Add pumping capability and migrate vendor backends by rickwierenga · Pull Request #958 · PyLabRobot/pylabrobot

rickwierenga · 2026-03-23T22:58:51Z

Summary

Adds PumpingCapability under the capability composition architecture with PumpBackend, calibration, and chatterbox
Migrates Cole Parmer Masterflex to pylabrobot/cole_parmer/ as a Device with a single PumpingCapability
Migrates Agrow dose pumps to pylabrobot/agrowpumps/ — models each channel as its own PumpingCapability backed by a per-channel adapter (AgrowChannelBackend) over a shared AgrowDriver
No PumpArrayCapability — pump arrays are just List[PumpingCapability]

Test plan

pytest pylabrobot/capabilities/pumping/pumping_tests.py — 10 tests pass
pytest pylabrobot/agrowpumps/agrowdosepump_tests.py — 4 tests pass

🤖 Generated with Claude Code

- PumpingCapability with calibration, chatterbox, tests - AgrowDriver (extends Driver), AgrowDosePumpArray device - Cole Parmer Masterflex backend - PumpBackend extends CapabilityBackend Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Follow CLARIOstar pattern: Driver owns connection, Backend owns capability operations. Remove stale setup/stop from capability backends. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Legacy Pump.run_revolutions, run_continuously, halt were not awaiting the backend coroutines. Fixed + updated test mock accordingly. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Adapter pattern: _PumpAdapter and _ChannelAdapter wrap legacy backends into new CapabilityBackend interface. Frontends delegate to PumpingCapability — no duplicated orchestration logic. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Copilot

Pull request overview

This PR introduces a new PumpingCapability under the capabilities architecture and migrates pump integrations (Cole Parmer Masterflex + Agrow dose pumps) from legacy backends into first-class Device implementations, while keeping legacy adapters in place.

Changes:

Added a new pumping capability module (PumpBackend, PumpingCapability, calibration helpers, chatterbox backend) with unit tests.
Added new device/driver-based implementations for Cole Parmer Masterflex and Agrow dose pump arrays.
Updated legacy Pump/PumpArray and legacy pump backends to adapt to the new pumping capability architecture.

Reviewed changes

Copilot reviewed 18 out of 18 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
pylabrobot/legacy/pumps/pumparray.py	Adapts legacy pump arrays to expose per-channel `PumpingCapability` and routes operations through it.
pylabrobot/legacy/pumps/pump_tests.py	Updates legacy pump tests to align with the new capability-based wiring.
pylabrobot/legacy/pumps/pump.py	Wraps a legacy `PumpBackend` with a `PumpingCapability` adapter.
pylabrobot/legacy/pumps/cole_parmer/masterflex_backend.py	Replaces legacy Masterflex implementation with a delegating wrapper to the new backend/driver.
pylabrobot/legacy/pumps/agrowpumps/agrowdosepump_tests.py	Adjusts legacy Agrow tests to the new driver-based implementation while keeping legacy entrypoints.
pylabrobot/legacy/pumps/agrowpumps/agrowdosepump_backend.py	Replaces legacy Agrow backend internals with a wrapper over the new `AgrowDriver` + channel backends.
pylabrobot/cole_parmer/masterflex_backend.py	Adds new `MasterflexDriver`, `MasterflexBackend`, and `MasterflexPump` device.
pylabrobot/cole_parmer/init.py	Exports the new Cole Parmer Masterflex classes.
pylabrobot/capabilities/pumping/pumping_tests.py	Adds unit tests for the new `PumpingCapability`.
pylabrobot/capabilities/pumping/pumping.py	Implements `PumpingCapability` behavior and lifecycle hooks.
pylabrobot/capabilities/pumping/errors.py	Introduces a pumping-specific calibration error type.
pylabrobot/capabilities/pumping/chatterbox.py	Adds a pumping chatterbox backend for device-free usage.
pylabrobot/capabilities/pumping/calibration.py	Adds a new calibration model + loaders for pumping.
pylabrobot/capabilities/pumping/backend.py	Defines the capability backend ABC for pumping.
pylabrobot/capabilities/pumping/init.py	Re-exports pumping capability module public API.
pylabrobot/agrowpumps/agrowdosepump_tests.py	Adds tests for the new Agrow device implementation.
pylabrobot/agrowpumps/agrowdosepump_backend.py	Adds new `AgrowDriver`, `AgrowChannelBackend`, and `AgrowDosePumpArray` device.
pylabrobot/agrowpumps/init.py	Exports the new Agrow pump classes.

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Copilot · 2026-03-26T20:49:21Z

pylabrobot/legacy/pumps/pump_tests.py


  def setUp(self):
-    self.mock_backend = Mock(spec=PumpBackend)
+    self.mock_backend = AsyncMock()


TestPump.setUp() switched to a bare AsyncMock() which drops interface checking and also doesn't match the legacy PumpBackend contract (where run_revolutions/run_continuously/halt are synchronous methods). Once _PumpAdapter is fixed to handle legacy sync methods, this test should use a Mock(spec=PumpBackend) (and configure setup/stop as AsyncMocks) so it accurately models real legacy backends and catches API mismatches.

