Merge branch 'v3a' into api-direct-movements-within-well

api/opentrons/__init__.py

@@ -149,4 +149,4 @@ def _create_pipette_from_config(
 containers = ContainersWrapper(robot)
 labware = ContainersWrapper(robot)
 
-__all__ = [containers, instruments, robot, reset, __version__]
+__all__ = [containers, instruments, labware, robot, reset, __version__]

api/opentrons/api/calibration.py

@@ -31,7 +31,7 @@ def _set_state(self, state):
 
  def tip_probe(self, instrument):
  inst = instrument._instrument
- log.debug('Probing tip with {}'.format(instrument.name))
+ log.info('Probing tip with {}'.format(instrument.name))
  self._set_state('probing')
 
  measured_center = calibration_functions.probe_instrument(
@@ -45,7 +45,7 @@ def tip_probe(self, instrument):
  measured_center=measured_center
  )
 
- log.debug('New config: {0}'.format(config))
+ log.info('New config: {0}'.format(config))
 
  calibration_functions.move_instrument_for_probing_prep(
  inst, inst.robot
@@ -60,7 +60,7 @@ def pick_up_tip(self, instrument, container):
  .format(type(container)))
 
  inst = instrument._instrument
- log.debug('Picking up tip from {} in {} with {}'.format(
+ log.info('Picking up tip from {} in {} with {}'.format(
  container.name, container.slot, instrument.name))
  self._set_state('moving')
  inst.pick_up_tip(container._container[0])
@@ -73,22 +73,22 @@ def drop_tip(self, instrument, container):
  .format(type(container)))
 
  inst = instrument._instrument
- log.debug('Dropping tip from {} in {} with {}'.format(
+ log.info('Dropping tip from {} in {} with {}'.format(
  container.name, container.slot, instrument.name))
  self._set_state('moving')
  inst.drop_tip(container._container[0], home_after=True)
  self._set_state('ready')
 
  def return_tip(self, instrument):
  inst = instrument._instrument
- log.debug('Returning tip from {}'.format(instrument.name))
+ log.info('Returning tip from {}'.format(instrument.name))
  self._set_state('moving')
  inst.return_tip(home_after=True)
  self._set_state('ready')
 
  def move_to_front(self, instrument):
  inst = instrument._instrument
- log.debug('Moving {}'.format(instrument.name))
+ log.info('Moving {}'.format(instrument.name))
  self._set_state('moving')
  inst.robot.home()
  calibration_functions.move_instrument_for_probing_prep(
@@ -97,22 +97,21 @@ def move_to_front(self, instrument):
  self._set_state('ready')
 
  def move_to(self, instrument, container):
- # TODO (ben 20171115) Replace `isinstance` checks with typed params
  if not isinstance(container, Container):
  raise ValueError(
  'Invalid object type {0}. Expected models.Container'
  .format(type(container)))
 
  inst = instrument._instrument
- log.debug('Moving {} to {} in {}'.format(
+ log.info('Moving {} to {} in {}'.format(
  instrument.name, container.name, container.slot))
  self._set_state('moving')
  inst.move_to(container._container[0])
  self._set_state('ready')
 
  def jog(self, instrument, distance, axis):
  inst = instrument._instrument
- log.debug('Jogging {} by {} in {}'.format(
+ log.info('Jogging {} by {} in {}'.format(
  instrument.name, distance, axis))
  self._set_state('moving')
  calibration_functions.jog_instrument(
@@ -125,23 +124,20 @@ def jog(self, instrument, distance, axis):
 
  def home(self, instrument):
  inst = instrument._instrument
- log.debug('Homing {}'.format(instrument.name))
+ log.info('Homing {}'.format(instrument.name))
  self._set_state('moving')
  inst.home()
  self._set_state('ready')
 
  def update_container_offset(self, container, instrument):
  inst = instrument._instrument
- log.debug('Updating {} in {}'.format(container.name, container.slot))
+ log.info('Updating {} in {}'.format(container.name, container.slot))
  inst.robot.calibrate_container_with_instrument(
  container=container._container,
  instrument=inst,
  save=True
  )
 
- # TODO (artyom, 20171003): along with session, consider extracting this
- # into abstract base class or find any other way to keep notifications
- # consistent across all managers
  def _snapshot(self):
  return {
  'topic': CalibrationManager.TOPIC,

api/opentrons/api/models.py

@@ -21,7 +21,7 @@ def __init__(self, instrument, containers=None):
  self.name = instrument.name
  self.channels = instrument.channels
  self.mount = instrument.mount
- # TODO(artyom, 20171006): with axis removed from the instrument
+ # Although axis has been deprecated from the instrument
  # we still need to pass it to the UI for now
  # Warning: this does not correspond to the Smoothie axis!
  self.axis = 'a' if self.mount == 'right' else 'b'

api/opentrons/api/session.py

@@ -5,7 +5,7 @@
 from functools import reduce
 
 from opentrons.broker import publish, subscribe
-from opentrons.containers import get_container
+from opentrons.containers import get_container, location_to_list
 from opentrons.commands import tree, types
 from opentrons import robot
 
