Test

Merge pull request #140 from CompOmics/fix/various-io-fixes #463

	name: Test

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

	jobs:
	linting-and-coverage:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.10"

	- name: Lint with Ruff
	uses: astral-sh/ruff-action@v3
	with:
	args: check --exclude docs,tests

	- name: Check formatting with Ruff
	uses: astral-sh/ruff-action@v3
	with:
	args: format --check --diff --exclude docs,tests

	- name: Install package and its dependencies
	run: pip install --editable .[dev,io]

	- name: Static type checking with mypy
	run: mypy --non-interactive

	- name: Test with pytest and codecov
	run: \|
	pytest --cov=psm_utils --cov-report=xml tests/

	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v3
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: ./coverage.xml
	flags: unittests
	name: codecov-umbrella
	fail_ci_if_error: false

	test-platforms:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.10", "3.11", "3.12", "3.13"]
	steps:
	- uses: actions/checkout@v4

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install package and its dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install .[dev]

	- name: Install optional dependencies that might not be available
	continue-on-error: true
	run: pip install .[io]

	- name: Test imports
	run: python -c "import psm_utils"

	- name: Test with pytest
	run: \|
	pytest

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