From 452902f7a5e6c663d39cad7aa08701a826cd8a30 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Thu, 15 Aug 2024 12:46:13 -0400
Subject: [PATCH 01/48] Update parameters.py

---
 flepimop/gempyor_pkg/src/gempyor/parameters.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/flepimop/gempyor_pkg/src/gempyor/parameters.py b/flepimop/gempyor_pkg/src/gempyor/parameters.py
index b01fb52ab..492404274 100644
--- a/flepimop/gempyor_pkg/src/gempyor/parameters.py
+++ b/flepimop/gempyor_pkg/src/gempyor/parameters.py
@@ -23,6 +23,7 @@
 
 ## TODO: ideally here path_prefix should not be used and all files loaded from modinf
 
+# Test comment to check for proper branch creation
 
 class Parameters:
     # Minimal object to be easily picklable for // runs

From 9a7f4a3b466da346623349887156f223f94b4bf6 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Thu, 15 Aug 2024 14:21:22 -0400
Subject: [PATCH 02/48] Update parameters.py

---
 flepimop/gempyor_pkg/src/gempyor/parameters.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/parameters.py b/flepimop/gempyor_pkg/src/gempyor/parameters.py
index 492404274..b01fb52ab 100644
--- a/flepimop/gempyor_pkg/src/gempyor/parameters.py
+++ b/flepimop/gempyor_pkg/src/gempyor/parameters.py
@@ -23,7 +23,6 @@
 
 ## TODO: ideally here path_prefix should not be used and all files loaded from modinf
 
-# Test comment to check for proper branch creation
 
 class Parameters:
     # Minimal object to be easily picklable for // runs

From d063762f99fc6cbb64e9053f6c22fbd1d3ab68e2 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 16 Sep 2024 15:58:22 -0400
Subject: [PATCH 03/48] Improved readability/consistency of errors/exceptions
 in 5 gempyor files.

Adjusted formatting, punctuation, clarity, syntax, etc. in the errors/exceptions in `gempyor`'s initial_conditions.py, parameters.py, compartments.py, config_validator.py, inference.py. This will likely be one of three pulls to address GH-281.
---
 .../gempyor_pkg/src/gempyor/compartments.py   | 54 +++++++++++------
 .../src/gempyor/config_validator.py           | 59 ++++++++++++++-----
 flepimop/gempyor_pkg/src/gempyor/inference.py |  6 +-
 .../src/gempyor/initial_conditions.py         | 35 +++++++----
 .../gempyor_pkg/src/gempyor/parameters.py     | 25 ++++----
 5 files changed, 117 insertions(+), 62 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/compartments.py b/flepimop/gempyor_pkg/src/gempyor/compartments.py
index ec87cf7e5..027ea671c 100644
--- a/flepimop/gempyor_pkg/src/gempyor/compartments.py
+++ b/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]
 
@@ -395,7 +397,7 @@ def get_transition_array(self):
                             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 compartments.")
                     transition_array[cit, it] = rc
 
             unique_strings = []
@@ -424,8 +426,11 @@ 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 +469,11 @@ 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 +498,10 @@ 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 +565,10 @@ 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 +614,10 @@ 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 operator: ^,*,/,+,-. "
+                f"The defined parameters are {parameter_names}."
             )
 
         split_strings = [x.split(operators[0]) for x in string_list]
@@ -710,12 +724,14 @@ 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):
diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index 95f6e3029..3b8b9a36d 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -52,7 +52,7 @@ 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(f'Error in InitialConditions: a plugin file path is required when method is plugin.')
         return values
 
 
@@ -70,11 +70,20 @@ 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')
@@ -82,7 +91,10 @@ 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('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('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
 
 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')
@@ -331,7 +356,9 @@ 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 greater than `start_date` ({start_date})).'
+                )
         return values
     
     @model_validator(mode='before')
@@ -339,5 +366,7 @@ 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
diff --git a/flepimop/gempyor_pkg/src/gempyor/inference.py b/flepimop/gempyor_pkg/src/gempyor/inference.py
index 81b1c22d0..d1f3397d7 100644
--- a/flepimop/gempyor_pkg/src/gempyor/inference.py
+++ b/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]
diff --git a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
index 554f3910c..1b50c0988 100644
--- a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
+++ b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
@@ -99,7 +99,7 @@ def get_from_config(self, sim_id: int, modinf) -> np.ndarray:
                 allow_missing_subpops=self.allow_missing_subpops,
             )
         else:
-            raise NotImplementedError(f"unknown initial conditions method [got: {method}]")
+            raise NotImplementedError(f"Unknown initial conditions method [recieved: {method}].")
 
         # check that the inputed values sums to the subpop population:
         check_population(y0=y0, modinf=modinf, ignore_population_checks=self.ignore_population_checks)
@@ -122,16 +122,20 @@ def check_population(y0, modinf, ignore_population_checks=False):
         if abs(n_y0 - n_pop) > 1:
             error = True
             print(
-                f"ERROR: subpop_names {pl} (idx: pl_idx) has a population from initial condition of {n_y0} while population from geodata is {n_pop} (absolute difference should be < 1, here is {abs(n_y0-n_pop)})"
+                f"ERROR: subpop_names {pl} (idx: pl_idx) has a population from initial condition of {n_y0} "
+                f"while population from geodata is {n_pop}." 
+                f"(absolute difference should be < 1, here is {abs(n_y0-n_pop)})."
             )
 
     if error and not ignore_population_checks:
         raise ValueError(
-            """ geodata and initial condition do not agree on population size (see messages above). Use ignore_population_checks: True to ignore"""
+            f"Geodata and initial condition do not agree on population size (see messages above). "
+            f"Use `ignore_population_checks: True` to ignore."
         )
     elif error and ignore_population_checks:
         print(
-            """ Ignoring the previous population mismatch errors because you added flag 'ignore_population_checks'. This is dangerous"""
+            f"WARNING: population mismatch errors ignored because `ignore_population_checks` is set to `True`."
+            f"Execution will continue, but this is not recommended."
         )
 
 
@@ -162,8 +166,9 @@ def read_initial_condition_from_tidydataframe(
                         ic_df_compartment_val = 0.0
                     else:
                         raise ValueError(
-                            f"Initial Conditions: Could not set compartment {comp_name} (id: {comp_idx}) in subpop {pl} (id: {pl_idx}). The data from the init file is {states_pl}. \n \
-                                        Use 'allow_missing_compartments' to default to 0 for compartments without initial conditions"
+                            f"ERROR: Multiple rows ({len(ic_df_compartment_val)}) match for compartment '{comp_name}' in the initial conditions file. "
+                            f"Filters used: {filters.to_dict()}. Matches: {ic_df_compartment_val.tolist()}. "
+                            f"Ensure that each compartment has a unique initial condition entry."
                         )
                 if "rest" in str(ic_df_compartment_val).strip().lower():
                     rests.append([comp_idx, pl_idx])
@@ -177,7 +182,7 @@ def read_initial_condition_from_tidydataframe(
             logger.critical(
                 f"No initial conditions for for subpop {pl}, assuming everyone (n={modinf.subpop_pop[pl_idx]}) in the first metacompartment ({modinf.compartments.compartments['name'].iloc[0]})"
             )
-            raise ValueError("THERE IS A BUG; REPORT THIS MESSAGE. Past implemenation was buggy")
+            raise ValueError("THERE IS A BUG; REPORT THIS MESSAGE. Past implemenation was buggy.")
             # TODO: this is probably ok but highlighting for consistency
             if "proportional" in self.initial_conditions_config.keys():
                 if self.initial_conditions_config["proportional"].get():
@@ -188,7 +193,8 @@ def read_initial_condition_from_tidydataframe(
                 y0[0, pl_idx] = modinf.subpop_pop[pl_idx]
         else:
             raise ValueError(
-                f"subpop {pl} does not exist in initial_conditions::states_file. You can set allow_missing_subpops=TRUE to bypass this error"
+                f"Subpop {pl} does not exist in `initial_conditions::states_file`. "
+                f"You can set `allow_missing_subpops=TRUE` to bypass this error."
             )
     if rests:  # not empty
         for comp_idx, pl_idx in rests:
@@ -229,7 +235,7 @@ def read_initial_condition_from_seir_output(ic_df, modinf, allow_missing_subpops
 
     ic_df = ic_df[(ic_df["date"] == str(modinf.ti)) & (ic_df["mc_value_type"] == "prevalence")]
     if ic_df.empty:
-        raise ValueError(f"There is no entry for initial time ti in the provided initial_conditions::states_file.")
+        raise ValueError(f"No entry provided for initial time `ti` in the `initial_conditions::states_file.`")
     y0 = np.zeros((modinf.compartments.compartments.shape[0], modinf.nsubpops))
 
