Improve pangolin tests #36

	name: pytest

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

	jobs:
	build:
	runs-on: ubuntu-latest
	strategy:
	max-parallel: 5
	fail-fast: false
	matrix:
	python-version: ["3.10", "3.11"]

	steps:
	- uses: actions/checkout@v4
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'pip'
	- name: Add conda to system path
	run: \|
	# $CONDA is an environment variable pointing to the root of the miniconda directory
	echo $CONDA/bin >> $GITHUB_PATH
	- name: Install dependencies
	run: \|
	conda config --add channels conda-forge
	conda config --add channels bioconda
	conda install -y python=${{ matrix.python-version }} meme=5.5.5
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	- 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
	# Ignore tests that should use GPU
	pytest --ignore=tests/black_box_test.py --ignore=tests/prune_archive_test.py

Provide feedback