Optional deps should be optional

.github/actions/run-tests/action.yml

@@ -0,0 +1,30 @@
+name: "Run Tests"
+description: "Sets up Python, installs dependencies, and runs tests"
+inputs:
+  version:
+    description: "Python version"
+    required: true
+  extra:
+    description: "Optional dependency to install"
+    required: true
+runs:
+  using: "composite"
+  steps:
+    - name: Update packages
+      run: sudo apt-get update
+      shell: bash
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ inputs.version }}
+    - name: Install Dependencies
+      run: |
+        if [ "${{ inputs.extra }}" = "<none>" ]; then
+          pip install -e '.[test]'
+        else
+          pip install -e '.[test,${{ inputs.extra }}]'
+        fi
+      shell: bash
+    - name: Run Pytest
+      run: make test
+      shell: bash

.github/workflows/test.yml

@@ -3,30 +3,45 @@ name: Unit Tests
 on:
   push:
     branches:
-      - main
+     - main
   pull_request:
+  workflow_dispatch:
 
 jobs:
-  test:
+  test-all:
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
         version: [3.9, "3.10", 3.11, 3.12, 3.13, 3.14]
 
-    name: Tests
+    name: Tests (all, py${{ matrix.version }})
     runs-on: ${{ matrix.os }}
 
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v2
-      - name: Update packages
-        run: sudo apt-get update
-      - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/checkout@v6
+      - name: Run Tests
+        uses: ./.github/actions/run-tests
         with:
-          python-version: ${{ matrix.version }}
-      - name: Install Dependencies
-        run: pip install -e '.[dev]'
-      - name: Run Pytest
-        run: make test
+          version: ${{ matrix.version }}
+          extra: all
+
+  test-extras:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        extra: ["<none>", serial, usb, ftdi, hid, modbus, opentrons, sila, microscopy, pico]
+
+    name: Tests (${{ matrix.extra }}, py3.12)
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v6
+      - name: Run Tests
+        uses: ./.github/actions/run-tests
+        with:
+          version: "3.12"
+          extra: ${{ matrix.extra }}

docs/user_guide/_getting-started/installation.md

@@ -49,6 +49,9 @@ Different machines use different communication modes. Replace `[usb]` with one o
 | `hid` | hid | HID devices: e.g. Inheco Incubator/Shaker (HID mode) |
 | `modbus` | pymodbus | Modbus devices: e.g. Agrow Pump Array |
 | `opentrons` | opentrons-http-api-client | e.g. Opentrons backend |
+| `microscopy` | numpy (1.26), opencv-python | e.g. Cytation imager |
+| `sila` | zeroconf, grpcio | SiLA devices |
+| `pico` | microscopy + sila | ImageXpress Pico microscope |
 | `dev` | All of the above + testing/linting tools | Development |
 
