tests

Modernising Build Process #1052

Workflow file for this run

.github/workflows/cicd_tests.yml at 7023df3

	name: tests

	on:
	# quick tests for pull requests and the releasing branches
	push:
	branches:
	- dev
	- main
	- releasing/*
	paths-ignore: # skip if only docs are modified
	- '**.md'
	- '**.rst'
	- 'docs/**'
	pull_request:
	branches:
	- dev
	- main
	- releasing/*
	paths-ignore: # skip if only docs are modified
	- '**.md'
	- '**.rst'
	- 'docs/**'

	concurrency:
	# automatically cancel the previously triggered workflows when there's a newer version
	group: cicd-tests-${{ github.event.pull_request.number \|\| github.ref }}
	cancel-in-progress: true

	# Supported versions of Python and PyTorch are listed here for use below and as documentation
	env:
	# supported versions of Python
	PYTHON_VER1: '3.10'
	PYTHON_VER2: '3.11'
	PYTHON_VER3: '3.12'
	PYTHON_VER4: '3.13'
	# PYTHON_VER5: '3.14' # TODO: not compatible with Torchscript, re-enable once Torchscript removed from MONAI
	# supported versions of PyTorch
	PYTORCH_VER1: '2.8.0'
	PYTORCH_VER2: '2.9.1'
	PYTORCH_VER3: '2.10.0'
	PYTORCH_VER4: '2.11.0'
	TORCHVISION_VER1: '0.23.0' # used for testing with lowest PyTorch version (PYTORCH_VER1), update as needed

	# versions of PyTorch/Torchvision to use for full-dep Windows tests, needed to get around a gloo bug
	WIN_FULLDEP_VER: '2.11.0'
	WIN_FULLDEP_VISION_VER: '0.26.0'

	PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354

	# These jobs run the CICD tests, type checking, and testing packaging. These use the minimum supported versions of
	# Python and PyTorch in many places using the above environment variables but also hard coded where necessary.
	# When support is dropped for a version it is important to update these as appropriate.

	jobs:
	static-checks: # Perform static type and other checks using runtests.sh
	runs-on: ubuntu-latest
	strategy:
	matrix:
	opt: ["codeformat", "pyrefly"]
	steps:
	- name: Clean unused tools
	run: \|
	find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
	sudo rm -rf /usr/share/dotnet
	sudo rm -rf /usr/local/lib/android
	sudo rm -rf /opt/ghc /usr/local/.ghcup
	sudo docker system prune -f

	- uses: actions/checkout@v7
	- name: Set up Python ${{ env.PYTHON_VER1 }}
	uses: actions/setup-python@v6
	with:
	python-version: ${{ env.PYTHON_VER1 }}
	cache: 'pip'
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip wheel
	python -m pip install .[all,testing]
	- name: Lint and type check
	run: \|
	# clean up temporary files
	$(pwd)/runtests.sh --build --clean
	$(pwd)/runtests.sh --build --${{ matrix.opt }}

	min-dep: # Test with minumum dependencies installed for different OS, Python, and PyTorch combinations
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	# Base test cases are to test on all three OSes with the lowest versions of Python and PyTorch, other cases are
	# added below as special cases to cover other Python and PyTorch versions under Ubuntu
	os: [windows-latest, macOS-latest, ubuntu-latest]
	python-version: ['3.10']
	pytorch-version: ['2.8.0']
	include:
	# Test Python versions under Ubuntu with lowest PyTorch version supported
	- os: ubuntu-latest
	pytorch-version: '2.8.0'
	python-version: '3.11'
	- os: ubuntu-latest
	pytorch-version: '2.8.0'
	python-version: '3.12'
	- os: ubuntu-latest
	pytorch-version: '2.8.0'
	python-version: '3.13'
	# - os: ubuntu-latest
	# pytorch-version: '2.9.1'
	# python-version: '3.14'

	# Test PyTorch versions under Ubuntu with lowest Python version supported
	- os: ubuntu-latest
	python-version: '3.10'
	pytorch-version: '2.9.1'
	- os: ubuntu-latest
	python-version: '3.10'
	pytorch-version: '2.10.0'
	- os: ubuntu-latest
	python-version: '3.10'
	pytorch-version: '2.11.0'

