Bump version to 1.1.2 #44
Workflow file for this run
This file contains hidden or 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: BarcodeForge CI | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| permissions: | |
| contents: read | |
| jobs: | |
| testsuite: | |
| name: Test Package (Python ${{ matrix.python-version }} | ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: [ "3.10", "3.11", "3.12", "3.13" ] | |
| steps: | |
| # Downloads a copy of the code in your repository before running CI tests | |
| - name: Check out repository code | |
| uses: actions/checkout@v6 | |
| - name: Setup for conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| channels: bioconda,conda-forge | |
| channel-priority: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: test | |
| - name: Install | |
| shell: bash -l {0} | |
| run: | | |
| conda install -n base conda-libmamba-solver | |
| conda config --set solver libmamba | |
| conda config --add channels bioconda | |
| conda config --add channels conda-forge | |
| conda install usher ucsc-fatovcf -y | |
| pip install '.[dev-requirements,test-requirements]' | |
| - name: Test | |
| shell: bash -l {0} | |
| run: | | |
| conda activate test | |
| pytest -vvv --tb=short | |
| - name: Run barcode generation test | |
| shell: bash -l {0} | |
| run: | | |
| barcodeforge --debug barcode barcodeforge/assets/reference.fasta barcodeforge/assets/aligned.fasta barcodeforge/assets/tree.nwk barcodeforge/assets/lineages.tsv --matutils-overlap 0.8 --threads 4 --prefix RSVa | |
| diff -q RSVa-barcode.csv barcodeforge/assets/RSVa-barcode.csv || (echo "Files are not identical!" && exit 1) | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - name: Set up Python | |
| uses: actions/setup-python@v6 | |
| with: | |
| python-version: '3.10' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install black | |
| - name: Lint with Black | |
| run: | | |
| black --check . |