Merge branch 'edge' into fix_deck-view-size-issue

Author: koji

api/docs/v1/pipettes.rst

@@ -55,12 +55,12 @@ same behavior as before.
 The P20 Single GEN2 is back-compatible with the P10 Single in this regard. If your protocol
 specifies an ``instruments.P10_Single`` and your robot has an ``instruments.P20_Single_GEN2``
 attached, you can run your protocol, and the robot will act as if the maximum volume of the P20
-Single GEN2 is 10 μl.
+Single GEN2 is 10 µl.
 
 If you have a P50 Single specified in your protocol, there is no automatic backwards compatibility.
 If you want to use a Gen2 Pipette, you must change your protocol to load either a P300 Single GEN2
-(if you are using volumes between 20 and 50 μl) or a P20 Single GEN2 (if you are using volumes
-below 20 μl).
+(if you are using volumes between 20 and 50 µl) or a P20 Single GEN2 (if you are using volumes
+below 20 µl).
 
 
 Plunger Flow Rates
@@ -99,92 +99,92 @@ The given defaults for every pipette model is the following:
 P10_Single
 ----------
 
-- Aspirate Default: 5 μl/s
-- Dispense Default: 10 μl/s
-- Blow Out Default: 1000 μl/s
-- Minimum Volume: 1 μl
-- Maximum Volume: 10 μl
+- Aspirate Default: 5 µl/s
+- Dispense Default: 10 µl/s
+- Blow Out Default: 1000 µl/s
+- Minimum Volume: 1 µl
+- Maximum Volume: 10 µl
 
 P10_Multi
 ---------
 
-- Aspirate Default: 5 μl/s
-- Dispense Default: 10 μl/s
-- Blow Out Default: 1000 μl/s
-- Minimum Volume: 1 μl
-- Maximum Volume: 10 μl
+- Aspirate Default: 5 µl/s
+- Dispense Default: 10 µl/s
+- Blow Out Default: 1000 µl/s
+- Minimum Volume: 1 µl
+- Maximum Volume: 10 µl
 
 P50_Single
 ----------
 
-- Aspirate Default: 25 μl/s
-- Dispense Default: 50 μl/s
-- Blow Out Default: 1000 μl/s
-- Minimum Volume: 5 μl
-- Maximum Volume: 50 μl
+- Aspirate Default: 25 µl/s
+- Dispense Default: 50 µl/s
+- Blow Out Default: 1000 µl/s
+- Minimum Volume: 5 µl
+- Maximum Volume: 50 µl
 
 P50_Multi
 ---------
 
-- Aspirate Default: 25 μl/s
-- Dispense Default: 50 μl/s
-- Blow Out Default: 1000 μl/s
-- Minimum Volume: 5 μl
-- Maximum Volume: 50 μl
+- Aspirate Default: 25 µl/s
+- Dispense Default: 50 µl/s
+- Blow Out Default: 1000 µl/s
+- Minimum Volume: 5 µl
+- Maximum Volume: 50 µl
 
 P300_Single
 -----------
 
-- Aspirate Default: 150 μl/s
-- Dispense Default: 300 μl/s
-- Blow Out Default: 1000 μl/s
-- Minimum Volume: 30 μl
-- Maximum Volume: 300 μl
+- Aspirate Default: 150 µl/s
+- Dispense Default: 300 µl/s
+- Blow Out Default: 1000 µl/s
+- Minimum Volume: 30 µl
+- Maximum Volume: 300 µl
 
 P300_Multi
 ----------
 
-- Aspirate Default: 150 μl/s
-- Dispense Default: 300 μl/s
-- Blow Out Default: 1000 μl/s
-- Minimum Volume: 30 μl
-- Maximum Volume: 300 μl
+- Aspirate Default: 150 µl/s
+- Dispense Default: 300 µl/s
+- Blow Out Default: 1000 µl/s
+- Minimum Volume: 30 µl
+- Maximum Volume: 300 µl
 
