doc-build.yml

---
# Workflow to build the documentation.
name: Build documentation
on:
    push:
        branches:
        -   main
    pull_request:
        branches:
        -   '*'
jobs:
  # Steps to build the documentation.
    build_docs:
    # This prevents this workflow from running on a fork.
        if: github.repository == 'parietal-INRIA/fmralign'
        runs-on: ubuntu-latest
        timeout-minutes: 360
        defaults:
            run:
                shell: bash -el {0}
        steps:
        -   name: Source caching
            uses: actions/cache@v3
            with:
                path: .git
                key: source-cache-${{ runner.os }}-${{ github.run_id }}
                restore-keys: |
                    source-cache-${{ runner.os }}
        -   name: Checkout fmralign
            uses: actions/checkout@v3
            with:
          # If pull request, checkout HEAD commit with all commit history
                ref: ${{ github.event.pull_request.head.sha }}
                fetch-depth: 0
        -   name: Complete checkout
            run: |
                set -x
                if ! git remote -v | grep upstream; then
                  git remote add upstream https://github.com/parietal-INRIA/fmralign.git
                fi
                git fetch upstream
        -   name: Merge with upstream
            run: |
                set -x
                echo $(git log -1 --pretty=%B) | tee gitlog.txt
                echo "gitlog.txt = $(cat gitlog.txt)"
                echo $GITHUB_REF_NAME | tee merge.txt
                if [ "$GITHUB_REF_NAME" != "main" ]; then
                    echo "Merging $(cat merge.txt)";
                    git pull --ff-only upstream "refs/pull/$(cat merge.txt)";
                fi
      # Set up environment
        -   name: Install apt packages
            run: |
                sudo -E apt-get -yq update
                sudo -E apt-get -yq --no-install-suggests --no-install-recommends install \
                    dvipng texlive-latex-base texlive-latex-extra
        -   name: Setup conda
            uses: conda-incubator/setup-miniconda@v2
            with:
                auto-activate-base: true
                activate-environment: ''
                miniconda-version: latest
                channels: conda-forge
        -   name: Install packages in conda env
            run: |
                conda init bash
                echo "conda version = $(conda --version)"
                conda create -n testenv
                conda install -n testenv -yq python=3.9
                source activate testenv
                python -m pip install --user --upgrade --progress-bar off pip
                # See pyproject.toml for dependency group options
                python -m pip install .[jax,test,doc]

      # Run the doc build. 
        -   name: Build docs
            run: |
                source activate testenv
                echo "Conda active env = $CONDA_DEFAULT_ENV";
                cd doc;
                set -o pipefail;
                make html | tee log.txt;
        -   name: Upload documentation
            uses: actions/upload-artifact@v3
            with:
                name: doc
                path: doc/_build/html

    # Deploy the documentation to GitHub Pages.
    deploy_docs:
        if: github.repository == 'parietal-INRIA/fmralign'
        needs: build_docs
        runs-on: ubuntu-latest
        steps:
        -   uses: actions/checkout@v2
    
        -   name: Download artifacts
            uses: actions/download-artifact@v4
            with:
                name: DocHTML
                path: doc/_build/html/

        -   name: Commit to documentation branch
            run: |
                git clone --depth 1 https://github.com/${{ github.repository }}.git --branch gh-pages --single-branch gh-pages
                cp -r doc/_build/html/* gh-pages/
                cd gh-pages
                touch .nojekyll
                git config --local user.email "fmralign@github.com"
                git config --local user.name "fmralign GitHub Action"
                git add .
                git commit -m "Update documentation" -a || true

        -   name: Push changes
            uses: ad-m/github-push-action@v0.6.0
            with:
                branch: gh-pages
                directory: gh-pages
                github_token: ${{ secrets.GITHUB_TOKEN }}