Merge pull request #107 from cokelaer/main #460

	name: Tests wrappers

	on:
	push:
	branches:
	- main
	- dev
	workflow_dispatch:
	pull_request:
	branches-ignore: []
	schedule:
	- cron: '0 0 4 * *'

	jobs:
	testing:
	runs-on: ubuntu-latest
	strategy:
	max-parallel: 5
	matrix:
	python: ['3.10']



	steps:
	- name: checkout git repo
	uses: actions/checkout@v4
	with:
	# by default fetch depth is 1 leading to error
	# when using git diff HEAD^ --name-only so we need to set
	# fetch depth to 0 manualy
	fetch-depth: '0'

	- name: mamba
	uses: "mamba-org/setup-micromamba@v1"
	with:
	# snakemake complains it cannot find mamba. the micromamba does not seem
	# to install mamba by itself so we add it specifically
	create-args: >-
	python=${{ matrix.python }}
	snakemake-minimal
	pytest
	mamba
	environment-name: snakemake
	init-shell: >-
	bash
	condarc: \|
	channels:
	- conda-forge
	- bioconda
	channel_priority: strict

	- name: Fetch main
	shell: bash -el {0}
	if: ${{ github.ref != 'refs/heads/main' }}
	run: \|
	git fetch origin main
	- name: Test with pytest
	shell: micromamba-shell {0}
	env:
	DIFF_MASTER: ${{ github.event_name == 'pull_request' }}
	DIFF_LAST_COMMIT: ${{ github.ref == 'refs/heads/main' }}
	run: \|
	if [ $(git rev-parse --verify HEAD^ > /dev/null 2>&1; echo $?) -eq 0 ]; then
	git diff HEAD^ --name-only
	else
	echo "No parent commit. Skipping git diff."
	fi
	pytest test.py -vv

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