     for comp_idx, comp_name in modinf.compartments.compartments["name"].items():
@@ -244,18 +250,20 @@ def read_initial_condition_from_seir_output(ic_df, modinf, allow_missing_subpops
         if len(ic_df_compartment) > 1:
             # ic_df_compartment = ic_df_compartment.iloc[0]
             raise ValueError(
-                f"ERROR: Several ({len(ic_df_compartment)}) rows are matches for compartment {mc_name} in init file: filter {filters} returned {ic_df_compartment}"
+                f"ERROR: Several ({len(ic_df_compartment)}) rows are matches for compartment {mc_name} in init file: filter {filters}. "
+                f"returned: {ic_df_compartment}."
             )
         elif ic_df_compartment.empty:
             if allow_missing_compartments:
                 ic_df_compartment = pd.DataFrame(0, columns=ic_df_compartment.columns, index=[0])
             else:
                 raise ValueError(
-                    f"Initial Conditions: Could not set compartment {comp_name} (id: {comp_idx}) in subpop {pl} (id: {pl_idx}). The data from the init file is {ic_df_compartment[pl]}."
+                    f"Initial Conditions: could not set compartment {comp_name} (id: {comp_idx}) in subpop {pl} (id: {pl_idx}). "
+                    f"The data from the init file is {ic_df_compartment[pl]}."
                 )
         elif ic_df_compartment["mc_name"].iloc[0] != comp_name:
             print(
-                f"WARNING: init file mc_name {ic_df_compartment['mc_name'].iloc[0]} does not match compartment mc_name {comp_name}"
+                f"WARNING: init file `mc_name` {ic_df_compartment['mc_name'].iloc[0]} does not match compartment `mc_name` {comp_name}."
             )
 
         for pl_idx, pl in enumerate(modinf.subpop_struct.subpop_names):
@@ -273,6 +281,7 @@ def read_initial_condition_from_seir_output(ic_df, modinf, allow_missing_subpops
                 y0[0, pl_idx] = modinf.subpop_pop[pl_idx]
             else:
                 raise ValueError(
-                    f"subpop {pl} does not exist in initial_conditions::states_file. You can set allow_missing_subpops=TRUE to bypass this error"
+                    f"Subpop {pl} does not exist in `initial_conditions::states_file`. "
+                    f"You can set `allow_missing_subpops=TRUE` to bypass this error."
                 )
     return y0
diff --git a/flepimop/gempyor_pkg/src/gempyor/parameters.py b/flepimop/gempyor_pkg/src/gempyor/parameters.py
index b01fb52ab..2243039b4 100644
--- a/flepimop/gempyor_pkg/src/gempyor/parameters.py
+++ b/flepimop/gempyor_pkg/src/gempyor/parameters.py
@@ -74,8 +74,9 @@ def __init__(
                     print("loaded col :", sorted(list(df.columns)))
                     print("geodata col:", sorted(subpop_names))
                     raise ValueError(
-                        f"""ERROR loading file {fn_name} for parameter {pn}: the number of non 'date'
-                    columns are {len(df.columns)}, expected {len(subpop_names)} (the number of subpops) or one."""
+                        f"Error loading file {fn_name} for parameter {pn}: "
+                        f"the number of non-'date' columns is {len(df.columns)}, "
+                        f"expected {len(subpop_names)} (number of subpopulations) or one."
                     )
 
                 df = df[str(ti) : str(tf)]
@@ -83,21 +84,21 @@ def __init__(
                     print("config dates:", pd.date_range(ti, tf))
                     print("loaded dates:", df.index)
                     raise ValueError(
-                        f"""ERROR loading file {fn_name} for parameter {pn}: 
-                    the 'date' entries of the provided file do not include all the days specified to be modeled by 
-                    the config. the provided file includes {len(df.index)} days between {str(df.index[0])} to {str(df.index[-1])}, 
-                    while there are {len(pd.date_range(ti, tf))} days in the config time span of {ti}->{tf}. The file must contain entries for the
-                    the exact start and end dates from the config. """
+                        f"ERROR loading file {fn_name} for parameter {pn}: " 
+                        f"the 'date' entries of the provided file do not include all the days specified to be modeled by " 
+                        f"the config. the provided file includes {len(df.index)} days between {str(df.index[0])} to {str(df.index[-1])}, " 
+                        f"while there are {len(pd.date_range(ti, tf))} days in the config time span of {ti}->{tf}. The file must contain entries for the "
+                        f"the exact start and end dates from the config."
                     )
                 if not (pd.date_range(ti, tf) == df.index).all():
                     print("config dates:", pd.date_range(ti, tf))
                     print("loaded dates:", df.index)
                     raise ValueError(
-                        f"""ERROR loading file {fn_name} for parameter {pn}: 
-                    the 'date' entries of the provided file do not include all the days specified to be modeled by 
-                    the config. the provided file includes {len(df.index)} days between {str(df.index[0])} to {str(df.index[-1])}, 
-                    while there are {len(pd.date_range(ti, tf))} days in the config time span of {ti}->{tf}. The file must contain entries for the
-                    the exact start and end dates from the config. """
+                        f"ERROR loading file {fn_name} for parameter {pn}: "
+                        f"the 'date' entries of the provided file do not include all the days specified to be modeled by "
+                        f" the config. the provided file includes {len(df.index)} days between {str(df.index[0])} to {str(df.index[-1])}, "
+                        f"while there are {len(pd.date_range(ti, tf))} days in the config time span of {ti}->{tf}. The file must contain entries for the "
+                        f"the exact start and end dates from the config."
                     )
 
                 self.pdata[pn]["ts"] = df

From add67d1e4378c540004052a1049067aaf8857458 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 20 Sep 2024 16:26:09 -0400
Subject: [PATCH 04/48] Attempting to fix errors by changing the regexs in some
 of the test files.

---
 .../tests/parameters/test_parameters_class.py          | 10 +++++-----
 flepimop/gempyor_pkg/tests/seir/test_ic.py             |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index 4bfb86fd2..af8d186ef 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -237,9 +237,9 @@ def test_timeseries_parameter_has_insufficient_columns_value_error(
         with pytest.raises(
             ValueError,
             match=(
-                rf"^ERROR loading file {tmp_file} for parameter sigma\: the number of "
-                rf"non 'date'\s+columns are {actual_columns}, expected "
-                rf"{mock_inputs.number_of_subpops()} \(the number of subpops\) or "
+                rf"^Error loading file {tmp_file} for parameter sigma\: the number of "
+                rf"non- 'date'\s+columns is {actual_columns}, expected "
+                rf"{mock_inputs.number_of_subpops()} \(number of subpops\) or "
                 rf"one\.$"
             ),
         ):
@@ -288,10 +288,10 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
                 rf"to be modeled by\s+the config\. the provided file includes "
                 rf"{(timeseries_end_date - timeseries_start_date).days + 1} days "
                 rf"between {timeseries_start_date}( 00\:00\:00)? to "
-                rf"{timeseries_end_date}( 00\:00\:00)?,\s+while there are "
+                rf"{timeseries_end_date}( 00\:00\:00)?, while there are "
                 rf"{mock_inputs.number_of_days()} days in the config time span of "
                 rf"{mock_inputs.ti}->{mock_inputs.tf}\. The file must contain entries "
-                rf"for the\s+the exact start and end dates from the config\. $"
+                rf"for the the exact start and end dates from the config\. $"
             ),
         ):
             mock_inputs.create_parameters_instance()
diff --git a/flepimop/gempyor_pkg/tests/seir/test_ic.py b/flepimop/gempyor_pkg/tests/seir/test_ic.py
index b4cd240ee..e2d78eb35 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_ic.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_ic.py
@@ -44,7 +44,7 @@ def test_IC_allow_missing_node_compartments_success(self):
         sic.get_from_config(sim_id=100, modinf=s)
 
     def test_IC_IC_notImplemented_fail(self):
-        with pytest.raises(NotImplementedError, match=r".*unknown.*initial.*conditions.*"):
+        with pytest.raises(NotImplementedError, match=r"^Unknown initial conditions method \[received: .*\]\.$"):
             config.clear()
             config.read(user=False)
             config.set_file(f"{DATA_DIR}/config.yml")

From 3b4e4909890fa79b0e5ae030421e6fc7f8b22a19 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 27 Sep 2024 15:28:34 -0400
Subject: [PATCH 05/48] Another attempt to fix RegExs in test files