 P1000_Single
 ------------
 
-- Aspirate Default: 500 μl/s
-- Dispense Default: 1000 μl/s
-- Blow Out Default: 1000 μl/s
-- Minimum Volume: 100 μl
-- Maximum Volume: 1000 μl
+- Aspirate Default: 500 µl/s
+- Dispense Default: 1000 µl/s
+- Blow Out Default: 1000 µl/s
+- Minimum Volume: 100 µl
+- Maximum Volume: 1000 µl
 
 P20_Single_GEN2
 ---------------
 
-- Aspirate Default: 3.78 μl/s
-- Dispense Default: 3.78 μl/s
-- Blow Out Default: 3.78 μl/s
-- Minimum Volume: 1 μl
-- Maximum Volume: 20 μl
+- Aspirate Default: 3.78 µl/s
+- Dispense Default: 3.78 µl/s
+- Blow Out Default: 3.78 µl/s
+- Minimum Volume: 1 µl
+- Maximum Volume: 20 µl
 
 P300_Single_GEN2
 ----------------
 
-- Aspirate Default: 46.43 μl/s
-- Dispense Default: 46.43 μl/s
-- Blow Out Default: 46.43 μl/s
-- Minimum Volume: 20 μl
-- Maximum Volume: 300 μl
+- Aspirate Default: 46.43 µl/s
+- Dispense Default: 46.43 µl/s
+- Blow Out Default: 46.43 µl/s
+- Minimum Volume: 20 µl
+- Maximum Volume: 300 µl
 
 P1000_Single_GEN2
 -----------------
 
-- Aspirate Default: 137.35 μl/s
-- Dispense Default: 137.35 μl/s
-- Blow Out Default: 137.35 μl/s
-- Minimum Volume: 100 μl
-- Maximum Volume: 1000 μl
+- Aspirate Default: 137.35 µl/s
+- Dispense Default: 137.35 µl/s
+- Blow Out Default: 137.35 µl/s
+- Minimum Volume: 100 µl
+- Maximum Volume: 1000 µl
 
 Old Pipette Constructor
 =======================

api/docs/v2/complex_commands/parameters.rst

@@ -62,7 +62,7 @@ One reason to set ``new_tip="always"`` is to avoid cross-contamination between w
 
 :py:meth:`~.InstrumentContext.transfer` will pick up a new tip before *every* aspirate when ``new_tip="always"``. This includes when :ref:`tip refilling <complex-tip-refilling>` requires multiple aspirations from a single source well.
 
-:py:meth:`~.InstrumentContext.distribute` and :py:meth:`~.InstrumentContext.consolidate` only pick up one tip, even when ``new_tip="always"``. For example, this distribute command returns to the source well a second time, because the amount to be distributed (400 µL total plus disposal volume) exceeds the pipette capacity (300 μL)::
+:py:meth:`~.InstrumentContext.distribute` and :py:meth:`~.InstrumentContext.consolidate` only pick up one tip, even when ``new_tip="always"``. For example, this distribute command returns to the source well a second time, because the amount to be distributed (400 µL total plus disposal volume) exceeds the pipette capacity (300 µL)::
 
     pipette.distribute(
         volume=200,

api/docs/v2/modules/temperature_module.rst

@@ -98,11 +98,11 @@ The Temperature Module supports these 96-well block and labware combinations for
 
    * - 96-well block contents
      - API Load Name
-   * - Bio-Rad well plate 200 μL
+   * - Bio-Rad well plate 200 µL
      - ``opentrons_96_aluminumblock_biorad_wellplate_200uL``
-   * - Generic PCR strip 200 μL
+   * - Generic PCR strip 200 µL
      - ``opentrons_96_aluminumblock_generic_pcr_strip_200uL``
-   * - NEST well plate 100 μL
+   * - NEST well plate 100 µL
      - ``opentrons_96_aluminumblock_nest_wellplate_100uL``
 
 This command loads the same physical adapter and labware as the example in the Standalone Adapters section above, but it is also compatible with earlier API versions::

api/docs/v2/tutorial.rst

@@ -30,7 +30,7 @@ Hardware and Labware
 
 Before running a protocol, you’ll want to have the right kind of hardware and labware ready for your Flex or OT-2.
 
