ci.yaml

name: CI

on: [pull_request, push, workflow_dispatch]

jobs:
  frontend-test:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout source
        uses: actions/checkout@v6

      - name: Setup node
        uses: actions/setup-node@v6
        with:
          node-version: "25"
          cache: npm
          cache-dependency-path: frontend/package-lock.json

      - name: Run frontend tests
        run: |
          make frontend-test

  backend-test:
    runs-on: ubuntu-latest
    env:
      TESTING: 1
      DOT_PIOREACTOR: ${{ github.workspace }}/.pioreactor
      GLOBAL_CONFIG: ${{ github.workspace }}/.pioreactor/config.ini
      RUN_PIOREACTOR: ${{ github.workspace }}/run/pioreactor
      LG_WD: ${{ github.workspace }}/run/pioreactor
      TMPDIR: /tmp/
      PIO_VENV: ${{ github.workspace }}/.venv
      VIRTUAL_ENV: ${{ github.workspace }}/.venv
      PIO_EXECUTABLE: ${{ github.workspace }}/.venv/bin/pio
      PIOS_EXECUTABLE: ${{ github.workspace }}/.venv/bin/pios
      PLUGINS_DEV: ${{ github.workspace }}/plugins_dev
      HARDWARE: 1.2
      FIRMWARE: 0.5
      BLINKA_FORCECHIP: BCM2XXX
      BLINKA_FORCEBOARD: RASPBERRY_PI_3A_PLUS
      MODEL_NAME: pioreactor_40ml
      MODEL_VERSION: 1.5

    steps:
      - name: Checkout source
        uses: actions/checkout@v4

      - name: Setup python
        uses: actions/setup-python@v5
        with:
          python-version: "3.13"

      - name: Install python libraries into env
        run: |
          # env create in make install
          make install
          wget https://github.com/Gadgetoid/PY_LGPIO/releases/download/0.2.2.0/lgpio-0.2.2.0.tar.gz -O lgpio-0.2.2.0.tar.gz
          tar -xvzf lgpio-0.2.2.0.tar.gz
          # Install lgpio into the venv created by `make install`.
          # Note: keep working directory at repo root so `.venv` is resolvable.
          .venv/bin/python -m pip install -e ./lgpio-0.2.2.0

          .venv/bin/pip list

      - name: Mosquitto MQTT Broker in GitHub Actions
        uses: Namoshek/mosquitto-github-action@v1
        with:
          version: '1.6'

      - name: Install any other required linux software
        run: |
          sudo apt-get update
          sudo apt-get install avahi-daemon avahi-discover avahi-utils mosquitto-clients

      - name: Create pioreactor folders
        run: |
          mkdir -p "$RUN_PIOREACTOR"
          mkdir -p "$RUN_PIOREACTOR/cache"
          touch "$RUN_PIOREACTOR/cache/huey.db"


          mkdir -p "$DOT_PIOREACTOR"
          mv config.dev.ini "$DOT_PIOREACTOR"/config.ini
          mkdir -p "$DOT_PIOREACTOR"/storage


          mkdir -p "$DOT_PIOREACTOR"/hardware/hats/1.2
          mkdir -p "$DOT_PIOREACTOR"/hardware/models/pioreactor_40ml/1.5
          cat <<'EOF_HW' > "$DOT_PIOREACTOR"/hardware/hats/1.2/pwm.yaml
          heater_pwm_channel: "5"
          pwm_to_pin:
            "1": 17
            "2": 13
            "3": 16
            "4": 12
            "5": 18
          EOF_HW
          cat <<'EOF_HW' > "$DOT_PIOREACTOR"/hardware/hats/1.2/dac.yaml
          address: 0x2C
          EOF_HW
          cat <<'EOF_HW' > "$DOT_PIOREACTOR"/hardware/hats/1.2/temp.yaml
          address: 0x4F
          EOF_HW
          cat <<'EOF_HW' > "$DOT_PIOREACTOR"/hardware/hats/1.2/adc.yaml
          aux:
            driver: pico
            address: 0x2C
            channel: 1
          version:
            driver: pico
            address: 0x2C
            channel: 0
          pd1:
            driver: pico
            address: 0x2C
            channel: 2
          pd2:
            driver: pico
            address: 0x2C
            channel: 3
          EOF_HW
          cat <<'EOF_HW' > "$DOT_PIOREACTOR"/hardware/hats/1.2/gpio.yaml
          pcb_led_pin: 23
          pcb_button_pin: 4
          hall_sensor_pin: 21
          sda_pin: 2
          scl_pin: 3
          EOF_HW
          cat <<'EOF_HW' > "$DOT_PIOREACTOR"/hardware/models/pioreactor_40ml/1.5/adc.yaml
          pd1:
            driver: ads1114
            address: 0x48
            channel: 0
          pd2:
            driver: ads1114
            address: 0x49
            channel: 0
          EOF_HW

