docs(): Satisfy mkdocs warnings

Author: gegnew

cellengine/resources/attachment.py

@@ -62,7 +62,7 @@ def from_dict(cls, data: dict):
     def to_dict(self):
         return converter.unstructure(self)
 
-    def download(self, to_file: str = None):
+    def download(self, to_file: Optional[str] = None) -> Optional[bytes]:
         """Download the attachment.
 
         Defaults to returning the file as a blob. If ``to_file`` is specified,

cellengine/resources/compensation.py

@@ -1,5 +1,5 @@
 from __future__ import annotations
-from typing import List, Optional, TYPE_CHECKING, Tuple, cast
+from typing import List, Optional, TYPE_CHECKING, Tuple, Union, cast
 
 from attr import define, field
 from numpy import array, linalg
@@ -146,14 +146,16 @@ def dataframe_as_html(self):
         """Return the compensation matrix dataframe as HTML."""
         return self.dataframe._repr_html_()
 
-    def apply(self, file: FcsFile, inplace: bool = True, **kwargs):
+    def apply(
+        self, file: FcsFile, inplace: bool = True, **kwargs
+    ) -> Union[DataFrame, None]:
         """Compensate an FcsFile's data.
 
         Args:
             file (FcsFile): The FcsFile to compensate.
             inplace (bool): If True, modify the `FcsFile.events` with the result.
                 If False, return the compensated events.
-            kwargs (Dict):
+            **kwargs (Dict):
                 All arguments accepted by `FcsFile.get_events` are accepted here.
                 If the file's events have already been retrieved with the same
                 kwargs provided here, those stored events will be used.

cellengine/resources/experiment.py

@@ -2,6 +2,7 @@
 from datetime import datetime
 
 from marshmallow import fields
+from pandas.core.frame import DataFrame
 
 from cellengine.utils.dataclass_mixin import DataClassMixin, ReadOnly
 from dataclasses import dataclass, field
@@ -180,7 +181,7 @@ def update(self):
         res = ce.APIClient().update_experiment(self._id, self.to_dict())
         self.__dict__.update(Experiment.from_dict(res).__dict__)
 
-    def clone(self, props: Optional[Dict[str, Any]] = None):
+    def clone(self, props: Optional[Dict[str, Any]] = None) -> Experiment:
         """
         Saves a deep copy of the experiment and all of its resources, including
         attachments, FCS files, gates and populations.
@@ -331,7 +332,7 @@ def get_statistics(
         layout: str = None,
         percent_of: Union[str, List[str]] = None,
         population_ids: List[str] = None,
-    ):
+    ) -> Union[Dict, str, DataFrame]:
         """
         Request Statistics from CellEngine.
 
@@ -369,6 +370,7 @@ def get_statistics(
                 those populations.
             population_ids: List[str]: List of population IDs.
                 Defaults to ungated.
+
         Returns:
             statistics: Dict, String, or pandas.Dataframe
         """

cellengine/resources/fcs_file.py

@@ -283,12 +283,13 @@ def spill_string(self):
         return self._spill_string
 
     def get_events(
-        self, inplace: bool = False, destination=None, **kwargs
+        self, inplace: bool = False, destination=None, **kwargs: Any
     ) -> Union[DataFrame, None]:
         """
         Fetch a DataFrame containing this file's data.
 
         Args:
+            inplace: bool
             **kwargs:
                 - compensatedQ (bool): If true, applies the compensation
                     specified in compensationId to the exported events.

cellengine/resources/gate.py

@@ -64,37 +64,6 @@ def bulk_create(cls, experiment_id, gates: List) -> List[Gate]:
 
