Merge pull request #3 from instituteofcancerresearch/analysis-ssb192 #27

	name: SOPRANO Tests

	on:
	push:
	branches:
	- python-dev
	pull_request:
	branches:
	- python

	jobs:
	lint:
	strategy:
	matrix:
	os: ["ubuntu-latest"]
	python-version: ["3.11"]
	name: lint with python ${{ matrix.python-version }} on ${{ matrix.os }}
	runs-on: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install ruff and black
	run: \|
	python -m pip install --upgrade pip
	pip install ruff black
	- name: Lint check with ruff
	run: \|
	ruff --format=github --target-version=py311 --line-length 79 .
	- name: Style check with black
	run: \|
	black ./ --check --line-length 79
	test:
	strategy:
	matrix:
	os: ["ubuntu-latest"] # To include macos-latest
	python-version: ["3.11"]
	name: test with python ${{ matrix.python-version }} on ${{ matrix.os }}
	runs-on: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v3
	- uses: mamba-org/setup-micromamba@v1
	with:
	environment-file: src/SOPRANO/local.yml
	init-shell: bash
	- name: Install SOPRANO
	shell: bash -l {0}
	run: \|
	micromamba activate soprano-dev
	pip install -e .[ci]
	- name: Test conda environment
	shell: bash -l {0}
	run: \|
	micromamba activate soprano-dev
	pytest tests/test_configuration
	- name: Test units
	shell: bash -l {0}
	run: \|
	micromamba activate soprano-dev
	pytest tests/test_units
	# - name: Test integration
	# shell: bash -l {0}
	# run: \|
	# micromamba activate soprano-dev
	# pytest tests/test_integrations

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