Suggested change

self.mock_backend = AsyncMock()

# Use a spec'd Mock so we enforce the PumpBackend interface and keep

# run_revolutions/run_continuously/halt as synchronous methods.

self.mock_backend = Mock(spec=PumpBackend)

# setup and stop are asynchronous in the adapter, so model them as AsyncMocks.

self.mock_backend.setup = AsyncMock()

self.mock_backend.stop = AsyncMock()

Copilot · 2026-03-26T20:49:22Z

pylabrobot/legacy/pumps/pumparray.py

-    await self.backend.run_revolutions(num_revolutions=num_revolutions, use_channels=use_channels)
+    channels = self._normalize_channels(use_channels)
+    if isinstance(num_revolutions, (float, int)):
+      num_revolutions = [float(num_revolutions)] * len(channels)


run_revolutions() zips channels with num_revolutions without validating list length. If a list is provided with a different length than use_channels, extra values will be silently ignored or channels will be skipped. Add an explicit length check (similar to _normalize_speeds) and normalize values to floats before iterating.

Suggested change

num_revolutions = [float(num_revolutions)] * len(channels)

num_revolutions = [float(num_revolutions)] * len(channels)

else:

if len(num_revolutions) != len(channels):

raise ValueError("num_revolutions and use_channels must be the same length.")

num_revolutions = [float(rev) for rev in num_revolutions]

Copilot · 2026-03-26T20:49:22Z

pylabrobot/capabilities/pumping/pumping.py

+    if self.calibration is None:
+      raise TypeError(
+        "Pump is not calibrated. Volume based pumping and related functions unavailable."
+      )


pumping/errors.py defines NotCalibratedError, but PumpingCapability.pump_volume() raises TypeError when calibration is missing. Exception type is part of the public API and this currently diverges from the legacy pumping APIs (which raise NotCalibratedError). Consider raising NotCalibratedError here (and updating the tests accordingly) or removing the unused error type/export.

Copilot · 2026-03-26T20:49:22Z

pylabrobot/capabilities/pumping/chatterbox.py

+from .backend import PumpBackend
+
+
+class PumpChatterboxBackend(PumpBackend):
+  """Chatterbox backend for device-free testing."""
+
+  async def setup(self):
+    print("Setting up the pump.")
+
+  async def stop(self):
+    print("Stopping the pump.")
+
+  async def run_revolutions(self, num_revolutions: float):
+    print(f"Running {num_revolutions} revolutions.")
+
+  async def run_continuously(self, speed: float):
+    print(f"Running continuously at speed {speed}.")
+
+  async def halt(self):
+    print("Halting the pump.")


This chatterbox backend prints directly to stdout on every call. In the rest of the capabilities package, chatterbox/mock backends typically avoid printing and instead return dummy data (or use logging) to keep tests and library usage quiet. Consider switching to logging or making these methods no-ops to avoid noisy output when used in unit tests or notebooks.

Suggested change

from .backend import PumpBackend

class PumpChatterboxBackend(PumpBackend):

"""Chatterbox backend for device-free testing."""

async def setup(self):

print("Setting up the pump.")

async def stop(self):

print("Stopping the pump.")

async def run_revolutions(self, num_revolutions: float):

print(f"Running {num_revolutions} revolutions.")

async def run_continuously(self, speed: float):

print(f"Running continuously at speed {speed}.")

async def halt(self):

print("Halting the pump.")

import logging

from .backend import PumpBackend

logger = logging.getLogger(__name__)

class PumpChatterboxBackend(PumpBackend):

"""Chatterbox backend for device-free testing."""

async def setup(self):

logger.info("Setting up the pump.")

async def stop(self):

logger.info("Stopping the pump.")

async def run_revolutions(self, num_revolutions: float):

logger.info(f"Running {num_revolutions} revolutions.")

async def run_continuously(self, speed: float):

logger.info(f"Running continuously at speed {speed}.")

async def halt(self):

logger.info("Halting the pump.")

Copilot · 2026-03-26T20:49:22Z

pylabrobot/legacy/pumps/cole_parmer/masterflex_backend.py

-
-  async def stop(self):
-    await self.io.stop()
+    return self._driver.serialize()


MasterflexBackend.serialize() now returns self._driver.serialize(), which sets type to MasterflexDriver. Since this class is a legacy MachineBackend, MachineBackend.deserialize() expects the serialized type to be a MachineBackend subclass name (e.g., MasterflexBackend). Returning the driver serialization will break deserialization of legacy Pump/Machine objects. Keep the legacy backend serialization shape (include super().serialize() and com_port) or otherwise ensure the type remains MasterflexBackend.

