main.yml

name: main
on: [push]

jobs:
  test:
    strategy:
      matrix:
        python-version: ["3.8", "3.9", "3.10"]
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: git setup
      # Set up git and export env vars to be used in later steps.
      id: git-setup
      run: |
        git config --global user.email "action@github.com"
        git config --global user.name "GitHub Action"
        echo "BRANCH=${GITHUB_REF##*/}" >> $GITHUB_ENV
        echo "WORKDIR=$(pwd)" >> $GITHUB_ENV

    - name: build new conda env
      run: |
        eval "$(conda shell.bash hook)"
        conda install -n base mamba -y --channel conda-forge
        mamba create -p ./env -y python=${{ matrix.python-version }} --file test-requirements.txt --channel conda-forge --channel bioconda
        conda activate ./env
        pip install -e .

    - name: run pytests
      # pytests and doctests happen here
      run: |
        eval "$(conda shell.bash hook)"
        conda activate ./env
        pytest -vv --doctest-modules trackhub

    - name: build docs
      run: |
        # To make sure that the links in the built docs refer to the correct
        # branch on the trackhub-demo repo, we replace the branch names in the
        # .rst files. Note if we're on master branch then this is a no-op.
        eval "$(conda shell.bash hook)"
        conda activate ./env
        conda env export
        (
          cd doc
          find . -name "*.rst" | xargs sed -i "s|trackhub-demo/master|trackhub-demo/$BRANCH|g"
          make doctest html
        )

    - name: test command-line script
      # Ensure that the installed command-line script can be run and creates
      # the correct files
      run: |
        eval "$(conda shell.bash hook)"
        conda activate ./env
        trackhub_from_excel --template
        trackhub_from_excel --create-example a.xlsx
        trackhub_from_excel --excel-file a.xlsx
        err=0
        for f in template.xlsx a.xlsx staging staging/test_excel_to_trackhub.hub.txt; do
          if [ ! -e $f ]; then
            echo "file $f not present!"
            err=1
          fi
        done
        if [ $err == 1 ]; then
          exit 1
        fi


    - name: upload the just-built docs as an artifact
      uses: actions/upload-artifact@v4
      with:
        name: docs-${{matrix.python-version}}-${{ github.run_id }}
        path: doc/build/html
        overwrite: true  # v4 requires unique names; this will delete existing before uploading


    - name: commit built docs to gh-pages
      # The changes aren't actually pushed unless we're on the master branch
      # (see next step).
      #
      # Note that cloning just the gh-pages branch to a new directory ended
      # up being easier than staying in this directory and copying stuff
      # around within it.
      run: |
        git clone \
          --single-branch \
          --branch gh-pages "https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY" \
          /tmp/docs

        # recall that this does leave hidden files
        rm -rf /tmp/docs/*
        cp -r doc/build/html/* /tmp/docs
        touch /tmp/docs/.nojekyll
        cd /tmp/docs
        git add .

        if git diff --cached --quiet; then
          echo "no changes; nothing to commit"
        else
          git commit -m 'update docs'
        fi

        cd $WORKDIR


    - name: push docs to gh-pages branch
      # Push to gh-pages.
      #   (but only if we're on the master branch)
      #   This is how the docs get hosted on https://github.io/daler/trackhub.
      if: ${{ github.ref == 'refs/heads/master' }}
      run: |
        cd /tmp/docs
        git push "https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/daler/trackhub" gh-pages
        cd $WORKDIR


    - name: build example hubs
      # Build example hubs into the "example_hubs" directory.
      #   See the ci/build_examples.py script for details. Also note that since
      #   we were last on the gh-pages branch from the last step, we need to
      #   explicitly check out the branch that this PR is for.
      run: |
        git branch
        git checkout $BRANCH
        eval "$(conda shell.bash hook)"
        conda activate ./env
        ci/build_examples.py


    - name: start ssh agent
      # Start the SSH agent so that subsequent steps don't need additional SSH
      # setup.
      #   The private key has been added as a secret to the trackhub repo (the
      #   one running these tests), and the public key has been added as an
      #   allowed deploy key for the trackhub-demo repo (the one accepting
      #   pushes from this test). Note that this method ensures that the key is
      #   never saved to disk, and GitHub Actions automatically protects the
      #   secrets from being echoed.
      env:
        SSH_AUTH_SOCK: /tmp/ssh_agent.sock
      run: |
        mkdir -p ~/.ssh
        ssh-keyscan github.com >> ~/.ssh/known_hosts
        ssh-agent -a $SSH_AUTH_SOCK > /dev/null
        ssh-add - <<< "${{ secrets.SSH_PRIVATE_KEY }}"


    - name: push built hubs to trackhub-demo repo
      # Push to the trackhub-demo repo
      #   This creates a matching branch on the trackhub-demo repo, cleans out
      #   everything, and copies over the contents of the just-built
      #   "example_hubs" directory to that matching branch. This lets us
      #   inspect the hubs and correct them if needed on a branch before
      #   merging to master.
      env:
        SSH_AUTH_SOCK: /tmp/ssh_agent.sock
      run: |
        set -x
        here=$(pwd)
        git clone git@github.com:daler/trackhub-demo.git /tmp/trackhub-demo
        cd /tmp/trackhub-demo
        git checkout -B $BRANCH
        git rm -rf ./*

        # Note -L to follow links
        cp -rLv $here/example_hubs/* /tmp/trackhub-demo
        git add -f .
        ls
        git status

        # It's possible that the $BRANCH here in the trackhub repo does not yet
        # exist over in the trackhub-demo repo. In that case, we should be good
        # to push immediately.
        if [[ -z $(git ls-remote --heads origin $BRANCH) ]]; then
          echo "remote branch $BRANCH does not exist"
          git commit -m 'update hub'
          git push origin $BRANCH --force
          exit 0
        fi

        # Otherwise, only push to existing branch if there are changes.
        if git diff origin/$BRANCH --quiet; then
            echo "no changes to push to branch $BRANCH!";
        else
          echo "Diffs will be pushed to remote branch $BRANCH"
          git commit -m 'update hub'
          git push origin $BRANCH --force
        fi
        set +x

    - name: hubChecks
      # Check hubs
      #   Once hubs are uploaded to trackhub-demo repo, we need to check them
      #   to make sure they're accessible and have no glaring errors.
      #
      #   See ci/check_hubs.py for details.
      run: |
        git checkout $BRANCH
        eval "$(conda shell.bash hook)"
        conda activate ./env
        ci/check_hubs.py


    - name: cleanup
      # Remove all the ssh stuff we set up.
      if: always()
      env:
        SSH_AUTH_SOCK: /tmp/ssh_agent.sock
      run: |
        ssh-add -D
        rm -Rf  *