feat(api, shared-data): add location-based gripper offsets to final labware movement offsets

[sanni-t]

Closes RLAB-295

Overview

Takes the location-based offsets we have been using in protocols and puts them in definitions so that they are included by default while calculating total gripper offsets.

Test Plan

• Test the well-tested science protocols that do labware movement with gripper and verify that they work the same without any offsets provided in the protocol.

Changelog

• adds a new field of gripperOffsets to deck, labware & module schemas
• updates all the relevant definition models
• adds offset getters to engine module & labware state views
• updates the final gripper offset calculations to include these offsets

Review requests

• make sure the calculations are being done correctly
• does the shape of the new fields look okay?
• Updated definition models look fine or can they be improved?

Risk assessment

Medium. The offset calculations are unit tested & will be robot tested well so that's not a risk. But we should make sure the actual offsets being added are correct.

[codecov]

Codecov Report

Merging #13186 (4658923) into internal-release_0.14.0 (fcab19c) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@                     Coverage Diff                     @@
##           internal-release_0.14.0   #13186      +/-   ##
===========================================================
+ Coverage                    72.51%   72.53%   +0.01%     
===========================================================
  Files                         2392     2392              
  Lines                        66004    66032      +28     
  Branches                      7327     7327              
===========================================================
+ Hits                         47865    47895      +30     
+ Misses                       16392    16391       -1     
+ Partials                      1747     1746       -1     

Flag	Coverage Δ
app	71.31% <ø> (+<0.01%)	⬆️
g-code-testing	96.44% <ø> (ø)
labware-library	49.17% <ø> (ø)
notify-server	89.13% <ø> (ø)
protocol-designer	47.30% <ø> (ø)
shared-data	79.02% <100.00%> (+0.21%)	⬆️
step-generation	87.18% <ø> (ø)

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

Files Changed	Coverage Δ
api/src/opentrons/motion_planning/waypoints.py	100.00% <ø> (ø)
...pi/src/opentrons/protocol_engine/state/geometry.py	100.00% <ø> (ø)
api/src/opentrons/protocol_engine/state/labware.py	100.00% <ø> (ø)
api/src/opentrons/protocol_engine/state/modules.py	91.48% <ø> (ø)
api/src/opentrons/protocol_engine/types.py	97.56% <ø> (ø)
...ata/python/opentrons_shared_data/deck/dev_types.py	100.00% <100.00%> (ø)
.../python/opentrons_shared_data/labware/dev_types.py	100.00% <100.00%> (ø)
...pentrons_shared_data/labware/labware_definition.py	100.00% <100.00%> (ø)
...a/python/opentrons_shared_data/module/dev_types.py	100.00% <100.00%> (ø)

... and 1 file with indirect coverage changes

[sanni-t]

add default as required

[sanni-t]

Change this assigned TypedDict to class-based and see if anything breaks. If not, switch to that and split it into required vs optional typed dicts

[sanni-t]

punting this to later

[sanni-t]

Tagging @andySigler @ChrisYarka for verification

[sanni-t]

Tagging @andySigler @ChrisYarka for verification

[sanni-t]

Tagging @andySigler @ChrisYarka for verification

[sanni-t]

Tagging @andySigler @ChrisYarka for verification

[b-cooper]

Changes look good to me 👍

[SyntaxColoring]

Here are my results from testing the PR as-is, and from testing it with adjusted offsets that @andySigler gave me in this spreadsheet.

Pickup/drop location	Sanniti's original offsets	Andy's offsets
armadillo_96_wellplate_200ul_pcr_full_skirt on bare deck slot	✅	✅
armadillo_96_wellplate_200ul_pcr_full_skirt on thermocyclerModuleV2	❌ In the jaw-open immediately after the drop, the jaws collide with the TC. Pickup not attempted.	❌ Same.
armadillo_96_wellplate_200ul_pcr_full_skirt on temperatureModuleV2	❌ During both pickup and drop, it collides with the ~2mm lip around the edge of the module's slot.	❌ Same.
armadillo_96_wellplate_200ul_pcr_full_skirt on magneticBlockV1	🤷‍♂️ It seems to think the labware sits ~2 mm higher than it actually does.	🤷‍♂️ Same.
corning_384_wellplate_112ul_flat on opentrons_universal_flat_adapter on heaterShakerModuleV1	✅	✅
armadillo_96_wellplate_200ul_pcr_full_skirt on opentrons_96_pcr_adapter on heaterShakerModuleV1	✅	✅

Here are the Python files that I used.

[SyntaxColoring]

Recap from in-person work with @sanni-t, @andySigler, and @jbleon95:

• thermocyclerModuleV2: A pickup and drop offset of z=4.6 avoids the collision, and happens to align with the official value for how far up the Thermocycler pops the labware. We've added that to this PR.
• magneticBlockV1: This problem will remain unresolved for this PR.
• temperatureModuleV2: This problem will remain unresolved for this PR. This might be lower-priority because realistic protocols would load the PCR plate atop an adapter atop the module, which would happen to avoid this problem. We couldn't test with that setup because that adapter hasn't yet been split into its own definition.

Thinking continues on where we should take this work in the medium/long-term.

• If you pick up closer to the top of a labware, theoretically, you should also drop it higher to compensate.
• Defining these offsets like we are now is probably not appropriate for labware other than armadillo_96_wellplate_200ul_pcr_full_skirt, with different heights.