Bump existing package versions and add tests. #105

	name: Python CI

	on:
	push:
	branches: [ main, dev]
	pull_request:
	branches: [ main, dev]

	jobs:
	build:
	runs-on: ubuntu-latest
	timeout-minutes: 10
	strategy:
	matrix:
	python-version: ["3.11", "3.12"]

	steps:
	- uses: actions/checkout@v3

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Cache pip
	uses: actions/cache@v3
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-

	- name: Install dependencies
	run: \|
	sudo apt-get install -qq phyml
	python -m pip install --upgrade pip setuptools>=77.0.3 wheel
	pip install --only-binary=numpy,scipy numpy scipy
	pip install matplotlib ipython jupyter sympy pytest codecov pytest-cov
	pip install -r requirements.txt
	pip install -e .

	- name: Run tests
	run: pytest --cov=OrthoEvol --cov-report=xml --junitxml=junit.xml tests/

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

	- name: Upload test results to Codecov
	if: ${{ !cancelled() }}
	uses: codecov/test-results-action@v1
	with:
	token: ${{ secrets.CODECOV_TOKEN }}

	- name: Notify failure
	if: failure()
	run: echo "Build failed"

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