HSSM base class

src/hssm/config.py

@@ -31,7 +31,6 @@
     "list_params",
     "bounds",
     "params_default",
-    "data",
     "choices",
     "decision_process",
     "learning_process",
@@ -217,7 +216,7 @@ def update_config(self, user_config: ModelConfig) -> None:
             User specified ModelConfig used update self.
         """
         if user_config.response is not None:
-            self.response = user_config.response
+            self.response = list(user_config.response)  # type: ignore[assignment]
         if user_config.list_params is not None:
             self.list_params = user_config.list_params
         if user_config.choices is not None:
@@ -326,8 +325,8 @@ def from_rlssm_dict(cls, model_name: str, config_dict: dict[str, Any]):
                 raise ValueError(f"{field_name} must be provided in config_dict")
 
         return cls(
-            model_name=model_name,
-            description=config_dict.get("description"),
+            model_name=config_dict["model_name"],
+            description=config_dict["description"],
             list_params=config_dict["list_params"],
             extra_fields=config_dict.get("extra_fields"),
             params_default=config_dict["params_default"],
@@ -451,7 +450,7 @@ def to_config(self) -> Config:
 class ModelConfig:
     """Representation for model_config provided by the user."""
 
-    response: list[str] | None = None
+    response: tuple[str, ...] | None = None
     list_params: list[str] | None = None
     choices: tuple[int, ...] | None = None
     default_priors: dict[str, ParamSpec] = field(default_factory=dict)

src/hssm/data_validator.py

@@ -128,51 +128,6 @@ def _post_check_data_sanity(self):
     # remaining check on missing data
     # which are coming AFTER the data validation
     # in the HSSM class, into this function?
-    def _handle_missing_data_and_deadline(self):
-        """Handle missing data and deadline."""
-        if not self.missing_data and not self.deadline:
-            # In the case where missing_data is set to False, we need to drop the
-            # cases where rt = na_value
-            if pd.isna(self.missing_data_value):
-                na_dropped = self.data.dropna(subset=["rt"])
-            else:
-                na_dropped = self.data.loc[
-                    self.data["rt"] != self.missing_data_value, :
-                ]
-
-            if len(na_dropped) != len(self.data):
-                warnings.warn(
-                    "`missing_data` is set to False, "
-                    + "but you have missing data in your dataset. "
-                    + "Missing data will be dropped.",
-                    stacklevel=2,
-                )
-            self.data = na_dropped
-
-        elif self.missing_data and not self.deadline:
-            # In the case where missing_data is set to True, we need to replace the
-            # missing data with a specified na_value
-
-            # Create a shallow copy to avoid modifying the original dataframe
-            if pd.isna(self.missing_data_value):
-                self.data["rt"] = self.data["rt"].fillna(-999.0)
-            else:
-                self.data["rt"] = self.data["rt"].replace(
-                    self.missing_data_value, -999.0
-                )
-
-        else:  # deadline = True
-            if self.deadline_name not in self.data.columns:
-                raise ValueError(
-                    "You have specified that your data has deadline, but "
-                    + f"`{self.deadline_name}` is not found in your dataset."
-                )
-            else:
-                self.data.loc[:, "rt"] = np.where(
-                    self.data["rt"] < self.data[self.deadline_name],
-                    self.data["rt"],
-                    -999.0,
-                )
 
     def _update_extra_fields(self, new_data: pd.DataFrame | None = None):
         """Update the extra fields data in self.model_distribution.
@@ -195,45 +150,6 @@ def _update_extra_fields(self, new_data: pd.DataFrame | None = None):
                 new_data[field].values for field in self.extra_fields
             ]
 
-    @staticmethod
-    def _set_missing_data_and_deadline(
-        missing_data: bool, deadline: bool, data: pd.DataFrame
-    ) -> MissingDataNetwork:
-        """Set missing data and deadline."""
-        network = MissingDataNetwork.NONE
-        if not missing_data:
-            return network
-        if missing_data and not deadline:
-            network = MissingDataNetwork.CPN
-        elif missing_data and deadline:
-            network = MissingDataNetwork.OPN
-        # AF-TODO: GONOGO case not yet correctly implemented
-        # else:
-        #     # TODO: This won't behave as expected yet, GONOGO needs to be split
-        #     # into a deadline case and a non-deadline case.
-        #     network = MissingDataNetwork.GONOGO
-
-        if np.all(data["rt"] == -999.0):
-            if network in [MissingDataNetwork.CPN, MissingDataNetwork.OPN]:
-                # AF-TODO: I think we should allow invalid-only datasets.
-                raise ValueError(
-                    "`missing_data` is set to True, but you have no valid data in your "
-                    "dataset."
-                )
-            # AF-TODO: This one needs refinement for GONOGO case
-            # elif network == MissingDataNetwork.OPN:
-            #     raise ValueError(
-            #         "`deadline` is set to True and `missing_data` is set to True, "
-            #         "but ."
-            #     )
-            # else:
-            #     raise ValueError(
-            #         "`missing_data` and `deadline` are both set to True,
-            #         "but you have "
-            #         "no missing data and/or no rts exceeding the deadline."
-            #     )
-        return network
-
     def _validate_choices(self):
         """
         Ensure that `choices` is provided (not None).