-- **Flex users** should review Chapter 2: Installation and Relocation in the `instruction manual <https://insights.opentrons.com/hubfs/Products/Flex/Opentrons%20Flex%20Manual.pdf>`_. Specifically, see the pipette information in the "Instrument Installation and Calibration" section. You can use either a 1-channel or 8-channel pipette for this tutorial. Most Flex code examples will use a `Flex 1-Channel 1000 μL pipette <https://shop.opentrons.com/opentrons-flex-1-channel-pipette/>`_.
+- **Flex users** should review Chapter 2: Installation and Relocation in the `instruction manual <https://insights.opentrons.com/hubfs/Products/Flex/Opentrons%20Flex%20Manual.pdf>`_. Specifically, see the pipette information in the "Instrument Installation and Calibration" section. You can use either a 1-channel or 8-channel pipette for this tutorial. Most Flex code examples will use a `Flex 1-Channel 1000 µL pipette <https://shop.opentrons.com/opentrons-flex-1-channel-pipette/>`_.
 
 - **OT-2 users** should review the robot setup and pipette information on the `Get Started page <https://support.opentrons.com/s/ot2-get-started>`_. Specifically, see `attaching pipettes <https://support.opentrons.com/s/article/Get-started-Attach-pipettes>`_ and `initial calibration <https://support.opentrons.com/s/article/Get-started-Calibrate-the-deck>`_. You can use either a single-channel or 8-channel pipette for this tutorial. Most OT-2 code examples will use a `P300 Single-Channel GEN2 <https://shop.opentrons.com/single-channel-electronic-pipette-p20/>`_ pipette.
 

api/src/opentrons/hardware_control/api.py

@@ -1039,6 +1039,7 @@ async def aspirate(
         mount: top_types.Mount,
         volume: Optional[float] = None,
         rate: float = 1.0,
+        correction_volume: float = 0.0,
     ) -> None:
         """
         Aspirate a volume of liquid (in microliters/uL) using this pipette.
@@ -1073,6 +1074,7 @@ async def dispense(
         volume: Optional[float] = None,
         rate: float = 1.0,
         push_out: Optional[float] = None,
+        correction_volume: float = 0.0,
     ) -> None:
         """
         Dispense a volume of liquid in microliters(uL) using this pipette.

api/src/opentrons/hardware_control/instruments/ot3/pipette_handler.py

@@ -502,10 +502,19 @@ def ready_for_tip_action(
         self._ihp_log.debug(f"{action} on {target.name}")
 
     def plunger_position(
-        self, instr: Pipette, ul: float, action: "UlPerMmAction"
+        self,
+        instr: Pipette,
+        ul: float,
+        action: "UlPerMmAction",
+        correction_volume: float = 0.0,
     ) -> float:
-        mm = ul / instr.ul_per_mm(ul, action)
-        position = instr.plunger_positions.bottom - mm
+        if ul == 0:
+            position = instr.plunger_positions.bottom
+        else:
+            multiplier = 1.0 + (correction_volume / ul)
+            mm_dist_from_bottom = ul / instr.ul_per_mm(ul, action)
+            mm_dist_from_bottom_corrected = mm_dist_from_bottom * multiplier
+            position = instr.plunger_positions.bottom - mm_dist_from_bottom_corrected
         return round(position, 6)
 
     def plunger_speed(
@@ -531,6 +540,7 @@ def plan_check_aspirate(
         mount: OT3Mount,
         volume: Optional[float],
         rate: float,
+        correction_volume: float = 0.0,
     ) -> Optional[LiquidActionSpec]:
         """Check preconditions for aspirate, parse args, and calculate positions.
 
