Add dnabert #107
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| 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 |