Merge branch 'refactor-bind-path-singularity' into fix-snakemake-rerun #5315

	name: pytests
	on:
	push:
	paths-ignore:
	- "CHANGELOG.rst"
	- "docs/**"
	pull_request:
	paths-ignore:
	- "CHANGELOG.rst"
	- "docs/**"
	jobs:
	pytest_coveralls:
	name: run PyTest
	runs-on: ubuntu-20.04
	steps:
	# Checkout BALSAMIC
	- name: Git checkout
	id: git_checkout
	uses: actions/checkout@v3
	# Get branch name
	- name: Get branch name
	id: get_branch_name
	shell: bash
	run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF##*/})"
	# Conda env create
	- name: setup conda
	id: setup_conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	activate-environment: balsamic
	environment-file: BALSAMIC/conda/balsamic.yaml
	# Install BALSAMIC
	- name: Install BALSAMIC
	id: install_balsamic
	shell: bash -l {0}
	run: \|
	conda activate balsamic
	pip install --no-cache-dir .
	# Install pytest coveralls dependencies
	- name: Install PyTest and Coveralls
	id: install_pytest
	shell: bash -l {0}
	run: \|
	conda activate balsamic
	pip install --no-cache-dir -r requirements-dev.txt
	# Run PyTest
	- name: Run PyTest
	id: pytest
	shell: bash -l {0}
	run: \|
	conda activate balsamic
	py.test --cov-report=xml --cov=BALSAMIC -rsxv tests/*
	env:
	SENTIEON_LICENSE: dummy_license
	SENTIEON_INSTALL_DIR: dummy_install_dir
	# Run Codecov
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v3
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: ./coverage.xml
	flags: unittests
	fail_ci_if_error: true
	verbose: true

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