Improving readability/consistency of errors/exceptions in gempyor.

flepimop/gempyor_pkg/src/gempyor/compartments.py

@@ -25,7 +25,7 @@ def __init__(self, seir_config=None, compartments_config=None, compartments_file
             self.times_set += 1
 
         if self.times_set == 0:
-            raise ValueError("Compartments object not set, no config or file provided")
+            raise ValueError("Compartments object not set, no config or file provided.")
         return
 
     def constructFromConfig(self, seir_config, compartment_config):
@@ -375,7 +375,9 @@ def get_comp_idx(self, comp_dict: dict, error_info: str = "no information") -> i
         comp_idx = self.compartments[mask].index.values
         if len(comp_idx) != 1:
             raise ValueError(
-                f"The provided dictionary does not allow to isolate a compartment: {comp_dict} isolate {self.compartments[mask]} from options {self.compartments}. The get_comp_idx function was called by'{error_info}'."
+                f"The provided dictionary does not allow to isolate a compartment: {comp_dict} "
+                f" isolate {self.compartments[mask]} from options {self.compartments}. "
+                f"The get_comp_idx function was called by '{error_info}'."
             )
         return comp_idx[0]
 
@@ -394,8 +396,7 @@ def get_transition_array(self):
                         if self.compartments["name"][compartment] == elem:
                             rc = compartment
                     if rc == -1:
-                        print(self.compartments)
-                        raise ValueError(f"Could not find {colname} defined by {elem} in compartments")
+                        raise ValueError(f"Could not find {colname} defined by {elem} in {self.compartments}.")
                     transition_array[cit, it] = rc
 
             unique_strings = []
@@ -424,8 +425,11 @@ def get_transition_array(self):
                 candidate = reduce(lambda a, b: a + "*" + b, elem)
                 candidate = candidate.replace(" ", "")
                 # candidate = candidate.replace("*1", "")
-                if not candidate in unique_strings:
-                    raise ValueError("Something went wrong")
+                if candidate not in unique_strings:
+                    raise ValueError(
+                        f"Candidate '{candidate}' from 'rate' column is not in the list of unique strings. "
+                        f"Unique strings: {unique_strings}"
+                    )
                 rc = [it for it, x in enumerate(unique_strings) if x == candidate][0]
                 transition_array[2][it] = rc
 
@@ -464,8 +468,11 @@ def get_transition_array(self):
                     candidate = reduce(lambda a, b: a + "*" + b, y)
                     candidate = candidate.replace(" ", "")
                     # candidate = candidate.replace("*1", "")
-                    if not candidate in unique_strings:
-                        raise ValueError("Something went wrong")
+                    if candidate not in unique_strings:
+                        raise ValueError(
+                            f"Proportion exponent '{candidate}' is not found in the list of unique strings. "
+                            f"Unique strings: {unique_strings}"
+                            )
                     rc = [it for it, x in enumerate(unique_strings) if x == candidate][0]
                     proportion_info[2][proportion_compartment_index] = rc
                     proportion_compartment_index += 1
@@ -490,7 +497,10 @@ def get_transition_array(self):
                             if self.compartments["name"][compartment] == elem3:
                                 rc = compartment
                         if rc == -1:
-                            raise ValueError(f"Could not find proportional_to {elem3} in compartments")
+                            raise ValueError(
+                                f"Could not find proportional_to {elem3} in compartments. "
+                                f"Available compartments: {self.compartments}"
+                            )
 
                         proportion_array[proportion_index] = rc
                         proportion_index += 1
@@ -554,7 +564,10 @@ def parse_parameter_strings_to_numpy_arrays_v2(self, parameters, parameter_names
                 f = sp.sympify(formula, locals=symbolic_parameters_namespace)
                 parsed_formulas.append(f)
             except Exception as e:
-                print(f"Cannot parse formula: '{formula}' from parameters {parameter_names}")
+                print(
+                    f"Cannot parse formula: '{formula}' :" 
+                    f"from parameters: {parameter_names}."
+                )
                 raise (e)  # Print the error message for debugging
 
