physionet-build-test.yml

# Installs PhysioNet dependencies on Debian 10 and runs tests on the `dev` branch and PRs against the `dev` branch.

name: Debian / Build and Test

on:
  push:
    branches:
      - dev
  pull_request:
    branches:
      - dev
  merge_group:
    types:
      - checks_requested

jobs:
  test:
    name: Test
    runs-on: ubuntu-latest
    container: ${{ matrix.container }}
    env:
      DJANGO_SETTINGS_MODULE: physionet.settings.settings
      TEST_GCS_INTEGRATION: false
      PHYSIONET_TEST_HTML_DIR: /tmp/pn-test-html-output
    defaults:
      run:
        shell: bash
    strategy:
      fail-fast: false
      matrix:
        pip3: ['poetry', 'requirements.txt']
        container: ['debian:11', 'debian:12']
    steps:

      - name: Update packages
        run: apt-get update --yes

      - name: Install and configure needed software
        run: |
          apt-get install --yes \
                  build-essential \
                  flake8 \
                  git \
                  libcap-dev \
                  libffi-dev \
                  libflac-dev \
                  libpq-dev \
                  libseccomp-dev \
                  postgresql \
                  python3-dev \
                  sudo \
                  virtualenv \
                  wget \
                  zip

      # Note: run checkout after updating git
      - name: Checkout physionet-build repo
        uses: actions/checkout@v3
        with:
          fetch-depth: 0

      - name: Mark git repository as trusted
        run: |
          git config --global --add safe.directory $(pwd)

      - name: Create .env file
        run: |
          ln -sT .env.example .env

      - name: Install repo dependencies
        # add virtual env path to github_path so each run: process will see it
        run: |
          export VIRTUAL_ENV=/env3
          virtualenv -ppython3 $VIRTUAL_ENV
          echo "$VIRTUAL_ENV/bin" >> $GITHUB_PATH
          source $VIRTUAL_ENV/bin/activate
          if [ ${{matrix.pip3}} = 'poetry' ]; then
            pip3 install poetry
            poetry config virtualenvs.create false
            poetry install --no-root
          else
            pip3 install -r requirements.txt
          fi
          pip3 freeze

      - name: Setup postgres
        run: |
          service postgresql start
          sudo -u postgres psql -c "create user physionet with superuser password 'password';" -U postgres
          sudo -u postgres psql -c "create database physionet;" -U postgres

      - name: Install and setup wfdb
        run: |
          wget https://github.com/bemoody/wfdb/archive/10.7.0.tar.gz -O wfdb.tar.gz
          tar -xf wfdb.tar.gz
          (cd wfdb-* && ./configure --without-netfiles && make -C lib install && make -C data install)

      - name: Run linker for newly installed software
        run: ldconfig

      - name: Install and setup lightwave
        run: |
          wget https://github.com/bemoody/lightwave/archive/0.72.tar.gz -O lightwave.tar.gz
          tar -xf lightwave.tar.gz
          (cd lightwave-* && make CGIDIR=/usr/local/bin sandboxed-server)

      - name: Setup and test physionet, check amount of code tested
        run: |
          cd physionet-django
          python manage.py makemigrations --dry-run --no-input --check
          python manage.py resetdb
          python manage.py loaddemo
          coverage run --source='.' manage.py test --verbosity=3 --keepdb
          coverage report -m

      - name: Run Theme File Generation & SCSS Compilation
        run: |
          cd physionet-django
          python manage.py compilestatic

      - name: Run code style check on changed files relative to PR base branch
        if: github.event_name == 'pull_request'
        run: |
          git rev-parse --verify ${{ github.event.pull_request.base.sha }}
          git diff -U0 ${{ github.event.pull_request.base.sha }} HEAD | \
              flake8 --diff | \
              perl -ne '
                print; if (/^([^:]+):(\d+):(\d+):/) {
                  $path = $1; $line = $2; $col = $3;
                  open F, $path or die;
                  print "\n";
                  while (<F>) {
                    next if $. < $line - 2;
                    print " $_";
                    if ($. == $line) { print " " x $col . "^\n\n"; last; }
                  }
                  close F;
                  $status = 1;
                }
                END { exit $status }'

      - name: Run code style check relative to local dev branch
        if: github.event_name != 'pull_request'
        run: |
          git fetch origin dev
          git diff -U0 origin/dev HEAD | \
              flake8 --diff | \
              perl -ne '
                print; if (/^([^:]+):(\d+):(\d+):/) {
                  $path = $1; $line = $2; $col = $3;
                  open F, $path or die;
                  print "\n";
                  while (<F>) {
                    next if $. < $line - 2;
                    print " $_";
                    if ($. == $line) { print " " x $col . "^\n\n"; last; }
                  }
                  close F;
                  $status = 1;
                }
                END { exit $status }'