Merge pull request #524 from fbaensch-beilstein/main #53

	name: API workflow

	on:
	push:
	branches:
	- main
	- development
	pull_request:
	branches:
	- main
	- development

	jobs:
	test:
	runs-on: ubuntu-latest
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
	strategy:
	matrix:
	python-version: ["3.10"]
	steps:
	- uses: actions/[email protected]
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v3
	with:
	python-version: ${{ matrix.python-version }}
	- name: Print all environment variables
	run: printenv
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip3 install --upgrade setuptools pip
	pip3 install --no-cache-dir -r requirements.txt
	pip3 install rdkit
	python3 -m pip uninstall -y imantics
	pip3 install imantics==0.1.12
	pip3 install openbabel-wheel
	pip3 install --no-deps decimer-segmentation==1.1.3
	pip3 install --no-deps decimer==2.3.0
	pip3 install --no-deps STOUT-pypi==2.0.5
	pip install flake8 pytest
	pip install pytest-cov
	wget -O surge "https://github.com/StructureGenerator/surge/releases/download/v1.0/surge-linux-v1.0"
	chmod +x surge
	sudo mv surge /usr/bin
	- name: Analysing the code with pylint
	run: \|
	flake8 --per-file-ignores="__init__.py:F401" --ignore E402,E501,W503 $(git ls-files '*.py') .
	- name: Run tests and collect coverage
	run: \|
	python3 -m pytest --cov=./ --cov-report=xml
	- name: Upload coverage reports to Codecov
	uses: codecov/[email protected]
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
	with:
	file: ./coverage.xml
	fail_ci_if_error: true
	flags: service
	name: codecov-umbrella
	verbose: true

Provide feedback