gh-ci.yaml

name: Cookiecutter CI

on:
  push:
    branches:
      - "main"
  pull_request:
    branches:
      - "main"
  schedule:
    # weekly tests
    - cron: "0 0 * * 0"

defaults:
  run:
    shell: bash

env:
    ARTIFACT_NAME: demo-mdakit-repos
    OUTPUT_DIRECTORY: /home/runner/example_outputs
    OUTPUT_COOKIE_SUBDIRECTORY: TestMDAKit_with_host_MDAnalysis_condaforge-deps_and_ReadTheDocs/mdakit-Cookie
    GH_USER: github-actions
    GH_EMAIL: "github-action@users.noreply.github.com"
    GH_REPOSITORY: "github.com/${{ github.repository }}.git"

jobs:
  cookiecutter-main-tests:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macOS-latest, windows-latest]
        # check last three versions of Python
        last-n-minor-python-release: [2, 1, 0]

    steps:
      - uses: actions/checkout@v4

      - id: get-python-version
        uses: MDAnalysis/get-latest-python-version@main
        with:
          last-n-minor-release: ${{ matrix.last-n-minor-python-release }}

      - name: Environment information
        run: |
          uname -a
          df -h
          ulimit -a
          echo "Using Python ${{ steps.get-python-version.outputs.python-version }}"
      
      - name: Set up Python ${{ steps.get-python-version.outputs.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ steps.get-python-version.outputs.python-version }}

      - name: Install dependencies
        run: |
          python -m pip install -U pytest pyyaml cookiecutter
          
      - name: Run cookiecutter tests
        run: |
          # --keep-test-outputs also saves the generated repositories
          if [[ ${{ matrix.os }} == "ubuntu-latest" ]] ; then
            PYTEST_FLAGS="--keep-test-outputs ${{ env.OUTPUT_DIRECTORY }}"
          else
            PYTEST_FLAGS=""
          fi
          echo "PYTEST_FLAGS=${PYTEST_FLAGS}"
          
          pytest tests/ $PYTEST_FLAGS

      - name: check cookie CI presence
        if: ${{ matrix.os == 'ubuntu-latest' }}
        run: |
          ls -la ${{ env.OUTPUT_DIRECTORY }}/
          ls -la ${{ env.OUTPUT_DIRECTORY }}/${{ env.OUTPUT_COOKIE_SUBDIRECTORY }}/

      - name: Run cookie CI
        if: ${{ matrix.os == 'ubuntu-latest' }}
        uses: ./.github/actions/run-cookie-ci
        with:
          source-directory: ${{ env.OUTPUT_DIRECTORY }}/${{ env.OUTPUT_COOKIE_SUBDIRECTORY }}
          CODECOV_TOKEN: ${{ secrets.COOKIE_CODECOV_TOKEN }}

      - name: Upload artifact
        if: ${{ matrix.os == 'ubuntu-latest' && matrix.last-n-minor-python-release == 0 }}
        uses: actions/upload-artifact@v4
        with:
          name: ${{ env.ARTIFACT_NAME }}
          path: ${{ env.OUTPUT_DIRECTORY }}
          retention-days: 3

  update-repo-examples:
    if: github.event_name != 'pull_request'
    needs: cookiecutter-main-tests
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Make output directory
        run: mkdir $OUTPUT_DIRECTORY

      - name: Download artifact
        uses: actions/download-artifact@v4
        with:
          name: ${{ env.ARTIFACT_NAME }}
          path: ${{ env.OUTPUT_DIRECTORY }}

      - name: Push to cookie repo
        uses: ./.github/actions/push-to-cookie
        with:
          source-directory: ${{ env.OUTPUT_DIRECTORY }}
          target-repository: mdakit-cookie
          source-package: mdakit-Cookie
          target-ssh-deploy-key: ${{ secrets.MDAKIT_COOKIE_SSH_DEPLOY_KEY }}

      - name: Push to remote
        env:
          GH_USER: github-actions
          GH_EMAIL: "github-action@users.noreply.github.com"
          GH_REPOSITORY: "github.com/${{ github.repository }}.git"
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        run: |
          # dynamic vars
          BRANCH="${GITHUB_REF#refs/heads/}"
          REV=$(git rev-parse --short HEAD)
          cd $HOME
          mkdir examples
          cd examples
          # set up git
          git init
          git config user.name $GH_USER
          git config user.email $GH_EMAIL
          git remote add upstream "https://${GH_USER}:${GH_TOKEN}@${GH_REPOSITORY}"
          git fetch --depth 50 upstream $BRANCH examples
          git reset upstream/examples
          # update examples
          for keep in README.md ; do
            if [[ -e $keep ]] ; then
              cp $keep ${{ env.OUTPUT_DIRECTORY }}/
            fi
          done
          rm -rf *
          mv ${{ env.OUTPUT_DIRECTORY }}/* .
          # push back to GitHub
          git add .
          git diff-index --quiet HEAD -- || git commit -m "rebuilt examples from branch ${BRANCH} with CI at ${REV}"
          git push -q upstream HEAD:examples

  build_docs:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Install conda dependencies
        uses: conda-incubator/setup-miniconda@v3
        with:
          environment-file: docs/requirements.yaml
          add-pip-as-python-dependency: true
          architecture: x64
          miniforge-variant: Mambaforge
          use-mamba: true
          channels: conda-forge, defaults
          activate-environment: cookiecutter-mdakit-docs
          auto-update-conda: true
          show-channel-urls: true
      
      - name: Build docs
        shell: bash -l {0}
        working-directory: docs
        run: make html

      - name: Deploy docs
        if: github.event_name != 'pull_request'
        working-directory: docs/_build/html
        run: |
          BRANCH="${GITHUB_REF#refs/heads/}"
          REV=$(git rev-parse --short HEAD)
          git init
          git config user.name $GH_USER
          git config user.email $GH_EMAIL
          git remote add upstream "https://${GH_USER}:${{ secrets.GITHUB_TOKEN }}@${GH_REPOSITORY}"
          git fetch --depth 50 upstream $BRANCH gh-pages
          git reset upstream/gh-pages

          touch .
          touch .nojekyll
          git add .

          git diff-index --quiet HEAD -- || git commit -m "rebuilt html docs from branch ${BRANCH} with sphinx at ${REV}"
          git push -q upstream HEAD:gh-pages