---
 .../tests/parameters/test_parameters_class.py | 23 ++++++++-----------
 flepimop/gempyor_pkg/tests/seir/test_ic.py    |  2 +-
 2 files changed, 11 insertions(+), 14 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index af8d186ef..e66aca4c2 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -237,10 +237,9 @@ def test_timeseries_parameter_has_insufficient_columns_value_error(
         with pytest.raises(
             ValueError,
             match=(
-                rf"^Error loading file {tmp_file} for parameter sigma\: the number of "
-                rf"non- 'date'\s+columns is {actual_columns}, expected "
-                rf"{mock_inputs.number_of_subpops()} \(number of subpops\) or "
-                rf"one\.$"
+                rf"^Error loading file {tmp_file} for parameter sigma: " 
+                rf"the number of non-'date' columns is {actual_columns}, expected {mock_inputs.number_of_subpops()} " 
+                rf"\(number of subpopulations\) or one\.$"
             ),
         ):
             mock_inputs.create_parameters_instance()
@@ -283,15 +282,13 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
         with pytest.raises(
             ValueError,
             match=(
-                rf"^ERROR loading file {tmp_file} for parameter sigma\:\s+the \'date\' "
-                rf"entries of the provided file do not include all the days specified "
-                rf"to be modeled by\s+the config\. the provided file includes "
-                rf"{(timeseries_end_date - timeseries_start_date).days + 1} days "
-                rf"between {timeseries_start_date}( 00\:00\:00)? to "
-                rf"{timeseries_end_date}( 00\:00\:00)?, while there are "
-                rf"{mock_inputs.number_of_days()} days in the config time span of "
-                rf"{mock_inputs.ti}->{mock_inputs.tf}\. The file must contain entries "
-                rf"for the the exact start and end dates from the config\. $"
+                rf"^ERROR loading file {tmp_file} for parameter sigma: " 
+                rf"the 'date' entries of the provided file do not include " 
+                rf"all the days specified to be modeled by the config\. the provided file includes " 
+                rf"{(timeseries_end_date - timeseries_start_date).days + 1} days between " 
+                rf"{timeseries_start_date} to {timeseries_end_date}, while there are " 
+                rf"{mock_inputs.number_of_days()} days in the config time span of {mock_inputs.ti}->{mock_inputs.tf}\. " 
+                rf"The file must contain entries for the exact start and end dates from the config\.$"
             ),
         ):
             mock_inputs.create_parameters_instance()
diff --git a/flepimop/gempyor_pkg/tests/seir/test_ic.py b/flepimop/gempyor_pkg/tests/seir/test_ic.py
index e2d78eb35..a24f141ea 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_ic.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_ic.py
@@ -44,7 +44,7 @@ def test_IC_allow_missing_node_compartments_success(self):
         sic.get_from_config(sim_id=100, modinf=s)
 
     def test_IC_IC_notImplemented_fail(self):
-        with pytest.raises(NotImplementedError, match=r"^Unknown initial conditions method \[received: .*\]\.$"):
+        with pytest.raises(NotImplementedError, match=r"^Unknown initial conditions method \[received: .*?\]\.$"):
             config.clear()
             config.read(user=False)
             config.set_file(f"{DATA_DIR}/config.yml")

From e3df5d8e11332e043bab71d5a22e169e7b9938f6 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 2 Oct 2024 16:18:21 -0400
Subject: [PATCH 06/48] Update initial_conditions.py

---
 flepimop/gempyor_pkg/src/gempyor/initial_conditions.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
index 1b50c0988..c17fd78be 100644
--- a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
+++ b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
@@ -99,7 +99,7 @@ def get_from_config(self, sim_id: int, modinf) -> np.ndarray:
                 allow_missing_subpops=self.allow_missing_subpops,
             )
         else:
-            raise NotImplementedError(f"Unknown initial conditions method [recieved: {method}].")
+            raise NotImplementedError(f"Unknown initial conditions method [received: {method}].")
 
         # check that the inputed values sums to the subpop population:
         check_population(y0=y0, modinf=modinf, ignore_population_checks=self.ignore_population_checks)

From 2066ee43776706fcb4ca2055415eb74a324cf810 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 2 Oct 2024 16:45:19 -0400
Subject: [PATCH 07/48] Update parameters.py

---
 flepimop/gempyor_pkg/src/gempyor/parameters.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/parameters.py b/flepimop/gempyor_pkg/src/gempyor/parameters.py
index 02f4bbba6..c9d1886ec 100644
--- a/flepimop/gempyor_pkg/src/gempyor/parameters.py
+++ b/flepimop/gempyor_pkg/src/gempyor/parameters.py
@@ -136,7 +136,7 @@ def __init__(
                         f"ERROR loading file {fn_name} for parameter {pn}: " 
                         f"the 'date' entries of the provided file do not include all the days specified to be modeled by " 
                         f"the config. the provided file includes {len(df.index)} days between {str(df.index[0])} to {str(df.index[-1])}, " 
-                        f"while there are {len(pd.date_range(ti, tf))} days in the config time span of {ti}->{tf}. The file must contain entries for the "
+                        f"while there are {len(pd.date_range(ti, tf))} days in the config time span of {ti}->{tf}. The file must contain entries for "
                         f"the exact start and end dates from the config."
                     )
                 if not (pd.date_range(ti, tf) == df.index).all():
@@ -145,8 +145,8 @@ def __init__(
                     raise ValueError(
                         f"ERROR loading file {fn_name} for parameter {pn}: "
                         f"the 'date' entries of the provided file do not include all the days specified to be modeled by "
-                        f" the config. the provided file includes {len(df.index)} days between {str(df.index[0])} to {str(df.index[-1])}, "
-                        f"while there are {len(pd.date_range(ti, tf))} days in the config time span of {ti}->{tf}. The file must contain entries for the "
+                        f"the config. the provided file includes {len(df.index)} days between {str(df.index[0])} to {str(df.index[-1])}, "
+                        f"while there are {len(pd.date_range(ti, tf))} days in the config time span of {ti}->{tf}. The file must contain entries for "
                         f"the exact start and end dates from the config."
                     )
 

From 2b3feedd668dc952d9eab11be6e6e3335798b54b Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 4 Oct 2024 14:03:07 -0400
Subject: [PATCH 08/48] Update
 flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index e66aca4c2..f5b5fe150 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -286,7 +286,7 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
                 rf"the 'date' entries of the provided file do not include " 
                 rf"all the days specified to be modeled by the config\. the provided file includes " 
                 rf"{(timeseries_end_date - timeseries_start_date).days + 1} days between " 
-                rf"{timeseries_start_date} to {timeseries_end_date}, while there are " 
+                rf"{timeseries_start_date}( 00:00:00)? to {timeseries_end_date}( 00:00:00)?, while there are " 
                 rf"{mock_inputs.number_of_days()} days in the config time span of {mock_inputs.ti}->{mock_inputs.tf}\. " 
                 rf"The file must contain entries for the exact start and end dates from the config\.$"
             ),

From 72aaa843bbd907b570d1b0ca8694fb6f762d25c4 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 4 Oct 2024 15:03:10 -0400
Subject: [PATCH 09/48] Small adjustments to compartments.py

---
 flepimop/gempyor_pkg/src/gempyor/compartments.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/compartments.py b/flepimop/gempyor_pkg/src/gempyor/compartments.py
index 027ea671c..d9be0f8ef 100644
--- a/flepimop/gempyor_pkg/src/gempyor/compartments.py
+++ b/flepimop/gempyor_pkg/src/gempyor/compartments.py
@@ -396,8 +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 = []
@@ -616,7 +615,7 @@ def parse_parameter_strings_to_numpy_arrays(
             raise ValueError(
                 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 operator: ^,*,/,+,-. "
+                f"or that it contains an operator that is not in the list of supported operators: ^,*,/,+,-. "
                 f"The defined parameters are {parameter_names}."
             )
 

From 4639721d846e4bce477f3326f4a9872823d9c09c Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 4 Oct 2024 15:44:58 -0400
Subject: [PATCH 10/48] Some more small syntactical adjustments.

---
 .../src/gempyor/config_validator.py           | 50 +++++++++----------
 .../src/gempyor/initial_conditions.py         |  5 +-
 2 files changed, 28 insertions(+), 27 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index 3b8b9a36d..acacd8b35 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -42,9 +42,9 @@ 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')
@@ -52,7 +52,7 @@ 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(f'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
 
 
@@ -71,18 +71,18 @@ 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} '
-                f'Current value: {lambda_file}.'
+                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(
-                f'Error in Seeding: A seeding_file_type is required when method is FolderDraw'
-                f'Current value: {seeding_file_type}.'
+                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(
-                f'Error in Seeding: A seeding_file is required when method is FromFile '
-                f'Current value: {seeding_file}.'
+                f"Error in Seeding: A seeding_file is required when method is FromFile "
+                f"Current value: {seeding_file}."
             )
         return values
     
@@ -92,8 +92,8 @@ def plugin_filecheck(cls, values):
         plugin_file_path = values.get('plugin_file_path')   
         if method == 'plugin' and not plugin_file_path:
             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.'
+                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
     
@@ -119,11 +119,11 @@ def check_distr(cls, values):
         b = values.get('b')
         if distr != 'fixed':
             if not mean and not sd:
-                raise ValueError('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('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('Value must be provided for fixed distributions')
+            raise ValueError(f"Value must be provided for fixed distributions")
         return values
 
 class BaseParameterConfig(BaseModel):
@@ -143,8 +143,8 @@ def which_value(cls, values):
         timeseries = values.get('timeseries') is not None
         if value and timeseries:
             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}.'
+                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
     
@@ -219,9 +219,9 @@ def which_source(cls, values):
         prevalence = values.get('prevalence')
         if incidence and prevalence:
             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}.'
+                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
 
@@ -340,13 +340,13 @@ 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(
-                f'Inference mode is enabled, but no groundtruth dates are provided.'
-                f'Please provide groundtruth dates.'
+                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(
-                f'Groundtruth dates are provided, but inference mode is not enabled.'
-                f'Please enable inference mode.'
+                f"Groundtruth dates are provided, but inference mode is not enabled."
+                f"Please enable inference mode."
             )
         return values
     