 Or install all dependencies:
@@ -57,6 +60,8 @@ Or install all dependencies:
 pip install 'pylabrobot[all]'
 ```
 
+Microscopy is not included in the `all` group because it requires an older version of numpy. If you want to use microscopy features, you need to install those dependencies separately through `pip install "pylabrobot[microscopy]"`.
+
 ### From source
 
 You can install PyLabRobot from source. This is particularly useful if you want to contribute to the project or if you want to use the latest features that haven't been released on PyPI yet.

pylabrobot/barcode_scanners/keyence/keyence_backend.py

@@ -2,7 +2,13 @@
 import logging
 import time
 
-import serial
+try:
+  import serial
+
+  HAS_SERIAL = True
+except ImportError as e:
+  HAS_SERIAL = False
+  _SERIAL_IMPORT_ERROR = e
 
 from pylabrobot.barcode_scanners.backend import (
   BarcodeScannerBackend,
@@ -24,6 +30,11 @@ def __init__(
     self,
     port: str,
   ):
+    if not HAS_SERIAL:
+      raise RuntimeError(
+        "pyserial is not installed. Install with: pip install pylabrobot[serial]. "
+        f"Import error: {_SERIAL_IMPORT_ERROR}"
+      )
     super().__init__()
 
     # BL-1300 Barcode reader factory default serial communication settings

pylabrobot/io/sila/discovery_tests.py

@@ -5,6 +5,7 @@
 from unittest.mock import MagicMock, patch
 
 from pylabrobot.io.sila.discovery import (
+  HAS_ZEROCONF,
   SiLADevice,
   _decode_nbns_name,
   _discover_sila2,
@@ -137,9 +138,9 @@ def test_no_zeroconf_returns_empty(self):
     devices = asyncio.run(_discover_sila2(timeout=0.1))
     self.assertEqual(devices, [])
 
-  @patch("pylabrobot.io.sila.discovery.HAS_ZEROCONF", True)
-  @patch("pylabrobot.io.sila.discovery.Zeroconf")
-  @patch("pylabrobot.io.sila.discovery.ServiceBrowser")
+  @unittest.skipIf(not HAS_ZEROCONF, "zeroconf not installed")
+  @patch("pylabrobot.io.sila.discovery.Zeroconf", create=True)
+  @patch("pylabrobot.io.sila.discovery.ServiceBrowser", create=True)
   def test_discovers_device(self, mock_browser_cls, mock_zc_cls):
     mock_zc = MagicMock()
     mock_zc_cls.return_value = mock_zc

pylabrobot/liquid_handling/backends/opentrons_backend_tests.py

@@ -1,6 +1,10 @@
 import unittest
 from unittest.mock import patch
 
+import pytest
+
+pytest.importorskip("ot_api")
+
 from pylabrobot.liquid_handling import LiquidHandler
 from pylabrobot.liquid_handling.backends.opentrons_backend import (
   OpentronsOT2Backend,

pylabrobot/microscopes/molecular_devices/pico/backend_tests.py

@@ -14,7 +14,12 @@
 from typing import Dict, List, Tuple
 from unittest.mock import patch
 
-import numpy as np
+import pytest
+
+pytest.importorskip("numpy")
+pytest.importorskip("grpc")
+
+import numpy as np  # type: ignore[import-not-found]
 
 from pylabrobot.io.sila.grpc import (
   decode_fields,

pylabrobot/peeling/xpeel_backend.py

@@ -3,7 +3,13 @@
 from dataclasses import dataclass
 from typing import List, Literal, Tuple
 
-import serial  # type: ignore
+try:
+  import serial  # type: ignore
+
+  HAS_SERIAL = True
+except ImportError as e:
+  HAS_SERIAL = False
+  _SERIAL_IMPORT_ERROR = e
 
 from pylabrobot.io.serial import Serial
 from pylabrobot.peeling.backend import PeelerBackend
@@ -43,6 +49,11 @@ class ErrorInfo:
   }
 
   def __init__(self, port: str, logger=None, timeout=None):
+    if not HAS_SERIAL:
+      raise RuntimeError(
+        "pyserial is not installed. Install with: pip install pylabrobot[serial]. "
+        f"Import error: {_SERIAL_IMPORT_ERROR}"
+      )
     self.logger = logger or logging.getLogger(__name__)
     self.port = port
     self.response_timeout = timeout if timeout is not None else self.RESPONSE_TIMEOUT

pylabrobot/plate_reading/agilent/biotek_synergyh1_backend.py

@@ -3,7 +3,13 @@
 import time
 from typing import Optional
 
-from pylibftdi import FtdiError
+try:
+  from pylibftdi import FtdiError
+
+  HAS_PYLIBFTDI = True
+except ImportError:
+  HAS_PYLIBFTDI = False
+  FtdiError = Exception  # type: ignore[misc,assignment]
 
 from pylabrobot.plate_reading.agilent.biotek_backend import BioTekPlateReaderBackend
 

pylabrobot/plate_reading/agilent/biotek_tests.py

@@ -6,6 +6,10 @@
 import unittest.mock
 from typing import Iterator
 
+import pytest
+
+pytest.importorskip("pylibftdi")
+
