action to pip #7

	# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: Python package

	on:
	push:
	paths:
	- 'src/**'
	- 'tests/**'
	workflow_dispatch:

	jobs:
	build:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.12"]

	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 dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install pysmiles pytest ruff ty pytest-cov
	pip install -e .

	- name: Lint with ruff
	run: ruff check src

	- name: Type check with ty
	run: ty check src

	- name: Test with pytest
	run: \|
	pytest tests --cov=src --cov-branch --cov-report=term-missing --cov-report=html --cov-report=xml
	pytest tests --cov=src --junitxml=junit.xml -o junit_family=legacy

	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v5
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	slug: tacular-omics/paftacular
	fail_ci_if_error: false

	- name: Upload test results to Codecov
	if: ${{ !cancelled() }}
	uses: codecov/codecov-action@v5
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	slug: tacular-omics/paftacular
	report_type: test_results
	fail_ci_if_error: false

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