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updated CI/CD deployment workflow
- directly use pypa workflow (instead of MDAnalysis deployment workflow) - use different steps for build and deploy - introduce environments testpypi and pypi - test before upload
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‎.github/workflows/deploy.yaml‎

Lines changed: 174 additions & 35 deletions
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name: Build and upload to PyPi
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name: Build and Deploy Package
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on:
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push:
@@ -9,49 +9,188 @@ on:
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- published
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jobs:
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test_pypi_push:
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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@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.x"
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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@v4
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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-install:
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name: Test package installation
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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@v5
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with:
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python-version: "3.x"
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- name: Download dist files
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uses: actions/download-artifact@v4
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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
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run: |
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python -m pip install --upgrade pip
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pip install dist/*.whl
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- name: Test import
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run: |
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python -c "import gromacs; print('Package imported successfully')"
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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@v5
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with:
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python-version: "3.x"
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- name: Download dist files
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uses: actions/download-artifact@v4
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with:
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name: dist-files
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path: dist/
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- name: Install system dependencies (GROMACS)
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run: |
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sudo apt-get update
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sudo apt-get install -y gromacs
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- name: Install package with test dependencies
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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: Run tests
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run: |
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pytest -n auto --verbose --pyargs gromacs
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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-install, test-pytest]
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if: |
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github.repository == 'Becksteinlab/GromacsWrapper' &&
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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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name: testpypi
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url: https://test.pypi.org/p/GromacsWrapper
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permissions:
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id-token: write
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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@v4
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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@v1.12.4
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with:
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repository-url: https://test.pypi.org/legacy/
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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-install, test-pytest]
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if: |
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github.repository == 'Becksteinlab/GromacsWrapper' &&
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(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
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name: "TestPyPi: Build and upload pure Python wheels"
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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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- name: testpypi_deploy
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uses: MDAnalysis/pypi-deployment@main
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
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with:
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test_submission: true
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package_name: 'GromacsWrapper'
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module_name: 'gromacs'
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tests: false
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pypi_push:
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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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name: pypi
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url: https://pypi.org/p/GromacsWrapper
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permissions:
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id-token: write
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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@v4
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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@v1.12.4
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test-deployed-testpypi:
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name: Test deployed package (TestPyPI)
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runs-on: ubuntu-latest
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needs: deploy-testpypi
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if: |
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github.repository == 'Becksteinlab/GromacsWrapper' &&
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(github.event_name == 'release' && github.event.action == 'published')
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name: "PyPi: Build and upload pure Python wheels"
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runs-on: ubuntu-latest
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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@v5
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with:
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python-version: "3.x"
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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/ GromacsWrapper[test]
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- name: Test import
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run: |
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python -c "import gromacs; print('Package imported successfully from TestPyPI')"
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- name: Run basic tests
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run: |
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python -c "import gromacs; print('Package version:', gromacs.__version__)"
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test-deployed-pypi:
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name: Test deployed package (PyPI)
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runs-on: ubuntu-latest
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needs: deploy-pypi
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if: |
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github.repository == 'Becksteinlab/GromacsWrapper' &&
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(github.event_name == 'release' && github.event.action == 'published')
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steps:
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- uses: actions/checkout@v4
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- name: pypi_deploy
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uses: MDAnalysis/pypi-deployment@main
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if: github.event_name == 'release' && github.event.action == 'published'
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with:
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package_name: 'GromacsWrapper'
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module_name: 'gromacs'
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tests: false
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.x"
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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 GromacsWrapper[test]
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- name: Test import
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run: |
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python -c "import gromacs; print('Package imported successfully from PyPI')"
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- name: Run basic tests
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run: |
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python -c "import gromacs; print('Package version:', gromacs.__version__)"

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