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Merge pull request #82 from MDAnalysis/update-python-and-gh
update Python and workflows - NEP: removed 3.9, 3.10, added 3.13, 3.14 - update workflows - actions versions updated - improved automatic deployment - fix update package metadata #83
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‎.github/actions/wait-for-pypi-version/action.yaml‎

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name: 'Wait for PyPI version'
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description: 'Wait for a specific package version to become available on PyPI or TestPyPI'
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inputs:
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repository:
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description: 'PyPI repository type: "pypi" or "testpypi"'
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required: true
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package:
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description: 'Package name'
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required: true
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version:
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description: 'Package version to wait for'
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required: true
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max_attempts:
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description: 'Maximum number of retry attempts'
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required: false
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default: '30'
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wait_seconds:
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description: 'Seconds to wait between attempts'
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required: false
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default: '10'
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runs:
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using: composite
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steps:
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- name: Install requests
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shell: bash
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run: |
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python -m pip install --upgrade pip
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pip install requests
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- name: Wait for version to be available
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shell: python
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env:
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REPOSITORY: ${{ inputs.repository }}
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PACKAGE: ${{ inputs.package }}
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VERSION: ${{ inputs.version }}
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MAX_ATTEMPTS: ${{ inputs.max_attempts }}
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WAIT_SECONDS: ${{ inputs.wait_seconds }}
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run: |
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import os
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import sys
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import time
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import requests
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repository = os.environ["REPOSITORY"].strip().lower()
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package = os.environ["PACKAGE"]
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version = os.environ["VERSION"]
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max_attempts = int(os.environ.get("MAX_ATTEMPTS", "30"))
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wait_seconds = int(os.environ.get("WAIT_SECONDS", "10"))
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if repository == "testpypi":
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api_url = f"https://test.pypi.org/pypi/{package}/json"
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repo_name = "TestPyPI"
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elif repository == "pypi":
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api_url = f"https://pypi.org/pypi/{package}/json"
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repo_name = "PyPI"
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else:
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print(
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f"ERROR: repository must be 'pypi' or 'testpypi', got {repository!r}",
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file=sys.stderr,
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)
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sys.exit(1)
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for attempt in range(max_attempts):
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try:
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r = requests.get(api_url, timeout=10)
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r.raise_for_status()
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data = r.json()
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versions = data.get("releases", {})
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keys = list(versions.keys())
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print("Available versions:", keys[-10:]) # Show last 10 versions
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if version in versions:
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print(f"✓ Version {version} is available on {repo_name}")
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print(f"Version {version} is now available on {repo_name}")
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sys.exit(0)
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print(f"✗ Version {version} is NOT available on {repo_name}")
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except Exception as e:
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print(f"Error checking version: {e}")
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current = attempt + 1
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print(
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f"Attempt {current}/{max_attempts}: Version {version} not yet available "
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f"on {repo_name}, waiting {wait_seconds} seconds..."
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)
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time.sleep(wait_seconds)
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print(
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f"ERROR: Version {version} did not become available on {repo_name} "
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f"after {max_attempts} attempts",
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file=sys.stderr,
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)
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sys.exit(1)

‎.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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outputs:
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version: ${{ steps.extract-version.outputs.version }}
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steps:
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- name: Checkout
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uses: actions/checkout@v6
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with:
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fetch-depth: 0
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fetch-tags: true
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: "3.14"
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- name: Install build dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build twine
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- name: Build package (binary wheel and source distribution package)
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run: python -m build
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- name: Check package
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run: twine check dist/*
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- name: Extract package version
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id: extract-version
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run: |
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WHEEL_FILE=$(ls dist/*.whl)
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VERSION=$(basename "$WHEEL_FILE" | sed -n 's/mdanalysisdata-\([^-]*\)-.*/\1/p')
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if [ -z "$VERSION" ]; then
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python -m pip install --upgrade pip
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pip install "$WHEEL_FILE" --quiet
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VERSION=$(python -c "import MDAnalysisData; print(MDAnalysisData.__version__)")
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pip uninstall -y MDAnalysisData --quiet
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fi
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echo "version=$VERSION" >> "$GITHUB_OUTPUT"
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echo "Extracted version: $VERSION"
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- name: Upload dist files
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uses: actions/upload-artifact@v7
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with:
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name: dist-files
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path: dist/
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retention-days: 1
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test-pytest:
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name: Run tests
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runs-on: ubuntu-latest
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needs: build
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steps:
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: "3.14"
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- name: Download dist files
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uses: actions/download-artifact@v8
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with:
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name: dist-files
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path: dist/
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- name: Install package with test dependencies and tests
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run: |
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python -m pip install --upgrade pip
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WHEEL_FILE=$(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 tests (without data file downloads)
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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: [build, 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: Checkout repository for actions
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uses: actions/checkout@v6
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with:
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path: source # put code under different path and do not cd to avoid interference with pytest invocation (missing authors.py)
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- name: Wait for version to be available on TestPyPI
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uses: ./source/.github/actions/wait-for-pypi-version
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with:
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repository: testpypi
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package: MDAnalysisData
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version: ${{ needs.build.outputs.version }}
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- name: Install from TestPyPI
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run: |
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python -m pip install --upgrade pip
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pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ "MDAnalysisData[test]==${{ needs.build.outputs.version }}"
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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 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: [build, 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: Checkout repository for actions
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uses: actions/checkout@v6
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with:
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path: source # put code under different path and do not cd to avoid interference with pytest invocation (missing authors.py)
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- name: Wait for version to be available on PyPI
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uses: ./source/.github/actions/wait-for-pypi-version
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with:
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repository: pypi
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package: MDAnalysisData
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version: ${{ needs.build.outputs.version }}
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- name: Install from PyPI
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run: |
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python -m pip install --upgrade pip
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pip install "MDAnalysisData[test]==${{ needs.build.outputs.version }}"
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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 tests
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run: |
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pytest --verbose -m "not online" --pyargs MDAnalysisData

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