@@ -199,7 +199,7 @@ def turn_off_rail_lights(self):
  robot.turn_off_rail_lights()
 
  def set_state(self, state):
- log.info("State set to {}".format(state))
+ log.debug("State set to {}".format(state))
  if state not in VALID_STATES:
  raise ValueError(
  'Invalid state: {0}. Valid states are: {1}'
@@ -275,8 +275,9 @@ def _get_labware(command):
  containers.append(get_container(location))
 
  if locations:
+ list_of_locations = location_to_list(locations)
  containers.extend(
- [get_container(location) for location in locations])
+ [get_container(location) for location in list_of_locations])
 
  containers = [c for c in containers if c is not None]
 

api/opentrons/commands/commands.py

@@ -2,8 +2,7 @@
 from ..broker import broker
 import functools
 import inspect
-from opentrons.containers import Well, Container, Slot, WellSeries,\
- unpack_location
+from opentrons.containers import Well, Container, Slot, location_to_list
 
 
 def stringify_location(location):
@@ -23,7 +22,7 @@ def get_slot(location):
  if location is None:
  return '?'
 
- location = _location_to_list(location)
+ location = location_to_list(location)
  multiple = len(location) > 1
 
  return '{object_text}{suffix} {first}{last} in "{slot_text}"'.format(
@@ -35,32 +34,6 @@ def get_slot(location):
  )
 
 
-def _location_to_list(loc):
- # might be a location tuple, or list of location tuples
- # like what's returned from well.top()
- if isinstance(loc, tuple):
- loc = unpack_location(loc)[0]
- elif isinstance(loc, list):
- loc = [
- unpack_location(l)[0]
- for l in loc
- ]
-
- if isinstance(loc, WellSeries):
- # TODO(artyom, 20171107): this is to handle a case when
- # container.rows('1', '2') returns a WellSeries of WellSeries
- # the data structure should be fixed when WellSeries is phased out
- if isinstance(loc[0], WellSeries):
- loc = [well for series in loc for well in series]
- else:
- loc = list(loc)
-
- # ensure it returns either list or tuple
- if not (isinstance(loc, list) or isinstance(loc, tuple)):
- loc = [loc]
- return loc
-
-
 def make_command(name, payload):
  return {'name': name, 'payload': payload}
 
@@ -117,11 +90,14 @@ def consolidate(instrument, volume, source, dest):
  source=stringify_location(source),
  dest=stringify_location(dest)
  )
+ # incase either source or dest is list of tuple location
+ # strip both down to simply lists of Placeables
+ locations = [] + location_to_list(source) + location_to_list(dest)
  return make_command(
  name=types.CONSOLIDATE,
  payload={
  'instrument': instrument,
- 'locations': [source, dest],
+ 'locations': locations,
  'volume': volume,
  'source': source,
  'dest': dest,
@@ -136,11 +112,14 @@ def distribute(instrument, volume, source, dest):
  source=stringify_location(source),
  dest=stringify_location(dest)
  )
+ # incase either source or dest is list of tuple location
+ # strip both down to simply lists of Placeables
+ locations = [] + location_to_list(source) + location_to_list(dest)
  return make_command(
  name=types.DISTRIBUTE,
  payload={
  'instrument': instrument,
- 'locations': [source, dest],
+ 'locations': locations,
  'volume': volume,
  'source': source,
  'dest': dest,
@@ -155,11 +134,14 @@ def transfer(instrument, volume, source, dest):
  source=stringify_location(source),
  dest=stringify_location(dest)
  )
+ # incase either source or dest is list of tuple location
+ # strip both down to simply lists of Placeables
+ locations = [] + location_to_list(source) + location_to_list(dest)
  return make_command(
  name=types.TRANSFER,
  payload={
  'instrument': instrument,
- 'locations': [source, dest],
+ 'locations': locations,
  'volume': volume,
  'source': source,
  'dest': dest,

api/opentrons/containers/__init__.py

@@ -11,6 +11,7 @@
  Well,
  WellSeries,
  unpack_location,
+ location_to_list,
  get_container
 )
 from opentrons.containers.calibrator import apply_calibration
@@ -24,6 +25,7 @@
  Well,
  WellSeries,
  unpack_location,
+ location_to_list,
  apply_calibration,
  get_container]
 

api/opentrons/containers/placeable.py

@@ -29,6 +29,35 @@ def unpack_location(location):
  return (placeable, Vector(coordinates))
 
 
+def location_to_list(loc):
+ # might be a location tuple, or list of location tuples
+ # like what's returned from well.top()
+ if isinstance(loc, tuple):
+ loc = unpack_location(loc)[0]
+ if isinstance(loc, list):
+ if isinstance(loc[0], (WellSeries, list)):
+ loc = [well for series in loc for well in series]
+ else:
+ loc = [
+ unpack_location(l)[0]
+ for l in loc
+ ]
+
+ if isinstance(loc, WellSeries):
+ # TODO(artyom, 20171107): this is to handle a case when
+ # container.rows('1', '2') returns a WellSeries of WellSeries
+ # the data structure should be fixed when WellSeries is phased out
+ if isinstance(loc[0], WellSeries):
+ loc = [well for series in loc for well in series]
+ else:
+ loc = list(loc)
+
+ # ensure it returns either list or tuple
+ if not (isinstance(loc, list) or isinstance(loc, tuple)):
+ loc = [loc]
+ return loc
+
+
 def get_container(location):
  obj, _ = unpack_location(location)