ENH: Add three new parameters to run_amrfinderplus_n #89
Workflow file for this run
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| name: Test | |
| on: | |
| pull_request: | |
| branches: ["main"] | |
| push: | |
| branches: ["main"] | |
| env: | |
| DISTRO: shotgun | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| latest-dev-tag: 2024.5.0.dev0 | |
| latest-stable-tag: 2024.2.0 | |
| 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)" >> $GITHUB_OUTPUT | |
| - name: Install dependencies | |
| run: python -m pip install requests yq | |
| - name: Create conda yaml | |
| id: create-conda-yaml | |
| run: | | |
| commit_msg="${{ steps.get-commit-msg.outputs.commit-msg }}" | |
| if [[ "$commit_msg" == *"[stable]"* ]] || [[ "$commit_msg" == *"[prod]"* ]]; then | |
| tag="2024.2.0" | |
| else | |
| tag="2024.5.0.dev0" | |
| 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)" >> $GITHUB_OUTPUT | |
| - name: Setup miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: 3.8 | |
| mamba-version: "*" | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| activate-environment: conda-env | |
| condarc-file: utilities/ci/condarc | |
| # use-only-tar-bz2: true | |
| - name: Get date | |
| id: get-date | |
| run: echo "today=$(/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 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 |