Add dnabert #113
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: pipeline | |
| on: [pull_request] | |
| #on: | |
| # push: | |
| # branches: | |
| # - main | |
| jobs: | |
| # test: | |
| # runs-on: ubuntu-latest | |
| # container: | |
| # image: quay.io/qiime2/core:2023.2 | |
| # strategy: | |
| # fail-fast: false | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # - name: Set up Python ${{ matrix.python-version }} | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| # - name: Install dependencies | |
| # run: | | |
| # python -m pip install --upgrade pip | |
| # python -m pip install pytest | |
| # python -m pip install flake8 | |
| # python -m pip install pydocstyle | |
| # python -m pip install pytest-cov | |
| # python -m pip install . | |
| # - name: Test with pytest | |
| # run: | | |
| # flake8 hitac tests | |
| # pydocstyle hitac | |
| # pytest -v --cov=hitac --cov-fail-under=70 --cov-report html | |
| # coverage xml | |
| # - name: Upload Coverage to Codecov | |
| # uses: codecov/codecov-action@v2 | |
| bump: | |
| # needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: '0' | |
| - name: Bump version and push tag | |
| id: tag | |
| uses: anothrNick/github-tag-action@1.36.0 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| WITH_V: false | |
| DEFAULT_BUMP: patch | |
| outputs: | |
| new_tag: ${{steps.tag.outputs.new_tag}} | |
| docker: | |
| needs: bump | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # container: [blca, btop, usearch, hitac, knn, spingo, rdp, microclass, pandas, metaxa2] | |
| container: [hitac] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Docker meta | |
| id: meta | |
| uses: docker/metadata-action@v4 | |
| with: | |
| images: mirand863/${{ matrix.container }} | |
| # tags: | | |
| # type=raw,value=${{needs.bump.outputs.new_tag}} | |
| # type=raw,value=latest,enable={{is_default_branch}} | |
| tags: | | |
| type=raw,value=2.0.31 | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v2 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and push | |
| uses: docker/build-push-action@v4 | |
| with: | |
| file: benchmark/dockerfiles/${{ matrix.container }}.dockerfile | |
| context: . | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| # pypi: | |
| # needs: bump | |
| # name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - uses: actions/checkout@v1 | |
| # - name: Set up Python 3.8 | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.8 | |
| # - name: Install pypa/build | |
| # run: | | |
| # git fetch --tags | |
| # git branch --create-reflog main origin/main | |
| # python -m pip install build --user . | |
| # - name: Build a binary wheel and a source tarball | |
| # run: | | |
| # python -m build --sdist --wheel --outdir dist/ . | |
| # - name: Publish distribution 📦 to PyPI | |
| # uses: pypa/gh-action-pypi-publish@release/v1 | |
| # with: | |
| # user: __token__ | |
| # password: ${{ secrets.PYPI_API_TOKEN }} | |
| # verbose: true |