@@ -357,7 +357,7 @@ def check_dates(cls, values):
         if start_date and end_date:
             if end_date <= start_date:
                 raise ValueError(
-                    f'`end_date` ({end_date}) must be greater than `start_date` ({start_date})).'
+                    f"`end_date` ({end_date}) must be later than `start_date` ({start_date}))."
                 )
         return values
     
@@ -367,6 +367,6 @@ def init_or_seed(cls, values):
         seed = values.get('seeding')
         if not init or seed:
             raise ValueError(
-                f'At least one of `initial_conditions` or `seeding` must be provided.'
+                f"At least one of `initial_conditions` or `seeding` must be provided."
                 )
         return values
diff --git a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
index c17fd78be..396308ee4 100644
--- a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
+++ b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
@@ -182,7 +182,7 @@ def read_initial_condition_from_tidydataframe(
             logger.critical(
                 f"No initial conditions for for subpop {pl}, assuming everyone (n={modinf.subpop_pop[pl_idx]}) in the first metacompartment ({modinf.compartments.compartments['name'].iloc[0]})"
             )
-            raise ValueError("THERE IS A BUG; REPORT THIS MESSAGE. Past implemenation was buggy.")
+            raise ValueError(f"THERE IS A BUG; REPORT THIS MESSAGE. Past implemenation was buggy.")
             # TODO: this is probably ok but highlighting for consistency
             if "proportional" in self.initial_conditions_config.keys():
                 if self.initial_conditions_config["proportional"].get():
@@ -235,7 +235,8 @@ def read_initial_condition_from_seir_output(ic_df, modinf, allow_missing_subpops
 
     ic_df = ic_df[(ic_df["date"] == str(modinf.ti)) & (ic_df["mc_value_type"] == "prevalence")]
     if ic_df.empty:
-        raise ValueError(f"No entry provided for initial time `ti` in the `initial_conditions::states_file.`")
+        raise ValueError(f"No entry provided for initial time `ti` in the `initial_conditions::states_file.` "
+                         f"`ti`: {modinf.ti}.")
     y0 = np.zeros((modinf.compartments.compartments.shape[0], modinf.nsubpops))
 
     for comp_idx, comp_name in modinf.compartments.compartments["name"].items():

From 064ec7ef1226a982acd2c1a759d212d4313f4b2c Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Mon, 14 Oct 2024 12:24:09 -0400
Subject: [PATCH 11/48] Update flepimop/gempyor_pkg/src/gempyor/compartments.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/compartments.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/compartments.py b/flepimop/gempyor_pkg/src/gempyor/compartments.py
index d9be0f8ef..43f5aa5e3 100644
--- a/flepimop/gempyor_pkg/src/gempyor/compartments.py
+++ b/flepimop/gempyor_pkg/src/gempyor/compartments.py
@@ -427,8 +427,7 @@ def get_transition_array(self):
                 # candidate = candidate.replace("*1", "")
                 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}"
+                        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

From f614127688a634e5639a11774a0e48799e17f69c Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 16 Oct 2024 09:56:35 -0400
Subject: [PATCH 12/48] Continuing to evolve error/exception messags

Making '' and `` conventions consistent, removing unnecessary f-strings, added some warnings.warn() statements instead of print() statements.
---
 .../gempyor_pkg/src/gempyor/compartments.py   | 62 +++++++++----------
 .../src/gempyor/config_validator.py           | 47 +++++++-------
 flepimop/gempyor_pkg/src/gempyor/inference.py |  8 +--
 .../src/gempyor/initial_conditions.py         | 52 ++++++++--------
 .../gempyor_pkg/src/gempyor/parameters.py     | 18 +++---
 5 files changed, 91 insertions(+), 96 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/compartments.py b/flepimop/gempyor_pkg/src/gempyor/compartments.py
index d9be0f8ef..ac15e2de4 100644
--- a/flepimop/gempyor_pkg/src/gempyor/compartments.py
+++ b/flepimop/gempyor_pkg/src/gempyor/compartments.py
@@ -127,10 +127,10 @@ 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}")
-                print(f">>> this transition source is: {single_transition_config['source']}")
-                print(f">>> this transition destination is: {single_transition_config['destination']}")
-                print(f"transition_dimension: {problem_dimension}")
+                print(f">>> in expand_transition_elements for `source:` at index '{it.multi_index}'")
+                print(f">>> this transition source is: '{single_transition_config['source']}'")
+                print(f">>> this transition destination is: '{single_transition_config['destination']}'")
+                print(f"transition_dimension: '{problem_dimension}'")
                 raise e
 
             try:
@@ -139,10 +139,10 @@ 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}")
-                print(f">>> this transition source is: {single_transition_config['source']}")
-                print(f">>> this transition destination is: {single_transition_config['destination']}")
-                print(f"transition_dimension: {problem_dimension}")
+                print(f">>> in expand_transition_elements for `destination:` at index '{it.multi_index}'")
+                print(f">>> this transition source is: '{single_transition_config['source']}'")
+                print(f">>> this transition destination is: '{single_transition_config['destination']}'")
+                print(f"transition_dimension: '{problem_dimension}'")
                 raise e
             
             try:
@@ -151,10 +151,10 @@ 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}")
-                print(f">>> this transition source is: {single_transition_config['source']}")
-                print(f">>> this transition destination is: {single_transition_config['destination']}")
-                print(f"transition_dimension: {problem_dimension}")
+                print(f">>> in expand_transition_elements for `rate:` at index '{it.multi_index}'")
+                print(f">>> this transition source is: '{single_transition_config['source']}'")
+                print(f">>> this transition destination is: '{single_transition_config['destination']}'")
+                print(f"transition_dimension: '{problem_dimension}'")
                 raise e
 
             try:
@@ -173,10 +173,10 @@ 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}")
-                print(f">>> this transition source is: {single_transition_config['source']}")
-                print(f">>> this transition destination is: {single_transition_config['destination']}")
-                print(f"transition_dimension: {problem_dimension}")
+                print(f">>> in expand_transition_elements for `proportional_to:` at index '{it.multi_index}'")
+                print(f">>> this transition source is: '{single_transition_config['source']}'")
+                print(f">>> this transition destination is: '{single_transition_config['destination']}'")
+                print(f"transition_dimension: '{problem_dimension}'")
                 raise e
             
             if "proportion_exponent" in single_transition_config: # if proportion_exponent is not defined, it is set to 1
@@ -198,10 +198,10 @@ 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}")
-                    print(f">>> this transition source is: {single_transition_config['source']}")
-                    print(f">>> this transition destination is: {single_transition_config['destination']}")
-                    print(f"transition_dimension: {problem_dimension}")
+                    print(f">>> in expand_transition_elements for `proportion_exponent:` at index '{it.multi_index}'")
+                    print(f">>> this transition source is: '{single_transition_config['source']}'")
+                    print(f">>> this transition destination is: '{single_transition_config['destination']}'")
+                    print(f"transition_dimension: '{problem_dimension}'")
                     raise e
             else:
                 new_transition_config["proportion_exponent"][it.multi_index] = ["1"] * proportion_size
@@ -375,8 +375,8 @@ 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} "
-                f" isolate {self.compartments[mask]} from options {self.compartments}. "
+                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]
@@ -396,7 +396,7 @@ def get_transition_array(self):
                         if self.compartments["name"][compartment] == elem:
                             rc = compartment
                     if rc == -1:
-                        raise ValueError(f"Could not find {colname} defined by {elem} in {self.compartments}.")
+                        raise ValueError(f"Could not find '{colname}' defined by '{elem}' in '{self.compartments}'.")
                     transition_array[cit, it] = rc
 
             unique_strings = []
@@ -428,7 +428,7 @@ def get_transition_array(self):
                 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}"
+                        f"Unique strings: '{unique_strings}'"
                     )
                 rc = [it for it, x in enumerate(unique_strings) if x == candidate][0]
                 transition_array[2][it] = rc
@@ -470,8 +470,7 @@ def get_transition_array(self):
                     # candidate = candidate.replace("*1", "")
                     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}"
+                            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
@@ -565,8 +564,7 @@ def parse_parameter_strings_to_numpy_arrays_v2(self, parameters, parameter_names
                 parsed_formulas.append(f)
             except Exception as e:
                 print(
-                    f"Cannot parse formula: '{formula}' :" 
-                    f"from parameters: {parameter_names}."
+                    f"Cannot parse formula: '{formula}' from parameters: '{parameter_names}'."
                 )
                 raise (e)  # Print the error message for debugging
 
