setup.py -> pyproject.toml #303
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |