cleaning dependencies #3

	name: runTest

	on: [push]

	jobs:
	test-python-app:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- name: Set up Python 3.10
	uses: actions/setup-python@v3
	with:
	python-version: '3.10'
	- name: Add conda to system path
	run: \|
	# $CONDA is an environment variable pointing to the root of the miniconda directory
	echo $CONDA/bin >> $GITHUB_PATH
	- name: create environment 4 yacht
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-activate-base: false
	activate-environment: yacht
	environment-file: env/yacht_env.yaml
	- name: Install dependencies
	run: \|
	pip install scipy==1.11.2
	pip install numpy==1.25
	pip install wget==3.2
	pip install pandas
	pip install sourmash
	pip install loguru
	- 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 --ref_matrix 'gtdb_ani_thresh_0.95_ref_matrix_processed.npz' --ksize 31 --sample_file 'tests/testdata/sample.sig' --ani_thresh 0.95 --significance 0.99 --min_coverage 1 --outfile 'yacht_results.csv'

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