@@ -613,10 +611,10 @@ 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}. " 
+                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}."
+                f"The defined parameters are '{parameter_names}'."
             )
 
         split_strings = [x.split(operators[0]) for x in string_list]
@@ -725,10 +723,10 @@ def list_access_element_safe(thing, idx, dimension=None, encapsulate_as_list=Fal
     except Exception as e:
         raise Exception(
             f"Error {e}: "
-            f"in list_access_element_safe for {thing} at index {idx}. "
+            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}."
+            f"dimension: '{dimension}'."
         )
 
 
diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index acacd8b35..b1bcd7cce 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -42,9 +42,9 @@ 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')
@@ -52,7 +52,7 @@ 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(f"Error in InitialConditions: a plugin file path is required when method is plugin.")
+            raise ValueError("Error in InitialConditions: a plugin file path is required when method is plugin.")
         return values
 
 
@@ -71,18 +71,18 @@ 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} "
-                f"Current value: {lambda_file}."
+                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(
-                f"Error in Seeding: A seeding_file_type is required when method is FolderDraw"
-                f"Current value: {seeding_file_type}."
+                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(
-                f"Error in Seeding: A seeding_file is required when method is FromFile "
-                f"Current value: {seeding_file}."
+                f"Error in Seeding: A seeding_file is required when method is FromFile. "
+                f"Current value: '{seeding_file}'."
             )
         return values
     
@@ -92,8 +92,8 @@ def plugin_filecheck(cls, values):
         plugin_file_path = values.get('plugin_file_path')   
         if method == 'plugin' and not plugin_file_path:
             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."
+                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
     
@@ -119,11 +119,11 @@ def check_distr(cls, values):
         b = values.get('b')
         if distr != 'fixed':
             if not mean and not sd:
-                raise ValueError(f"Mean and sd must be provided for non-fixed distributions.")
+                raise ValueError("Mean and sd must be provided for non-fixed distributions.")
             if distr == 'truncnorm' and not a and not b:
-                raise ValueError(f"a and b must be provided for truncated normal distributions.")
+                raise ValueError("a and b must be provided for truncated normal distributions.")
         if distr == 'fixed' and not value:
-            raise ValueError(f"Value must be provided for fixed distributions")
+            raise ValueError("Value must be provided for fixed distributions.")
         return values
 
 class BaseParameterConfig(BaseModel):
@@ -144,7 +144,7 @@ def which_value(cls, values):
         if value and timeseries:
             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}."
+                f"Current values - value: '{values.get('value')!r}', timeseries: '{values.get('timeseries')!r}'."
             )
         return values
     
@@ -221,7 +221,7 @@ def which_source(cls, values):
             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}."
+                f"Current values - incidence: '{values.get('incidence')!r}', prevalence: '{values.get('prevalence')!r}'."
                 )
         return values
 
@@ -258,9 +258,9 @@ 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("Error in outcome: Both 'sum' and 'source' are present. 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("Error in outcome: Neither 'sum' nor 'source' is present. Choose one.")
         return values
 
 class OutcomesConfig(BaseModel):
@@ -275,7 +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("Error in outcome: `param_subpop_file` is required when `param_from_file` is 'True'.")
         return values
 
 class ResampleConfig(BaseModel):
@@ -339,14 +339,11 @@ 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(
-                f"Inference mode is enabled, but no groundtruth dates are provided."
-                f"Please provide groundtruth dates."
+            raise ValueError("Inference mode is enabled, but no groundtruth dates are provided. Please provide groundtruth dates."
             )
         elif start_date_groundtruth and not inference_present:
             raise ValueError(
-                f"Groundtruth dates are provided, but inference mode is not enabled."
-                f"Please enable inference mode."
+                f"Groundtruth dates are provided, but inference mode is not enabled. Please enable inference mode."
             )
         return values
     
@@ -357,7 +354,7 @@ def check_dates(cls, values):
         if start_date and end_date:
             if end_date <= start_date:
                 raise ValueError(
-                    f"`end_date` ({end_date}) must be later than `start_date` ({start_date}))."
+                    f"`end_date` ('{end_date}') must be later than `start_date` ('{start_date}'))."
                 )
         return values
     
diff --git a/flepimop/gempyor_pkg/src/gempyor/inference.py b/flepimop/gempyor_pkg/src/gempyor/inference.py
index a03239e5b..fa28991de 100644
--- a/flepimop/gempyor_pkg/src/gempyor/inference.py
+++ b/flepimop/gempyor_pkg/src/gempyor/inference.py
@@ -269,8 +269,8 @@ def autodetect_scenarios(config):
     if len(seir_modifiers_scenarios) != 1 or len(outcome_modifiers_scenarios) != 1:
         raise ValueError(
             f"Inference only supports configuration files with one scenario, recieved:\n"
-            f"SEIR modifiers: {seir_modifiers_scenarios}."
-            f"Outcomes modifiers: {outcome_modifiers_scenarios}."
+            f"SEIR modifiers: '{seir_modifiers_scenarios}'."
+            f"Outcomes modifiers: '{outcome_modifiers_scenarios}'."
         )
 
     return seir_modifiers_scenarios[0], outcome_modifiers_scenarios[0]
@@ -417,7 +417,7 @@ def get_all_sim_arguments(self):
     def get_logloss(self, proposal):
         if not self.inferpar.check_in_bound(proposal=proposal):
             if not self.silent:
-                print("OUT OF BOUND!!")
+                print("OUT OF BOUNDS!!")
             return -np.inf, -np.inf, -np.inf
 
         snpi_df_mod, hnpi_df_mod = self.inferpar.inject_proposal(
@@ -438,7 +438,7 @@ def get_logloss(self, proposal):
             model_df=outcomes_df, subpop_names=self.modinf.subpop_struct.subpop_names
         )
         if not self.silent:
-            print(f"llik is {ll_total}")
+            print(f"llik is '{ll_total}' ")
 
         return ll_total, logloss, regularizations
 
diff --git a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
index 396308ee4..3e5b67490 100644
--- a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
+++ b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
@@ -8,6 +8,7 @@
 from .simulation_component import SimulationComponent
 from . import utils
 from .utils import read_df
+import warnings
 import os
 
 logger = logging.getLogger(__name__)
@@ -99,7 +100,7 @@ def get_from_config(self, sim_id: int, modinf) -> np.ndarray:
                 allow_missing_subpops=self.allow_missing_subpops,
             )
         else:
-            raise NotImplementedError(f"Unknown initial conditions method [received: {method}].")
+            raise NotImplementedError(f"Unknown initial conditions method [received: '{method}'].")
 
         # check that the inputed values sums to the subpop population:
         check_population(y0=y0, modinf=modinf, ignore_population_checks=self.ignore_population_checks)
@@ -121,21 +122,20 @@ def check_population(y0, modinf, ignore_population_checks=False):
         n_pop = modinf.subpop_pop[pl_idx]
         if abs(n_y0 - n_pop) > 1:
             error = True
-            print(
-                f"ERROR: subpop_names {pl} (idx: pl_idx) has a population from initial condition of {n_y0} "
-                f"while population from geodata is {n_pop}." 
-                f"(absolute difference should be < 1, here is {abs(n_y0-n_pop)})."
+            warnings.warn(
+                f"ERROR: subpop_names {pl} (idx: plx_idx) has a population from  initial condition of {n_y0} "
+                f"while population geodata is {n_pop}. "
+                f"(absolute difference should be <1, here is {abs(n_y0-n_pop)})."
             )
 
     if error and not ignore_population_checks:
-        raise ValueError(
-            f"Geodata and initial condition do not agree on population size (see messages above). "
-            f"Use `ignore_population_checks: True` to ignore."
+        raise ValueError("Geodata and initial condition do not agree on population size. Use `ignore_population_checks: True` to ignore."
         )
     elif error and ignore_population_checks:
-        print(
-            f"WARNING: population mismatch errors ignored because `ignore_population_checks` is set to `True`."
-            f"Execution will continue, but this is not recommended."
+        warnings.warn(
+        "WARNING: Population mismatch errors ignored because `ignore_population_checks` is set to `True`. "
+        "Execution will continue, but this is not recommended.",
+        UserWarning
         )
 