	timeout-minutes: 40
	steps:
	- if: runner.os == 'Linux'
	name: Clean unused tools
	run: \|
	find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
	sudo rm -rf /usr/share/dotnet
	sudo rm -rf /usr/local/lib/android
	sudo rm -rf /opt/ghc /usr/local/.ghcup
	sudo docker system prune -f
	- uses: actions/checkout@v7
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v6
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'pip'
	- name: Prepare pip wheel
	run: \|
	which python
	python -m pip install --upgrade pip wheel tomli
	- name: Install the minimum dependencies
	run: \|
	# min. requirements
	python -m pip install torch==${{ matrix.pytorch-version }}
	python monai/config/print_dependencies.py build-system \| xargs pip install --no-build-isolation
	python -m pip install --no-build-isolation .[testing]
	python -m pip list
	shell: bash
	- if: matrix.os == 'linux-gpu-runner'
	name: Print GPU Info
	run: \|
	nvidia-smi
	python -c 'import torch; print(torch.rand(2,2).to("cuda:0"))'
	shell: bash
	- name: Run quick tests
	run: \|
	python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
	python -c "import monai; monai.config.print_config()"
	./runtests.sh --min
	shell: bash
	env:
	QUICKTEST: True
	NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
	NGC_ORG: ${{ secrets.NGC_ORG }}
	NGC_TEAM: ${{ secrets.NGC_TEAM }}

	full-dep: # Test with full dependencies installed for different OS runners
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	os: [windows-latest, ubuntu-latest, macOS-latest] # macOS-latest is very slow (#8864), testing install only
	timeout-minutes: 120
	env:
	QUICKTEST: True
	steps:
	- if: runner.os == 'Linux'
	name: Clean unused tools
	run: \|
	find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
	sudo rm -rf /usr/share/dotnet
	sudo rm -rf /usr/local/lib/android
	sudo rm -rf /opt/ghc /usr/local/.ghcup
	sudo docker system prune -f
	- if: runner.os == 'windows'
	name: Config pagefile (Windows only)
	uses: al-cheb/configure-pagefile-action@v1.5
	with:
	minimum-size: 8GB
	maximum-size: 16GB
	disk-root: "D:"
	- uses: actions/checkout@v7
	- name: Set up Python ${{ env.PYTHON_VER1 }}
	uses: actions/setup-python@v6
	with:
	python-version: ${{ env.PYTHON_VER1 }}
	cache: 'pip'
	- name: Prepare pip wheel
	run: \|
	which python
	python -m pip install --upgrade pip wheel
	- if: runner.os == 'windows'
	name: Install torch cpu from pytorch.org (Windows only)
	run: \|
	python -m pip install torch==${WIN_FULLDEP_VER} torchvision==${WIN_FULLDEP_VISION_VER}+cpu --index-url https://download.pytorch.org/whl/cpu
	shell: bash
	- if: runner.os != 'windows'
	name: Install torch gpu
	run: \|
	# install the lowest version of PyTorch supported
	python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER1}
	shell: bash
	- if: runner.os == 'Linux'
	name: Install itk pre-release (Linux only)
	run: \|
	python -m pip install --pre -U itk
	shell: bash
	- name: Install the complete dependencies
	run: \|
	python -m pip install --user --upgrade pip wheel tomli
	python monai/config/print_dependencies.py build-system \| xargs pip install --no-build-isolation
	python -m pip install --no-build-isolation .[all,testing]
	python -m pip list
	shell: bash
	- name: Run compiled (${{ runner.os }})
	run: \|
	python -m pip uninstall -y monai
	BUILD_MONAI=1 python -m pip install --no-build-isolation -e . # compile the cpp extensions in-place with -e
	# ensure extensions were compiled
	python -c 'import monai._C' > /dev/null
	shell: bash
	- if: runner.os != 'macOS'
	name: Run full tests
	run: \|
	python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
	python -c "import monai; monai.config.print_config()"
	python -m unittest -v
	shell: bash
	- if: runner.os == 'macOS'
	name: Run min tests
	run: \|
	python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
	python -c "import monai; monai.config.print_config()"
	# TODO: enable large range of macOS tests which don't take a very long time
	./runtests.sh --min
	shell: bash

