	name: Tests

	on:
	push:
	branches:
	- develop
	- feature_prepare/**
	- main

	pull_request:
	branches:
	- '**'
	workflow_dispatch:

	concurrency:
	group: test-${{ github.ref }}
	cancel-in-progress: true

	jobs:
	actionlint:
	name: Action lint
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Check workflow files
	run: \|
	bash <(curl https://raw.githubusercontent.com/rhysd/actionlint/main/scripts/download-actionlint.bash)
	./actionlint -color -ignore SC2129
	shell: bash

	download_data:
	name: Download test data
	runs-on: ubuntu-22.04
	steps:
	- uses: actions/checkout@v4
	- shell: bash
	run: bash build_utils/download_data.sh
	- name: Upload test data
	uses: actions/upload-artifact@v4
	with:
	name: test_data
	path: test_data
	retention-days: 5

	base-test:
	name: Base py${{ matrix.python_version }}
	if: github.event_name == 'pull_request'
	uses: ./.github/workflows/base_test_workflow.yml
	needs: download_data
	strategy:
	fail-fast: false
	matrix:
	python_version: ["3.9", "3.10", "3.11", "3.12"]
	os: ["ubuntu-24.04"]
	qt_backend: ["PyQt5"]
	tox_args: [ "" ]
	include:
	- python_version: "3.11"
	os: "macos-13"
	qt_backend: "PyQt5"
	- python_version: "3.12"
	os: "macos-14"
	qt_backend: "PyQt6"
	- python_version: "3.11"
	os: "windows-latest"
	qt_backend: "PyQt5"
	- python_version: "3.10"
	os: "ubuntu-22.04"
	qt_backend: "PySide2"
	- python_version: "3.10"
	os: "ubuntu-24.04"
	qt_backend: "PySide6"
	- python_version: "3.12"
	os: "ubuntu-22.04"
	qt_backend: "PyQt6"
	- python_version: "3.10"
	os: "ubuntu-22.04"
	qt_backend: "PyQt5"
	pydantic: "_pydantic_1"
	with:
	test_data: True
	python_version: ${{ matrix.python_version }}
	os: ${{ matrix.os }}
	qt_backend: ${{ matrix.qt_backend }}
	tox_args: ${{ matrix.tox_args }}
	pydantic: ${{ matrix.pydantic }}

	base-test-main:
	name: Base py${{ matrix.python_version }}
	if: github.event_name == 'push'
	uses: ./.github/workflows/base_test_workflow.yml
	needs: download_data
	strategy:
	fail-fast: false
	matrix:
	python_version: ["3.9", "3.10", "3.11", "3.12"]
	os: ["ubuntu-24.04", "macos-14", "windows-2022"]
	qt_backend: ["PySide2", "PyQt5"]
	include:
	- python_version: "3.12"
	qt_backend: "PyQt5"
	os: "ubuntu-22.04"
	- python_version: "3.10"
	os: "ubuntu-22.04"
	qt_backend: "PySide6"
	- python_version: "3.11"
	os: "ubuntu-22.04"
	qt_backend: "PyQt6"
	- python_version: "3.11"
	os: "ubuntu-22.04"
	qt_backend: "PyQt5"
	pydantic: "_pydantic_1"
	exclude:
	- python_version: "3.11"
	qt_backend: "PySide2"
	- python_version: "3.12"
	qt_backend: "PySide2"
	- os: "macos-14"
	qt_backend: "PySide2"
	- os: "macos-14"
	python_version: "3.9"
	with:
	test_data: True
	python_version: ${{ matrix.python_version }}
	os: ${{ matrix.os }}
	qt_backend: ${{ matrix.qt_backend }}
	pydantic: ${{ matrix.pydantic }}
	artifact_suffix: "-main"
	pytest_args: "-v"

	test_coverage:
	needs: download_data
	uses: ./.github/workflows/base_test_workflow.yml
	with:
	test_data: True
	python_version: "3.12"
	tox_args: "-e py312-PyQt5-coverage"
	coverage: true

	test_minimal:
	name: Test PartSeg minimal
	needs: download_data
	uses: ./.github/workflows/base_test_workflow.yml
	with:
	test_data: True
	python_version: "3.9"
	tox_args: "-e py39-PyQt5-minimal"
	coverage: true

	coverage_prepare:
	name: Prepare coverage
	runs-on: ubuntu-latest
	needs: [test_coverage, test_minimal]
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: "3.x"
	cache-dependency-path: pyproject.toml
	cache: 'pip'
	- name: Install Dependencies
	run: \|
	pip install --upgrade pip
	pip install codecov

	- name: Download coverage data
	uses: actions/download-artifact@v4
	with:
	pattern: cov-reports-*
	path: coverage
	merge-multiple: true
	- name: combine coverage data
	run: \|
	python -Im coverage combine coverage
	python -Im coverage xml -o coverage.xml
	# Report and write to summary.
	python -Im coverage report --format=markdown --skip-empty --skip-covered >> "$GITHUB_STEP_SUMMARY"

	- name: Upload coverage artifact
	uses: actions/upload-artifact@v4
	with:
	name: coverage_xml
	path: coverage.xml
	retention-days: 5

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

	test_conda:
	name: Test PartSeg conda
	runs-on: ubuntu-24.04
	needs: download_data
	steps:
	- uses: actions/checkout@v4
	- name: Setup Miniconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	miniforge-version: latest
	use-mamba: true
	channels: conda-forge
	channel-priority: strict
	python-version: "3.12"

	- uses: tlambert03/setup-qt-libs@v1

	- name: Download test data
	uses: actions/download-artifact@v4
	with:
	name: test_data
	path: test_data

	- name: Use mamba solver
	shell: "bash -el {0}"
	run: \|
	conda install -n base conda-libmamba-solver
	conda config --set solver libmamba

	- name: Install dependencies
	shell: "bash -el {0}"
	run: \|
	mamba install -y "tox-conda>=0.10.0"

	- name: List environment packages
	shell: "bash -el {0}"
	run: conda list

	- name: create environment
	shell: "bash -el {0}"
	run: bash build_utils/create_environment_yml.sh

	- name: Upload environment file
	uses: actions/upload-artifact@v4
	with:
	name: environment
	path: environment.yml
	retention-days: 5

	- name: patch tox.ini
	shell: "bash -el {0}"
	run: sed -e "s/{sys_platform}/{platform}/g" tox.ini -i

	- name: Test with tox
	uses: aganders3/headless-gui@v2
	with:
	run: conda run -n test --no-capture-output tox -e py312-PySide2-conda
	timeout-minutes: 60

	check-package:
	name: Build & inspect our package.
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- uses: hynek/build-and-inspect-python-package@v2

test: [Automatic] Constraints upgrades: ipython, napari, numpy, packaging, pydantic, sentry-sdk, simpleitk, sympy, xlsxwriter #5558

Workflow file

Workflow file for this run

test: [Automatic] Constraints upgrades: `ipython`, `napari`, `numpy`, `packaging`, `pydantic`, `sentry-sdk`, `simpleitk`, `sympy`, `xlsxwriter` #5558