fix: add processed sample paths to mapping #328
Workflow file for this run
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| name: ci | |
| on: [push, pull_request] | |
| jobs: | |
| static-code-analysis: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: check out repository | |
| uses: actions/checkout@v4 | |
| - name: set up miniconda and env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: "3.9" | |
| mamba-version: "*" | |
| auto-update-conda: true | |
| activate-environment: htsinfer | |
| environment-file: environment-dev.yml | |
| auto-activate-base: false | |
| - name: display env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: flake8 | |
| run: flake8 | |
| - name: pylint | |
| run: pylint --rcfile pylint.cfg setup.py htsinfer/ | |
| - name: mypy | |
| run: mypy htsinfer | |
| unit-testing: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [ '3.8', '3.9', '3.10' ] | |
| name: unit-testing-Python-${{ matrix.python-version }} | |
| steps: | |
| - name: check out repository | |
| uses: actions/checkout@v3 | |
| - name: set up miniconda and env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| mamba-version: "*" | |
| auto-update-conda: true | |
| activate-environment: htsinfer | |
| environment-file: environment-dev.yml | |
| auto-activate-base: false | |
| - name: display env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: run unit tests | |
| run: | | |
| coverage run --source htsinfer -m pytest | |
| coverage xml | |
| - name: submit coverage report | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./coverage.xml | |
| fail_ci_if_error: true | |
| verbose: true | |
| integration-testing: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [ '3.8', '3.9', '3.10' ] | |
| name: integration-testing-Python-${{ matrix.python-version }} | |
| steps: | |
| - name: check out repository | |
| uses: actions/checkout@v4 | |
| - name: set up miniconda and env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| mamba-version: "*" | |
| auto-update-conda: true | |
| activate-environment: htsinfer | |
| environment-file: environment-dev.yml | |
| auto-activate-base: false | |
| - name: display env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: integration test - help screen | |
| run: htsinfer --help | |
| - name: integration test - single-ended library | |
| run: htsinfer --cleanup-regime=KEEP_NONE --verbosity=DEBUG tests/files/adapter_single.fastq | |
| - name: integration test - paired-ended library | |
| run: htsinfer --cleanup-regime=KEEP_NONE --verbosity=DEBUG tests/files/adapter_{1,2}.fastq | |
| publish: | |
| name: build and publish app image | |
| runs-on: ubuntu-latest | |
| if: | | |
| github.event_name == 'push' && | |
| github.ref == format('refs/heads/{0}', github.event.repository.default_branch) | |
| steps: | |
| - name: check out repository | |
| uses: actions/checkout@v3 | |
| - name: generate tag | |
| run: | | |
| echo "TAG=$(date '+%Y%m%d')" >> $GITHUB_ENV | |
| - name: build and publish image | |
| id: docker | |
| uses: philips-software/[email protected] | |
| with: | |
| dockerfile: . | |
| image-name: "htsinfer" | |
| 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" |