Make molecules from SMILES where possible #113

	name: ci

	on:
	push:
	branches:
	- "main"
	pull_request:
	branches:
	- "main"
	workflow_dispatch:

	defaults:
	run:
	shell: bash -l {0}

	jobs:
	test:
	name: Test
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	os:
	- macOS-latest
	- ubuntu-latest
	python-version:
	- "3.10"
	- "3.11"

	env:
	OE_LICENSE: ${{ github.workspace }}/oe_license.txt

	steps:
	- uses: actions/checkout@v4

	- name: Set up conda environment
	uses: mamba-org/setup-micromamba@v1
	with:
	environment-file: devtools/conda-envs/dev.yaml
	create-args: >-
	python=${{ matrix.python-version }}

	- name: Install package
	run: python -m pip install -e .

	- name: Install and license OpenEye Toolkits
	run: \|
	echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE}
	python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()"
	env:
	SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }}

	- name: Run tests
	run: \|
	pytest -r fEx -n logical --durations=10 \
	--cov=yammbs/ --cov-report=xml --cov-config=setup.cfg \
	yammbs/

	- name: CodeCov
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: ./coverage.xml
	flags: unittests

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