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feat(step-generation): py command generation for mix() #17833

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merged 8 commits into from
Mar 24, 2025
Merged

feat(step-generation): py command generation for mix() #17833

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24b1ae0
feat(step-generation): py command generation for mix()
jerader Mar 20, 2025
ff5563e
add support for x and y offsets
jerader Mar 20, 2025
ea5b138
remove unneeded comment
jerader Mar 20, 2025
23bf086
Merge branch 'edge' into sg_mix-py
jerader Mar 20, 2025
849d8a1
adjust touch_tip cosmetics
jerader Mar 20, 2025
d4d09bd
refactor flow rates to define from the pipette
jerader Mar 21, 2025
4439db3
fix unit test and add the flow rates
jerader Mar 21, 2025
0015389
check if delay seconds === 0
jerader Mar 24, 2025
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14 changes: 6 additions & 8 deletions protocol-designer/src/timelineMiddleware/__tests__/generateRobotStateTimeline.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -208,16 +208,14 @@ mockPythonName.drop_tip()
// Step c:
`
mockPythonName.pick_up_tip(location=mockPythonName)
mockPythonName.aspirate(...)
mockPythonName.dispense(...)
mockPythonName.aspirate(...)
mockPythonName.dispense(...)
mockPythonName.flow_rate.aspirate = 3.78
mockPythonName.flow_rate.dispense = 3.78
mockPythonName.mix(...)
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Oh wow, we already had a test for a Mix step. That's nice :)

mockPythonName.drop_tip()
mockPythonName.pick_up_tip(location=mockPythonName)
mockPythonName.aspirate(...)
mockPythonName.dispense(...)
mockPythonName.aspirate(...)
mockPythonName.dispense(...)
mockPythonName.flow_rate.aspirate = 3.78
mockPythonName.flow_rate.dispense = 3.78
mockPythonName.mix(...)
mockPythonName.drop_tip()
`.trim(),
])
Expand Down
2 changes: 1 addition & 1 deletion shared-data/command/types/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ export * from './pipetting'
export * from './setup'
export * from './timing'
export * from './unsafe'

export * from './support'
// NOTE: these key/value pairs will only be present on commands at analysis/run time
// they pertain only to the actual execution status of a command on hardware, as opposed to
// the command's identity and parameters which can be known prior to runtime
Expand Down
195 changes: 189 additions & 6 deletions step-generation/src/__tests__/mix.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,7 @@ describe('mix: change tip', () => {
wells: ['A1', 'B1', 'C1'],
changeTip,
} as MixArgs)
it('changeTip="always"', () => {
it('changeTip="always" with no advanced settings', () => {
const args = makeArgs('always')
const result = mix(args, invariantContext, robotStateWithTip)
const res = getSuccessResult(result)
Expand All @@ -100,6 +100,36 @@ describe('mix: change tip', () => {
dispenseHelper(well, volume, mockWellLocation),
])
)
expect(res.python).toBe(
`
mockPythonName.drop_tip()
mockPythonName.pick_up_tip(location=mockPythonName)
mockPythonName.flow_rate.aspirate = 2.1
mockPythonName.flow_rate.dispense = 2.2
mockPythonName.mix(
repetitions=2,
volume=5,
location=mockPythonName["A1"].bottom(z=3.2),
)
mockPythonName.drop_tip()
mockPythonName.pick_up_tip(location=mockPythonName)
mockPythonName.flow_rate.aspirate = 2.1
mockPythonName.flow_rate.dispense = 2.2
mockPythonName.mix(
repetitions=2,
volume=5,
location=mockPythonName["B1"].bottom(z=3.2),
)
mockPythonName.drop_tip()
mockPythonName.pick_up_tip(location=mockPythonName)
mockPythonName.flow_rate.aspirate = 2.1
mockPythonName.flow_rate.dispense = 2.2
mockPythonName.mix(
repetitions=2,
volume=5,
location=mockPythonName["C1"].bottom(z=3.2),
)`.trimStart()
)
})

it('changeTip="once"', () => {
Expand Down Expand Up @@ -303,7 +333,7 @@ describe('mix: advanced options', () => {
)
})
describe('all advanced settings enabled', () => {
it('should create commands in the expected order with expected params', () => {
it('should create commands in the expected order with expected params with all args', () => {
const args: MixArgs = {
...mixinArgs,
touchTip: true,
Expand All @@ -314,21 +344,28 @@ describe('mix: advanced options', () => {
times,
changeTip: 'always',
wells: ['A1', 'B1', 'C1'],
yOffset: 1,
} as MixArgs
const mockWellLocationCustomXY: Partial<AspDispAirgapParams> = {
wellLocation: {
origin: 'bottom',
offset: { x: 0, y: 1, z: 3.2 },
},
}

