clean up comments. Note that #39 was already fixed in 4321efe Fixes #39 #79
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name: runTest | |
on: [push] | |
jobs: | |
test-python-app: | |
runs-on: ubuntu-20.04 | |
defaults: | |
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 | |
- name: make training data | |
run: python make_training_data_from_sketches.py --ref_file 'tests/testdata/20_genomes_sketches.zip' --ksize 31 --prefix 'gtdb_ani_thresh_0.95' --ani_thresh 0.95 --outdir ./ | |
- name: run YACHT | |
run: python 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 --outdir ./ | |
- name: test-unit | |
run: pytest tests/test_unit.py | |
- name: test-utils | |
run: pytest tests/test_utils.py | |
- name: test-workflow | |
run: pytest tests/test_workflow.py |