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Merge pull request #11 from Becksteinlab/ci-cd
updated GitHub Actions workflow for package deployment
2 parents e37accf + e14e78d commit 157fcac

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‎.github/workflows/deploy.yaml‎

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@@ -1,4 +1,4 @@
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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:
@@ -9,45 +9,188 @@ on:
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- published
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jobs:
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test_pypi_push:
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environment:
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name: deploy
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url: https://test.pypi.org/p/mdpow-molconfgen
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permissions:
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id-token: write
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if: |
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github.repository == 'Becksteinlab/mdpow-molconfgen' &&
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(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
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name: Build, upload and test pure Python wheels to TestPypi
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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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- 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: 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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- name: Download dist files
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uses: actions/download-artifact@v4
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with:
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test_submission: true
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package_name: 'molconfgen'
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name: dist-files
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path: dist/
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pypi_push:
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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 molconfgen; 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 molconfgen
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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/mdpow-molconfgen' &&
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(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
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environment:
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name: deploy
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url: https://pypi.org/p/mdpow-molconfgen
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name: testpypi
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url: https://test.pypi.org/p/mdpow-molconfgen
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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/mdpow-molconfgen' &&
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(github.event_name == 'release' && github.event.action == 'published')
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name: Build, upload and test pure Python wheels to PyPi
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/mdpow-molconfgen
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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@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/mdpow-molconfgen' &&
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(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
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steps:
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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: 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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- 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/ mdpow-molconfgen[test]
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- name: Test import
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run: |
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python -c "import molconfgen; 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 molconfgen; print('Package version:', molconfgen.__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/mdpow-molconfgen' &&
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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@v5
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with:
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package_name: 'molconfgen'
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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 mdpow-molconfgen[test]
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- name: Test import
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run: |
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python -c "import molconfgen; 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 molconfgen; print('Package version:', molconfgen.__version__)"

‎README.md‎

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@@ -26,7 +26,7 @@ Generation of conformers of small molecules.
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### Initial testing systems ###
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From the [COW dataset](https://github.com/Becksteinlab/sampl5-distribution-water-cyclohexane/tree/master/11_validation_dataset92):
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From the [COW dataset](https://github.com/Becksteinlab/cow-dataset):
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- V36-methylacetate : 1 dihedral
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- V46-2-methyl-1-nitrobenzene : steric hindrance
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Below we provide instructions both for `mamba` and
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for `pip`.
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#### With mamba
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Note that for some functionality you also need a working [GROMACS](https://www.gromacs.org) installation.
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#### With pip from PyPi
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You can directly install the [mdpow-molconfgen package](https://pypi.org/project/mdpow-molconfgen/) PyPi package with
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```
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pip install mdpow-molconfgen
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```
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This will install all dependencies (except GROMACS).
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#### With mamba from source
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Ensure that you have [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) installed.
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mamba deactivate
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```
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#### With pip
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#### With pip from source
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To build the package from source, run:
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‎pyproject.toml‎

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@@ -21,6 +21,7 @@ readme = "README.md"
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requires-python = ">=3.9"
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dependencies = [
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"MDAnalysis>=2.0.0",
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"pyedr",
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"rdkit",
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"numpy",
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"tqdm",
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"sphinx_rtd_theme",
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]
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# [project.urls]
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# source = "https://github.com/becksteinlab/mdpow-molconfgen"
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# documentation = "https://mdpow-molconfgen.readthedocs.io"
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[project.urls]
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source = "https://github.com/becksteinlab/mdpow-molconfgen"
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documentation = "https://mdpow-molconfgen.readthedocs.io"
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[tool.setuptools]
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packages = ["molconfgen", "molconfgen.tests", "molconfgen.data"]

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