diff --git a/.github/workflows/runTest.yml b/.github/workflows/runTest.yml index 4a737f3..3fba674 100644 --- a/.github/workflows/runTest.yml +++ b/.github/workflows/runTest.yml @@ -7,15 +7,15 @@ jobs: run: shell: bash -el {0} steps: -# - uses: actions/checkout@v4 -# - uses: conda-incubator/setup-miniconda@v2 -# with: -# activate-environment: yacht_env -# environment-file: env/yacht_env.yml + - uses: actions/checkout@v4 + - uses: conda-incubator/setup-miniconda@v2 + with: + activate-environment: yacht_env + environment-file: env/yacht_env.yml - name: make training data - run: python -m srcs.make_training_data_from_sketches --ref_file '../tests/testdata/20_genomes_sketches.zip' --ksize 31 --prefix 'gtdb_ani_thresh_0.95' --ani_thresh 0.95 --outdir ../ --force + run: python -m srcs.make_training_data_from_sketches --ref_file './tests/testdata/20_genomes_sketches.zip' --ksize 31 --prefix 'gtdb_ani_thresh_0.95' --ani_thresh 0.95 --outdir ./ --force - name: run YACHT - run: python srcs.run_YACHT.py --json ../gtdb_ani_thresh_0.95_config.json --sample_file '../tests/testdata/sample.sig.zip' --significance 0.99 --min_coverage_list 1 0.6 0.2 0.1 + run: python srcs.run_YACHT.py --json ./gtdb_ani_thresh_0.95_config.json --sample_file './tests/testdata/sample.sig.zip' --significance 0.99 --min_coverage_list 1 0.6 0.2 0.1 - name: test-unit run: pytest tests/test_unit.py --cov=./ --cov-report xml:covunit.xml - name: test-utils