 from pylabrobot.plate_reading.agilent.biotek_cytation_backend import CytationBackend
 from pylabrobot.resources import CellVis_24_wellplate_3600uL_Fb, CellVis_96_wellplate_350uL_Fb
 

pylabrobot/pumps/agrowpumps/agrowdosepump_backend.py

@@ -34,6 +34,11 @@ class AgrowPumpArrayBackend(PumpArrayBackend):
   """
 
   def __init__(self, port: str, address: Union[int, str]):
+    if _MODBUS_IMPORT_ERROR is not None:
+      raise RuntimeError(
+        "pymodbus is not installed. Install with: pip install pylabrobot[modbus]. "
+        f"Import error: {_MODBUS_IMPORT_ERROR}"
+      )
     if not isinstance(port, str):
       raise ValueError("Port must be a string")
     self.port = port

pylabrobot/pumps/agrowpumps/agrowdosepump_tests.py

@@ -1,6 +1,10 @@
 import unittest
 from unittest.mock import AsyncMock, call
 
+import pytest
+
+pytest.importorskip("pymodbus")
+
 from pymodbus.client import AsyncModbusSerialClient  # type: ignore
 
 from pylabrobot.pumps import PumpArray

pylabrobot/pumps/cole_parmer/masterflex_backend.py

@@ -1,4 +1,10 @@
-import serial  # type: ignore
+try:
+  import serial  # type: ignore
+
+  HAS_SERIAL = True
+except ImportError as e:
+  HAS_SERIAL = False
+  _SERIAL_IMPORT_ERROR = e
 
 from pylabrobot.io.serial import Serial
 from pylabrobot.pumps.backend import PumpBackend
@@ -24,6 +30,11 @@ class MasterflexBackend(PumpBackend):
   """
 
   def __init__(self, com_port: str):
+    if not HAS_SERIAL:
+      raise RuntimeError(
+        "pyserial is not installed. Install with: pip install pylabrobot[serial]. "
+        f"Import error: {_SERIAL_IMPORT_ERROR}"
+      )
     self.com_port = com_port
     self.io = Serial(
       port=self.com_port,

pylabrobot/sealing/a4s_backend.py

@@ -4,14 +4,25 @@
 import time
 from typing import Set
 
-import serial
+try:
+  import serial
+
+  HAS_SERIAL = True
+except ImportError as e:
+  HAS_SERIAL = False
+  _SERIAL_IMPORT_ERROR = e
 
 from pylabrobot.io.serial import Serial
 from pylabrobot.sealing.backend import SealerBackend
 
 
 class A4SBackend(SealerBackend):
   def __init__(self, port: str, timeout=20) -> None:
+    if not HAS_SERIAL:
+      raise RuntimeError(
+        "pyserial is not installed. Install with: pip install pylabrobot[serial]. "
+        f"Import error: {_SERIAL_IMPORT_ERROR}"
+      )
     super().__init__()
     self.port = port
     self.timeout = timeout

pylabrobot/storage/cytomat/cytomat.py

@@ -4,7 +4,13 @@
 import warnings
 from typing import List, Literal, Optional, Union, cast
 
-import serial
+try:
+  import serial
+
+  HAS_SERIAL = True
+except ImportError as e:
+  HAS_SERIAL = False
+  _SERIAL_IMPORT_ERROR = e
 
 from pylabrobot.io.serial import Serial
 from pylabrobot.resources import Plate, PlateCarrier, PlateHolder
@@ -49,6 +55,11 @@ class CytomatBackend(IncubatorBackend):
   serial_message_encoding = "utf-8"
 
   def __init__(self, model: Union[CytomatType, str], port: str):
+    if not HAS_SERIAL:
+      raise RuntimeError(
+        "pyserial is not installed. Install with: pip install pylabrobot[serial]. "
+        f"Import error: {_SERIAL_IMPORT_ERROR}"
+      )
     super().__init__()
 
     supported_models = [

pylabrobot/storage/cytomat/heraeus_cytomat_backend.py

@@ -4,7 +4,13 @@
 import warnings
 from typing import List, Tuple
 
-import serial
+try:
+  import serial
+
+  HAS_SERIAL = True
+except ImportError as e:
+  HAS_SERIAL = False
+  _SERIAL_IMPORT_ERROR = e
 
 from pylabrobot.io.serial import Serial
 from pylabrobot.resources import Plate, PlateHolder
@@ -31,6 +37,11 @@ class HeraeusCytomatBackend(IncubatorBackend):
   poll_interval = 0.2
 
   def __init__(self, port: str):
+    if not HAS_SERIAL:
+      raise RuntimeError(
+        "pyserial is not installed. Install with: pip install pylabrobot[serial]. "
+        f"Import error: {_SERIAL_IMPORT_ERROR}"
+      )
     super().__init__()
     self.io = Serial(
       port=port,

pylabrobot/storage/inheco/incubator_shaker_backend.py

@@ -148,6 +148,11 @@ def __init__(
     vid: int = 0x0403,
     pid: int = 0x6001,
   ):
+    if not HAS_SERIAL:
+      raise RuntimeError(
+        "pyserial is not installed. Install with: pip install pylabrobot[serial]. "
+        f"Import error: {_SERIAL_IMPORT_ERROR}"
+      )
     super().__init__()
 
     self.logger = logging.LoggerAdapter(