Implement collapse unifurcations feature #743

Workflow file for this run

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

	name: CI

	on:
	push:
	pull_request:
	branches: [ "main" ]

	permissions:
	contents: read

	jobs:
	test:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
	os: [windows-latest, macOS-latest, ubuntu-latest]
	steps:
	- uses: actions/checkout@v4
	with:
	submodules: "recursive"
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install oldest-supported-numpy==2023.10.25
	# --ignore-requires-python ensures docs deps don't break install on early python versions
	if [ -f requirements.txt ]; then pip install --ignore-requires-python -r requirements.txt; fi
	pip install -e .
	- name: Lint with flake8
	run: \|
	# 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: \|
	python -m pytest

	coverage:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.11"]
	os: [ubuntu-latest]
	steps:
	- uses: actions/checkout@v4
	with:
	submodules: "recursive"
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	# - name: Setup LCOV
	# uses: hrishikesh-kadam/setup-lcov@v1
	- name: Install dependencies
	run: \|
	sudo apt update -yy
	sudo apt install -yy lcov
	python -m pip install --upgrade pip
	pip install wheel
	pip install oldest-supported-numpy==2023.10.25
	# --ignore-requires-python ensures docs deps don't break install on early python versions
	if [ -f requirements.txt ]; then pip install --ignore-requires-python -r requirements.txt; fi
	rm -rf Empirical/.git
	- name: Build phylotrackpy
	run: \|
	make coverage
	- name: Test with pytest
	run: \|
	python -m pytest --cov=. --cov-report=lcov
	lcov --output-file coverage.cpp --capture --directory .
	lcov --output-file coverage.cpp --extract coverage.cpp "*"
	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v4
	with:
	files: "coverage.cpp, coverage.lcov, Empirical/include/emp/Evolve/Systematics.hpp"
	token: ${{ secrets.CODECOV_TOKEN }}
	verbose: true

	build_wheels:
	name: Build wheels on ${{ matrix.os }}
	needs: []
	# if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu-latest, windows-latest, macos-13, macos-14]

	steps:
	- uses: actions/checkout@v4
	with:
	submodules: "recursive"
	- name: Build wheels
	uses: pypa/[email protected]
	- uses: actions/upload-artifact@v4
	with:
	name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
	path: ./wheelhouse/*.whl

	build_sdist:
	name: Build source distribution
	needs: []
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	submodules: "recursive"
	- name: Build sdist
	run: pipx run build --sdist

	- uses: actions/upload-artifact@v4
	with:
	name: cibw-sdist
	path: dist/*.tar.gz

	# Regression test borrowed from https://github.com/mmore500/hstrat/blob/ba7b19d0f0561303b6bf789d5024a323aa5993fc/.github/workflows/ci.yaml#L201
	packaging-sdist:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	submodules: "recursive"
	- name: Build sdist
	run: \|
	python3 -m venv env
	source env/bin/activate
	python3 -m pip install -r requirements.txt
	python3 setup.py sdist
	tree dist
	deactivate
	- name: Upgrade pip
	run: python3 -m pip install pip --upgrade
	- name: Install from sdist
	run: python3 -m pip install dist/*.tar.gz
	- name: Test install
	run: \|
	find . -type f -name '*.py' -exec rm {} \;
	python3 -c "import phylotrackpy; print(phylotrackpy.__version__)"

	upload_pypi:
	needs: [build_wheels, build_sdist, test]
	runs-on: ubuntu-latest
	environment: pypi
	permissions:
	id-token: write
	# upload to PyPI on every tag starting with 'v'
	if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
	# alternatively, to publish when a GitHub Release is created, use the following rule:
	# if: github.event_name == 'release' && github.event.action == 'published'
	steps:
	- uses: actions/download-artifact@v4
	with:
	# unpacks default artifact into dist/
	# if `name: artifact` is omitted, the action will create extra parent dir
	pattern: cibw-*
	path: dist
	merge-multiple: true

	- uses: pypa/[email protected]
	with:
	user: __token__
	password: ${{ secrets.PYPI_API_TOKEN }}

	paper:
	runs-on: ubuntu-latest
	name: Paper Draft
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Build draft PDF
	uses: openjournals/openjournals-draft-action@master
	with:
	journal: joss
	# This should be the path to the paper within your repo.
	paper-path: joss/paper.md
	- name: Upload
	uses: actions/upload-artifact@v4
	with:
	name: paper
	# This is the output path where Pandoc will write the compiled
	# PDF. Note, this should be the same directory as the input
	# paper.md
	path: joss/paper.pdf

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Implement collapse unifurcations feature #743

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Implement collapse unifurcations feature #743

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Workflow file for this run