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orbeckstorbeckst
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Merge branch 'main' into fix-issue-72
2 parents 5b0bac4 + 410ff43 commit e810164

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Lines changed: 161 additions & 198 deletions

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‎.github/workflows/deploy.yaml‎

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defaults:
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run:
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shell: bash
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shell: bash -l {0}
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jobs:
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fail-fast: false
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matrix:
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buildplat:
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- [ubuntu-20.04, manylinux_x86_64, x86_64]
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- [macos-11, macosx_*, x86_64]
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- [windows-2019, win_amd64, AMD64]
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- [macos-14, macosx_*, arm64]
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python: ["cp39", "cp310", "cp311", "cp312"]
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- [ubuntu-22.04, manylinux_x86_64, x86_64]
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- [windows-2022, win_amd64, AMD64]
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- [macos-15, macosx_*, arm64]
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python: ["cp311", "cp312", "cp313", "cp314"]
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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: Build wheels
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uses: pypa/cibuildwheel@v2.16.5
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uses: pypa/cibuildwheel@v3.4.0
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env:
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CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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CIBW_ARCHS: ${{ matrix.buildplat[2] }}
@@ -53,8 +52,9 @@ jobs:
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if: |
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(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')) ||
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(github.event_name == 'release' && github.event.action == 'published')
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v7
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with:
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name: wheel-${{ matrix.buildplat[0] }}-${{ matrix.python }}
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path: wheelhouse/*.whl
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retention-days: 7
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@@ -63,20 +63,32 @@ jobs:
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name: build package source distribution
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runs-on: ubuntu-latest
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timeout-minutes: 10
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outputs:
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version: ${{ steps.extract-version.outputs.version }}
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v6
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with:
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fetch-depth: 0
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- name: Build sdist
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run: pipx run build --sdist
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- name: Extract package version
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id: extract-version
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run: |
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SDIST_FILE=$(ls dist/*.tar.gz)
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# Extract version from sdist archive (format: mdaencore-1.0.1rc1.tar.gz)
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VERSION=$(tar xf ${SDIST_FILE} -O --wildcards '*/*.egg-info/PKG-INFO' | awk '/^Version:/ {print $2}')
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echo "version=$VERSION" >> $GITHUB_OUTPUT
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echo "Extracted version: $VERSION"
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- name: upload artifacts
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if: |
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(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')) ||
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(github.event_name == 'release' && github.event.action == 'published')
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uses: actions/upload-artifact@v3
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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/*.tar.gz
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retention-days: 7
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@@ -93,16 +105,16 @@ jobs:
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runs-on: ubuntu-latest
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needs: [build_wheels, build_sdist]
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steps:
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- uses: actions/download-artifact@v3
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- uses: actions/download-artifact@v8
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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: upload_source_and_wheels
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uses: pypa/gh-action-pypi-publish@v1.8.10
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uses: pypa/gh-action-pypi-publish@v1.14.0
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with:
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skip_existing: true
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repository_url: https://test.pypi.org/legacy/
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skip-existing: true
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repository-url: https://test.pypi.org/legacy/
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upload_pypi:
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if: |
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runs-on: ubuntu-latest
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needs: [build_wheels, build_sdist]
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steps:
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- uses: actions/download-artifact@v3
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- uses: actions/download-artifact@v8
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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: upload_source_and_wheels
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uses: pypa/gh-action-pypi-publish@v1.8.10
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uses: pypa/gh-action-pypi-publish@v1.14.0
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check_testpypi:
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if: |
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name: testpypi check
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runs-on: ${{ matrix.os }}
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timeout-minutes: 60
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needs: upload_testpypi
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needs: [upload_testpypi, build_sdist]
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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, windows-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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steps:
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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: ${{ matrix.python-version }}
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- name: pip install
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- name: Wait for version to be available on TestPyPI (30 seconds)
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run: sleep 30
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- name: pip install mdaencore from testpypi (${{ needs.build_sdist.outputs.version }})
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run: |
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pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple mdaencore
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pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "mdaencore==${{ needs.build_sdist.outputs.version }}"
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- name: install test deps
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run: |

