add new env to build test #370
Workflow file for this run
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: Test Bin Chicken with Setup-Miniconda From Marketplace | |
| on: [push] | |
| jobs: | |
| miniconda: | |
| name: Miniconda ${{ matrix.os }} | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| matrix: | |
| python-version: ["3.10"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up environment with Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: test | |
| environment-file: binchicken.yml | |
| python-version: ${{ matrix.python-version }} | |
| auto-activate-base: false | |
| channels: conda-forge,bioconda | |
| channel-priority: true | |
| - run: | | |
| conda info | |
| conda list | |
| conda config --set channel_priority strict | |
| # Workaround to provide additional free space for testing. | |
| # https://github.com/actions/virtual-environments/issues/2840 | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Install Bin Chicken | |
| run: | | |
| pip install -e . | |
| - name: Run unit tests | |
| run: | | |
| python test/test_query_processing.py -b | |
| python test/test_sketch_samples.py -b | |
| python test/test_abundance_weighting.py -b | |
| python test/test_target_elusive.py -b | |
| python test/test_target_weighting.py -b | |
| python test/test_cluster_graph.py -b | |
| python test/test_collect_reference_bins.py -b | |
| python test/test_summarise_coassemblies.py -b | |
| python test/test_no_genomes.py -b | |
| python test/test_aviary_commands.py | |
| python test/test_is_interleaved.py | |
| python test/test_build.py | |
| python test/test_coassemble.py | |
| python test/test_update.py | |
| python test/test_iterate.py | |
| python test/test_evaluate.py | |
| python test/test_evaluate_script.py -b |