Tests

read from parquet and hdf5 input files #58

	name: Tests

	on:
	push:
	branches: [ main, dev ]
	pull_request:
	branches: [ main, dev ]

	jobs:
	tests:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.9', '3.10', '3.11']

	steps:
	- name: Checkout
	uses: actions/checkout@v3

	- name: Install poetry
	run: pipx install poetry

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'poetry'

	- name: Update poetry lock file
	run: poetry lock --no-update

	- name: Install dependencies
	run: poetry install

	- name: Run unit tests
	run: poetry run pytest -m "not slow" --cov=esce --cov-report=term

	- name: Run snakemake workflow test
	run: poetry run snakemake --configfile tests/test_config.yaml -F -c1 all

	- name: Run snakemake submodule test
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	BRANCH: ${{ github.head_ref }}
	run: poetry run snakemake -s tests/test_snakefile_submodule.smk -c1 -F all

	# Uncomment this step if you need to run tests with conda
	# - name: Run snakemake submodule test with conda
	# env:
	# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	# run: \|
	# poetry run snakemake -s tests/test_snakefile_submodule.smk -c1 -F --use-conda --conda-frontend conda all

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