Implement EM convergence with tolerance threshold of log-likelihood change #73

	name: Pytest-workflow
	on:
	push:
	branches: [main]
	paths:
	- 'irescue/**'
	- 'tests/**'
	- '.github/workflows/pytest-workflow.yml'
	pull_request:
	branches: [main]

	concurrency:
	group: ${{ github.workflow }}-${{ github.event.pull_request.number \|\| github.ref }}
	cancel-in-progress: true

	jobs:
	test:
	runs-on: ubuntu-22.04
	name: test
	strategy:
	matrix:
	python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
	steps:
	- name: Checkout
	uses: actions/[email protected]

	- name: Setup conda
	uses: conda-incubator/setup-miniconda@v3
	with:
	environment-file: tests/config/environment.yml
	python-version: ${{ matrix.python-version }}
	condarc-file: tests/config/condarc.yml
	auto-update-conda: true

	- name: Install Python dependencies
	shell: bash -el {0}
	run: \|
	python -m pip install --upgrade pip
	python -m pip install pytest-workflow
	python -m pip install .

	- name: Run pytest-workflow
	shell: bash -el {0}
	run: TMPDIR=~ pytest --symlink --kwdof --git-aware --color=yes

	- name: Output log on failure
	if: failure()
	shell: bash -el {0}
	run: \|
	cat /home/runner/pytest_workflow_//log.{out,err}
	env
	which bedtools && bedtools --version
	which samtools && samtools --version
	which python && python --version
	conda list -n test

	- name: Upload logs on failure
	if: failure()
	uses: actions/[email protected]
	with:
	path: \|
	/home/runner/pytest_workflow_//log.out
	/home/runner/pytest_workflow_//log.err
	/home/runner/pytest_workflow_//IRescue_out
	/home/runner/pytest_workflow_//IRescue_tmp

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