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Add thermocycling capability and Opentrons vendor module#959

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rickwierenga wants to merge 13 commits intov1b1from
thermocycling-capability-v2
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Add thermocycling capability and Opentrons vendor module#959
rickwierenga wants to merge 13 commits intov1b1from
thermocycling-capability-v2

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@rickwierenga rickwierenga commented Mar 23, 2026

Summary

  • Add pylabrobot/capabilities/thermocycling/ with thin ThermocyclingBackend (lid control, protocol execution, profile progress only — no temperature methods)
  • ThermocyclingCapability composes with block/lid TemperatureControlCapability instances
  • Own copies of Step/Stage/Protocol data types; translation functions in legacy standard.py
  • Legacy Thermocycler frontend delegates to capabilities via three adapters (_BlockTempAdapter, _LidTempAdapter, _ThermocyclingAdapter)
  • pylabrobot/opentrons/ vendor module with driver + 3 capability backends pattern:
    • OpentronsThermocyclerDriver — single class for all OT HTTP API calls
    • OpentronsBlockBackend, OpentronsLidBackend, OpentronsThermocyclingBackend
    • OpentronsThermocyclerV1 and V2 device classes
  • Legacy opentrons_backend.py delegates to new module

Usage (new API)

tc = OpentronsThermocyclerV1(name="tc", opentrons_id="...")
await tc.setup()

# Ad-hoc temperature control
await tc.block.set_temperature(95.0)
await tc.lid.set_temperature(105.0)

# Protocol execution
await tc.thermocycling.run_pcr_profile(
  denaturation_temp=[95.0], denaturation_time=30,
  annealing_temp=[55.0], annealing_time=30,
  extension_temp=[72.0], extension_time=60,
  num_cycles=30, block_max_volume=50,
  lid_temperature=105.0,
)
await tc.thermocycling.wait_for_profile_completion()

Test plan

  • All 4 legacy thermocycler tests pass
  • All imports verified (new + legacy)
  • Pre-commit hooks pass
  • CI tests pass

🤖 Generated with Claude Code

@rickwierenga @claude
Add pumping capability and migrate Masterflex/Agrow vendor backends
3ae4a20 
Introduces PumpingCapability under the new capability composition architecture.
Pump arrays (Agrow) are modeled as a list of PumpingCapability instances, one
per channel, each backed by a per-channel adapter over the shared hardware driver.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga rickwierenga changed the base branch from main to v1b1 March 23, 2026 23:13
rickwierenga and others added 11 commits March 26, 2026 17:44
@rickwierenga
Merge branch 'v1b1' into capability-pumps
8627187
@rickwierenga @claude
Merge v1b1 and fix pumps capability mypy errors
50af86c 
- Fix PumpBackend to extend CapabilityBackend instead of removed DeviceBackend
- Fix AgrowDriver to extend Driver, fix type annotations and attribute access
- Fix MasterflexPump to use driver= kwarg in Device.__init__

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga @claude
Add thermocycling capability with legacy adapters
80a86a0 
Capability:
- ThermocyclingBackend(DeviceBackend) — thin: lid control, protocol
  execution, and profile progress queries only. Block/lid temperature
  handled by separate TemperatureControllerBackend instances.
- ThermocyclingCapability composes with block/lid TemperatureControlCapability
- Own copies of Step/Stage/Protocol data types
- run_pcr_profile convenience method

Legacy:
- Translation functions (protocol_to_new, protocol_from_new) in legacy standard.py
- Three adapters in legacy thermocycler.py: _BlockTempAdapter,
  _LidTempAdapter, _ThermocyclingAdapter — wrap legacy ThermocyclerBackend
  for the new capability interfaces
- Legacy Thermocycler frontend delegates to capabilities via adapters
- All 4 legacy tests pass

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga @claude
Add Opentrons thermocycler vendor module
ea9de37 
- OpentronsThermocyclerDriver: single class for all OT HTTP API calls
- Three capability backends backed by the driver:
  - OpentronsBlockBackend (TemperatureControllerBackend)
  - OpentronsLidBackend (TemperatureControllerBackend)
  - OpentronsThermocyclingBackend (ThermocyclingBackend)
- OpentronsThermocyclerV1 and V2 device classes with self._driver
- Legacy opentrons_backend.py delegates to new module via driver

