feat(api): Support the new pipette configurations and 96 channel in the hardware controller #11830

Laura-Danielle · 2022-12-06T00:00:01Z

Overview

This PR is an initial pass at supporting the new pipette configurations from shared data in the hardware controller. As a result of this, we also get to control the 96 channel in the hardware controller. Another benefit is that the ot3 api can now switch between pipetting functions depending on the working volume of the pipette.

A lot of the work in this PR will require refactoring once we have the ot2 pipettes ported over to the new pipette configuration. I hope to combine a lot of repeat code at that time. The shape of the configurations is very different, so I did not bother trying to combine it at this time.

A separate PR will be put up to support full tip rack pick up with the 96 channel.

A few things that need more thought in the follow-ups:

Are we satisfied with how we handle major/minor version?
How can we make the caching more effective for the pipette information in shared data?
How should we actually store multiple tip types with their configurations?
What should we do about the pipette "name" and "model" given that they're very confusing and we're moving away from loading in pipettes by string name.
Should we keep track of the right mount's "position" while the 96 channel is moving?

Changelog

Block pipettes not supported on the OT3 from being loaded in an OT3 hardware controller
Separate the new configurations and use them in the Pipette object / hardware controller
Changed how pipettes are reset. Rather than reloading an object (which is a roundabout way of resetting state/offsets), we should actually reset state/offsets/configurations
Modified current/speeds for high throughput gantry load
Modified the gantry load function to not rely on the pipette dict and modified the functionality to only return HIGH_THROUGHPUT when a 96 channel is attached to the left (the only supported configuration)
Marked all tests that use non-ot3 pipettes as ot2_only for now. A lot of them were old protocol api tests which I'm assuming we plan to delete at some point as well.

Planned fast follows

Support the correct "versions" for the pipettes
Add the OT2 pipettes to the new pipette configuration format (will also need to change locations this is ported in for js as well)
Support updating pipette configurations for the OT2 pipettes
Re-combine pipette_handler and separate out pipette objects only where functionality diverges
Separate out the concept of "static" and "stateful" pipette information that consumers of the HC would be interested in. This will effectively remove the pipette state "dict" that we keep track of on top of the attributes stored in the Pipette object class.

Risk assessment

High. This changes where configurations are loaded in for pipettes. It should be thoroughly tested for all pipette types.

codecov · 2022-12-06T00:10:50Z

Codecov Report

Merging #11830 (9c19a98) into RLIQ-131-support-96-channel (e59f558) will increase coverage by 0.04%.
The diff coverage is 80.00%.

@@                       Coverage Diff                       @@
##           RLIQ-131-support-96-channel   #11830      +/-   ##
===============================================================
+ Coverage                        74.14%   74.19%   +0.04%     
===============================================================
  Files                             2106     2108       +2     
  Lines                            58491    58636     +145     
  Branches                          6218     6218              
===============================================================
+ Hits                             43371    43504     +133     
- Misses                           13654    13666      +12     
  Partials                          1466     1466

Flag	Coverage Δ
app	`72.60% <ø> (ø)`
hardware-testing	`∅ <ø> (∅)`
notify-server	`88.26% <ø> (ø)`
protocol-designer	`45.86% <ø> (ø)`
shared-data	`85.53% <78.00%> (+0.72%)`	⬆️
step-generation	`88.46% <ø> (ø)`

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
api/src/opentrons/config/defaults_ot3.py	`87.27% <0.00%> (ø)`
...entrons/hardware_control/backends/ot3controller.py	`64.63% <58.33%> (ø)`
api/src/opentrons/hardware_control/ot3api.py	`80.66% <73.33%> (ø)`
.../python/opentrons_shared_data/pipette/load_data.py	`93.10% <75.00%> (ø)`
...pentrons_shared_data/pipette/pipette_definition.py	`91.37% <78.57%> (ø)`
api/src/opentrons/hardware_control/__init__.py	`100.00% <100.00%> (ø)`
...pentrons/hardware_control/backends/ot3simulator.py	`88.57% <100.00%> (ø)`
api/src/opentrons/hardware_control/dev_types.py	`100.00% <100.00%> (ø)`
...ardware_control/protocols/instrument_configurer.py	`63.15% <100.00%> (ø)`
api/src/opentrons/protocols/api_support/util.py	`90.80% <100.00%> (ø)`
... and 10 more

…ed data We have a completely new shape for pipette configurations that need to be loaded in.

sfoster1

Couple inline changes; some are critical, like using floats for versions - we really shouldn't do that.

There's also a whole lot of tests that effectively get mark-skipped for the ot3. Is there any way at all we can avoid that? IMO we really shouldn't check in PRs that disable swathes of tests like this.

