Improving readability/consistency of errors/exceptions in gempyor.

flepimop/gempyor_pkg/src/gempyor/compartments.py

@@ -31,7 +31,7 @@ def __init__(
             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):
@@ -153,15 +153,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
             except Exception as e:
                 print(f"Error {e}:")
                 print(
-                    f">>> in expand_transition_elements for `source:` at index {it.multi_index}"
+                    f">>> in expand_transition_elements for `source:` at index '{it.multi_index}'"
                 )
                 print(
-                    f">>> this transition source is: {single_transition_config['source']}"
+                    f">>> this transition source is: '{single_transition_config['source']}'"
                 )
                 print(
-                    f">>> this transition destination is: {single_transition_config['destination']}"
+                    f">>> this transition destination is: '{single_transition_config['destination']}'"
                 )
-                print(f"transition_dimension: {problem_dimension}")
+                print(f"transition_dimension: '{problem_dimension}'")
                 raise e
 
             try:
@@ -175,15 +175,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
             except Exception as e:
                 print(f"Error {e}:")
                 print(
-                    f">>> in expand_transition_elements for `destination:` at index {it.multi_index}"
+                    f">>> in expand_transition_elements for `destination:` at index '{it.multi_index}'"
                 )
                 print(
-                    f">>> this transition source is: {single_transition_config['source']}"
+                    f">>> this transition source is: '{single_transition_config['source']}'"
                 )
                 print(
-                    f">>> this transition destination is: {single_transition_config['destination']}"
+                    f">>> this transition destination is: '{single_transition_config['destination']}'"
                 )
-                print(f"transition_dimension: {problem_dimension}")
+                print(f"transition_dimension: '{problem_dimension}'")
                 raise e
 
             try:
@@ -197,15 +197,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
             except Exception as e:
                 print(f"Error {e}:")
                 print(
-                    f">>> in expand_transition_elements for `rate:` at index {it.multi_index}"
+                    f">>> in expand_transition_elements for `rate:` at index '{it.multi_index}'"
                 )
                 print(
-                    f">>> this transition source is: {single_transition_config['source']}"
+                    f">>> this transition source is: '{single_transition_config['source']}'"
                 )
                 print(
-                    f">>> this transition destination is: {single_transition_config['destination']}"
+                    f">>> this transition destination is: '{single_transition_config['destination']}'"
                 )
-                print(f"transition_dimension: {problem_dimension}")
+                print(f"transition_dimension: '{problem_dimension}'")
                 raise e
 
             try:
@@ -225,15 +225,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
             except Exception as e:
                 print(f"Error {e}:")
                 print(
-                    f">>> in expand_transition_elements for `proportional_to:` at index {it.multi_index}"
+                    f">>> in expand_transition_elements for `proportional_to:` at index '{it.multi_index}'"
                 )
                 print(
-                    f">>> this transition source is: {single_transition_config['source']}"
+                    f">>> this transition source is: '{single_transition_config['source']}'"
                 )
                 print(
-                    f">>> this transition destination is: {single_transition_config['destination']}"
+                    f">>> this transition destination is: '{single_transition_config['destination']}'"
                 )
-                print(f"transition_dimension: {problem_dimension}")
+                print(f"transition_dimension: '{problem_dimension}'")
                 raise e
 
             if (
@@ -260,15 +260,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
                 except Exception as e:
                     print(f"Error {e}:")
                     print(
-                        f">>> in expand_transition_elements for `proportion_exponent:` at index {it.multi_index}"
+                        f">>> in expand_transition_elements for `proportion_exponent:` at index '{it.multi_index}'"
                     )
                     print(
-                        f">>> this transition source is: {single_transition_config['source']}"
+                        f">>> this transition source is: '{single_transition_config['source']}'"
                     )
                     print(
-                        f">>> this transition destination is: {single_transition_config['destination']}"
+                        f">>> this transition destination is: '{single_transition_config['destination']}'"
                     )
-                    print(f"transition_dimension: {problem_dimension}")
+                    print(f"transition_dimension: '{problem_dimension}'")
                     raise e
             else:
                 new_transition_config["proportion_exponent"][it.multi_index] = [
@@ -379,7 +379,6 @@ def unformat_proportion_exponent(
     def parse_single_transition(
         self, seir_config, single_transition_config, fake_config=False
     ):
-
         ## This method relies on having run parse_compartments
         if not fake_config:
             single_transition_config = single_transition_config.get()
@@ -483,7 +482,9 @@ 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 an isolated compartment: '{comp_dict}'. "
+                f"Isolate '{self.compartments[mask]}'. "
+                f"The `get_comp_idx` function was called by '{error_info}'."
             )
         return comp_idx[0]
 
@@ -503,9 +504,8 @@ 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"
+                            f"Could not find '{colname}' defined by '{elem}' in '{self.compartments}'."
                         )
                     transition_array[cit, it] = rc
 
@@ -539,8 +539,10 @@ 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: {unique_strings}."
+                    )
                 rc = [it for it, x in enumerate(unique_strings) if x == candidate][0]
                 transition_array[2][it] = rc
 
