Conversion bruker data #291

	# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
	# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

	name: Python package

	on:
	push:
	branches: [ master ]
	pull_request:
	branches: [ master ]

	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.7", "3.8", "3.9"]

	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 dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -r requirements.txt
	- name: Lint with flake8
	run: \|
	pip install flake8
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Test with pytest
	run: \|
	pip install pytest
	python setup.py install
	python sdrf_pipelines/tests/test_sdrfchecker.py
	- name: Test OpenMS converter
	run: \|
	cd sdrf_pipelines
	for sdrf in testdata//.sdrf.tsv
	do
	pushd $(dirname $sdrf)
	python ../../parse_sdrf.py convert-openms -s $(pwd)/../../$sdrf -t2
	diff -c experimental_design.tsv expected_experimental_design.tsv >> ../../failures.txt
	diff -c expected_openms.tsv openms.tsv >> ../../failures.txt
	popd
	done
	if [ -s failures.txt ]
	then
	exit 1
	fi

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