Fix: cdna-generator input and fragment-selector output (#19) #72
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: ci | |
| on: | |
| pull_request: | |
| branches: | |
| - dev | |
| push: | |
| branches: | |
| - '*' | |
| jobs: | |
| static-code-analysis: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Conda/Mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| auto-update-conda: true | |
| activate-environment: "scrnasim-toolz" | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| - name: Display environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: flake8 | |
| run: flake8 | |
| - name: pylint | |
| run: pylint --rcfile pylint.cfg setup.py scRNAsim_toolz/ | |
| - name: mypy | |
| run: mypy scRNAsim_toolz | |
| unit-testing: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Conda/Mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| auto-update-conda: true | |
| activate-environment: "scrnasim-toolz" | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| - name: Display environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Run unit tests | |
| run: | | |
| coverage run --source scRNAsim_toolz -m pytest | |
| coverage xml | |
| - name: Submit coverage report | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./coverage.xml | |
| verbose: true | |
| fail_ci_if_error: false | |
| publish: | |
| name: build and publish app image | |
| runs-on: ubuntu-latest | |
| if: | | |
| github.event_name == 'push' && | |
| github.ref == format('refs/heads/{0}', github.event.repository.default_branch) | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Generate tag | |
| run: | | |
| echo "TAG=$(date '+%Y%m%d')" >> $GITHUB_ENV | |
| - name: Build and publish image | |
| id: docker | |
| uses: philips-software/[email protected] | |
| with: | |
| dockerfile: . | |
| image-name: "scrnasim-toolz" | |
| tags: "latest ${{ env.TAG }}" | |
| push-branches: "${{ github.event.repository.default_branch }}" | |
| env: | |
| REGISTRY_USERNAME: ${{ secrets.DOCKERHUB_LOGIN }} | |
| REGISTRY_TOKEN: "${{ secrets.DOCKERHUB_TOKEN }}" | |
| DOCKER_ORGANIZATION: ${{ secrets.DOCKERHUB_ORG }} | |
| GITHUB_ORGANIZATION: ${{ github.repository_owner }} | |
| - name: Verify that image was pushed | |
| run: | | |
| echo "Push indicator: ${{ steps.docker.outputs.push-indicator }}" | |
| echo "# Set to 'true' if image was pushed, empty string otherwise" | |
| test "${{ steps.docker.outputs.push-indicator }}" == "true" |