Merge pull request #176 from CCBR/python-paths #26
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: build | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - main | |
| - develop | |
| pull_request: | |
| jobs: | |
| dryrun-lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: docker://snakemake/snakemake:v7.32.4 | |
| - name: Dry-run | |
| run: | | |
| docker run -v $PWD:/opt2 -w /opt2 snakemake/snakemake:v7.32.4 \ | |
| ./bin/renee run \ | |
| --input .tests/KO_S3.R1.fastq.gz .tests/KO_S3.R2.fastq.gz .tests/KO_S4.R1.fastq.gz .tests/KO_S4.R2.fastq.gz .tests/WT_S1.R1.fastq.gz .tests/WT_S1.R2.fastq.gz .tests/WT_S2.R1.fastq.gz .tests/WT_S2.R2.fastq.gz \ | |
| --output output \ | |
| --genome config/genomes/biowulf/hg38_30.json \ | |
| --shared-resources .tests/shared_resources/ \ | |
| --mode local \ | |
| --dry-run | |
| - name: Lint | |
| continue-on-error: true | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ | |
| snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \ | |
| echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.' | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.11"] | |
| snakemake-version: ["7.32.3"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: test | |
| cache-environment: true | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| snakemake=${{ matrix.snakemake-version }} | |
| setuptools | |
| pip | |
| pytest | |
| - name: check CLI basics | |
| run: | | |
| ./bin/renee --help | |
| ./bin/renee --version | |
| shell: micromamba-shell {0} | |
| - name: pip install python package | |
| run: | | |
| pip install .[dev,test] | |
| shell: micromamba-shell {0} | |
| - name: Test | |
| run: | | |
| python -m pytest | |
| env: | |
| TMPDIR: ${{ runner.temp }} | |
| shell: micromamba-shell {0} | |
| build-status: # https://github.com/orgs/community/discussions/4324#discussioncomment-3477871 | |
| runs-on: ubuntu-latest | |
| needs: [dryrun-lint, test] | |
| if: always() | |
| steps: | |
| - name: Successful build | |
| if: ${{ !(contains(needs.*.result, 'failure')) }} | |
| run: exit 0 | |
| - name: Failing build | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 |