     @classmethod
     def factory(cls, gates: Dict) -> List["Gate"]:
-        """Build a Gate object from a dict of properties.
-
-        Args:
-            experiment_id (str): The ID of the experiment to which to add the gate. Use
-                when calling this as a static method; not needed when calling from an
-                Experiment object.
-            name (str): The name of the gate
-            x_channel (str): The name of the x channel to which the gate applies.
-            y_channel (str): The name of the y channel to which the gate applies.
-            gid (str): Group ID of the gate, used for tailoring. If this is not
-                specified, then a new Group ID will be created. If you wish you create
-                a tailored gate, you must specify the gid of the global tailored gate.
-            parent_population_id (str): ID of the parent population. Use ``None`` for
-                the 'ungated' population. If specified, do not specify
-                ``parent_population``.
-            parent_population (str): Name of the parent population. An attempt will
-                be made to find the population by name.  If zero or more than
-                one population exists with the name, an error will be thrown.
-                If specified, do not specify ``parent_population_id``.
-            tailored_per_file (bool): Whether or not this gate is tailored per FCS file.
-            fcs_file_id (str): ID of FCS file, if tailored per file. Use ``None`` for
-                the global gate in a tailored gate group. If specified, do not
-                specify ``fcs_file``.
-            fcs_file (str): Name of FCS file, if tailored per file. An attempt will
-                be made to find the file by name. If zero or more than one file exists
-                with the name, an error will be thrown. Looking up files by name is
-                slower than using the ID, as this requires additional requests
-                to the server. If specified, do not specify ``fcs_file_id``.
-            locked (bool): Prevents modification of the gate via the web interface.
-            create_population (bool): Automatically create corresponding population.
-        """
         if type(gates) is list:
             return [cls._build_gate(gate) for gate in gates]
         else:
@@ -152,7 +121,7 @@ def delete_gates(
         ce.APIClient().delete_gate(experiment_id, _id, gid, exclude)
 
     @staticmethod
-    def update_gate_family(experiment_id, gid: str, body: Dict):
+    def update_gate_family(experiment_id: str, gid: str, body: Dict) -> None:
         """Update a given field for a gate family.
 
         Warning: This method does not modify local versions of gates; use the

cellengine/utils/api_client/APIClient.py

@@ -6,6 +6,7 @@
 from typing import Any, Dict, List, Optional, Tuple, TypeVar, Union, overload
 
 import pandas
+from pandas.core.frame import DataFrame
 from requests_toolbelt.multipart.encoder import MultipartEncoder
 
 from cellengine.utils import converter
@@ -76,7 +77,9 @@ def __repr__(self):
         else:
             return "Client(TOKEN)"
 
-    def _authenticate(self, username, password, token):
+    def _authenticate(
+        self, username: Optional[str], password: Optional[str], token: Optional[str]
+    ):
         """Authenticate with the CellEngine API.
 
         There are two ways of authenticating:
@@ -386,14 +389,14 @@ def create_fcs_file(self, experiment_id, body):
         return FcsFile.from_dict(self._post(url, json=body))
 
     def download_fcs_file(
-        self, experiment_id: str, fcs_file_id: str, **kwargs
+        self, experiment_id: str, fcs_file_id: str, **kwargs: Any
     ) -> bytes:
         """Download events for a specific FcsFile
 
         Parameters:
             experiment_id (str): ID of the experiment
             fcs_file_id (str): ID of the FcsFile
-            kwargs:
+            **kwargs:
                 - compensatedQ (bool): If true, applies the compensation
                   specified in compensationId to the exported events. For
                   TSV format, the numerical values will be the compensated
@@ -624,7 +627,7 @@ def get_statistics(
         layout: Optional[str] = None,
         percent_of: Optional[Union[str, List[str]]] = "PARENT",
         population_ids: Optional[List[str]] = None,
-    ):
+    ) -> Union[Dict, str, DataFrame]:
         """
         Request Statistics from CellEngine.
 
@@ -663,6 +666,7 @@ def get_statistics(
                 those populations.
             population_ids: List[str]: List of population IDs.
                 Defaults to ungated.
+
         Returns:
             statistics: Dict, String, or pandas.Dataframe
         """
@@ -710,3 +714,5 @@ def determine_format(f):
                 return pandas.DataFrame.from_dict(json.loads(raw_stats))
             except Exception as e:
                 raise ValueError("Invalid data format {} for pandas".format(format), e)
+        else:
+            raise ValueError("Invalid data format selected.")