 
@@ -159,16 +159,15 @@ def read_initial_condition_from_tidydataframe(
                         ]["amount"]
                 if len(ic_df_compartment_val) > 1:
                     raise ValueError(
-                        f"ERROR: Several ({len(ic_df_compartment_val)}) rows are matches for compartment {comp_name} in init file: filters returned {ic_df_compartment_val}"
+                        f"Several ('{len(ic_df_compartment_val)}') rows are matches for compartment '{comp_name}' in init file: filters returned '{ic_df_compartment_val}'"
                     )
                 elif ic_df_compartment_val.empty:
                     if allow_missing_compartments:
                         ic_df_compartment_val = 0.0
                     else:
                         raise ValueError(
-                            f"ERROR: Multiple rows ({len(ic_df_compartment_val)}) match for compartment '{comp_name}' in the initial conditions file. "
-                            f"Filters used: {filters.to_dict()}. Matches: {ic_df_compartment_val.tolist()}. "
-                            f"Ensure that each compartment has a unique initial condition entry."
+                            f"Multiple rows match for compartment '{comp_name}' in the initial conditions file; ensure each compartment has a unique entry. "
+                            f"Filters used: '{filters.to_dict()}'. Matches: '{ic_df_compartment_val.tolist()}'."
                         )
                 if "rest" in str(ic_df_compartment_val).strip().lower():
                     rests.append([comp_idx, pl_idx])
@@ -182,7 +181,7 @@ def read_initial_condition_from_tidydataframe(
             logger.critical(
                 f"No initial conditions for for subpop {pl}, assuming everyone (n={modinf.subpop_pop[pl_idx]}) in the first metacompartment ({modinf.compartments.compartments['name'].iloc[0]})"
             )
-            raise ValueError(f"THERE IS A BUG; REPORT THIS MESSAGE. Past implemenation was buggy.")
+            raise RuntimeError("There is a bug; report this message. Past implemenation was buggy.")
             # TODO: this is probably ok but highlighting for consistency
             if "proportional" in self.initial_conditions_config.keys():
                 if self.initial_conditions_config["proportional"].get():
@@ -193,7 +192,7 @@ def read_initial_condition_from_tidydataframe(
                 y0[0, pl_idx] = modinf.subpop_pop[pl_idx]
         else:
             raise ValueError(
-                f"Subpop {pl} does not exist in `initial_conditions::states_file`. "
+                f"Subpop '{pl}' does not exist in `initial_conditions::states_file`. "
                 f"You can set `allow_missing_subpops=TRUE` to bypass this error."
             )
     if rests:  # not empty
@@ -236,7 +235,7 @@ def read_initial_condition_from_seir_output(ic_df, modinf, allow_missing_subpops
     ic_df = ic_df[(ic_df["date"] == str(modinf.ti)) & (ic_df["mc_value_type"] == "prevalence")]
     if ic_df.empty:
         raise ValueError(f"No entry provided for initial time `ti` in the `initial_conditions::states_file.` "
-                         f"`ti`: {modinf.ti}.")
+                         f"`ti`: '{modinf.ti}'.")
     y0 = np.zeros((modinf.compartments.compartments.shape[0], modinf.nsubpops))
 
     for comp_idx, comp_name in modinf.compartments.compartments["name"].items():
@@ -251,27 +250,28 @@ def read_initial_condition_from_seir_output(ic_df, modinf, allow_missing_subpops
         if len(ic_df_compartment) > 1:
             # ic_df_compartment = ic_df_compartment.iloc[0]
             raise ValueError(
-                f"ERROR: Several ({len(ic_df_compartment)}) rows are matches for compartment {mc_name} in init file: filter {filters}. "
-                f"returned: {ic_df_compartment}."
+                f"Several ('{len(ic_df_compartment)}') rows are matches for compartment '{mc_name}' in init file: "
+                f"filter '{filters}'. "
+                f"returned: '{ic_df_compartment}'."
             )
         elif ic_df_compartment.empty:
             if allow_missing_compartments:
                 ic_df_compartment = pd.DataFrame(0, columns=ic_df_compartment.columns, index=[0])
             else:
                 raise ValueError(
-                    f"Initial Conditions: could not set compartment {comp_name} (id: {comp_idx}) in subpop {pl} (id: {pl_idx}). "
-                    f"The data from the init file is {ic_df_compartment[pl]}."
+                    f"Initial Conditions: could not set compartment '{comp_name}' (id: '{comp_idx}') in subpop '{pl}' (id: '{pl_idx}'). "
+                    f"The data from the init file is '{ic_df_compartment[pl]}'."
                 )
         elif ic_df_compartment["mc_name"].iloc[0] != comp_name:
-            print(
-                f"WARNING: init file `mc_name` {ic_df_compartment['mc_name'].iloc[0]} does not match compartment `mc_name` {comp_name}."
+            warnings.warn(
+                f"{ic_df_compartment['mc_name'].iloc[0]} does not match compartment `mc_name` {comp_name}."
             )
 
         for pl_idx, pl in enumerate(modinf.subpop_struct.subpop_names):
             if pl in ic_df.columns:
                 y0[comp_idx, pl_idx] = float(ic_df_compartment[pl].iloc[0])
             elif allow_missing_subpops:
-                raise ValueError("THERE IS A BUG; REPORT THIS MESSAGE. Past implemenation was buggy")
+                raise ValueError("There is a bug; report this message. Past implemenation was buggy")
                 # TODO this should set the full subpop, not just the 0th commpartment
                 logger.critical(
                     f"No initial conditions for for subpop {pl}, assuming everyone (n={modinf.subpop_pop[pl_idx]}) in the first metacompartments ({modinf.compartments.compartments['name'].iloc[0]})"
@@ -282,7 +282,7 @@ def read_initial_condition_from_seir_output(ic_df, modinf, allow_missing_subpops
                 y0[0, pl_idx] = modinf.subpop_pop[pl_idx]
             else:
                 raise ValueError(
-                    f"Subpop {pl} does not exist in `initial_conditions::states_file`. "
+                    f"Subpop '{pl}' does not exist in `initial_conditions::states_file`. "
                     f"You can set `allow_missing_subpops=TRUE` to bypass this error."
                 )
     return y0
diff --git a/flepimop/gempyor_pkg/src/gempyor/parameters.py b/flepimop/gempyor_pkg/src/gempyor/parameters.py
index c9d1886ec..248e9254c 100644
--- a/flepimop/gempyor_pkg/src/gempyor/parameters.py
+++ b/flepimop/gempyor_pkg/src/gempyor/parameters.py
@@ -123,9 +123,9 @@ def __init__(
                     print("loaded col :", sorted(list(df.columns)))
                     print("geodata col:", sorted(subpop_names))
                     raise ValueError(
-                        f"Error loading file {fn_name} for parameter {pn}: "
-                        f"the number of non-'date' columns is {len(df.columns)}, "
-                        f"expected {len(subpop_names)} (number of subpopulations) or one."
+                        f"Issue loading file '{fn_name}' for parameter '{pn}': "
+                        f"the number of non-'date' columns is '{len(df.columns)}', "
+                        f"expected '{len(subpop_names)}' (number of subpopulations) or one."
                     )
 
                 df = df[str(ti) : str(tf)]
@@ -133,20 +133,20 @@ def __init__(
                     print("config dates:", pd.date_range(ti, tf))
                     print("loaded dates:", df.index)
                     raise ValueError(
-                        f"ERROR loading file {fn_name} for parameter {pn}: " 
+                        f"Issue loading file '{fn_name}' for parameter '{pn}': " 
                         f"the 'date' entries of the provided file do not include all the days specified to be modeled by " 
-                        f"the config. the provided file includes {len(df.index)} days between {str(df.index[0])} to {str(df.index[-1])}, " 
-                        f"while there are {len(pd.date_range(ti, tf))} days in the config time span of {ti}->{tf}. The file must contain entries for "
+                        f"the config. the provided file includes '{len(df.index)}' days between '{str(df.index[0])}' to '{str(df.index[-1])}', " 
+                        f"while there are '{len(pd.date_range(ti, tf))}' days in the config time span of '{ti}->{tf}'. The file must contain entries for "
                         f"the exact start and end dates from the config."
                     )
                 if not (pd.date_range(ti, tf) == df.index).all():
                     print("config dates:", pd.date_range(ti, tf))
                     print("loaded dates:", df.index)
                     raise ValueError(
-                        f"ERROR loading file {fn_name} for parameter {pn}: "
+                        f"Issue loading file '{fn_name}' for parameter '{pn}': "
                         f"the 'date' entries of the provided file do not include all the days specified to be modeled by "
-                        f"the config. the provided file includes {len(df.index)} days between {str(df.index[0])} to {str(df.index[-1])}, "
-                        f"while there are {len(pd.date_range(ti, tf))} days in the config time span of {ti}->{tf}. The file must contain entries for "
+                        f"the config. the provided file includes '{len(df.index)}' days between '{str(df.index[0])}' to '{str(df.index[-1])}', "
+                        f"while there are '{len(pd.date_range(ti, tf))}' days in the config time span of '{ti}'->'{tf}'. The file must contain entries for "
                         f"the exact start and end dates from the config."
                     )
 

From 3b20e8af462efc1a33eee397c3acaf5f7a54fe12 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 16 Oct 2024 11:37:11 -0400
Subject: [PATCH 13/48] Fixing reg-exs

---
 .../tests/parameters/test_parameters_class.py          | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index f5b5fe150..8f8aaf7aa 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -237,8 +237,8 @@ def test_timeseries_parameter_has_insufficient_columns_value_error(
         with pytest.raises(
             ValueError,
             match=(
-                rf"^Error loading file {tmp_file} for parameter sigma: " 
-                rf"the number of non-'date' columns is {actual_columns}, expected {mock_inputs.number_of_subpops()} " 
+                rf"^Issue loading file '{tmp_file}' for parameter 'sigma': " 
+                rf"the number of non-'date' columns is '{actual_columns}', expected '{mock_inputs.number_of_subpops()}' " 
                 rf"\(number of subpopulations\) or one\.$"
             ),
         ):
@@ -282,12 +282,12 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
         with pytest.raises(
             ValueError,
             match=(
-                rf"^ERROR loading file {tmp_file} for parameter sigma: " 
+                rf"^Issue loading file '{tmp_file}' for parameter 'sigma': " 
                 rf"the 'date' entries of the provided file do not include " 
                 rf"all the days specified to be modeled by the config\. the provided file includes " 
                 rf"{(timeseries_end_date - timeseries_start_date).days + 1} days between " 
-                rf"{timeseries_start_date}( 00:00:00)? to {timeseries_end_date}( 00:00:00)?, while there are " 
-                rf"{mock_inputs.number_of_days()} days in the config time span of {mock_inputs.ti}->{mock_inputs.tf}\. " 
+                rf"'{timeseries_start_date}'( 00:00:00)? to '{timeseries_end_date}'( 00:00:00)?, while there are " 
+                rf"'{mock_inputs.number_of_days()}' days in the config time span of '{mock_inputs.ti}'->'{mock_inputs.tf}'\. " 
                 rf"The file must contain entries for the exact start and end dates from the config\.$"
             ),
         ):

