Updating unit tests, adding to pipeline (#24) #27

	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
	environment-file: env/yacht_env.yaml
	- name: make training data
	run: python make_training_data_from_sketches.py --ref_file 'tests/testdata/20_genomes_sketches.zip' --ksize 31 --out_prefix 'gtdb_ani_thresh_0.95' --ani_thresh 0.95
	- name: run YACHT
	run: python run_YACHT.py --json 'gtdb_ani_thresh_0.95_config.json' --sample_file 'tests/testdata/sample.sig' --significance 0.99 --min_coverage 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

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