deploy.yaml

name: Build and upload to PyPI

on:
  pull_request:
    branches:
      - "package-*"
  push:
    branches:
      - "package-*"
    tags:
      - "package-*"
  release:
    types:
      - published
  schedule:
    # 3 am Tuesdays and Fridays
    - cron: "0 3 * * 2,5"
  workflow_dispatch:


concurrency:
  group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}"
  cancel-in-progress: true


defaults:
  run:
    shell: bash -l {0}


jobs:
  build_wheels:
    if: "github.repository == 'MDAnalysis/mdanalysis'"
    name: Build wheels
    runs-on: ${{ matrix.buildplat[0] }}
    timeout-minutes: 15
    strategy:
      fail-fast: false
      matrix:
        buildplat:
          - [ubuntu-24.04, manylinux, x86_64]
          - [ubuntu-24.04-arm, manylinux, aarch64]
          - [windows-2025, win, AMD64]
          - [macos-15, macosx, arm64]
          - [macos-15-intel, macosx, x86_64]
        python: ["cp311", "cp312", "cp313", "cp314"]
    defaults:
      run:
        working-directory: ./package
    steps:
      - uses: actions/checkout@v7
        with:
          fetch-depth: 0

      - name: Build wheels
        uses: pypa/cibuildwheel@v4.3.0
        with:
          package-dir: package
        env:
          CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}_${{ matrix.buildplat[2] }}
          CIBW_ARCHS: ${{ matrix.buildplat[2] }}
          CIBW_BUILD_VERBOSITY: 1

      - name: upload artifacts
        if: |
          (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
          (github.event_name == 'release' && github.event.action == 'published')
        uses: actions/upload-artifact@v7
        with:
          name: wheel-${{ matrix.buildplat[0] }}-${{ matrix.python }}
          path: wheelhouse/*.whl
          retention-days: 7

  build_sdist:
    if: "github.repository == 'MDAnalysis/mdanalysis'"
    name: build package source distribution
    runs-on: ubuntu-latest
    timeout-minutes: 10
    defaults:
      run:
        working-directory: ./package
    steps:
      - uses: actions/checkout@v7
        with:
          fetch-depth: 0

      - name: Build sdist
        run: pipx run build --sdist

      - name: upload artifacts
        if: |
          (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
          (github.event_name == 'release' && github.event.action == 'published')
        uses: actions/upload-artifact@v7
        with:
          name: sdist
          path: package/dist/*.tar.gz
          retention-days: 7

  build_sdist_tests:
    if: "github.repository == 'MDAnalysis/mdanalysis'"
    name: build test source distribution
    runs-on: ubuntu-latest
    timeout-minutes: 10
    defaults:
      run:
        working-directory: ./testsuite
    steps:
      - uses: actions/checkout@v6
        with:
          fetch-depth: 0

      - name: Build sdist
        run: pipx run build --sdist

      - name: upload artifacts
        if: |
          (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
          (github.event_name == 'release' && github.event.action == 'published')
        uses: actions/upload-artifact@v7
        with:
          name: sdist_tests
          path: testsuite/dist/*.tar.gz
          retention-days: 7

  upload_testpypi_mdanalysis:
    if: |
      github.repository == 'MDAnalysis/mdanalysis' &&
      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package'))
    name: testpypi_upload_mdanalysis
    environment:
      name: deploy
      url: https://test.pypi.org/p/mdanalysis
    permissions:
      id-token: write
    runs-on: ubuntu-latest
    needs: [build_wheels, build_sdist, build_sdist_tests]
    steps:
      - uses: actions/download-artifact@v8
        with:
          path: dist
          merge-multiple: true

      - name: move_test_dist
        run: |
          mkdir -p testsuite/dist
          mv dist/mdanalysistests-* testsuite/dist

      - name: upload_source_and_wheels
        uses: pypa/gh-action-pypi-publish@v1.14.2
        with:
          skip_existing: true
          repository_url: https://test.pypi.org/legacy/

  upload_testpypi_mdanalysistests:
    if: |
      github.repository == 'MDAnalysis/mdanalysis' &&
      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package'))
    name: testpypi_upload_mdanalysistests
    environment:
      name: deploy
      url: https://test.pypi.org/p/mdanalysis
    permissions:
      id-token: write
    runs-on: ubuntu-latest
    needs: [build_wheels, build_sdist, build_sdist_tests]
    steps:
      - uses: actions/download-artifact@v8
        with:
          path: dist
          merge-multiple: true