@@ -566,7 +576,10 @@ def plan_check_aspirate(
         ), "Cannot aspirate more than pipette max volume"
 
         dist = self.plunger_position(
-            instrument, instrument.current_volume + asp_vol, "aspirate"
+            instr=instrument,
+            ul=instrument.current_volume + asp_vol,
+            action="aspirate",
+            correction_volume=correction_volume,
         )
         speed = self.plunger_speed(
             instrument, instrument.aspirate_flow_rate * rate, "aspirate"
@@ -591,6 +604,7 @@ def plan_check_dispense(
         volume: Optional[float],
         rate: float,
         push_out: Optional[float],
+        correction_volume: float = 0.0,
     ) -> Optional[LiquidActionSpec]:
         """Check preconditions for dispense, parse args, and calculate positions.
 
@@ -659,7 +673,10 @@ def plan_check_dispense(
             )
 
         dist = self.plunger_position(
-            instrument, instrument.current_volume - disp_vol, "dispense"
+            instr=instrument,
+            ul=instrument.current_volume - disp_vol,
+            action="dispense",
+            correction_volume=correction_volume,
         )
         speed = self.plunger_speed(
             instrument, instrument.dispense_flow_rate * rate, "dispense"

api/src/opentrons/hardware_control/ot3api.py

@@ -2046,12 +2046,16 @@ async def aspirate(
         mount: Union[top_types.Mount, OT3Mount],
         volume: Optional[float] = None,
         rate: float = 1.0,
+        correction_volume: float = 0.0,
     ) -> None:
         """
         Aspirate a volume of liquid (in microliters/uL) using this pipette."""
         realmount = OT3Mount.from_mount(mount)
         aspirate_spec = self._pipette_handler.plan_check_aspirate(
-            realmount, volume, rate
+            mount=realmount,
+            volume=volume,
+            rate=rate,
+            correction_volume=correction_volume,
         )
         if not aspirate_spec:
             return
@@ -2088,12 +2092,17 @@ async def dispense(
         volume: Optional[float] = None,
         rate: float = 1.0,
         push_out: Optional[float] = None,
+        correction_volume: float = 0.0,
     ) -> None:
         """
         Dispense a volume of liquid in microliters(uL) using this pipette."""
         realmount = OT3Mount.from_mount(mount)
         dispense_spec = self._pipette_handler.plan_check_dispense(
-            realmount, volume, rate, push_out
+            mount=realmount,
+            volume=volume,
+            rate=rate,
+            push_out=push_out,
+            correction_volume=correction_volume,
         )
         if not dispense_spec:
             return

api/src/opentrons/hardware_control/protocols/liquid_handler.py

@@ -98,6 +98,7 @@ async def aspirate(
         mount: MountArgType,
         volume: Optional[float] = None,
         rate: float = 1.0,
+        correction_volume: float = 0.0,
     ) -> None:
         """
         Aspirate a volume of liquid (in microliters/uL) using this pipette
@@ -117,6 +118,7 @@ async def aspirate(
         volume : [float] The number of microliters to aspirate
         rate : [float] Set plunger speed for this aspirate, where
             speed = rate * aspirate_speed
+        correction_volume : Correction volume in uL for the specified aspirate volume
         """
         ...
 
@@ -126,6 +128,7 @@ async def dispense(
         volume: Optional[float] = None,
         rate: float = 1.0,
         push_out: Optional[float] = None,
+        correction_volume: float = 0.0,
     ) -> None:
         """
         Dispense a volume of liquid in microliters(uL) using this pipette
@@ -136,6 +139,7 @@ async def dispense(
         volume : [float] The number of microliters to dispense
         rate : [float] Set plunger speed for this dispense, where
             speed = rate * dispense_speed
+        correction_volume : Correction volume in uL for the specified dispense volume
         """
         ...