ENH: Clarify work is not limited to CT (#14) #31

Workflow file for this run

	name: CI

	# Comprehensive CI workflow combining unit tests, integration tests, GPU tests, and code quality checks
	#
	# Test organization:
	# - Unit tests: Run on all PRs and pushes, cross-platform (Ubuntu + Windows), multiple Python versions
	# - Integration tests: Run with external data, Ubuntu only
	# - GPU tests: Self-hosted runners with CUDA support
	# - Code quality: Linting and formatting checks
	#
	# Test markers:
	# - requires_data: Tests that need external data downloads
	# - slow: Tests that are computationally intensive or require GPU

	on:
	push:
	branches: [ main, master, develop ]
	pull_request:
	branches: [ main, master, develop ]
	workflow_dispatch:

	jobs:
	# ============================================================================
	# Cross-Platform Unit Tests (Ubuntu + Windows)
	# ============================================================================
	unit-tests:
	name: Unit Tests (${{ matrix.os }}, Python ${{ matrix.python-version }})
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu-latest, windows-latest]
	python-version: ['3.10', '3.11', '3.12']

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Free up disk space on Ubuntu
	if: matrix.os == 'ubuntu-latest'
	run: \|
	echo "Disk space before cleanup:"
	df -h
	sudo rm -rf /usr/share/dotnet
	sudo rm -rf /usr/local/lib/android
	sudo rm -rf /opt/ghc
	sudo rm -rf /opt/hostedtoolcache/CodeQL
	sudo docker image prune --all --force
	echo "Disk space after cleanup:"
	df -h

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'pip'
	cache-dependency-path: pyproject.toml

	- name: Cache pip packages
	uses: actions/cache@v4
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
	restore-keys: \|
	${{ runner.os }}-pip-${{ matrix.python-version }}-
	${{ runner.os }}-pip-

	- name: Install system dependencies (Ubuntu)
	if: matrix.os == 'ubuntu-latest'
	run: \|
	sudo apt-get update
	sudo apt-get install -y \
	libgl1 \
	libglib2.0-0 \
	libgomp1 \
	libsm6 \
	libxrender1 \
	libxext6 \
	libxrandr2 \
	libxi6
	sudo apt-get clean
	sudo rm -rf /var/lib/apt/lists/*

	- name: Upgrade pip and build tools
	run: \|
	python -m pip install --upgrade pip setuptools wheel

	- name: Install PyTorch (CPU)
	run: \|
	pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu

	- name: Install package with test dependencies
	run: \|
	pip install -e ".[test]"

	- name: Clear pip cache
	run: \|
	pip cache purge \|\| true

	- name: List installed packages
	run: \|
	pip list

	- name: Run unit tests (fast, no external data)
	run: \|
	pytest tests/ -v -m "not slow and not requires_data" --cov=physiomotion4d --cov-report=xml --cov-report=term --cov-report=html

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10'
	with:
	file: ./coverage.xml
	flags: unittests
	name: codecov-unit-${{ matrix.os }}-py${{ matrix.python-version }}
	fail_ci_if_error: false

	- name: Upload coverage artifacts
	uses: actions/upload-artifact@v4
	if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10'
	with:
	name: coverage-report-unit-tests
	path: htmlcov/
	retention-days: 7

	# ============================================================================
	# Integration Tests with External Data (Ubuntu only, on PRs)
	# ============================================================================
	integration-tests:
	name: Integration Tests (with data)
	runs-on: ubuntu-latest
	needs: unit-tests
	if: github.event_name == 'pull_request'

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Free up disk space
	run: \|
	echo "Disk space before cleanup:"
	df -h
	sudo rm -rf /usr/share/dotnet
	sudo rm -rf /usr/local/lib/android
	sudo rm -rf /opt/ghc
	sudo rm -rf /opt/hostedtoolcache/CodeQL
	sudo docker image prune --all --force
	echo "Disk space after cleanup:"
	df -h

	- name: Set up Python 3.10
	uses: actions/setup-python@v5
	with:
	python-version: '3.10'
	cache: 'pip'
	cache-dependency-path: pyproject.toml

	- name: Cache pip packages
	uses: actions/cache@v4
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-integration-${{ hashFiles('pyproject.toml') }}
	restore-keys: \|
	${{ runner.os }}-pip-integration-
	${{ runner.os }}-pip-

	- name: Cache test data
	uses: actions/cache@v4
	with:
	path: \|
	tests/data/
	tests/results/
	key: test-data-${{ hashFiles('tests/test_*.py') }}-v2
	restore-keys: \|
	test-data-

	- name: Install system dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y \
	libgl1 \
	libglib2.0-0 \
	libgomp1 \
	libsm6 \
	libxrender1 \
	libxext6 \
	libxrandr2 \
	libxi6
	sudo apt-get clean
	sudo rm -rf /var/lib/apt/lists/*

	- name: Upgrade pip and build tools
	run: \|
	python -m pip install --upgrade pip setuptools wheel

	- name: Install PyTorch (CPU)
	run: \|
	pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu

	- name: Install package with test dependencies
	run: \|
	pip install -e ".[test]"

	- name: Clear pip cache
	run: \|
	pip cache purge \|\| true

	- name: Run data download tests
	run: \|
	pytest tests/test_download_heart_data.py -v --cov=physiomotion4d --cov-report=xml
	continue-on-error: true

	- name: Run data conversion tests
	run: \|
	pytest tests/test_convert_nrrd_4d_to_3d.py -v --cov=physiomotion4d --cov-append --cov-report=xml
	continue-on-error: true

