Merge remote-tracking branch 'origin/edge' into RSS-100-Robust620DB

* origin/edge: (31 commits)
  refactor(hardware): Update appropriate revision (#12130)
  fix(api): Fix accidental error on any PAPIv2.14 protocol (#12141)
  refactor(api): Allow homing after drop tip in engine core (#12124)
  fix(shared-data): remove newLocation and strategy from schemav6 (#12133)
  refactor(api): load pipette with useVirtualPipettes config option (#12117)
  chore(api): further speed up ot3controller tests and add profiling (#12132)
  docs(api): Settle in to leave Labware.default_magdeck_engage_height alone, for now (#12122)
  refactor(api): Improve error messages for JSONv6 and PAPIv2.14 protocols (#12131)
  refactor(robot-server): Note mistaken type in migration (#12126)
  chore(hardware): Remove docstring content checks (#12128)
  feat(hardware_control): Added firmware update mechanism for submodules (#12076)
  feat(app): remove feature flag for calibration dashboard and wizard updates (#12125)
  feat(app):  Calibration dashboard wizard data invalidation (#12097)
  feat(hardware): support new revision values (#12111)
  feat(app): add Chip component (#12090)
  docs(api): Officially remove the `height` parameter of `MagneticModuleContext.engage()` (#12114)
  feat(system-server): add persistent UUID generation (#12123)
  feat(odd): add manual connection for a hidden network (#12033)
  feat(hardware): add progress output to subsystem firmware update process (#12059)
  refactor(api): Improve OT3 instrument calibration process (#11807)
  ...

api/Pipfile

@@ -37,5 +37,6 @@ opentrons = { editable = true, path = "." }
 opentrons-hardware = { editable = true, path = "./../hardware" }
 # specify typing-extensions explicitly to force lockfile inclusion on Python >= 3.8
 typing-extensions = ">=4.0.0,<5"
+pytest-profiling = "~=1.7.0"
 # TODO(mc, 2022-03-31): upgrade sphinx, remove this subdep pin
 jinja2 = ">=2.3,<3.1"

api/conftest.py

@@ -5,7 +5,6 @@
 """
 import pytest
 
-
 # Options must be added at the root level for pytest to properly
 # pick them up. Technically, the main conftest that we use in
 # tests/opentrons is not the root level.

api/docs/static/override_sphinx.css

@@ -17,12 +17,22 @@ div.document {
  padding-top: 150px;
  margin-top: 0;
 }
+
+div.document [id] {
+ scroll-margin-top: 150px;
+}
+
 @media only screen and (min-device-width: 768px) and (min-width: 768px) and (max-width: 1023px) {
  div.document {
  padding-top: 100px;
  margin-top: 0;
  }
+
+ div.document [id] {
+ scroll-margin-top: 100px;
+ }
 }
+
 div.body p {
  line-height: 20pt;
  font-family: "Open Sans", "sans-serif";

api/docs/v2/new_protocol_api.rst

@@ -17,6 +17,8 @@ Protocols and Instruments
  :members:
  :exclude-members: delay
 
+.. autoclass:: opentrons.protocol_api.Liquid
+
 .. _protocol-api-labware:
 
 Labware and Wells
@@ -29,24 +31,25 @@ Labware and Wells
 
 Modules
 -------
+
 .. autoclass:: opentrons.protocol_api.TemperatureModuleContext
  :members:
- :exclude-members: start_set_temperature, await_temperature, broker, geometry
+ :exclude-members: start_set_temperature, await_temperature, broker, geometry, load_labware_object
  :inherited-members:
 
 .. autoclass:: opentrons.protocol_api.MagneticModuleContext
  :members:
- :exclude-members: broker, geometry
+ :exclude-members: calibrate, broker, geometry, load_labware_object
  :inherited-members:
 
 .. autoclass:: opentrons.protocol_api.ThermocyclerContext
  :members:
- :exclude-members: total_step_count, current_cycle_index, total_cycle_count, hold_time, ramp_rate, current_step_index, broker, geometry
+ :exclude-members: total_step_count, current_cycle_index, total_cycle_count, hold_time, ramp_rate, current_step_index, broker, geometry, load_labware_object
  :inherited-members:
 
 .. autoclass:: opentrons.protocol_api.HeaterShakerContext
  :members:
- :exclude-members: broker, geometry
+ :exclude-members: broker, geometry, load_labware_object
  :inherited-members:
 
 

api/docs/v2/versioning.rst

@@ -95,7 +95,7 @@ This table lists the correspondence between Protocol API versions and robot soft
 +-------------+------------------------------+
 | 2.13 | 6.1.0 |
 +-------------+------------------------------+
-| 2.14 | unreleased |
+| 2.14 |  6.3.0  |
 +-------------+------------------------------+
 
 Changes in API Versions
@@ -237,18 +237,42 @@ Version 2.13
 Version 2.14
 ++++++++++++
 
