Tests

Use PAT to clone private test-datasets submodule in CI. #872

	name: Tests

	on: [push]

	jobs:
	run-unit-tests:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v5
	with:
	submodules: recursive
	# chem-spectra-test-files is private; use a PAT with repo read access,
	# or enable org-wide GITHUB_TOKEN access, or make the dataset repo public.
	token: ${{ secrets.CHEMSPECTRA_TEST_FILES_PAT != '' && secrets.CHEMSPECTRA_TEST_FILES_PAT \|\| github.token }}
	- name: Verify test-datasets submodule
	run: \|
	if [ ! -f test-datasets/catalog/datasets.json ]; then
	echo "::error::Submodule test-datasets is missing."
	echo "chem-spectra-test-files is a private repository."
	echo "Fix options:"
	echo " 1. Add repo secret CHEMSPECTRA_TEST_FILES_PAT (read access to ComPlat/chem-spectra-test-files)"
	echo " 2. Enable org setting: Actions may access other repositories in ComPlat"
	echo " 3. Make ComPlat/chem-spectra-test-files public"
	exit 1
	fi
	- uses: actions/setup-python@v6
	with:
	check-latest: true
	cache: "pip"
	python-version: "3.12"
	- name: Install dependencies
	run: \|
	pip install --upgrade pip
	pip install .[dev]
	- name: Create tmp directory with permissions
	run: \|
	mkdir -p chem_spectra/tmp
	chmod -R 777 chem_spectra/tmp
	- name: Start msconvert Docker container
	run: \|
	docker run --detach --name msconvert_docker \
	--rm -it \
	-e WINEDEBUG=-all \
	-v ${{ github.workspace }}/chem_spectra/tmp:/data \
	proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses bash
	- name: Test with pytest
	shell: bash -el {0}
	run: \|
	python -m pytest

Provide feedback