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pythonapp.yml
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# 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