ENH: Specify Python 3.11 for nightly health / remote runner #310

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 (gated by opt-in pytest flags; default = skip):
	# - slow -> --run-slow
	# - requires_gpu -> --run-gpu
	# - requires_simpleware -> --run-simpleware (also implies GPU)
	# - requires_physicsnemo -> --run-physicsnemo (needs the [physicsnemo] extra)
	# - experiment -> --run-experiments
	# - tutorial -> --run-tutorials
	# --run-all enables every bucket above at once.
	# Tests that need external data download it automatically via fixtures.

	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: ['3.11', '3.12']

	steps:
	- name: Checkout code
	uses: actions/checkout@v6
	with:
	lfs: true

	- 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@v6
	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 \
	xvfb \
	libosmesa6
	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 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 GPU/slow/experiment) - Ubuntu
	if: matrix.os == 'ubuntu-latest'
	run: \|
	xvfb-run -a --server-args="-screen 0 1024x768x24" \
	pytest tests/ -v --cov=physiotwin4d --cov-report=xml --cov-report=term --cov-report=html

	- name: Run unit tests (fast, no GPU/slow/experiment) - Windows
	if: matrix.os == 'windows-latest'
	run: \|
	pytest tests/ -v --cov=physiotwin4d --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 == '3.11'
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: ./coverage.xml
	flags: unittests
	name: codecov-unit-${{ matrix.os }}-py${{ matrix.python-version }}
	fail_ci_if_error: false

	- name: Upload coverage artifacts
	uses: actions/upload-artifact@v6
	if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
	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@v6
	with:
	lfs: true

	- 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 3.11
	uses: actions/setup-python@v6
	with:
	python-version: '3.11'
	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 \
	xvfb \
	libosmesa6
	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 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=physiotwin4d --cov-report=xml
	continue-on-error: true

	- name: Run data conversion tests
	run: \|
	pytest tests/test_convert_image_4d_to_3d.py -v --cov=physiotwin4d --cov-append --cov-report=xml
	continue-on-error: true

	- name: Run contour tools tests
	run: \|
	pytest tests/test_contour_tools.py -v --cov=physiotwin4d --cov-append --cov-report=xml
	continue-on-error: true

	- name: Run USD conversion tests
	run: \|
	xvfb-run -a --server-args="-screen 0 1024x768x24" \
	pytest tests/test_convert_vtk_to_usd_polymesh.py -v --cov=physiotwin4d --cov-append --cov-report=xml
	continue-on-error: true

	- name: Run USD utility tests
	run: \|
	xvfb-run -a --server-args="-screen 0 1024x768x24" \
	pytest tests/test_usd_merge.py tests/test_usd_time_preservation.py -v --cov=physiotwin4d --cov-append --cov-report=xml
	continue-on-error: true

	- name: Run all integration tests
	run: \|
	xvfb-run -a --server-args="-screen 0 1024x768x24" \
	pytest tests/ -v
	continue-on-error: true

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	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
	runs-on: [self-hosted, Windows, X64, 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')
	continue-on-error: true

	steps:
	- name: Checkout code
	uses: actions/checkout@v6
	with:
	lfs: true

	- name: Create venv in RUNNER_TEMP
	# Python 3.11 is required because the [physicsnemo] extra pulls in
	# nvidia-physicsnemo, which requires Python >= 3.11.
	run: \|
	& "C:\Program Files\Python311\python.exe" -m venv "$env:RUNNER_TEMP\physiotwin4d-venv"
	echo "$env:RUNNER_TEMP\physiotwin4d-venv\Scripts" >> $env:GITHUB_PATH

	- name: Check GPU availability
	run: nvidia-smi

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

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

	- name: Install package with test dependencies
	# uv respects [tool.uv.sources], routing torch to pytorch-cu130 for cuda13.
	# The [physicsnemo] extra brings in nvidia-physicsnemo so Tutorial 9 and
	# requires_physicsnemo-marked tests can run on this GPU runner.
	# Invoke via python -m uv so uv targets the active venv interpreter.
	run: \|
	python -m uv pip install -e ".[test,cuda13,physicsnemo]"

	- name: Assert CUDA is accessible
	run: \|
	python -c "
	import sys, torch, cupy
	print(f'PyTorch {torch.__version__} \| CUDA toolkit {torch.version.cuda} \| CuPy {cupy.__version__}')
	if not torch.cuda.is_available():
	print('ERROR: torch.cuda.is_available() returned False', file=sys.stderr)
	sys.exit(1)
	n = torch.cuda.device_count()
	if n == 0:
	print('ERROR: torch.cuda.device_count() == 0', file=sys.stderr)
	sys.exit(1)
	cn = cupy.cuda.runtime.getDeviceCount()
	if cn == 0:
	print('ERROR: cupy.cuda.runtime.getDeviceCount() == 0', file=sys.stderr)
	sys.exit(1)
	print(f'OK: {n} GPU(s) visible to PyTorch and CuPy')
	"

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

	- name: Run GPU tests
	# External self-hosted GPU runner: enable every opt-in bucket via --run-all.
	# Tests whose host requirements (e.g. a licensed Simpleware install)
	# aren't met on the runner will runtime-skip cleanly via their
	# internal availability guards.
	run: \|
	pytest tests/ -v --run-all --cov=physiotwin4d --cov-report=xml --cov-report=term --cov-report=html
	env:
	CUDA_VISIBLE_DEVICES: 0

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: ./coverage.xml
	flags: gpu-tests
	name: codecov-gpu
	fail_ci_if_error: false

	- name: Upload coverage artifacts
	uses: actions/upload-artifact@v6
	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@v6
	with:
	lfs: true

	- name: Set up Python 3.11
	uses: actions/setup-python@v6
	with:
	python-version: "3.11"
	cache: 'pip'

	- name: Install dev dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install ruff mypy
	pip install -e ".[dev]"

	- name: Check formatting with Ruff
	run: \|
	ruff format --check .
	continue-on-error: false

	- name: Lint with Ruff
	run: \|
	ruff check .
	continue-on-error: false

	- name: Type check with mypy
	run: \|
	mypy src/
	continue-on-error: false

	# ==============================================================================
	# 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)
	#
	# Experiment tests (EXTREMELY SLOW - hours to complete):
	# - tests/test_experiments.py (runs all notebooks in experiments/ subdirectories)
	# These tests are NEVER run in CI/CD and must be run manually
	# They execute end-to-end workflows that may take multiple hours
	#
	# To run locally:
	# pytest tests/ -v --run-slow # Run all slow tests
	# pytest tests/ -v --run-gpu --run-slow # GPU + slow (typical local dev profile)
	# pytest tests/ -v --run-simpleware --run-gpu --run-slow # Full Simpleware coverage
	# pytest tests/test_register_images_ANTS.py -v --run-slow
	#
	# Self-hosted GPU runner enables ALL buckets via --run-all
	# (--run-gpu --run-slow --run-simpleware --run-physicsnemo --run-experiments --run-tutorials).
	# That runner installs the [physicsnemo] extra in addition to [test,cuda13].
	#
	# To run experiment tests (manual only, extremely slow):
	# pytest tests/test_experiments.py -v --run-experiments
	# pytest tests/test_experiments.py::test_experiment_heart_gated_ct_to_usd -v --run-experiments

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ENH: Specify Python 3.11 for nightly health / remote runner #310

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ENH: Specify Python 3.11 for nightly health / remote runner #310

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