         # the list order needs to be right.
@@ -600,10 +613,10 @@ def parse_parameter_strings_to_numpy_arrays(
             not operators
         ):  # empty list means all have been tried. Usually there just remains one string in string_list at that time.
             raise ValueError(
-                f"""Could not parse string {string_list}. 
-    This usually mean that '{string_list[0]}' is a parameter name that is not defined
-    or that it contains an operator that is not in the list of supported operator: ^,*,/,+,-.
-    The defined parameters are {parameter_names}."""
+                f"Could not parse string {string_list}. " 
+                f"This usually mean that '{string_list[0]}' is a parameter name that is not defined "
+                f"or that it contains an operator that is not in the list of supported operators: ^,*,/,+,-. "
+                f"The defined parameters are {parameter_names}."
             )
 
         split_strings = [x.split(operators[0]) for x in string_list]
@@ -710,12 +723,14 @@ def list_access_element_safe(thing, idx, dimension=None, encapsulate_as_list=Fal
     try:
         return list_access_element(thing, idx, dimension, encapsulate_as_list)
     except Exception as e:
-        print(f"Error {e}:")
-        print(f">>> in list_access_element_safe for {thing} at index {idx}")
-        print(">>> This is often, but not always because the object above is a list (there are brackets around it).")
-        print(">>> and in this case it is not broadcast, so if you want to it to be broadcasted, you need remove the brackets around it.")
-        print(f"dimension: {dimension}")
-        raise e
+        raise Exception(
+            f"Error {e}: "
+            f"in list_access_element_safe for {thing} at index {idx}. "
+            f"This is often, but not always because the object above is a list (there are brackets around it). "
+            f"and in this case it is not broadcast, so if you want to it to be broadcasted, you need remove the brackets around it. "
+            f"dimension: {dimension}."
+        )
+
 
 
 def list_access_element(thing, idx, dimension=None, encapsulate_as_list=False):

flepimop/gempyor_pkg/src/gempyor/config_validator.py

@@ -42,17 +42,17 @@ def validate_initial_file_check(cls, values):
         initial_conditions_file = values.get('initial_conditions_file')
         initial_file_type = values.get('initial_file_type')        
         if method in {'FromFile', 'SetInitialConditions'} and not initial_conditions_file:
-            raise ValueError(f'Error in InitialConditions: An initial_conditions_file is required when method is {method}')
+            raise ValueError(f"Error in InitialConditions: An initial_conditions_file is required when method is {method}")
         if method in {'InitialConditionsFolderDraw','SetInitialConditionsFolderDraw'} and not initial_file_type:
-            raise ValueError(f'Error in InitialConditions: initial_file_type is required when method is {method}')
+            raise ValueError(f"Error in InitialConditions: initial_file_type is required when method is {method}")
         return values
 
     @model_validator(mode='before')
     def plugin_filecheck(cls, values):
         method = values.get('method')
         plugin_file_path = values.get('plugin_file_path')   
         if method == 'plugin' and not plugin_file_path:
-            raise ValueError('Error in InitialConditions: a plugin file path is required when method is plugin')
+            raise ValueError(f"Error in InitialConditions: a plugin file path is required when method is plugin.")
         return values
 
 
@@ -70,19 +70,31 @@ def validate_seedingfile(cls, values):
         seeding_file_type = values.get('seeding_file_type')        
         seeding_file = values.get('seeding_file')        
         if method == 'PoissonDistributed' and not lambda_file:
-            raise ValueError(f'Error in Seeding: A lambda_file is required when method is {method}')
+            raise ValueError(
+                f"Error in Seeding: A lambda_file is required when method is {method} "
+                f"Current value: {lambda_file}."
+            )
         if method == 'FolderDraw' and not seeding_file_type:
-            raise ValueError('Error in Seeding: A seeding_file_type is required when method is FolderDraw')
+            raise ValueError(
+                f"Error in Seeding: A seeding_file_type is required when method is FolderDraw"
+                f"Current value: {seeding_file_type}."
+            )
         if method == 'FromFile' and not seeding_file:
-            raise ValueError('Error in Seeding: A seeding_file is required when method is FromFile')
+            raise ValueError(
+                f"Error in Seeding: A seeding_file is required when method is FromFile "
+                f"Current value: {seeding_file}."
+            )
         return values
 
