fix for new pdb2pqr #5

	name: Test code and publish package

	on: [push]

	jobs:
	test:
	runs-on: ${{ matrix.os }}

	strategy:
	fail-fast: false
	matrix:
	os: ["ubuntu-latest", "macos-latest", "macos-13", "windows-2019"]
	python-version: ["3.9", "3.10", "3.11", "3.12"]

	defaults: # Needed for conda
	run:
	shell: bash -l {0}

	steps:
	- uses: actions/checkout@v4
	with:
	lfs: true
	submodules: true

	- uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: ${{ matrix.python-version }}
	channels: acellera,conda-forge,defaults

	- name: Lint with flake8
	run: \|
	pip install flake8 coverage
	# 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: Install cdpkit
	# # if: ${{ matrix.os == 'ubuntu-latest' }}
	# run: \|
	# # for testing CDPKit SmallMol
	# pip install CDPKit

	- name: Install moleculekit
	run: \|
	pip install build pytest pytest-xdist
	python -m build
	pip install dist/moleculekit-*.whl

	- name: List conda environment
	run: conda list

	- name: Test
	run: \|
	pytest -n auto ./tests/ --durations=20
	env:
	LOCAL_PDB_REPO: ./tests/pdb/
	SKIP_SPEED_TESTS: True

	# - name: Upload coverage to Codecov
	# uses: codecov/codecov-action@v3

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