updates testing bug fixes #378

	name: cgat-apps

	on: [push, pull_request]

	jobs:
	build:
	name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }})
	runs-on: ${{ matrix.os }}

	strategy:
	fail-fast: false
	matrix:
	os: ["ubuntu-latest", "macos-latest"]
	python-version: ["3.11", "3.12"]

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

	steps:
	- uses: actions/checkout@v2

	- name: Cache conda
	uses: actions/cache@v3 # Updated to the latest cache action version
	env:
	# Increase this value to reset cache if conda/environments/cgat-core.yml has not changed
	CACHE_NUMBER: 0
	with:
	path: ~/conda_pkgs_dir
	key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda/environments/cgat-apps.yml') }}

	- name: Set up Conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	mamba-version: "*" # Optional: if you prefer using mamba
	python-version: ${{ matrix.python-version }}
	miniforge-version: "latest" # Added to ensure Miniforge is installed
	channels: conda-forge, bioconda, defaults
	channel-priority: true
	activate-environment: cgat-a
	environment-file: conda/environments/cgat-apps.yml

	- name: Show conda
	run: \|
	conda info
	conda list

	- name: Test
	run: \|
	pip install -e .
	pip install pytest
	pytest -v tests/test_style.py
	pytest -v tests/test_scripts.py
	pytest -v tests/test_import.py

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