From afee28512ded3c447831dee47daba9582ab4aba5 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 16 Oct 2024 11:45:07 -0400
Subject: [PATCH 14/48] Updating RegEx

---
 flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index 8f8aaf7aa..756d0cc92 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -285,7 +285,7 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
                 rf"^Issue loading file '{tmp_file}' for parameter 'sigma': " 
                 rf"the 'date' entries of the provided file do not include " 
                 rf"all the days specified to be modeled by the config\. the provided file includes " 
-                rf"{(timeseries_end_date - timeseries_start_date).days + 1} days between " 
+                rf"'{(timeseries_end_date - timeseries_start_date).days + 1}' days between " 
                 rf"'{timeseries_start_date}'( 00:00:00)? to '{timeseries_end_date}'( 00:00:00)?, while there are " 
                 rf"'{mock_inputs.number_of_days()}' days in the config time span of '{mock_inputs.ti}'->'{mock_inputs.tf}'\. " 
                 rf"The file must contain entries for the exact start and end dates from the config\.$"

From 2eaa42748e5266c44dd0b3c5f556de4ddebfe010 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 16 Oct 2024 12:17:46 -0400
Subject: [PATCH 15/48] Fixing RegExs again UGH!

---
 .../gempyor_pkg/tests/parameters/test_parameters_class.py     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index 756d0cc92..78fab1270 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -284,11 +284,11 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
             match=(
                 rf"^Issue loading file '{tmp_file}' for parameter 'sigma': " 
                 rf"the 'date' entries of the provided file do not include " 
-                rf"all the days specified to be modeled by the config\. the provided file includes " 
+                rf"all the days specified to be modeled by the config. the provided file includes " 
                 rf"'{(timeseries_end_date - timeseries_start_date).days + 1}' days between " 
                 rf"'{timeseries_start_date}'( 00:00:00)? to '{timeseries_end_date}'( 00:00:00)?, while there are " 
                 rf"'{mock_inputs.number_of_days()}' days in the config time span of '{mock_inputs.ti}'->'{mock_inputs.tf}'\. " 
-                rf"The file must contain entries for the exact start and end dates from the config\.$"
+                rf"The file must contain entries for the exact start and end dates from the config.$"
             ),
         ):
             mock_inputs.create_parameters_instance()

From 48a78ee60e203eac42ccfeeb607046abcbea0b48 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 16 Oct 2024 12:31:34 -0400
Subject: [PATCH 16/48] I'm losing my mind with this RegEx

---
 flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index 78fab1270..1df019049 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -287,7 +287,7 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
                 rf"all the days specified to be modeled by the config. the provided file includes " 
                 rf"'{(timeseries_end_date - timeseries_start_date).days + 1}' days between " 
                 rf"'{timeseries_start_date}'( 00:00:00)? to '{timeseries_end_date}'( 00:00:00)?, while there are " 
-                rf"'{mock_inputs.number_of_days()}' days in the config time span of '{mock_inputs.ti}'->'{mock_inputs.tf}'\. " 
+                rf"'{mock_inputs.number_of_days()}' days in the config time span of '{mock_inputs.ti}'->'{mock_inputs.tf}'. " 
                 rf"The file must contain entries for the exact start and end dates from the config.$"
             ),
         ):

From 6e1410f12ea732907731ae42398779e1ec5787b2 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 16 Oct 2024 12:43:51 -0400
Subject: [PATCH 17/48] Update test_parameters_class.py

---
 flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index 1df019049..bd7991c1e 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -286,7 +286,7 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
                 rf"the 'date' entries of the provided file do not include " 
                 rf"all the days specified to be modeled by the config. the provided file includes " 
                 rf"'{(timeseries_end_date - timeseries_start_date).days + 1}' days between " 
-                rf"'{timeseries_start_date}'( 00:00:00)? to '{timeseries_end_date}'( 00:00:00)?, while there are " 
+                rf"'{timeseries_start_date}( 00:00:00)?' to '{timeseries_end_date}( 00:00:00)?', while there are " 
                 rf"'{mock_inputs.number_of_days()}' days in the config time span of '{mock_inputs.ti}'->'{mock_inputs.tf}'. " 
                 rf"The file must contain entries for the exact start and end dates from the config.$"
             ),

From 5c09a3cf866278b89762fbd5cbda1222236256bd Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Wed, 16 Oct 2024 13:36:49 -0400
Subject: [PATCH 18/48] Update
 flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 .../tests/parameters/test_parameters_class.py     | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index bd7991c1e..25bdfc512 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -282,13 +282,14 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
         with pytest.raises(
             ValueError,
             match=(
-                rf"^Issue loading file '{tmp_file}' for parameter 'sigma': " 
-                rf"the 'date' entries of the provided file do not include " 
-                rf"all the days specified to be modeled by the config. the provided file includes " 
-                rf"'{(timeseries_end_date - timeseries_start_date).days + 1}' days between " 
-                rf"'{timeseries_start_date}( 00:00:00)?' to '{timeseries_end_date}( 00:00:00)?', while there are " 
-                rf"'{mock_inputs.number_of_days()}' days in the config time span of '{mock_inputs.ti}'->'{mock_inputs.tf}'. " 
-                rf"The file must contain entries for the exact start and end dates from the config.$"
+                f"^Issue loading file '{tmp_file}' for parameter 'sigma': the 'date' "
+                "entries of the provided file do not include all the days specified to "
+                f"be modeled by the config. the provided file includes '{file_days}' "
+                f"days between '{timeseries_start_date}( 00:00:00)?' to "
+                f"'{timeseries_end_date}( 00:00:00)?', while there are "
+                f"'{mock_inputs.number_of_days()}' days in the config time span of "
+                f"'{mock_inputs.ti}->{mock_inputs.tf}'. The file must contain "
+                "entries for the exact start and end dates from the config.$"
             ),
         ):
             mock_inputs.create_parameters_instance()

From 278543713bf491e3d8735605b6f889584021db13 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 16 Oct 2024 14:48:58 -0400
Subject: [PATCH 19/48] Shortening a verbose error

---
 flepimop/gempyor_pkg/src/gempyor/parameters.py | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/parameters.py b/flepimop/gempyor_pkg/src/gempyor/parameters.py
index 248e9254c..450a3638a 100644
--- a/flepimop/gempyor_pkg/src/gempyor/parameters.py
+++ b/flepimop/gempyor_pkg/src/gempyor/parameters.py
@@ -134,20 +134,14 @@ def __init__(
                     print("loaded dates:", df.index)
                     raise ValueError(
                         f"Issue loading file '{fn_name}' for parameter '{pn}': " 
-                        f"the 'date' entries of the provided file do not include all the days specified to be modeled by " 
-                        f"the config. the provided file includes '{len(df.index)}' days between '{str(df.index[0])}' to '{str(df.index[-1])}', " 
-                        f"while there are '{len(pd.date_range(ti, tf))}' days in the config time span of '{ti}->{tf}'. The file must contain entries for "
-                        f"the exact start and end dates from the config."
+                        f"The 'date' entries of the provided file do not include all the days specified to be modeled by the config."
                     )
                 if not (pd.date_range(ti, tf) == df.index).all():
                     print("config dates:", pd.date_range(ti, tf))
                     print("loaded dates:", df.index)
                     raise ValueError(
                         f"Issue loading file '{fn_name}' for parameter '{pn}': "
-                        f"the 'date' entries of the provided file do not include all the days specified to be modeled by "
-                        f"the config. the provided file includes '{len(df.index)}' days between '{str(df.index[0])}' to '{str(df.index[-1])}', "
-                        f"while there are '{len(pd.date_range(ti, tf))}' days in the config time span of '{ti}'->'{tf}'. The file must contain entries for "
-                        f"the exact start and end dates from the config."
+                        f"the 'date' entries of the provided file do not include all the days specified to be modeled by the config."
                     )
 
                 self.pdata[pn]["ts"] = df

From 4cc651f339de31139692371c1f56841231df6282 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 16 Oct 2024 16:20:35 -0400
Subject: [PATCH 20/48] RegEx update

---
 .../gempyor_pkg/tests/parameters/test_parameters_class.py  | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index 25bdfc512..4cc620a3b 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -284,12 +284,7 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
             match=(
                 f"^Issue loading file '{tmp_file}' for parameter 'sigma': the 'date' "
                 "entries of the provided file do not include all the days specified to "
-                f"be modeled by the config. the provided file includes '{file_days}' "
-                f"days between '{timeseries_start_date}( 00:00:00)?' to "
-                f"'{timeseries_end_date}( 00:00:00)?', while there are "
-                f"'{mock_inputs.number_of_days()}' days in the config time span of "
-                f"'{mock_inputs.ti}->{mock_inputs.tf}'. The file must contain "
-                "entries for the exact start and end dates from the config.$"
+                f"be modeled by the config.$"
             ),
         ):
             mock_inputs.create_parameters_instance()

From be85d72067403bad9440bb563d1cf01c588e9399 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 18 Oct 2024 09:50:54 -0400
Subject: [PATCH 21/48] Regex edit..

