Skip to content
premerge

Diffusion Model Encoder has an output layer set in forward method and this leads to problems #27234

Sign in to view logs

Diffusion Model Encoder has an output layer set in forward method and this leads to problems

Diffusion Model Encoder has an output layer set in forward method and this leads to problems #27234

Workflow file for this run

.github/workflows/pythonapp.yml at 7ca0676
# 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==2.5.1 torchvision==0.20.1+cpu --index-url https://download.pytorch.org/whl/cpu
- 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==2.5.1 torchvision==0.20.1
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>=2.5.1 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