repair CI

docs/source/_templates/custom-class-template.rst

@@ -3,6 +3,8 @@
 .. currentmodule:: {{ module }}
 
 .. inheritance-diagram:: {{ objname }}
+ :parts: 1
+
 |
 
 .. autoclass:: {{ objname }}

docs/source/conf.py

@@ -25,10 +25,11 @@
  'sphinx.ext.autodoc',
  'sphinx.ext.autosummary',
  'sphinx.ext.inheritance_diagram',
- 'sphinx.ext.todo',
+ 'sphinx.ext.viewcode',
 ]
-autodoc_typehints = 'description'
+autodoc_typehints = 'none'
 autosummary_generate = True
+autosummary_imported_members = False
 autosectionlabel_prefix_document = True
 source_suffix = ['.rst', '.md']
 exclude_patterns = []
@@ -65,7 +66,7 @@
 }
 
 # -- Napoleon Settings -------------------------------------------------------
-napoleon_google_docstring = False
+napoleon_google_docstring = True
 napoleon_numpy_docstring = True
 napoleon_include_init_with_doc = True
 napoleon_include_special_with_doc = False
@@ -74,7 +75,7 @@
 napoleon_use_admonition_for_references = True
 napoleon_use_ivar = True
 napoleon_use_param = True
-napoleon_use_rtype = False
+napoleon_use_rtype = True
 napoleon_preprocess_types = True
 napoleon_type_aliases = None
-napoleon_attr_annotations = True
+napoleon_attr_annotations = True

iblrig/base_choice_world.py

@@ -114,7 +114,6 @@ class ChoiceWorldSession(
  # task_params = ChoiceWorldParams()
  base_parameters_file = Path(__file__).parent.joinpath('base_choice_world_params.yaml')
 
- @property
  def get_trial_data_model(self):
  return ChoiceWorldTrialData
 
@@ -129,7 +128,7 @@ def __init__(self, *args, delay_secs=0, **kwargs):
  self.block_num = -1
  self.block_trial_num = -1
  # init the tables, there are 2 of them: a trials table and a ambient sensor data table
- self.trials_table = self.get_trial_data_model.preallocate_dataframe(NTRIALS_INIT)
+ self.trials_table = self.get_trial_data_model().preallocate_dataframe(NTRIALS_INIT)
 
  self.ambient_sensor_table = pd.DataFrame(
  {
@@ -543,7 +542,7 @@ def save_trial_data_to_json(self, bpod_data: dict):
  """
  # get trial's data as a dict, validate by passing through pydantic model
  trial_data = self.trials_table.iloc[self.trial_num].to_dict()
- trial_data = self.get_trial_data_model.model_validate(trial_data).model_dump()
+ trial_data = self.get_trial_data_model().model_validate(trial_data).model_dump()
 
  # add bpod_data as 'behavior_data'
  trial_data['behavior_data'] = bpod_data

iblrig/base_tasks.py

@@ -29,12 +29,11 @@
 from pythonosc import udp_client
 
 import ibllib.io.session_params as ses_params
-import iblrig
 import iblrig.graphic as graph
 import iblrig.path_helper
 import pybpodapi
 from ibllib.oneibl.registration import IBLRegistrationClient
-from iblrig import net, sound
+from iblrig import net, path_helper, sound
 from iblrig.constants import BASE_PATH, BONSAI_EXE, PYSPIN_AVAILABLE
 from iblrig.frame2ttl import Frame2TTL
 from iblrig.hardware import SOFTCODE, Bpod, MyRotaryEncoder, sound_device_factory
@@ -71,8 +70,8 @@ class BaseSession(ABC):
  extractor_tasks: list | None = None
  """list of str: An optional list of pipeline task class names to instantiate when preprocessing task data."""
 
- @abstractmethod
- def get_trial_data_model(self) -> type[TrialDataModel]: ...
+ def get_trial_data_model(self):
+  return TrialDataModel
 
  def __init__(
  self,
@@ -262,7 +261,7 @@ def _init_paths(self, append: bool = False) -> Bunch:
  * SETTINGS_FILE_PATH: contains the task settings
  `C:\iblrigv8_data\mainenlab\Subjects\SWC_043\2019-01-01\001\raw_task_data_00\_iblrig_taskSettings.raw.json`
  """
- rig_computer_paths = iblrig.path_helper.get_local_and_remote_paths(
+ rig_computer_paths = path_helper.get_local_and_remote_paths(
  local_path=self.iblrig_settings.iblrig_local_data_path,
  remote_path=self.iblrig_settings.iblrig_remote_data_path,
  lab=self.iblrig_settings.ALYX_LAB,
@@ -315,7 +314,8 @@ def _setup_loggers(self, level='INFO', level_bpod='WARNING', file=None):
  self._logger = setup_logger('iblrig', level=level, file=file) # logger attr used by create_session to determine log level
  setup_logger('pybpodapi', level=level_bpod, file=file)
 
- def _remove_file_loggers(self):
+ @staticmethod
+ def _remove_file_loggers():
  for logger_name in ['iblrig', 'pybpodapi']:
  logger = logging.getLogger(logger_name)
  file_handlers = [fh for fh in logger.handlers if isinstance(fh, logging.FileHandler)]

iblrig/serial_singleton.py

@@ -188,7 +188,7 @@ def query(self, query, data_specifier=1):
 
  Parameters
  ----------
- query : any
+ query : Any
  Query to be sent to the serial device.
  data_specifier : int or str, default: 1
  The number of bytes to receive from the serial device, or a format string
@@ -222,7 +222,7 @@ def to_bytes(data: Any) -> bytes:
 
  Parameters
  ----------
- data : any
+ data : Any
  Data to be converted to bytestring.
 
  Returns