      - name: move_test_dist
        run: |
          mkdir -p testsuite/dist
          mv dist/mdanalysistests-* testsuite/dist

      - name: upload_tests
        uses: pypa/gh-action-pypi-publish@v1.14.2
        with:
          packages_dir: testsuite/dist
          skip_existing: true
          repository_url: https://test.pypi.org/legacy/
 
  upload_pypi_mdanalysis:
    if: |
      github.repository == 'MDAnalysis/mdanalysis' &&
      github.event_name == 'release' && github.event.action == 'published'
    name: pypi_upload_mdanalysis
    environment:
      name: deploy
      url: https://pypi.org/p/mdanalysis
    permissions:
      id-token: write
    runs-on: ubuntu-latest
    needs: [build_wheels, build_sdist, build_sdist_tests]
    steps:
      - uses: actions/download-artifact@v8
        with:
          path: dist
          merge-multiple: true

      - name: move_test_dist
        run: |
          mkdir -p testsuite/dist
          mv dist/mdanalysistests-* testsuite/dist

      - name: upload_source_and_wheels
        uses: pypa/gh-action-pypi-publish@v1.14.2

  upload_pypi_mdanalysistests:
    if: |
      github.repository == 'MDAnalysis/mdanalysis' &&
      github.event_name == 'release' && github.event.action == 'published'
    name: pypi_upload_mdanalysistests
    environment:
      name: deploy
      url: https://pypi.org/p/mdanalysistests
    permissions:
      id-token: write
    runs-on: ubuntu-latest
    needs: [build_wheels, build_sdist, build_sdist_tests]
    steps:
      - uses: actions/download-artifact@v8
        with:
          path: dist
          merge-multiple: true

      - name: move_test_dist
        run: |
          mkdir -p testsuite/dist
          mv dist/mdanalysistests-* testsuite/dist

      - name: upload_tests
        uses: pypa/gh-action-pypi-publish@v1.14.2
        with:
          packages_dir: testsuite/dist

  check_testpypi:
    if: |
      github.repository == 'MDAnalysis/mdanalysis' &&
      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package'))
    name: testpypi check
    runs-on: ${{ matrix.os }}
    timeout-minutes: 60
    needs: [upload_testpypi_mdanalysis, upload_testpypi_mdanalysistests]
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-15, macos-15-intel, windows-latest]
        python-version: ["3.11", "3.12", "3.13", "3.14"]
        type: ["FULL", "MIN"]
        exclude:
          # Multiple deps don't like windows
          # no osx-arm64 packages for HOLE2
          - os: windows-latest
            type: "FULL"
          - os: "macos-latest"
            type: "FULL"
          - python-version: "3.14"
            type: "FULL"
    env:
      MPLBACKEND: agg

    steps:
      - uses: actions/checkout@v7

      - name: setup_micromamba
        uses: mamba-org/setup-micromamba@v3
        with:
          environment-name: mda
          create-args: >-
            python=${{ matrix.python-version }}
            packaging
            pip
          # bioconda for clustalw things
          condarc: |
            channels:
              - conda-forge
              - bioconda

      - name: install_full_deps
        uses: ./.github/actions/setup-deps
        if: "matrix.type == 'FULL'"
        with:
          micromamba: true
          full-deps: true

      - name: pip_install_mda
        run: |
          awk '/__version__ =/ {print $3; exit}' package/MDAnalysis/version.py | tr -d \" > version.dat
          ver=$(python maintainer/norm_version.py --file version.dat)
          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple MDAnalysis==$ver
          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple MDAnalysisTests==$ver

      - name: install_min_deps
        if: "matrix.type == 'MIN'"
        run: |
          pip install pytest-xdist pytest-timeout

      - name: run_tests
        run: |
          pytest --timeout=200 -n auto --pyargs MDAnalysisTests