     @model_validator(mode='before')
     def plugin_filecheck(cls, values):
         method = values.get('method')
         plugin_file_path = values.get('plugin_file_path')   
         if method == 'plugin' and not plugin_file_path:
-            raise ValueError('Error in Seeding: a plugin file path is required when method is plugin')
+            raise ValueError(
+                f"Error in Seeding: a plugin file path is required when method is plugin "
+                f"Current value: {plugin_file_path!r}. Please specify the path to the plugin file."
+            )
         return values
 
 class IntegrationConfig(BaseModel):
@@ -107,11 +119,11 @@ def check_distr(cls, values):
         b = values.get('b')
         if distr != 'fixed':
             if not mean and not sd:
-                raise ValueError('Error in value: mean and sd must be provided for non-fixed distributions')
+                raise ValueError(f"Mean and sd must be provided for non-fixed distributions.")
             if distr == 'truncnorm' and not a and not b:
-                raise ValueError('Error in value: a and b must be provided for truncated normal distributions')
+                raise ValueError(f"a and b must be provided for truncated normal distributions.")
         if distr == 'fixed' and not value:
-            raise ValueError('Error in value: value must be provided for fixed distributions')
+            raise ValueError(f"Value must be provided for fixed distributions")
         return values
 
 class BaseParameterConfig(BaseModel):
@@ -130,7 +142,10 @@ def which_value(cls, values):
         value = values.get('value') is not None
         timeseries = values.get('timeseries') is not None
         if value and timeseries:
-            raise ValueError('Error in seir::parameters: your parameter is both a timeseries and a value, please choose one')
+            raise ValueError(
+                f"Configuration error in seir::parameters: your parameter is both a timeseries and a value, please choose one. "
+                f"Current values - value: {values.get('value')!r}, timeseries: {values.get('timeseries')!r}."
+            )
         return values
 
 
@@ -203,7 +218,11 @@ def which_source(cls, values):
         incidence = values.get('incidence')
         prevalence = values.get('prevalence')
         if incidence and prevalence:
-            raise ValueError('Error in outcomes::source. Can only be incidence or prevalence, not both.')
+            raise ValueError(
+                f"Configuration error in outcomes::source." 
+                f"Value can only be incidence or prevalence, not both."
+                f"Current values - incidence: {values.get('incidence')!r}, prevalence: {values.get('prevalence')!r}."
+                )
         return values
 
     # @model_validator(mode='before') # DOES NOT WORK
@@ -256,7 +275,7 @@ def check_paramfromfile_type(cls, values):
         param_subpop_file = values.get('param_subpop_file') is not None
 
         if param_from_file and not param_subpop_file:
-            raise ValueError(f"Error in outcome: 'param_subpop_file' is required when 'param_from_file' is True")
+            raise ValueError(f"Error in outcome: 'param_subpop_file' is required when 'param_from_file' is True.")
         return values
 
 class ResampleConfig(BaseModel):
@@ -320,9 +339,15 @@ def verify_inference(cls, values):
         inference_present = values.get('inference') is not None
         start_date_groundtruth = values.get('start_date_groundtruth') is not None
         if inference_present and not start_date_groundtruth:
-            raise ValueError('Inference mode is enabled but no groundtruth dates are provided')
+            raise ValueError(
+                f"Inference mode is enabled, but no groundtruth dates are provided."
+                f"Please provide groundtruth dates."
+            )
         elif start_date_groundtruth and not inference_present:
-            raise ValueError('Groundtruth dates are provided but inference mode is not enabled')
+            raise ValueError(
+                f"Groundtruth dates are provided, but inference mode is not enabled."
+                f"Please enable inference mode."
+            )
         return values
 
     @model_validator(mode='before')
@@ -331,13 +356,17 @@ def check_dates(cls, values):
         end_date = values.get('end_date')
         if start_date and end_date:
             if end_date <= start_date:
-                raise ValueError('end_date must be greater than start_date')
+                raise ValueError(
+                    f"`end_date` ({end_date}) must be later than `start_date` ({start_date}))."
+                )
         return values
 
     @model_validator(mode='before')
     def init_or_seed(cls, values):
         init = values.get('initial_conditions')
         seed = values.get('seeding')
         if not init or seed:
-            raise ValueError('either initial_conditions or seeding must be provided')
+            raise ValueError(
+                f"At least one of `initial_conditions` or `seeding` must be provided."
+                )
         return values

flepimop/gempyor_pkg/src/gempyor/inference.py

@@ -268,9 +268,9 @@ def autodetect_scenarios(config):
 
     if len(seir_modifiers_scenarios) != 1 or len(outcome_modifiers_scenarios) != 1:
         raise ValueError(
-            f"Inference only support configurations files with one scenario, got"
-            f"seir: {seir_modifiers_scenarios}"
-            f"outcomes: {outcome_modifiers_scenarios}"
+            f"Inference only supports configuration files with one scenario, recieved:\n"
+            f"SEIR modifiers: {seir_modifiers_scenarios}."
+            f"Outcomes modifiers: {outcome_modifiers_scenarios}."
         )
 
     return seir_modifiers_scenarios[0], outcome_modifiers_scenarios[0]