ci.yaml

name: Test
on:
  pull_request:
    branches: ["main"]
  push:
    branches: ["main"]
env:
    DISTRO: metagenome

jobs:
  test:
    runs-on: ubuntu-latest
    outputs:
      latest-dev-tag: ${{ steps.fetch_latest_tags.outputs.latest-dev-tag }}
      latest-stable-tag: ${{ steps.fetch_latest_tags.outputs.latest-stable-tag }}
      commit-msg: ${{ steps.get-commit-msg.outputs.commit-msg }}
    steps:
      - uses: actions/checkout@v4
        with:
            fetch-depth: 0

      - name: Checkout utilities
        uses: actions/checkout@v4
        with:
          repository: bokulich-lab/utilities
          path: utilities

      - name: Get last commit
        id: get-commit-msg
        run: |
          echo "$(git log --pretty=%B -n 1 --skip 1)"
          echo "commit-msg=$(git log --pretty=%B -n 1 --skip 1)" >> $GITHUB_OUTPUT

      - name: Install dependencies
        run: python -m pip install requests yq

      - name: Fetch latest tags
        id: fetch-tags
        run: |
          latest_tags=$(python utilities/ci/get-tags.py)
          echo "$latest_tags" > tags.txt
          echo "latest-dev-tag=$(grep 'latest-dev-tag' tags.txt | cut -d '=' -f 2)" >> $GITHUB_OUTPUT
          echo "latest-stable-tag=$(grep 'latest-stable-tag' tags.txt | cut -d '=' -f 2)" >> $GITHUB_OUTPUT

      - name: Create conda yaml
        id: create-conda-yaml
        run: |
          commit_msg="${{ steps.get-commit-msg.outputs.commit-msg }}"
          if [[ "$commit_msg" == *"[stable]"* ]] || [[ "$commit_msg" == *"[prod]"* ]]; then
              tag="${{ steps.fetch-tags.outputs.latest-stable-tag }}"
          else
              tag="${{ steps.fetch-tags.outputs.latest-dev-tag }}"
          fi
          bash utilities/ci/get-dependencies.sh "$DISTRO" $tag utilities/ci/repositories.yaml
          cat environment.yml >> $GITHUB_STEP_SUMMARY
          echo "qiime-deps=$(tr '\n' ' ' < repo-urls.txt | xargs)" >> $GITHUB_OUTPUT

      - name: Setup miniconda
        uses: conda-incubator/setup-miniconda@v3
        with:
          python-version: "3.10"
          mamba-version: 1.5.10
          channels: conda-forge,defaults
          channel-priority: true
          activate-environment: conda-env
          condarc-file: utilities/ci/condarc
          # use-only-tar-bz2: true

      - name: Get date
        id: get-date
        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
        shell: bash

      - name: Cache conda env
        uses: actions/cache@v3
        with:
          path: /usr/share/miniconda/envs
          key:
            conda-${{ runner.os }}--${{ runner.arch }}--${{
            steps.get-date.outputs.today }}-${{
            hashFiles('environment.yml') }}-${{ env.CACHE_NUMBER
            }}
        env:
          # Increase this value to reset cache if environment.yml has not changed
          CACHE_NUMBER: 0
        id: cache

      - name: Update environment
        run: mamba env update -n conda-env -f environment.yml
        if: steps.cache.outputs.cache-hit != 'true'

      - name: Install dev versions of QIIME repos
        run: mamba run -n conda-env pip install ${{ steps.create-conda-yaml.outputs.qiime-deps }}

      - name: Update specific dependency, if requested
        if: contains(${{ steps.get-commit-msg.outputs.commit-msg }}, '[add:')
        run: |
            commit_msg="${{ steps.get-commit-msg.outputs.commit-msg }}"
            IFS=',' read -ra ADDR <<< "$commit_msg"
            for i in "${ADDR[@]}"; do
                pkg_name=$(echo "$i" | awk -F':' '/\[add/{print $2}')
                commit_hash=$(echo "$i" | awk -F':' '/\[add/{print $3}' | awk -F']' '{print $1}')
                if [[ $(yq '.repositories[].name' utilities/ci/repositories.yaml | grep -c $pkg_name) -eq 1 ]]; then
                    pkg_url=$(yq ".repositories[] | select(.name == \"$pkg_name\") | .url" utilities/ci/repositories.yaml | tr -d '"')
                    mamba run -n conda-env pip install "git+$pkg_url@$commit_hash"
                fi
            done

      - name: Install plugin
        run: |
          mamba run -n conda-env pip install .
          mamba run -n conda-env qiime dev refresh-cache

      - name: Install dev dependencies
        run: mamba run -n conda-env pip install pytest pytest-cov coverage parameterized

      - name: Run tests
        id: test
        run: mamba run -n conda-env make test-cov

      - name: Upload artifacts
        uses: actions/upload-artifact@v4
        if: steps.test.outcome == 'success'
        with:
          name: coverage
          path: coverage.xml