const result = mix(args, invariantContext, robotStateWithTip)
const res = getSuccessResult(result)

expect(res.commands).toEqual(
flatMap(args.wells, (well, idx) => [
...replaceTipCommands(idx),
aspirateHelper(well, volume, mockWellLocation),
aspirateHelper(well, volume, mockWellLocationCustomXY),
delayCommand(10),
dispenseHelper(well, volume, mockWellLocation),
dispenseHelper(well, volume, mockWellLocationCustomXY),
delayCommand(12),
aspirateHelper(well, volume, mockWellLocation),
aspirateHelper(well, volume, mockWellLocationCustomXY),
delayCommand(10),
dispenseHelper(well, volume, mockWellLocation),
dispenseHelper(well, volume, mockWellLocationCustomXY),
delayCommand(12),
blowoutHelper(blowoutLabwareId, {
wellLocation: {
Expand All @@ -341,8 +378,154 @@ describe('mix: advanced options', () => {
touchTipHelper(well),
])
)
expect(res.python).toBe(
`
mockPythonName.drop_tip()
mockPythonName.pick_up_tip(location=mockPythonName)
mockPythonName.aspirate(
volume=8,
location=mockPythonName["A1"].bottom(z=3.2).move(types.Point(y=1)),
rate=2.1 / mockPythonName.flow_rate.aspirate,
)
protocol.delay(seconds=10)
mockPythonName.dispense(
volume=8,
location=mockPythonName["A1"].bottom(z=3.2).move(types.Point(y=1)),
rate=2.2 / mockPythonName.flow_rate.dispense,
)
protocol.delay(seconds=12)
mockPythonName.aspirate(
volume=8,
location=mockPythonName["A1"].bottom(z=3.2).move(types.Point(y=1)),
rate=2.1 / mockPythonName.flow_rate.aspirate,
)
protocol.delay(seconds=10)
mockPythonName.dispense(
volume=8,
location=mockPythonName["A1"].bottom(z=3.2).move(types.Point(y=1)),
rate=2.2 / mockPythonName.flow_rate.dispense,
)
protocol.delay(seconds=12)
mockPythonName.flow_rate.blow_out = 2.3
mockPythonName.blow_out(mockPythonName["A1"].top(z=3.3))
mockPythonName.touch_tip(mockPythonName["A1"], v_offset=-3.4)
mockPythonName.drop_tip()
mockPythonName.pick_up_tip(location=mockPythonName)
mockPythonName.aspirate(
volume=8,
location=mockPythonName["B1"].bottom(z=3.2).move(types.Point(y=1)),
rate=2.1 / mockPythonName.flow_rate.aspirate,
)
protocol.delay(seconds=10)
mockPythonName.dispense(
volume=8,
location=mockPythonName["B1"].bottom(z=3.2).move(types.Point(y=1)),
rate=2.2 / mockPythonName.flow_rate.dispense,
)
protocol.delay(seconds=12)
mockPythonName.aspirate(
volume=8,
location=mockPythonName["B1"].bottom(z=3.2).move(types.Point(y=1)),
rate=2.1 / mockPythonName.flow_rate.aspirate,
)
protocol.delay(seconds=10)
mockPythonName.dispense(
volume=8,
location=mockPythonName["B1"].bottom(z=3.2).move(types.Point(y=1)),
rate=2.2 / mockPythonName.flow_rate.dispense,
)
protocol.delay(seconds=12)
mockPythonName.flow_rate.blow_out = 2.3
mockPythonName.blow_out(mockPythonName["A1"].top(z=3.3))
mockPythonName.touch_tip(mockPythonName["B1"], v_offset=-3.4)
mockPythonName.drop_tip()
mockPythonName.pick_up_tip(location=mockPythonName)
mockPythonName.aspirate(
volume=8,
location=mockPythonName["C1"].bottom(z=3.2).move(types.Point(y=1)),
rate=2.1 / mockPythonName.flow_rate.aspirate,
)
protocol.delay(seconds=10)
mockPythonName.dispense(
volume=8,
location=mockPythonName["C1"].bottom(z=3.2).move(types.Point(y=1)),
rate=2.2 / mockPythonName.flow_rate.dispense,
)
protocol.delay(seconds=12)
mockPythonName.aspirate(
volume=8,
location=mockPythonName["C1"].bottom(z=3.2).move(types.Point(y=1)),
rate=2.1 / mockPythonName.flow_rate.aspirate,
)
protocol.delay(seconds=10)
mockPythonName.dispense(
volume=8,
location=mockPythonName["C1"].bottom(z=3.2).move(types.Point(y=1)),
rate=2.2 / mockPythonName.flow_rate.dispense,
)
protocol.delay(seconds=12)
mockPythonName.flow_rate.blow_out = 2.3
mockPythonName.blow_out(mockPythonName["A1"].top(z=3.3))
mockPythonName.touch_tip(mockPythonName["C1"], v_offset=-3.4)`.trimStart()
)
})
})
it('should create python commands with mix() with touchTip and blowOut and no delay or x/y offset set', () => {
const args: MixArgs = {
...mixinArgs,
touchTip: true,
blowoutLocation: blowoutLabwareId,
volume,
times,
changeTip: 'always',
wells: ['A1', 'B1', 'C1'],
xOffset: 1,
yOffset: 1,
} as MixArgs

