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orbeckstorbeckst
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updated deployment workflow
- ensure proper version is installed for testing - wait for release to appear on PyPi - source: https://github.com/Becksteinlab/multibind
1 parent 9d1e73c commit 977b316

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Lines changed: 276 additions & 22 deletions

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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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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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testpypi_push:
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build:
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name: Build package
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if: github.repository == 'MDAnalysis/PathSimAnalysis'
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runs-on: ubuntu-latest
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outputs:
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version: ${{ steps.extract-version.outputs.version }}
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steps:
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- name: Checkout
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uses: actions/checkout@v7
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with:
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fetch-depth: 0
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fetch-tags: true
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: "3.11"
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- name: Install build dependencies
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run: |
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python -m pip install --upgrade pip
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pip install "setuptools>=61.2,<81" build twine
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- name: Build package (wheel and sdist)
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run: python -m build
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- name: Check package
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run: twine check dist/*
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- name: Extract package version
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id: extract-version
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run: |
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WHEEL_FILE=$(ls dist/*.whl)
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VERSION=$(basename "$WHEEL_FILE" | sed -n 's/pathsimanalysis-\([^-]*\)-.*/\1/p')
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if [ -z "$VERSION" ]; then
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pip install "$WHEEL_FILE" --quiet
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VERSION=$(python -c "import pathsimanalysis; print(pathsimanalysis.__version__)")
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pip uninstall -y pathsimanalysis --quiet
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fi
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echo "version=$VERSION" >> "$GITHUB_OUTPUT"
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echo "Extracted version: $VERSION"
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- name: Upload dist files
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uses: actions/upload-artifact@v7
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with:
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name: dist-files
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path: dist/
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retention-days: 1
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test-pytest:
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name: Run tests
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if: github.repository == 'MDAnalysis/PathSimAnalysis'
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runs-on: ubuntu-latest
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needs: build
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steps:
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: "3.11"
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- name: Download dist files
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uses: actions/download-artifact@v8
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with:
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name: dist-files
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path: dist/
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- name: Install wheel with test extras
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run: |
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python -m pip install --upgrade pip
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WHEEL_FILE=$(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 pathsimanalysis; print(f'Package {pathsimanalysis.__version__} imported successfully')"
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- name: Run tests
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run: pytest -v --pyargs pathsimanalysis.tests
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deploy-testpypi:
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name: Deploy to TestPyPI
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if: |
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github.repository == 'MDAnalysis/PathSimAnalysis' &&
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(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
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runs-on: ubuntu-latest
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needs: [build, test-pytest]
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environment:
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name: deploy
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url: https://test.pypi.org/p/pathsimanalysis
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permissions:
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id-token: write
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if: |
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github.repository == 'MDAnalysis/PathSimAnalysis' &&
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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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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v7
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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: testpypi_deploy
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uses: MDAnalysis/pypi-deployment@main
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- name: Publish to TestPyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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test_submission: true
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tests: true
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test_deps: 'pytest MDAnalysisTests'
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package_name: 'pathsimanalysis'
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repository-url: https://test.pypi.org/legacy/
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verbose: true
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skip-existing: true
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pypi_push:
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deploy-pypi:
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name: Deploy to PyPI
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if: |
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github.repository == 'MDAnalysis/PathSimAnalysis' &&
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(github.event_name == 'release' && github.event.action == 'published')
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runs-on: ubuntu-latest
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needs: [build, test-pytest]
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environment:
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name: deploy
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url: https://pypi.org/p/pathsimanalysis
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permissions:
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id-token: write
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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@release/v1
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test-deployed-testpypi:
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name: Test deployed package (TestPyPI)
41149
if: |
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github.repository == 'MDAnalysis/PathSimAnalysis' &&
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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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(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
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runs-on: ubuntu-latest
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needs: [build, deploy-testpypi]
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steps:
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- name: Checkout repository for actions
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uses: actions/checkout@v7
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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: "3.11"
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- name: Wait for version to be available on TestPyPI
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uses: ./.github/actions/wait-for-pypi-version
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with:
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repository: testpypi
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package: pathsimanalysis
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version: ${{ needs.build.outputs.version }}
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- name: Install from TestPyPI
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run: |
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python -m pip install --upgrade pip
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pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ "pathsimanalysis[test]==${{ needs.build.outputs.version }}"
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- name: Test import
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run: |
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python -c "import pathsimanalysis; print(f'Package {pathsimanalysis.__version__} imported successfully from TestPyPI')"
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- name: Run tests
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run: pytest -v --pyargs pathsimanalysis.tests
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test-deployed-pypi:
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name: Test deployed package (PyPI)
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if: |
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github.repository == 'MDAnalysis/PathSimAnalysis' &&
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(github.event_name == 'release' && github.event.action == 'published')
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runs-on: ubuntu-latest
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needs: [build, deploy-pypi]
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steps:
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- uses: actions/checkout@v7
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- name: Checkout repository for actions
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uses: actions/checkout@v7
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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: "3.11"
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- name: pypi_deploy
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uses: MDAnalysis/pypi-deployment@main
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- name: Wait for version to be available on PyPI
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uses: ./.github/actions/wait-for-pypi-version
52200
with:
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package_name: 'pathsimanalysis'
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tests: false
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repository: pypi
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package: pathsimanalysis
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version: ${{ needs.build.outputs.version }}
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- name: Install from PyPI
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run: |
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python -m pip install --upgrade pip
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pip install "pathsimanalysis[test]==${{ needs.build.outputs.version }}"
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- name: Test import
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run: |
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python -c "import pathsimanalysis; print(f'Package {pathsimanalysis.__version__} imported successfully from PyPI')"
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- name: Run tests
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run: pytest -v --pyargs pathsimanalysis.tests

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