          mkdir -p "$DOT_PIOREACTOR/plugins"
          mkdir -p "$DOT_PIOREACTOR/ui/jobs"
          mkdir -p "$DOT_PIOREACTOR/ui/automations/dosing"
          mkdir -p "$DOT_PIOREACTOR/plugins/ui/jobs"
          mkdir -p "$DOT_PIOREACTOR/plugins/ui/automations/dosing"

          cat <<'EOF_UI' > "$DOT_PIOREACTOR"/ui/jobs/00_stirring.yaml
          ---
          display_name: Stirring
          job_name: stirring
          display: true
          source: app
          description: Start the stirring on the Pioreactor.
          published_settings:
            - key: target_rpm
              unit: RPM
              label: Target stir RPM
              description: Modify the target RPM of stirring.
              type: numeric
              display: true
          EOF_UI
          cat <<'EOF_UI' > "$DOT_PIOREACTOR"/ui/jobs/50_self_test.yaml
          ---
          display_name: Self test
          job_name: self_test
          display: true
          source: app
          description: Run the hardware and software self test suite.
          published_settings: []
          EOF_UI
          cat <<'EOF_UI' > "$DOT_PIOREACTOR"/ui/automations/dosing/chemostat.yaml
          ---
          display_name: Chemostat
          automation_name: chemostat
          description: Add and remove a constant volume of media on a fixed schedule.
          fields:
            - key: duration
              default: 20
              unit: min
              label: Time between dosing
              type: numeric
            - key: exchange_volume_ml
              default: 0.5
              unit: mL
              label: Exchange volume
              type: numeric
          EOF_UI
          cat <<'EOF_UI' > "$DOT_PIOREACTOR"/ui/automations/dosing/turbidostat.yaml
          ---
          display_name: Turbidostat
          automation_name: turbidostat
          description: Keep the culture near a target biomass by exchanging media.
          fields:
            - key: target_normalized_od
              default: 1.0
              unit: AU
              label: Target normalized OD
              type: numeric
          EOF_UI

          cat <<'EOF_UI' > "$DOT_PIOREACTOR"/plugins/ui/jobs/90_example_plugin.yaml
          ---
          display_name: Example plugin
          job_name: example_plugin
          display: true
          source: my-example-plugin
          description: Example plugin job descriptor for CI.
          published_settings: []
          EOF_UI
          cat <<'EOF_UI' > "$DOT_PIOREACTOR"/plugins/ui/automations/dosing/90_example_plugin_automation.yaml
          ---
          display_name: Example plugin automation
          automation_name: example_plugin_automation
          source: my-example-plugin
          description: Example plugin automation descriptor for CI.
          fields:
            - key: target
              default: 0.5
              unit: AU
              label: Target
              type: numeric
          EOF_UI

          ls "$DOT_PIOREACTOR"

          make check-env

      - name: Create plugin folder and seed it
        run: |
          mkdir -p "$PLUGINS_DEV"
          cat <<'EOF_PLUGIN' > "$PLUGINS_DEV"/example_plugin.py
          import click
          from pioreactor.background_jobs.base import BackgroundJob

          __plugin_version__ = "0.2.0"
          __plugin_name__ = "my-example-plugin"


          class ExamplePlugin(BackgroundJob):
              job_name = "example_plugin"

              def __init__(self):
                  super().__init__(unit="test", experiment="test")


          @click.command(name="example_plugin")
          def click_example_plugin():
              job = ExamplePlugin()
          EOF_PLUGIN

      - name: Start web API
        run: |
          make web-dev &
          sleep 5

      - name: Run fast tests
        run: |
          make fast-test

      - name: Run slow tests
        run: |
          make slow-test

      - name: Run flakey tests
        run: |
          make flakey-test || true