gh-ci-cron.yaml

name: GH Actions Cron CI
on:
  push:
    branches:
      - main
  schedule:
    # once a week at midnight on Sunday
    - cron: "0 3 * * 0"

concurrency:
  # Commits to develop/master will cancel each other, but PRs will only cancel
  # commits within the same PR
  group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}"
  cancel-in-progress: true

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

jobs:
  gen_matrix:
    runs-on: ubuntu-22.04
    outputs:
      matrix: ${{ steps.get-mdakits.outputs.matrix }}
    steps:
      - uses: actions/checkout@v3

      - id: get-python
        uses: actions/setup-python@v3
        with:
          python-version: 3.9

      - id: get-mdakits
        run: |
          mdakit=$(python utils/get_dir_matrix.py)
          echo "matrix=${mdakit}" >> $GITHUB_OUTPUT

  mdakit-ci:
    needs: gen_matrix
    runs-on: ubuntu-22.04
    strategy:
      fail-fast: false
      matrix:
        mdakit: ${{fromJSON(needs.gen_matrix.outputs.matrix)}}
        jobstep: ['latest', 'develop']
    steps:
      - uses: actions/checkout@v3

      - id: prev-python-ver
        name: prev-python-ver
        uses: MDAnalysis/get-latest-python-version@main
        with:
          last-n-minor-release: 1

      - id: get-base-python-deps
        name: get-base-python-deps
        run: |
          pip install requests setuptools packaging pyyaml pydantic PyGithub

      - id: check-set-python-bounds
        name: check-set-python-bounds
        continue-on-error: true
        run: |
          basepy=${{steps.prev-python-ver.outputs.python-version}}
          pyver=$(python utils/check_python_ver.py --mdakit "${{matrix.mdakit}}" --maxpyver ${basepy})
          echo "PYVER=${pyver}" >> $GITHUB_ENV
          
      - id: install-conda-env
        name: install-conda-env
        uses: conda-incubator/setup-miniconda@v2
        with:
          python-version: ${{ env.PYVER }}
          add-pip-as-python-dependency: true
          architecture: x64
          use-mamba: true
          miniforge-variant: Mambaforge
          channels: conda-forge, defaults
          channel-priority: flexible
          auto-update-conda: true
          show-channel-urls: true

      - id: install-conda-base-deps
        name: install-conda-base-deps
        run: |
          mamba install requests setuptools packaging pyyaml pydantic
          pip install PyGithub

      - id: install-mdakit
        name: install-mdakit
        continue-on-error: true
        run: |
         if [[ ${{ matrix.jobstep }} == "develop" ]]; then
           type="src"
         else
           type="install"
         fi

         install=$(python utils/get_install.py --itype ${type} --mdakit ${{matrix.mdakit}})
         echo "install=${install}"
         eval ${install}

      - id: install-test-deps
        name: install-test-deps
        continue-on-error: true
        run: |
          install=$(python utils/get_testdeps.py --mdakit ${{matrix.mdakit}})
          echo "install tests:${install}"
          eval ${install}

      - id: install-mdanalysis
        name: install-mdanalysis
        uses: MDAnalysis/install-mdanalysis@main
        continue-on-error: true
        with:
          version: ${{ matrix.jobstep }}
          install-tests: true
          installer: mamba
          shell: bash -l {0}

      - id: run-tests
        name: run-tests
        continue-on-error: true
        run: |
          tests=$(python utils/get_runtests.py --mdakit ${{matrix.mdakit}} --runtype ${{matrix.jobstep}})
          echo "tests: ${tests}"
          eval ${tests}

      - id: store-errors
        name: store-errors
        run: |
          echo "install_python=${{ steps.check-set-python-bounds.outcome }}" >> $GITHUB_ENV
          echo "install_mdakit=${{ steps.install-mdakit.outcome }}" >> $GITHUB_ENV
          echo "install_test_deps=${{ steps.install-test-deps.outcome }}" >> $GITHUB_ENV
          echo "install_mdanalysis=${{ steps.install-mdanalysis.outcome }}" >> $GITHUB_ENV
          echo "run_tests=${{ steps.run-tests.outcome }}" >> $GITHUB_ENV

      - id: write-errors
        name: write-errors
        run: |
          python utils/write-ci-status-json.py --tag ${{ matrix.jobstep }} --mdakit ${{ matrix.mdakit }}

      - id: upload-artifacts
        name: upload-artifacts
        uses: actions/upload-artifact@v3
        with:
          name: cron-statuses-${{ matrix.mdakit }}-${{ matrix.jobstep }}
          path: ${{ matrix.mdakit }}-${{ matrix.jobstep }}-statuses.json
          retention-days: 1
          if-no-files-found: error
 
  process_results:
    if: ${{ always() }}
    needs: mdakit-ci
    runs-on: ubuntu-22.04
    permissions:
      contents: write
      pull-requests: write 
      packages: none
      issues: write
    steps:
      - uses: actions/checkout@v3

      - uses: actions/download-artifact@v3
        with:
          path: json-statuses/

      - name: list-temp-files
        run: ls -l json-statuses/*/

      - id: get-base-python-deps
        name: get-base-python-deps
        run: |
          pip install requests setuptools packaging pyyaml pydantic PyGithub

      - id: combine-write-raise-issues
        name: combine-write-raise-issues
        run: |
          python utils/handle-status.py 
        env:
          GITHUB_TOKEN:  ${{ github.token }}

      - uses: stefanzweifel/git-auto-commit-action@v4
        with:
          commit_message: commit changes to status files
          skip_dirty_check: false
          skip_fetch: false

  deploy_docs:
    if: ${{ always() }}
    needs: process_results
    runs-on: ubuntu-22.04
    steps:
      - uses: actions/checkout@v3
      - name: setup_miniconda
        uses: conda-incubator/setup-miniconda@v2
        with:
          python-version: 3.9
          auto-update-conda: true
          channel-priority: flexible
          channels: conda-forge
          add-pip-as-python-dependency: true
          architecture: x64
          use-mamba: true
          miniforge-variant: Mambaforge
          environment-file: docs/requirements.yaml
      - name: build_docs
        run: |
          cd docs && sphinx-build -b html source build
      - name: deploy docs
        uses: peaceiris/actions-gh-pages@v3
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          publish_dir: ./docs/build
          cname: mdakits.mdanalysis.org
          user_name: 'github-actions'
          user_email: 'github-action@users.noreply.github.com'