Suggested change

return self._driver.serialize()

data = self._driver.serialize()

# Ensure legacy deserialization sees this as a MasterflexBackend,

# not as the underlying MasterflexDriver.

data["type"] = type(self).__name__

return data

Copilot · 2026-03-26T20:49:23Z

pylabrobot/cole_parmer/masterflex_backend.py

+  async def send_command(self, command: str):
+    command = "\x02P02" + command + "\x0d"
+    await self.io.write(command.encode())
+    return self.io.read()


MasterflexDriver.send_command() returns self.io.read() without awaiting it. Since Serial.read() is async, this causes send_command() to return a coroutine object rather than the bytes response (and callers that await send_command() will receive that coroutine instead of data). Update this to await the read (or otherwise ensure the response is awaited) before returning.

Suggested change

return self.io.read()

return await self.io.read()

Copilot · 2026-03-26T20:49:23Z

pylabrobot/legacy/pumps/pump.py

+  async def run_revolutions(self, num_revolutions: float):
+    await self._legacy.run_revolutions(num_revolutions=num_revolutions)
+
+  async def run_continuously(self, speed: float):
+    await self._legacy.run_continuously(speed=speed)
+
+  async def halt(self):
+    await self._legacy.halt()


_PumpAdapter is awaiting legacy.run_revolutions/run_continuously/halt, but the legacy PumpBackend interface defines these methods as synchronous (e.g., PumpChatterboxBackend implements them as normal def). Awaiting a non-coroutine will raise at runtime. Consider calling the legacy methods directly, or supporting both sync/async by checking inspect.isawaitable() and only awaiting when needed.

Copilot · 2026-03-26T20:49:23Z

pylabrobot/legacy/pumps/pumparray.py

+    if any(ch not in range(0, self.num_channels) for ch in use_channels):
+      raise ValueError(
+        f"Pump address out of range for this pump array. "
+        f"Value should be between 0 and {self.num_channels}"


The out-of-range message says the channel should be between 0 and {self.num_channels}, but valid indices are 0..self.num_channels-1. Adjust the message to avoid off-by-one confusion for users.

Suggested change

f"Value should be between 0 and {self.num_channels}"

f"Value should be between 0 and {self.num_channels - 1}"

Copilot · 2026-03-26T20:49:23Z

pylabrobot/capabilities/pumping/calibration.py

+    """
+
+    if any(value <= 0 for value in calibration):
+      raise ValueError("A value in the calibration is is outside expected parameters.")


Typo in this error message: duplicated "is".

Suggested change

raise ValueError("A value in the calibration is is outside expected parameters.")

raise ValueError("A value in the calibration is outside expected parameters.")

Legacy PumpCalibration now re-exports from new module to avoid type mismatch when passing calibration to PumpingCapability. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

rickwierenga force-pushed the capability-pumps branch 6 times, most recently from 8927a8f to b3fb9f7 Compare March 26, 2026 07:33

rickwierenga and others added 5 commits March 26, 2026 00:33

Merge remote-tracking branch 'origin/v1b1' into capability-pumps

98cbe2d

Split MasterflexDriver from MasterflexBackend, merge v1b1

51d60b5

Follow CLARIOstar pattern: Driver owns connection, Backend owns capability operations. Remove stale setup/stop from capability backends. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Fix missing awaits in legacy Pump frontend

0f7e6a0

Legacy Pump.run_revolutions, run_continuously, halt were not awaiting the backend coroutines. Fixed + updated test mock accordingly. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

rickwierenga requested a review from Copilot March 26, 2026 20:43

Copilot started reviewing on behalf of rickwierenga March 26, 2026 20:44 View session

Copilot AI reviewed Mar 26, 2026

View reviewed changes

Fix lint and type errors: remove unused import, unify PumpCalibration

82d1a35

Legacy PumpCalibration now re-exports from new module to avoid type mismatch when passing calibration to PumpingCapability. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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Add pumping capability and migrate vendor backends#958

Add pumping capability and migrate vendor backends#958
rickwierenga wants to merge 6 commits intov1b1from
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-    self.mock_backend = AsyncMock()
+    # Use a spec'd Mock so we enforce the PumpBackend interface and keep
+    # run_revolutions/run_continuously/halt as synchronous methods.
+    self.mock_backend = Mock(spec=PumpBackend)
+    # setup and stop are asynchronous in the adapter, so model them as AsyncMocks.
+    self.mock_backend.setup = AsyncMock()
+    self.mock_backend.stop = AsyncMock()

-      num_revolutions = [float(num_revolutions)] * len(channels)
+      num_revolutions = [float(num_revolutions)] * len(channels)
+    else:
+      if len(num_revolutions) != len(channels):
+        raise ValueError("num_revolutions and use_channels must be the same length.")
+      num_revolutions = [float(rev) for rev in num_revolutions]

-    return self._driver.serialize()
+    data = self._driver.serialize()
+    # Ensure legacy deserialization sees this as a MasterflexBackend,
+    # not as the underlying MasterflexDriver.
+    data["type"] = type(self).__name__
+    return data

	f"Value should be between 0 and {self.num_channels}"
	f"Value should be between 0 and {self.num_channels - 1}"

	raise ValueError("A value in the calibration is is outside expected parameters.")
	raise ValueError("A value in the calibration is outside expected parameters.")

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rickwierenga commented Mar 23, 2026

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