |
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python -m build
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- name: Check package
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run: |
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twine check dist/*
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- name: Upload dist files
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uses: actions/upload-artifact@v7
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with:
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name: dist-files
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path: dist/
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retention-days: 1
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test-pytest:
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name: Run tests
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runs-on: ubuntu-latest
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needs: build
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steps:
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: "3.14"
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- name: Download dist files
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uses: actions/download-artifact@v8
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with:
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name: dist-files
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path: dist/
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- name: Install package with test dependencies and tests
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run: |
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python -m pip install --upgrade pip
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WHEEL_FILE=$(ls dist/*.whl)
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pip install "$WHEEL_FILE"[test]
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- name: Test import
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run: |
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python -c "import MDAnalysisData; print(f'Package {MDAnalysisData.__version__} imported successfully')"
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- name: Run basic tests
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run: |
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pytest --verbose -m "not online" --pyargs MDAnalysisData
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deploy-testpypi:
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name: Deploy to TestPyPI
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runs-on: ubuntu-latest
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needs: [build, test-pytest]
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if: |
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github.repository == 'MDAnalysis/MDAnalysisData' &&
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(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
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environment:
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name: testpypi
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url: https://test.pypi.org/p/MDAnalysisData
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permissions:
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id-token: write # IMPORTANT: mandatory for trusted publishing
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steps:
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- name: Download dist files
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uses: actions/download-artifact@v8
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with:
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name: dist-files
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path: dist/
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- name: Publish to TestPyPI
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uses: pypa/gh-action-pypi-publish@v1.13.0
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with:
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repository-url: https://test.pypi.org/legacy/
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verbose: true # useful debugging info (eg wrong classifiers)
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skip-existing: true # allows repeated testing with same tag
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deploy-pypi:
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name: Deploy to PyPI
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runs-on: ubuntu-latest
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needs: [build, test-pytest]
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if: |
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github.repository == 'MDAnalysis/MDAnalysisData' &&
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(github.event_name == 'release' && github.event.action == 'published')
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environment:
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name: pypi
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url: https://pypi.org/p/MDAnalysisData
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permissions:
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id-token: write # IMPORTANT: mandatory for trusted publishing
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steps:
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- name: Download dist files
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uses: actions/download-artifact@v8
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with:
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name: dist-files
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path: dist/
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@v1.13.0
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test-deployed-testpypi:
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name: Test deployed package (TestPyPI)
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest]
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needs: deploy-testpypi
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if: |
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github.repository == 'MDAnalysis/MDAnalysisData' &&
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(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
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steps:
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: "3.14"
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- name: Install from TestPyPI
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run: |
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python -m pip install --upgrade pip
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pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ MDAnalysisData[test]
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- name: Test import
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run: |
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python -c "import MDAnalysisData; print(f'Package {MDAnalysisData.__version__} imported successfully from TestPyPi')"
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- name: Run basic tests
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run: |
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pytest --verbose -m "not online" --pyargs MDAnalysisData
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test-deployed-pypi:
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name: Test deployed package (PyPI)
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest]
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needs: deploy-pypi
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if: |
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github.repository == 'MDAnalysis/MDAnalysisData' &&
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(github.event_name == 'release' && github.event.action == 'published')
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steps:
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: "3.14"
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- name: Install from PyPI
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run: |
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python -m pip install --upgrade pip
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pip install MDAnalysisData[test]
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- name: Test import
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run: |
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python -c "import MDAnalysisData; print(f'Package {MDAnalysisData.__version__} imported successfully from PyPi')"
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- name: Run basic tests
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run: |
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pytest --verbose -m "not online" --pyargs MDAnalysisData

‎.github/workflows/docs.yml‎

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v6
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with:
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fetch-depth: 0
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- name: Setup python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v6
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with:
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python-version: 3.9
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python-version: 3.14
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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make html
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- name: deploy docs
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uses: peaceiris/actions-gh-pages@v3
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uses: peaceiris/actions-gh-pages@v4
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./docs/_build/html

‎.github/workflows/gh-ci.yml‎

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fail-fast: false
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matrix:
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os: [ubuntu-latest]
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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python-version: ["3.11", "3.12", "3.13", "3.14"]
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include:
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- os: macOS-latest
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python-version: "3.9"
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python-version: "3.11"
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- os: macOS-latest
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python-version: "3.12"
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python-version: "3.14"
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- os: windows-latest
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python-version: "3.9"
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python-version: "3.11"
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- os: windows-latest
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python-version: "3.12"
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python-version: "3.14"
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v6
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with:
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fetch-depth: 0
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- name: Setup python
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install package dependencies
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run: |
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python -m pip install six setuptools tqdm
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python -m pip install setuptools tqdm
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- name: Install package
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run: |
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- name: Codecov
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if: github.event_name != 'schedule'
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uses: codecov/codecov-action@v4
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uses: codecov/codecov-action@v6
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with:
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name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
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token: ${{ secrets.CODECOV_TOKEN }}

‎CHANGELOG.md‎

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## Unreleased
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## Changes
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### Changes
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- Update package to only support NEP29 range (Python 3.11 - 3.14 as of writing)
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- Update packaging to be PEP518 compliant.
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### Fixes
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- removed deprecated pkg_resources use (#75)
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## [0.9.0] - 2023-10-30
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### Changes

‎pyproject.toml‎

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"Operating System :: Microsoft :: Windows ",
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"Programming Language :: Python",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Programming Language :: Python :: 3.13",
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"Programming Language :: Python :: 3.14",
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"Topic :: Scientific/Engineering",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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"Topic :: Scientific/Engineering :: Chemistry",
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"Topic :: Software Development :: Libraries :: Python Modules",
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]
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readme = {file = "README.md", content-type = "text/markdown"}
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requires-python = ">=3.9"
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requires-python = ">=3.11"
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dependencies = [
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"tqdm",
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]

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