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga @claude
Add Thermo Fisher thermocycler vendor module (ProFlex/ATC)
2ea50f0 
- ThermoFisherThermocyclerDriver: single class for all SCPI I/O, auth,
  block discovery, power, temperature control, protocol execution
- Three capability backends per block:
  - ThermoFisherBlockBackend (TemperatureControllerBackend)
  - ThermoFisherLidBackend (TemperatureControllerBackend)
  - ThermoFisherThermocyclingBackend (ThermocyclingBackend)
- ThermoFisherThermocycler device with factory classmethods:
  proflex_single_block (1 block/6 zones), proflex_three_block (3 blocks/2 zones),
  atc (1 block/3 zones + lid control)
- Each block gets its own ThermocyclingCapability — run 3 PCR protocols simultaneously
- Legacy ThermoFisherThermocyclerBackend gutted to thin adapter (~275 lines, was ~1050)
- All 7 legacy tests pass

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga @claude
Make driver a DeviceBackend, split factory functions into separate files
9b30ed7 
- ThermoFisherThermocyclerDriver now extends DeviceBackend — passed
  directly to Device.__init__, no first_tc_backend hack
- Remove _supports_lid_control from device class (backend concern only)
- Split factory functions into separate files:
  - proflex.py: ProFlexSingleBlock(), ProFlexThreeBlock()
  - atc.py: ATC()
- Simplify _capabilities list construction

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga @claude
Add Inheco ODTC thermocycler vendor module
5d094d4 
- ODTCDriver(DeviceBackend): SiLA communication, setup/stop, sensor reading
- ODTCBlockBackend: block temperature control via PreMethod
- ODTCLidBackend: lid temperature control (coupled with block via PreMethod)
- ODTCThermocyclingBackend: protocol execution, lid open/close
- ODTC device class with block, lid, and thermocycling capabilities
- Legacy ExperimentalODTCBackend delegates to new module

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga @claude
Restructure ThermoFisher thermocycler into multi-file package
24b321b 
Split pylabrobot/thermo_fisher/thermocycler.py into:
- thermocyclers/driver.py — raw SCPI IO, auth, block discovery, power
- thermocyclers/block_backend.py — per-block temp control via send_command
- thermocyclers/lid_backend.py — per-block lid temp control via send_command
- thermocyclers/thermocycling_backend.py — protocol execution, run progress
- thermocyclers/thermocycler.py — device class
- thermocyclers/utils.py — XML/SCPI helpers, RunProgress
- thermocyclers/proflex.py, atc.py — factory functions

Backends call driver.send_command() directly — driver is pure IO layer.
Backward-compat shim at thermocycler.py re-exports from package.
All 3 legacy proflex tests pass.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga @claude
Make all legacy backends thin adapters, move universal methods to driver
022fca2 
- OT legacy backend: now delegates to new driver/backend (was self-contained)
- OT tests: updated patch targets to new module location
- TF legacy backend: delegates to per-block backends via lazy cache
- Move check_run_exists, create_run, get_log_by_runname,
  get_elapsed_run_time_from_log to TF driver (device-level, not per-block)
- All 19 legacy tests pass

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga @claude
Fix issues from review
bec4a2a 
- Fix empty backward compat shims (thermo_fisher/atc.py, proflex.py)
- Make OT driver a DeviceBackend (consistent with TF)
- OT device classes now pass driver to Device.__init__()
- Remove duplicate deactivate calls from OT thermocycling backend stop()
- Move dynamic imports to module level (ODTC legacy, thermocycler frontend)
- All 19 tests pass

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga @claude
Fix empty backward compat shims for TF atc.py and proflex.py
e8a4dd0 
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga rickwierenga force-pushed the thermocycling-capability-v2 branch from 5732d7b to 3a31244 Compare March 27, 2026 02:54
@rickwierenga @claude
Fix bugs and align with v1b1 architecture (Driver, CapabilityBackend,…
3a31244 
… BackendParams)

- DeviceBackend → Driver for ODTC and ThermoFisher drivers
- Remove setup()/stop()/super().__init__() from capability backends (CapabilityBackend pattern)
- Add BackendParams: ODTCRunProtocolParams for ODTC-specific run_protocol params
- Thread backend_params through ThermocyclingBackend → ThermocyclingCapability → backends
- Fix _run_pre_method: restore dynamic_time parameter (was hardcoded to true)
- Fix legacy ODTC adapter: cache ODTCBlockBackend instead of creating throwaway instances
- Fix is_profile_running: simplify hold > 0 check
- Fix wait_for_block/wait_for_lid: restore polling logic, handle missing target temps gracefully
- Replace print() with logging in ODTC module

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@rickwierenga rickwierenga force-pushed the v1b1 branch 5 times, most recently from 475dbab to 588abbb Compare April 2, 2026 21:12
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