	hyena-dep: # Optional HyenaND dependency + the no-CUDA Hyena tests.
	# nvsubquadratic >= 0.1.1 supports Python >= 3.10 and keeps its CUDA-kernel sdist
	# (subquadratic-ops-torch-cu12) plus the megatron / dali / timm packages in opt-in
	# extras, so it installs on a CPU runner. We still pass ``--no-deps`` deliberately:
	# (1) the HyenaND operators import only torch + einops + omegaconf at runtime, so
	# skipping the (still batteries-included: datasets/lightning/wandb) core deps
	# keeps this job lean; and
	# (2) nvsubquadratic pins torch>=2.10,<2.11, which would otherwise upgrade/clash
	# with the torch this job (and MONAI's matrix) installs.
	# CUDA-required Hyena tests skip cleanly here; the GPU surface is covered by
	# ``.github/workflows/pythonapp-hyena-gpu.yml``.
	runs-on: ubuntu-latest
	timeout-minutes: 30
	steps:
	- name: Clean unused tools
	run: \|
	find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
	sudo rm -rf /usr/share/dotnet
	sudo rm -rf /usr/local/lib/android
	sudo rm -rf /opt/ghc /usr/local/.ghcup
	sudo docker system prune -f
	- uses: actions/checkout@v6
	- name: Set up Python ${{ env.PYTHON_VER1 }}
	uses: actions/setup-python@v6
	with:
	python-version: ${{ env.PYTHON_VER1 }}
	cache: 'pip'
	- name: Install dependencies + nvsubquadratic (no-deps)
	run: \|
	python -m pip install --upgrade pip wheel tomli pytest
	# need a specific version of torch for nvsubquadratic
	python monai/config/print_dependencies.py build-system \| \
	xargs -d '\n' pip install --no-build-isolation torch==2.10.0 torchvision==0.25.0
	# # nvsubquadratic runtime imports need only torch + einops + omegaconf; install
	# # the package itself without its core dependency tree (see job comment above).
	python -m pip install --no-build-isolation omegaconf
	python -m pip install --no-build-isolation --no-deps 'nvsubquadratic>=0.1.1'
	python -m pip install --no-build-isolation .[hyena,testing]
	python -m pip list
	shell: bash
	- name: Run Hyena tests (CUDA-required cases skip cleanly)
	run: \|
	python -c "from monai.networks.blocks.hyena import is_nvsubquadratic_available; \
	assert is_nvsubquadratic_available(), 'nvsubquadratic must be importable'"
	python -m pytest -v \
	tests/networks/blocks/test_hyena_block.py \
	tests/networks/nets/test_hyena_nd_unetr.py \
	tests/networks/nets/test_swin_unetr.py
	shell: bash

	packaging: # Test package generation
	runs-on: ubuntu-latest
	env:
	QUICKTEST: True
	INDEX_URL: "https://download.pytorch.org/whl/cpu"
	steps:
	- name: Clean unused tools
	run: \|
	find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
	sudo rm -rf /usr/share/dotnet
	sudo rm -rf /usr/local/lib/android
	sudo rm -rf /opt/ghc /usr/local/.ghcup
	sudo docker system prune -f
	- uses: actions/checkout@v7
	with:
	fetch-depth: 0
	- name: Set up Python ${{ env.PYTHON_VER1 }}
	uses: actions/setup-python@v6
	with:
	python-version: ${{ env.PYTHON_VER1 }}
	cache: 'pip'
	- name: Install dependencies
	run: \|
	python -m pip install --user --upgrade pip setuptools wheel twine packaging tomli
	# install the latest pytorch for testing
	python monai/config/print_dependencies.py build-system all testing \| \
	xargs -d '\n' pip install --no-build-isolation torch==${PYTORCH_VER1} --extra-index-url $INDEX_URL
	- name: Check packages
	run: \|
	python -m pip uninstall -y monai
	python -m pip list \| grep -iv monai
	git fetch --depth=1 origin +refs/tags/:refs/tags/
	set -e

	# build tar.gz and wheel
	python setup.py check -m -s
	python setup.py sdist bdist_wheel
	python -m twine check dist/*
	- run: echo "pwd=$PWD" >> $GITHUB_OUTPUT
	id: root
	- run: echo "tmp_dir=$(mktemp -d)" >> $GITHUB_OUTPUT
	id: mktemp
	- name: Move packages
	run: \|
	printf ${{ steps.root.outputs.pwd }}
	printf ${{ steps.mktemp.outputs.tmp_dir }}
	# move packages to a temp dir
	cp dist/monai* "${{ steps.mktemp.outputs.tmp_dir }}"
	rm -r build dist monai.egg-info
	cd "${{ steps.mktemp.outputs.tmp_dir }}"
	ls -al
	- name: Install wheel file
	working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
	run: \|
	# install from wheel
	python -m pip install --no-build-isolation monai*.whl --extra-index-url $INDEX_URL
	python -c 'import monai; monai.config.print_config()' 2>&1 \| grep -iv "unknown"
	python -c 'import monai; print(monai.__file__)'
	python -m pip uninstall -y monai
	rm monai*.whl
	- name: Install source archive
	working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
	run: \|
	for name in *.tar.gz; do break; done
	echo $name
	python -m pip install --no-build-isolation ${name}[all] --extra-index-url $INDEX_URL
	python -c 'import monai; monai.config.print_config()' 2>&1 \| grep -iv "unknown"
	python -c 'import monai; print(monai.__file__)'
	python -m pip uninstall -y monai
	- name: Install using uv
	working-directory: ${{ steps.root.outputs.pwd }}
	run: \|
	pip install uv
	uv pip install --system --no-build-isolation .[all] --extra-index-url $INDEX_URL
	python -c 'import monai; monai.config.print_config()' 2>&1 \| grep -iv "unknown"
	python -c 'import monai; print(monai.__file__)'

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Modernising Build Process #1052

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Modernising Build Process #1052

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