const result = mix(args, invariantContext, robotStateWithTip)
const res = getSuccessResult(result)

expect(res.python).toBe(
`
mockPythonName.drop_tip()
mockPythonName.pick_up_tip(location=mockPythonName)
mockPythonName.flow_rate.aspirate = 2.1
mockPythonName.flow_rate.dispense = 2.2
mockPythonName.mix(
repetitions=2,
volume=8,
location=mockPythonName["A1"].bottom(z=3.2).move(types.Point(x=1, y=1)),
)
mockPythonName.flow_rate.blow_out = 2.3
mockPythonName.blow_out(mockPythonName["A1"].top(z=3.3))
mockPythonName.touch_tip(mockPythonName["A1"], v_offset=-3.4)
mockPythonName.drop_tip()
mockPythonName.pick_up_tip(location=mockPythonName)
mockPythonName.flow_rate.aspirate = 2.1
mockPythonName.flow_rate.dispense = 2.2
mockPythonName.mix(
repetitions=2,
volume=8,
location=mockPythonName["B1"].bottom(z=3.2).move(types.Point(x=1, y=1)),
)
mockPythonName.flow_rate.blow_out = 2.3
mockPythonName.blow_out(mockPythonName["A1"].top(z=3.3))
mockPythonName.touch_tip(mockPythonName["B1"], v_offset=-3.4)
mockPythonName.drop_tip()
mockPythonName.pick_up_tip(location=mockPythonName)
mockPythonName.flow_rate.aspirate = 2.1
mockPythonName.flow_rate.dispense = 2.2
mockPythonName.mix(
repetitions=2,
volume=8,
location=mockPythonName["C1"].bottom(z=3.2).move(types.Point(x=1, y=1)),
)
mockPythonName.flow_rate.blow_out = 2.3
mockPythonName.blow_out(mockPythonName["A1"].top(z=3.3))
mockPythonName.touch_tip(mockPythonName["C1"], v_offset=-3.4)`.trimStart()
)
})
})

describe('mix: errors', () => {
Expand Down
3 changes: 3 additions & 0 deletions step-generation/src/commandCreators/compound/consolidate.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -331,6 +331,7 @@
xOffset: aspirateXOffset,
yOffset: aspirateYOffset,
nozzles,
invariantContext,
})
: []
const preWetTipCommands = args.preWetTip // Pre-wet tip is equivalent to a single mix, with volume equal to the consolidate volume.
Expand All @@ -349,6 +350,7 @@
xOffset: aspirateXOffset,
yOffset: aspirateYOffset,
nozzles,
invariantContext,

Check warning on line 353 in step-generation/src/commandCreators/compound/consolidate.ts

View check run for this annotation

Codecov / codecov/patch

step-generation/src/commandCreators/compound/consolidate.ts#L353 

Added line #L353 was not covered by tests
})
: []
// can not mix in a waste chute
Expand All @@ -369,6 +371,7 @@
xOffset: dispenseXOffset,
yOffset: dispenseYOffset,
nozzles,
invariantContext,
})
: []

Expand Down
2 changes: 2 additions & 0 deletions step-generation/src/commandCreators/compound/distribute.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -464,6 +464,7 @@ export const distribute: CommandCreator<DistributeArgs> = (
xOffset: aspirateXOffset,
yOffset: aspirateYOffset,
nozzles,
invariantContext,
})
: []

Expand Down Expand Up @@ -502,6 +503,7 @@ export const distribute: CommandCreator<DistributeArgs> = (
xOffset: aspirateXOffset,
yOffset: aspirateYOffset,
nozzles,
invariantContext,
})
: []
return [
Expand Down
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