Are the ot3 variants of pipette and pipette_handler straight copies of the ot2 variants? if not, can you point at where they're different?

api/src/opentrons/config/ot3_pipette_config.py

api/src/opentrons/hardware_control/backends/ot3controller.py

api/src/opentrons/hardware_control/backends/ot3simulator.py

api/src/opentrons/hardware_control/dev_types.py

sfoster1 · 2022-12-07T17:13:50Z

api/src/opentrons/hardware_control/instruments/ot2/pipette_handler.py

-            )
-            new_p.act_as(p.acting_as)
-            self._attached_instruments[m] = new_p
+            if isinstance(m, OT3Mount):


the linter will also be satisfied if you make reset_pipette_offset generic across mount

All of the code is separated -- including calibration stuff right now. Would rather address this when I'm recombining all the instruments code.

api/src/opentrons/hardware_control/ot3api.py

api/tests/opentrons/hardware_control/test_instruments.py

sfoster1 · 2022-12-07T17:18:59Z

api/tests/opentrons/hardware_control/test_instruments.py

@@ -670,26 +671,50 @@ async def test_blowout_flow_rate(sim_and_instr):


 async def test_reset_instruments(monkeypatch, sim_and_instr):
-    sim_builder, dummy_instruments = sim_and_instr
+    instruments = {


we should have a version of this for ot2 and ot3, since those are now separate pieces of code

api/tests/opentrons/protocols/advanced_control/test_transfers.py

Laura-Danielle · 2022-12-07T17:48:53Z

Are the ot3 variants of pipette and pipette_handler straight copies of the ot2 variants? if not, can you point at where they're different?

The main differences include:

some new static properties to make is easier to look up things like plunger positions and pick up configurations
the shape of the pipette configurations passed in

Other than that both of those files are straight copies that I hope to be able to merge back together once the OT2 pipette configurations are ported over.

sfoster1

This looks good as a first step to me, yeah. I think your refactor plans will help the other stuff I like less.

sfoster1 · 2022-12-08T16:19:55Z

api/src/opentrons/config/ot3_pipette_config.py

+    return PipetteVersionType(major, minor)
+
+
+def version_from_int(version: int) -> PipetteVersionType:


When do we end up using this?

…he hardware controller (#11830) * feat(api): change pipette functions based on the tip working volume * feat(api): do not use "pipette name" and "pipette model" to look up pipettes via configurations

Laura-Danielle added 25 commits December 6, 2022 15:24

feat(shared-data): properly load new pipette configurations from shar…

6ff8630

…ed data We have a completely new shape for pipette configurations that need to be loaded in.

fix shared data linting

0fae508

fix more linting issues

715f8af

pr change requests

c7a167e

fixup test

2a21071

split out pipette object, controller uses ot3 load function

2a36f29

support ot3 configs in a pipette object

4858c04

Add new temporary ot3 pipette object and handler

539bc02

Support backwards compatible pipette name

7e547e8

support backwards compatible pipette model

a2238bd

fix validate errors in pipette definition

063a4c4

address linter errors

c2e6371

support changing tip functions with working volume

79e6ccd

Resolve all ot3 linter errors

0320af6

add tip physical configurations

b1b33d4

add more configs for backwards compatibility purposes

adbf062

Modify gantry load for 96 channel on left mount

e2b2ab1

modify current and ensure model and version stringable

2cfc368

bump up plunger current

2029017

fix simulator attach pipettes

b1ced01

fix instrument tests and max volume

5a61202

reset state of pipette also

2a30aaa

format the load name a little better for pipettes

882a393

fix up expected pipette spec and other linter errors

d301e05

fix unused imports

63a8e4a

Laura-Danielle force-pushed the RLIQ-60-support-96-channel-hc branch from 0e86423 to 63a8e4a Compare December 6, 2022 20:44

Laura-Danielle added 3 commits December 6, 2022 16:44

modify gantry load test

1db0cdf

Mark all tests with non-ot3 pipettes as ot2 only

6334a2b

Throw a key error if version does not match supported versions

cfd5057

Laura-Danielle added 5 commits December 7, 2022 09:13

support older tip overlap format

3e9043b

fix robot server linting

17a17dc

fix hardware testing simulation files

91ba392

fix shared data lint

f416345

fix api lint

e489086

Laura-Danielle marked this pull request as ready for review December 7, 2022 16:19

Laura-Danielle requested a review from a team as a code owner December 7, 2022 16:19

sfoster1 requested changes Dec 7, 2022

View reviewed changes

Laura-Danielle added 3 commits December 8, 2022 10:45

do not use floats to refer to versions

fbe0ee1

skip entire file if only ot2 compatibility

541b338

hardware testing lint

91c8fba

Laura-Danielle requested a review from sfoster1 December 8, 2022 16:17

delete unused code

9b21a6f

sfoster1 approved these changes Dec 8, 2022

View reviewed changes

Laura-Danielle added 5 commits December 8, 2022 11:49

skip whole module for test file

af65208

formatting

1935b80

fix hardware testing test suit

b29c40e

fix linter

2ab4ef6

do not need int version of model

9c19a98

Laura-Danielle merged commit 3a3035b into RLIQ-131-support-96-channel Dec 8, 2022

Laura-Danielle deleted the RLIQ-60-support-96-channel-hc branch December 8, 2022 19:37

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feat(api): Support the new pipette configurations and 96 channel in the hardware controller #11830

feat(api): Support the new pipette configurations and 96 channel in the hardware controller #11830

Laura-Danielle commented Dec 6, 2022 •

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Laura-Danielle Dec 8, 2022

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sfoster1 Dec 8, 2022

		return PipetteVersionType(major, minor)


		def version_from_int(version: int) -> PipetteVersionType:

feat(api): Support the new pipette configurations and 96 channel in the hardware controller #11830

feat(api): Support the new pipette configurations and 96 channel in the hardware controller #11830

Conversation

Laura-Danielle commented Dec 6, 2022 • edited Loading

Overview

Changelog

Planned fast follows

Risk assessment

codecov bot commented Dec 6, 2022 • edited Loading

Codecov Report

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Laura-Danielle commented Dec 6, 2022 •

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