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setupapp.yml
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# Jenkinsfile.monai-postmerge
name: deploy
on:
# full tests for all the important branches
push:
branches:
- main
- releasing/*
- feature/*
- dev
concurrency:
# automatically cancel the previously triggered workflows when there's a newer version
group: deploy-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
jobs:
# caching of these jobs:
# - docker-py3-pip- (shared)
# - ubuntu 37 38 39 310-pip-
# - os-latest-pip (shared)
coverage-py3:
# if: github.repository == 'Project-MONAI/MONAI'
if: ${{ false }} # disable self-hosted job project-monai/monai#7039
container:
image: nvcr.io/nvidia/pytorch:22.04-py3
options: --gpus all
runs-on: [self-hosted, linux, x64, integration]
steps:
- uses: actions/checkout@v4
- name: cache weekly timestamp
id: pip-cache
run: |
echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
- name: cache for pip
if: ${{ startsWith(github.ref, 'refs/heads/dev') }}
uses: actions/cache@v4
id: cache
with:
path: |
~/.cache/pip
~/.cache/torch
key: docker-py3-pip-${{ steps.pip-cache.outputs.datew }}
- name: Install the dependencies
run: |
which python
python -m pip install --upgrade pip wheel
python -m pip install --upgrade torch torchvision
python -m pip install -r requirements-dev.txt
- name: Run unit tests report coverage
env:
NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
NGC_ORG: ${{ secrets.NGC_ORG }}
NGC_TEAM: ${{ secrets.NGC_TEAM }}
run: |
python -m pip list
git config --global --add safe.directory /__w/MONAI/MONAI
git clean -ffdx
df -h
# python -m pip cache info
nvidia-smi
export CUDA_VISIBLE_DEVICES=$(python -m tests.utils | tail -n 1)
echo $CUDA_VISIBLE_DEVICES
trap 'if pgrep python; then pkill python; fi;' ERR
python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
BUILD_MONAI=1 ./runtests.sh --build --coverage --unittests --disttests # unit tests with coverage report
BUILD_MONAI=1 ./runtests.sh --build --coverage --net # integration tests with coverage report
coverage xml --ignore-errors
if pgrep python; then pkill python; fi
shell: bash
- name: Upload coverage
uses: codecov/codecov-action@v4
with:
fail_ci_if_error: false
files: ./coverage.xml
test-py3x:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9', '3.10', '3.11']
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: cache weekly timestamp
id: pip-cache
run: |
echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
- name: cache for pip
uses: actions/cache@v4
id: cache
with:
path: |
~/.cache/pip
~/.cache/torch
key: ${{ runner.os }}-${{ matrix.python-version }}-pip-${{ steps.pip-cache.outputs.datew }}
- name: Install the 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: Run quick tests CPU ubuntu
env:
NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
NGC_ORG: ${{ secrets.NGC_ORG }}
NGC_TEAM: ${{ secrets.NGC_TEAM }}
run: |
python -m pip list
python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
BUILD_MONAI=0 ./runtests.sh --build --quick --unittests
BUILD_MONAI=1 ./runtests.sh --build --quick --min
coverage xml --ignore-errors
- name: Upload coverage
uses: codecov/codecov-action@v4
with:
fail_ci_if_error: false
files: ./coverage.xml
install: # pip install from github url, the default branch is dev
runs-on: ubuntu-latest
steps:
- name: Set up Python 3.9
uses: actions/setup-python@v5
with:
python-version: '3.9'
- name: cache weekly timestamp
id: pip-cache
run: |
echo "datew=$(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 the default branch no build (dev branch only)
if: github.ref == 'refs/heads/dev'
run: |
BUILD_MONAI=0 pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
python -c 'import monai; monai.config.print_config()'
cd $(python -c 'import monai; import os; print(os.path.dirname(monai.__file__))')
ls .
pip uninstall -y monai
- name: Install the default branch with build (dev branch only)
if: github.ref == 'refs/heads/dev'
run: |
find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
BUILD_MONAI=1 pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
python -c 'import monai; monai.config.print_config()'
- name: Get the test cases (dev branch only)
if: github.ref == 'refs/heads/dev'
uses: actions/checkout@v4
with:
ref: dev
- name: Quick test installed (dev branch only)
if: github.ref == 'refs/heads/dev'
run: |
cd $GITHUB_WORKSPACE
rm -rf monai/
ls -al .
python -m pip install -r requirements-min.txt
python -m tests.min_tests
env:
QUICKTEST: True