pythonapp.yml

# 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: ["3.9", "3.10", "3.11"]
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v5
        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: ["3.9", "3.10", "3.11"]
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v5
        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@v4
        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: ["3.9", "3.10", "3.11"]
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - uses: actions/setup-node@v4
      - name: Set up Python
        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: ${{ runner.os }}-pip-${{ 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: ["3.9"]
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        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: ${{ runner.os }}-pip-${{ 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