Update ['pixdim'] after Spacing transform in meta dict. #26177

Workflow file for this run

.github/workflows/pythonapp.yml at cdb8391

	# Jenkinsfile.monai-premerge
	name: premerge

	on:
	# quick tests for pull requests and the releasing branches
	push:
	branches:
	- dev
	- main
	- releasing/*
	pull_request:
	head_ref-ignore:
	- dev

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

	jobs:
	# caching of these jobs:
	# - docker-py3-pip- (shared)
	# - ubuntu py37 pip-
	# - os-latest-pip- (shared)
	flake8-py3:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	opt: ["codeformat", "pytype", "mypy"]
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python 3.9
	uses: actions/setup-python@v5
	with:
	python-version: '3.9'
	- name: cache weekly timestamp
	id: pip-cache
	run: \|
	echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
	- name: cache for pip
	uses: actions/cache@v4
	id: cache
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
	- name: Install dependencies
	run: \|
	find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
	python -m pip install --upgrade pip wheel
	python -m pip install -r requirements-dev.txt
	- name: Lint and type check
	run: \|
	# clean up temporary files
	$(pwd)/runtests.sh --build --clean
	# Github actions have 2 cores, so parallelize pytype
	$(pwd)/runtests.sh --build --${{ matrix.opt }} -j 2

	quick-py3: # full dependencies installed tests for different OS
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	os: [windows-latest, macOS-latest, ubuntu-latest]
	timeout-minutes: 120
	steps:
	- if: runner.os == 'windows'
	name: Config pagefile (Windows only)
	uses: al-cheb/[email protected]
	with:
	minimum-size: 8GB
	maximum-size: 16GB
	disk-root: "D:"
	- uses: actions/checkout@v4
	- name: Set up Python 3.9
	uses: actions/setup-python@v5
	with:
	python-version: '3.9'
	- name: Prepare pip wheel
	run: \|
	which python
	python -m pip install --upgrade pip wheel
	- name: cache weekly timestamp
	id: pip-cache
	run: \|
	echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
	echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
	shell: bash
	- name: cache for pip
	uses: actions/cache@v4
	id: cache
	with:
	path: ${{ steps.pip-cache.outputs.dir }}
	key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
	- if: runner.os == 'windows'
	name: Install torch cpu from pytorch.org (Windows only)
	run: \|
	python -m pip install torch==1.13.1+cpu torchvision==0.14.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
	- if: runner.os == 'Linux'
	name: Install itk pre-release (Linux only)
	run: \|
	python -m pip install --pre -U itk
	find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
	- name: Install the dependencies
	run: \|
	python -m pip install --user --upgrade pip wheel
	python -m pip install torch==1.13.1 torchvision==0.14.1
	cat "requirements-dev.txt"
	python -m pip install -r requirements-dev.txt
	python -m pip list
	python setup.py develop # test no compile installation
	shell: bash
	- name: Run compiled (${{ runner.os }})
	run: \|
	python setup.py develop --uninstall
	BUILD_MONAI=1 python setup.py develop # compile the cpp extensions
	shell: bash
	- name: Run quick tests (CPU ${{ runner.os }})
	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
	env:
	QUICKTEST: True
	PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354

	packaging:
	runs-on: ubuntu-latest
	env:
	QUICKTEST: True
	shell: bash
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: Set up Python 3.9
	uses: actions/setup-python@v5
	with:
	python-version: '3.9'
	- name: cache weekly timestamp
	id: pip-cache
	run: \|
	echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
	- name: cache for pip
	uses: actions/cache@v4
	id: cache
	with:
	path: \|
	~/.cache/pip
	~/.cache/torch
	key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
	- name: Install dependencies
	run: \|
	find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
	python -m pip install --user --upgrade pip setuptools wheel twine packaging
	# install the latest pytorch for testing
	# however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
	# fresh torch installation according to pyproject.toml
	python -m pip install torch>=1.9 torchvision
	- name: Check packages
	run: \|
	pip uninstall monai
	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 monai*.whl
	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: ${{ steps.mktemp.outputs.tmp_dir }}
	run: \|
	# install from tar.gz
	name=$(ls *.tar.gz \| head -n1)
	echo $name
	python -m pip install $name[all]
	python -c 'import monai; monai.config.print_config()' 2>&1 \| grep -iv "unknown"
	python -c 'import monai; print(monai.__file__)'
	- name: Quick test
	working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
	run: \|
	# run min tests
	cp ${{ steps.root.outputs.pwd }}/requirements*.txt .
	cp -r ${{ steps.root.outputs.pwd }}/tests .
	ls -al
	python -m pip install -r requirements-dev.txt
	python -m unittest -v
	env:
	PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354

	build-docs:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python 3.9
	uses: actions/setup-python@v5
	with:
	python-version: '3.9'
	- name: cache weekly timestamp
	id: pip-cache
	run: \|
	echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
	- name: cache for pip
	uses: actions/cache@v4
	id: cache
	with:
	path: \|
	~/.cache/pip
	~/.cache/torch
	key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip wheel
	python -m pip install -r docs/requirements.txt
	- name: Make html
	run: \|
	cd docs/
	make clean
	make html 2>&1 \| tee tmp_log
	if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "found errors"; grep "ERROR:" tmp_log; exit 1; fi
	sed '/WARNING.*pip/d' tmp_log > tmp_log1; mv tmp_log1 tmp_log # monai#7133
	if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "found warnings"; grep "WARNING:" tmp_log; exit 1; fi
	shell: bash

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Update ['pixdim'] after Spacing transform in meta dict. #26177

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Update ['pixdim'] after Spacing transform in meta dict. #26177

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