‎.github/workflows/docs.yaml‎

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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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_miniconda
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uses: conda-incubator/setup-miniconda@v2
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uses: conda-incubator/setup-miniconda@v4
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with:
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python-version: 3.11
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python-version: 3.14
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environment-file: docs/requirements.yaml
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auto-update-conda: true
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channel-priority: flexible
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channels: conda-forge
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miniforge-variant: Mambaforge
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miniforge-version: latest
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use-mamba: true
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- name: Build and install package
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user_name: 'github-actions'
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user_email: 'github-action@users.noreply.github.com'
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v7
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if: github.event_name == 'pull_request'
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with:
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name: pr_docs

‎.github/workflows/gh-ci.yaml‎

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defaults:
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run:
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shell: bash -l {0}
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shell: bash -el {0}
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jobs:
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main-tests:
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strategy:
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fail-fast: false
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matrix:
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# macos-13 is x86_64 and macos-14 is arm64
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os: [ubuntu-latest, windows-latest, macos-14, macos-13]
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python-version: ["3.10", "3.11", "3.12"]
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# macos-latest = arm64, macos-15-intel = x86_64
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os: [ubuntu-latest, windows-latest, macos-latest, macos-15-intel]
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python-version: ["3.11", "3.12", "3.13", "3.14"]
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mdanalysis-version: ["latest", "develop"]
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# Manually exclude any combinations of the test matrix that can't be run
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exclude:
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# The latest release of MDAnalysis only supports up to Python 3.11
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# so we exclude 3.12 from the test matrix (issue #68)
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- python-version: "3.12"
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mdanalysis-version: "latest"
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#exclude:
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# - python-version: "3.12"
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# mdanalysis-version: "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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# More info on options: https://github.com/conda-incubator/setup-miniconda
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- name: Install conda dependencies
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uses: conda-incubator/setup-miniconda@v3
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uses: conda-incubator/setup-miniconda@v4
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with:
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python-version: ${{ matrix.python-version }}
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environment-file: devtools/conda-envs/test_env.yaml
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add-pip-as-python-dependency: true
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miniforge-variant: Mambaforge
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miniforge-version: latest
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use-mamba: true
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channels: conda-forge, defaults
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channels: conda-forge
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activate-environment: mdaencore-test
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auto-update-conda: true
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with:
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version: ${{ matrix.mdanalysis-version }}
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install-tests: true
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installer: mamba
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shell: bash -l {0}
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installer: conda
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shell: bash -el {0}
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- name: Install package
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run: |
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- name: codecov
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if: github.repository == 'MDAnalysis/mdaencore' && github.event_name != 'schedule'
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uses: codecov/codecov-action@v4
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uses: codecov/codecov-action@v6
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with:
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file: coverage.xml
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files: coverage.xml
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name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
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token: ${{ secrets.CODECOV_TOKEN }}
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verbose: True
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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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- name: Set up 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: "3.11"
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python-version: "3.14"
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- name: Install Pylint
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run: |
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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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- name: Set up 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: "3.11"
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python-version: "3.14"
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- name: Install dependencies
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run: |

‎CHANGELOG.md‎

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- ianmkenney
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- tylerjereddy
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- IAlibay
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- orbeckst
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- chr-sa
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### Added
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<!-- Added functionality -->
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3031
### Fixed
32+
- Fix "NameError" for "long" in mdaencore/clustering/affinityprop.pyx (#72, PR #78)
3133
- All dependencies added to pyproject.toml, setup.py, and conda envs (#57)
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- Temporary fix for Windows integer size default change in NumPy 2.0.0
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- Temporary fix for Windows integer size default change in NumPy 2.0.0 (PR #60)
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### Changed
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- Update CI and wheel deployment to include macos-arm64 and py3.12 (PR #63)
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- Minimum Python version has been raised to 3.10 (PR #66)
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- Minimum Python version has been raised to 3.11 (PR #66, PR #76)
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- Minimum MDAnalysis version has been raised to 2.1.0 (PR #66)
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### Deprecated

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