Add batch infer method to main function for demos #3337
Workflow file for this run
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# Copyright (c) MONAI Consortium | |
# Licensed under the Apache License, Version 2.0 (the "License"); | |
# you may not use this file except in compliance with the License. | |
# You may obtain a copy of the License at | |
# http://www.apache.org/licenses/LICENSE-2.0 | |
# Unless required by applicable law or agreed to in writing, software | |
# distributed under the License is distributed on an "AS IS" BASIS, | |
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
# See the License for the specific language governing permissions and | |
# limitations under the License. | |
# This workflow will install Python dependencies, run tests and lint with a single version of Python | |
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
name: build | |
on: | |
push: | |
branches: [ main ] | |
pull_request: | |
branches: [ main ] | |
workflow_dispatch: | |
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: | |
deps_check: | |
runs-on: ${{ matrix.os }} | |
strategy: | |
matrix: | |
os: [windows-latest, ubuntu-latest] | |
python-version: ["3.8", "3.9"] | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip wheel | |
pip install -r requirements.txt | |
build: | |
runs-on: ubuntu-latest | |
env: | |
MONAI_ZOO_AUTH_TOKEN: ${{ github.token }} | |
strategy: | |
matrix: | |
python-version: ["3.8", "3.9"] | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Install dependencies | |
run: | | |
sudo apt-get install openslide-tools -y | |
python -m pip install --upgrade pip wheel | |
pip install -r requirements-dev.txt | |
- name: Clean | |
run: | | |
$(pwd)/runtests.sh --clean | |
- name: PyType | |
run: | | |
echo $(pwd)/runtests.sh --pytype | |
- name: Unit Tests | |
run: | | |
$(pwd)/runtests.sh --unittests | |
- name: Upload coverage | |
uses: codecov/codecov-action@v3 | |
with: | |
fail_ci_if_error: false | |
file: ./coverage.xml | |
packaging: | |
runs-on: ubuntu-latest | |
env: | |
MONAI_ZOO_AUTH_TOKEN: ${{ github.token }} | |
strategy: | |
matrix: | |
python-version: ["3.8", "3.9"] | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- uses: actions/setup-node@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
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@v3 | |
id: cache | |
with: | |
path: | | |
~/.cache/pip | |
~/.cache/torch | |
key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }} | |
- name: Install dependencies | |
run: | | |
sudo apt-get install openslide-tools -y | |
python -m pip install --user --upgrade pip setuptools wheel | |
python -m pip install torch>=1.7 torchvision | |
- name: Build Package | |
run: | | |
./runtests.sh --clean | |
BUILD_OHIF=true python setup.py sdist bdist_wheel | |
ls -l dist | |
- name: Verify Package | |
run: | | |
tmp_dir=$(mktemp -d) | |
cp dist/monailabel* "$tmp_dir" | |
rm -r build monailabel*.egg-info | |
# install from wheel | |
python -m pip install "$tmp_dir"/monailabel*.whl | |
python -c 'import monailabel; monailabel.print_config()' 2>&1 | grep -iv "unknown" | |
python -c 'import monailabel; print(monailabel.__file__)' | |
# install test utilities | |
python -m pip install pytest | |
# start the monailabel server in the background and run the integration tests | |
./runtests.sh --net | |
# cleanup | |
python -m pip uninstall -y monailabel | |
rm -r "$tmp_dir" | |
env: | |
shell: bash | |
build-docs: | |
runs-on: ubuntu-latest | |
env: | |
MONAI_ZOO_AUTH_TOKEN: ${{ github.token }} | |
strategy: | |
matrix: | |
python-version: ["3.8", "3.9"] | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
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@v3 | |
id: cache | |
with: | |
path: | | |
~/.cache/pip | |
~/.cache/torch | |
key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }} | |
- name: Install dependencies | |
run: | | |
sudo apt-get install openslide-tools -y | |
python -m pip install --upgrade pip wheel | |
python -m pip install -r docs/requirements.txt | |
- name: Make html | |
run: | | |
export PYTHONPATH=$(pwd) | |
cd docs/ | |
make clean | |
make html 2>&1 | tee tmp_log | |
if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "found warnings"; grep "WARNING:" tmp_log; exit 1; fi | |
shell: bash |