-Upcoming, not yet released.
-
-- :py:meth:`.ProtocolContext.define_liquid` and :py:meth:`.Well.load_liquid` added will allow you to define different liquid types and add them to wells at the beginning of your protocol.
-- :py:class:`.Labware` and :py:class:`.Well` objects will adhere to the protocol's API level setting. Prior to this version, they incorrectly ignore the setting.
-- :py:meth:`.ModuleContext.load_labware_object` will be deprecated.
-- :py:meth:`.MagneticModuleContext.calibrate` will be deprecated.
-- The ``presses`` and ``increment`` arguments of :py:meth:`.InstrumentContext.pick_up_tip` will be deprecated. Configure your pipettes pick-up settings with the Opentrons App, instead.
-- Several internal properties of :py:class:`.Labware`, :py:class:`.Well`, and :py:class:`.ModuleContext` will be deprecated and/or removed:
- - ``Labware.separate_calibration`` and ``ModuleContext.separate_calibration``, which are holdovers from a calibration system that no longer exists.
- - The ``Well.has_tip`` setter, which will cease to function in a future upgrade to the Python protocol execution system. The corresponding ``Well.has_tip`` getter will not be deprecated.
-- :py:meth:`.ModuleContext.geometry` will be deprecated
- - The ``model`` and ``type`` properties of this interface will be replaced by :py:meth:`.ModuleContext.model` and :py:meth:`.ModuleContext.type`, respectively
-- :py:meth:`.ProtocolContext.load_labware` will favor loading custom labware over Opentrons defaults if a name shadows a default and no namespace is included.
- - :py:meth:`.InstrumentContext.touch_tip` will end with the pipette tip in the center of the well instead of on the edge closest to the front of the machine.
-
+This version introduces a new protocol runtime. Several older parts of the Protocol API were deprecated as part of this switchover.
+If you specify an API version of 2.13 or lower, your protocols will continue to execute on the old runtime.
+
+- Feature additions
+
+ - :py:meth:`.ProtocolContext.define_liquid` and :py:meth:`.Well.load_liquid` added
+ to define different liquid types and add them to wells, respectively.
+
+- Bug fixes
+
+ - :py:class:`.Labware` and :py:class:`.Well` now adhere to the protocol's API level setting.
+ Prior to this version, they incorrectly ignored the setting.
+
+ - :py:meth:`.InstrumentContext.touch_tip` will end with the pipette tip in the center of the well
+ instead of on the edge closest to the front of the machine.
+
+ - :py:meth:`.ProtocolContext.load_labware` now prefers loading user-provided labware definitions
+ rather than built-in definitions if no explicit ``namespace`` is specified.
+
+- Deprecations and removals
+
+ - ``ModuleContext.load_labware_object`` was deprecated as an unnecessary internal method.
+
+ - ``ModuleContext.geometry`` was deprecated in favor of
+ :py:attr:`.ModuleContext.model` and :py:attr:`.ModuleContext.type`
+
+ - ``MagneticModuleContext.calibrate`` was deprecated since it was never needed nor implemented.
+
+ - The ``height`` parameter of :py:meth:`MagneticModuleContext.engage` was deprecated.
+ Use ``offset`` or ``height_from_base`` instead.
+
+ - ``Labware.separate_calibration`` and ``ModuleContext.separate_calibration`` were removed,
+ since they were holdovers from a calibration system that no longer exists.
+
+ - The :py:attr:`.Well.has_tip` setter was deprecated. The getter is not deprecated.
+ Use :py:meth:`.Labware.reset` to reset your tip rack's state, instead.
+
+ - The ``presses`` and ``increment`` arguments of :py:meth:`.InstrumentContext.pick_up_tip` were deprecated.
+ Configure your pipette pick-up settings with the Opentrons App, instead.

api/src/opentrons/__init__.py

@@ -159,13 +159,21 @@ async def _blink() -> None:
  # is returned. Do our own blinking here to keep it going while we home the robot.
  blink_task = asyncio.create_task(_blink())
 
+ # check for and start firmware updates if OT3
+ async def _do_updates() -> None:
+ if should_use_ot3() and ff.enable_ot3_firmware_updates():
+ log.info("Checking firmware updates")
+ await hardware.do_firmware_updates()
+
+ await asyncio.create_task(_do_updates())
+
  try:
+
  if not ff.disable_home_on_boot():
  log.info("Homing Z axes")
  await hardware.home_z()
 
  await hardware.set_lights(button=True)
-
  return hardware
  finally:
  blink_task.cancel()

api/src/opentrons/config/advanced_settings.py

@@ -176,14 +176,6 @@ class Setting(NamedTuple):
  ),
  restart_required=True,
  ),
- SettingDefinition(
- _id="enableProtocolEnginePAPICore",
- title="Enable experimental execution core for Python protocols",
- description=(
- "This is an Opentrons-internal setting to test new execution logic."
- " Do not enable."
- ),
- ),
  SettingDefinition(
  _id="enableOT3FirmwareUpdates",
  title="Enable experimental OT-3 firmware updates",
@@ -518,6 +510,16 @@ def _migrate19to20(previous: SettingsMap) -> SettingsMap:
  return newmap
 
 
+def _migrate20to21(previous: SettingsMap) -> SettingsMap:
+ """Migrate to version 21 of the feature flags file.
+
+ - Removes deprecated enableProtocolEnginePAPICore option
+ """
+ removals = ["enableProtocolEnginePAPICore"]
+ newmap = {k: v for k, v in previous.items() if k not in removals}
+ return newmap
+
+
 _MIGRATIONS = [
  _migrate0to1,
  _migrate1to2,
@@ -539,6 +541,7 @@ def _migrate19to20(previous: SettingsMap) -> SettingsMap:
  _migrate17to18,
  _migrate18to19,
  _migrate19to20,
+ _migrate20to21,
 ]
 """
 List of all migrations to apply, indexed by (version - 1). See _migrate below