	- name: Run contour tools tests
	run: \|
	pytest tests/test_contour_tools.py -v -m "not slow" --cov=physiomotion4d --cov-append --cov-report=xml
	continue-on-error: true

	- name: Run USD conversion tests
	run: \|
	pytest tests/test_convert_vtk_4d_to_usd_polymesh.py -v -m "not slow" --cov=physiomotion4d --cov-append --cov-report=xml
	continue-on-error: true

	- name: Run USD utility tests
	run: \|
	pytest tests/test_usd_merge.py tests/test_usd_time_preservation.py -v --cov=physiomotion4d --cov-append --cov-report=xml
	continue-on-error: true

	- name: Run all integration tests
	run: \|
	pytest tests/ -v -m "not slow"
	continue-on-error: true

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	with:
	file: ./coverage.xml
	flags: integration-tests
	name: codecov-integration
	fail_ci_if_error: false

	# ============================================================================
	# GPU Tests (Self-hosted runners with CUDA)
	# ============================================================================
	# NOTE: GPU tests are DISABLED for automatic runs because they wait indefinitely
	# if no self-hosted runner is available. Enable manually via workflow_dispatch
	# or by setting the 'run-gpu-tests' label on the PR.
	gpu-tests:
	name: GPU Tests (Python ${{ matrix.python-version }})
	runs-on: [self-hosted, linux, gpu]
	needs: unit-tests
	timeout-minutes: 30
	# Only run GPU tests on manual trigger or if 'run-gpu-tests' label is present
	if: github.event_name == 'workflow_dispatch' \|\| contains(github.event.pull_request.labels.*.name, 'run-gpu-tests')
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.10", "3.11"]
	continue-on-error: true

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

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

	- name: Check GPU availability
	run: \|
	nvidia-smi \|\| echo "No GPU available"
	python -c "import torch; print(f'PyTorch CUDA available: {torch.cuda.is_available()}')" \|\| echo "PyTorch not installed yet"

	- name: Cache pip packages
	uses: actions/cache@v4
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-gpu-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
	restore-keys: \|
	${{ runner.os }}-pip-gpu-${{ matrix.python-version }}-
	${{ runner.os }}-pip-gpu-
	${{ runner.os }}-pip-

	- name: Upgrade pip and build tools
	run: \|
	python -m pip install --upgrade pip setuptools wheel

	- name: Install PyTorch (CUDA 12.6)
	run: \|
	pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu126

	- name: Install package with test dependencies
	run: \|
	pip install -e ".[test]"

	- name: Verify GPU setup
	run: \|
	python -c "import torch; print(f'PyTorch version: {torch.__version__}')"
	python -c "import torch; print(f'CUDA available: {torch.cuda.is_available()}')"
	python -c "import torch; print(f'CUDA version: {torch.version.cuda}')" \|\| echo "CUDA not available"
	python -c "import torch; print(f'Number of GPUs: {torch.cuda.device_count()}')" \|\| echo "No GPUs"

	- name: List installed packages
	run: \|
	pip list

	- name: Run GPU tests
	run: \|
	pytest tests/ -v -m "not slow" --cov=physiomotion4d --cov-report=xml --cov-report=term --cov-report=html
	env:
	CUDA_VISIBLE_DEVICES: 0

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	if: matrix.python-version == '3.10'
	with:
	file: ./coverage.xml
	flags: gpu-tests
	name: codecov-gpu-py${{ matrix.python-version }}
	fail_ci_if_error: false

	- name: Upload coverage artifacts
	uses: actions/upload-artifact@v4
	if: matrix.python-version == '3.10'
	with:
	name: coverage-report-gpu
	path: htmlcov/
	retention-days: 7

	# ============================================================================
	# Code Quality Checks
	# ============================================================================
	code-quality:
	name: Code Quality Checks
	runs-on: ubuntu-latest

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

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

	- name: Install dev dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install black isort ruff flake8 pylint mypy

	- name: Check code formatting with Black
	run: \|
	black --check src/ tests/ \|\| echo "Black check failed"
	continue-on-error: true

	- name: Check import sorting with isort
	run: \|
	isort --check-only src/ tests/ \|\| echo "isort check failed"
	continue-on-error: true

	- name: Lint with Ruff
	run: \|
	ruff check src/ tests/ \|\| echo "Ruff check failed"
	continue-on-error: true

	- name: Lint with Flake8
	run: \|
	flake8 src/ tests/ \|\| echo "Flake8 check failed"
	continue-on-error: true

	# ==============================================================================
	# Notes on Excluded Tests
	# ==============================================================================
	#
	# The following tests are excluded from CI and should be run locally:
	#
	# Slow/GPU-intensive tests:
	# - tests/test_register_images_ants.py (slow, computationally intensive)
	# - tests/test_register_images_icon.py (requires CUDA for ICON)
	# - tests/test_transform_tools.py (depends on slow registration tests)
	# - tests/test_segment_chest_total_segmentator.py (requires CUDA for TotalSegmentator)
	# - tests/test_segment_chest_vista_3d.py (requires CUDA for VISTA-3D, 20GB+ RAM)
	#
	# To run locally:
	# pytest tests/ -v -m "slow" # Run all slow tests
	# pytest tests/test_register_images_ants.py -v
	# pytest tests/test_register_images_icon.py -v
	# pytest tests/test_segment_chest_total_segmentator.py -v

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ENH: Clarify work is not limited to CT (#14) #31

Workflow file

ENH: Clarify work is not limited to CT (#14) #31

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Workflow file for this run