@@ -583,8 +585,10 @@ 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: '{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
@@ -610,7 +614,8 @@ def get_transition_array(self):
                                 rc = compartment
                         if rc == -1:
                             raise ValueError(
-                                f"Could not find proportional_to {elem3} in compartments"
+                                f"Could not find `proportional_to` '{elem3}' in compartments. "
+                                f"Available compartments: '{self.compartments}'."
                             )
 
                         proportion_array[proportion_index] = rc
@@ -682,7 +687,7 @@ def parse_parameter_strings_to_numpy_arrays_v2(
                 parsed_formulas.append(f)
             except Exception as e:
                 print(
-                    f"Cannot parse formula: '{formula}' from parameters {parameter_names}"
+                    f"Cannot parse formula '{formula}' from parameters: '{parameter_names}'."
                 )
                 raise (e)  # Print the error message for debugging
 
@@ -733,10 +738,10 @@ 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 means 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: '{operators}'. "
+                f"The defined parameters are '{parameter_names}'."
             )
 
         split_strings = [x.split(operators[0]) for x in string_list]
@@ -851,16 +856,13 @@ 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."
+        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}'."
         )
-        print(f"dimension: {dimension}")
-        raise e
 
 
 def list_access_element(thing, idx, dimension=None, encapsulate_as_list=False):

flepimop/gempyor_pkg/src/gempyor/config_validator.py

@@ -70,14 +70,14 @@ def validate_initial_file_check(cls, values):
         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}"
+                f"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}"
+                f"An `initial_file_type` is required when method is '{method}'."
             )
         return values
 
@@ -86,9 +86,7 @@ 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("A plugin file path is required when method is plugin.")
         return values
 
 
@@ -121,16 +119,14 @@ def validate_seedingfile(cls, values):
         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}"
+                "A `lambda_file` is required when method is 'PoissonDistributed'."
             )
         if method == "FolderDraw" and not seeding_file_type:
             raise ValueError(
-                "Error in Seeding: A seeding_file_type is required when method is FolderDraw"
+                "A `seeding_file_type` is required when method is 'FolderDraw'."
             )
         if method == "FromFile" and not seeding_file:
-            raise ValueError(
-                "Error in Seeding: A seeding_file is required when method is FromFile"
-            )
+            raise ValueError("A `seeding_file` is required when method is 'FromFile'.")
         return values
 
     @model_validator(mode="before")
@@ -139,7 +135,8 @@ def plugin_filecheck(cls, values):
         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"
+                f"A plugin file path is required when method is 'plugin', "
+                f"was given '{plugin_file_path!r}'."
             )
         return values
 
@@ -173,16 +170,14 @@ def check_distr(cls, values):
         if distr != "fixed":
             if not mean and not sd:
                 raise ValueError(
-                    "Error in value: mean and sd must be provided for non-fixed distributions"
+                    "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"
+                    "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("Value must be provided for fixed distributions.")
         return values
 
 
@@ -211,7 +206,7 @@ def which_value(cls, values):
         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"
+                f"Parsed a parameter with both a timeseries, '{values.get('timeseries')!r}', and a value, '{values.get('value')!r}', please choose one."
             )
         return values
 
@@ -301,7 +296,7 @@ def which_source(cls, values):
         prevalence = values.get("prevalence")
         if incidence and prevalence:
             raise ValueError(
-                "Error in outcomes::source. Can only be incidence or prevalence, not both."
+                f"Parsed a source with both an incidence, '{values.get('incidence')!r}', and prevalence, '{values.get('prevalence')!r}', please choose one."
             )
         return values
 
@@ -339,13 +334,9 @@ def check_outcome_type(cls, values):
         source_present = values.get("source") is not None
 
         if sum_present and source_present:
-            raise ValueError(
-                f"Error in outcome: Both 'sum' and 'source' are present. Choose one."
-            )
+            raise ValueError("Both 'sum' and 'source' are present, please choose one.")
         elif not sum_present and not source_present:
-            raise ValueError(
-                f"Error in outcome: Neither 'sum' nor 'source' is present. Choose one."
-            )
+            raise ValueError("Neither 'sum' nor 'source' is present, please choose one.")
         return values
 
 
@@ -364,7 +355,7 @@ def check_paramfromfile_type(cls, values):
 
         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"
+                "A `param_subpop_file` is required when `param_from_file` is 'True'."
             )
         return values
 
@@ -450,11 +441,11 @@ def verify_inference(cls, values):
         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"
+                "Inference mode is enabled, but no groundtruth dates are provided. Please provide groundtruth dates."
             )
         elif start_date_groundtruth and not inference_present:
             raise ValueError(
-                "Groundtruth dates are provided but inference mode is not enabled"
+                "Groundtruth dates are provided, but inference mode is not enabled. Please enable inference mode."
             )
         return values
 
@@ -464,13 +455,17 @@ 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")
+        if not (init or seed):
+            raise ValueError(
+                f"At least one of `initial_conditions` or `seeding` must be provided."
+            )
         return values