fix(api): connect context to real thermocycler during calibration

[b-cooper]

The calibration session currently picks up the simulated context from the beginning of the session.
This means that the simulated modules are also usedduring labware calibration. This temporarily
connect the thermocycler during calibration so the session is aware of the lid's open/close state.
This is a short term patch that will be removed in place of better session management to replace the
current RPC over HTTP session communication.

review requests

Please ensure that you are able to proceed to calibrating the labware loaded onto the Thermocycler in these 2 cases (via the run app):

• Your last protocol step is a call to thermocycler.open_lid()
• Your last protocol step is a call to thermocycler.close_lid()

stub protocol:

metadata = {"apiLevel": "2.0"}


def run(protocol):
    # Labware Setup
    reagents = protocol.load_labware('usascientific_12_reservoir_22ml', '1')
    p300rack = protocol.load_labware('opentrons_96_tiprack_300ul', '2')

    p300 = protocol.load_instrument(
        'p20_single_gen2', 'right', tip_racks=[p300rack])
    thermocycler = protocol.load_module('thermocycler')

    reaction_plate = thermocycler.load_labware('biorad_96_wellplate_200ul_pcr')

    thermocycler.set_block_temperature(4)
    p300.pick_up_tip()
    p300.aspirate(10, reagents.wells_by_name()['A1'])
    p300.dispense(10, reaction_plate.wells_by_name()['A1'])
    thermocycler.set_lid_temperature(50)
    thermocycler.deactivate_lid()
    thermocycler.set_lid_temperature(90)

    thermocycler.set_block_temperature(40, hold_time_seconds=10)
    thermocycler.deactivate_block()
    thermocycler.set_block_temperature(80, hold_time_minutes=0.5)
    thermocycler.deactivate()
    thermocycler.set_block_temperature(
        60, hold_time_seconds=30, hold_time_minutes=0.5)
    thermocycler.set_lid_temperature(30)

    thermocycler.close_lid()
    #thermocycler.open_lid()

[sfoster1]

LGTM

[codecov]

Codecov Report

Merging #4454 into edge will increase coverage by 0.39%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             edge    #4454      +/-   ##
==========================================
+ Coverage   55.55%   55.95%   +0.39%     
==========================================
  Files         903      903              
  Lines       26019    26662     +643     
==========================================
+ Hits        14456    14919     +463     
- Misses      11563    11743     +180

Impacted Files	Coverage Δ
...designer/src/components/KnowledgeBaseLink/index.js	50% <0%> (-16.67%)	⬇️
opentrons/protocol_api/execute.py	82.85% <0%> (-1.36%)	⬇️
opentrons/protocol_api/contexts.py	86.15% <0%> (-1.15%)	⬇️
...ol-designer/src/components/modules/CrashInfoBox.js	0% <0%> (ø)	⬆️
opentrons/protocol_api/geometry.py	100% <0%> (+0.67%)	⬆️
opentrons/protocol_api/labware.py	91.95% <0%> (+1.67%)	⬆️
.../protocol_api/legacy_wrapper/containers_wrapper.py	31.29% <0%> (+4.78%)	⬆️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 222cf37...78e8c8c. Read the comment docs.