---
 flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index 4cc620a3b..5fa8364c3 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -282,7 +282,7 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
         with pytest.raises(
             ValueError,
             match=(
-                f"^Issue loading file '{tmp_file}' for parameter 'sigma': the 'date' "
+                f"^Issue loading file '{tmp_file}' for parameter 'sigma': Tßhe 'date' "
                 "entries of the provided file do not include all the days specified to "
                 f"be modeled by the config.$"
             ),

From fb549c4f308243c14e53d3a23cb6e97e0cc1ffd6 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 18 Oct 2024 10:03:24 -0400
Subject: [PATCH 22/48] Regex edit

---
 flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index 5fa8364c3..377bb800e 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -282,7 +282,7 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
         with pytest.raises(
             ValueError,
             match=(
-                f"^Issue loading file '{tmp_file}' for parameter 'sigma': Tßhe 'date' "
+                f"Issue loading file '{tmp_file}' for parameter 'sigma': The 'date' "
                 "entries of the provided file do not include all the days specified to "
                 f"be modeled by the config.$"
             ),

From 135aa542f7b06f1d58f74089db19c9b2ae71cf9f Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:29:23 -0400
Subject: [PATCH 23/48] Update flepimop/gempyor_pkg/src/gempyor/compartments.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/compartments.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/compartments.py b/flepimop/gempyor_pkg/src/gempyor/compartments.py
index 6842d7e26..ac8ac4d33 100644
--- a/flepimop/gempyor_pkg/src/gempyor/compartments.py
+++ b/flepimop/gempyor_pkg/src/gempyor/compartments.py
@@ -427,7 +427,7 @@ def get_transition_array(self):
                 # candidate = candidate.replace("*1", "")
                 if candidate not in unique_strings:
                     raise ValueError(
-                        f"Candidate '{candidate}' from 'rate' column is not in the list of unique strings: {unique_strings}"
+                        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

From 681ff790471619f3f05fdd9aeb2d20e495c9714b Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:29:50 -0400
Subject: [PATCH 24/48] Update flepimop/gempyor_pkg/src/gempyor/compartments.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/compartments.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/compartments.py b/flepimop/gempyor_pkg/src/gempyor/compartments.py
index ac8ac4d33..02b7c3d05 100644
--- a/flepimop/gempyor_pkg/src/gempyor/compartments.py
+++ b/flepimop/gempyor_pkg/src/gempyor/compartments.py
@@ -469,7 +469,7 @@ def get_transition_array(self):
                     # candidate = candidate.replace("*1", "")
                     if candidate not in unique_strings:
                         raise ValueError(
-                            f"Proportion exponent '{candidate}' is not found in the list of unique strings: '{unique_strings}'"
+                            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

From 1549b5bc4e4b696ed3f422b4a9b9a7aa60c27449 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:34:30 -0400
Subject: [PATCH 25/48] Update flepimop/gempyor_pkg/src/gempyor/compartments.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/compartments.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/compartments.py b/flepimop/gempyor_pkg/src/gempyor/compartments.py
index 02b7c3d05..85ec66a54 100644
--- a/flepimop/gempyor_pkg/src/gempyor/compartments.py
+++ b/flepimop/gempyor_pkg/src/gempyor/compartments.py
@@ -497,7 +497,7 @@ def get_transition_array(self):
                         if rc == -1:
                             raise ValueError(
                                 f"Could not find proportional_to {elem3} in compartments. "
-                                f"Available compartments: {self.compartments}"
+                                f"Available compartments: {self.compartments}."
                             )
 
                         proportion_array[proportion_index] = rc

From cbfd0934f8450573f6317bf7148554da5cfc289b Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:34:40 -0400
Subject: [PATCH 26/48] Update flepimop/gempyor_pkg/src/gempyor/compartments.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/compartments.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/compartments.py b/flepimop/gempyor_pkg/src/gempyor/compartments.py
index 85ec66a54..35b907c25 100644
--- a/flepimop/gempyor_pkg/src/gempyor/compartments.py
+++ b/flepimop/gempyor_pkg/src/gempyor/compartments.py
@@ -563,7 +563,7 @@ def parse_parameter_strings_to_numpy_arrays_v2(self, parameters, parameter_names
                 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
 

From ccfb6e01f482fdb319fe40fc5be2e1406dde0dc0 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:34:57 -0400
Subject: [PATCH 27/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index b1bcd7cce..6475ebfb2 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -42,7 +42,7 @@ 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"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}'.")
         return values

From e83f250bd32087f4e90af673f280ee076c366086 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:35:36 -0400
Subject: [PATCH 28/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index 6475ebfb2..b5da57514 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -44,7 +44,7 @@ def validate_initial_file_check(cls, values):
         if method in {'FromFile', 'SetInitialConditions'} and not initial_conditions_file:
             raise ValueError(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}'.")
+            raise ValueError(f"An `initial_file_type` is required when method is '{method}'.")
         return values
     
     @model_validator(mode='before')

From 6eed1e30612659cbb148db407548f446cccfad06 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:35:57 -0400
Subject: [PATCH 29/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index b5da57514..c41a979b8 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -52,7 +52,7 @@ 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
 
 

From 08e25a3cbfb1c02d7dad70447d7420805ea0d55d Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:37:59 -0400
Subject: [PATCH 30/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index c41a979b8..19c95d91e 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -71,8 +71,8 @@ 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}'. "
-                f"Current value: '{lambda_file}'."
+                f"A `lambda_file` is required when method is '{method}', "
+                f"was given '{lambda_file}'."
             )
         if method == 'FolderDraw' and not seeding_file_type:
             raise ValueError(

From e68dc8a26d9a724c1594111210b239503f8ef105 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:38:20 -0400
Subject: [PATCH 31/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index 19c95d91e..d5acabc79 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -76,8 +76,8 @@ def validate_seedingfile(cls, values):
             )
         if method == 'FolderDraw' and not seeding_file_type:
             raise ValueError(
-                f"Error in Seeding: A seeding_file_type is required when method is FolderDraw. "
-                f"Current value: '{seeding_file_type}'."
+                f"A `seeding_file_type` is required when method is 'FolderDraw', "
+                f"was given '{seeding_file_type}'."
             )
         if method == 'FromFile' and not seeding_file:
             raise ValueError(

From 960f4d230b72f0e835f44066fbaefc2598930d22 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:39:42 -0400
Subject: [PATCH 32/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index d5acabc79..cbc14b450 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -81,8 +81,8 @@ def validate_seedingfile(cls, values):
             )
         if method == 'FromFile' and not seeding_file:
             raise ValueError(
-                f"Error in Seeding: A seeding_file is required when method is FromFile. "
-                f"Current value: '{seeding_file}'."
+                f"A `seeding_file` is required when method is 'FromFile', "
+                f"was given '{seeding_file}'."
             )
         return values
     

From 2b75d6adce2d60e3fe09cfcd8458b6151cfcb0bf Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:41:54 -0400
Subject: [PATCH 33/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index cbc14b450..775f2811b 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -92,8 +92,8 @@ def plugin_filecheck(cls, values):
         plugin_file_path = values.get('plugin_file_path')   
         if method == 'plugin' and not plugin_file_path:
             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."
+                f"A plugin file path is required when method is 'plugin', "
+                f"was given '{plugin_file_path!r}'."
             )
         return values
     

From 5d999ddb7e814eda021fff81357084dd041f8aa2 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:42:16 -0400
Subject: [PATCH 34/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index 775f2811b..02cf695c0 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -143,8 +143,7 @@ def which_value(cls, values):
         timeseries = values.get('timeseries') is not None
         if value and timeseries:
             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}'."
+                f"Parsed a parameter with both a timeseries, '{values.get('timeseries')!r}', and a value, '{values.get('value')!r}', please choose one."
             )
         return values
     

From a15184ec2955da52ad724af5ac24b20e13404508 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:43:21 -0400
Subject: [PATCH 35/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index 02cf695c0..1157bcbb5 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -218,9 +218,7 @@ def which_source(cls, values):
         prevalence = values.get('prevalence')
         if incidence and prevalence:
             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}'."
+                f"Parsed a source with both an incidence, '{values.get('incidence')!r}', and prevalence, '{values.get('prevalence')!r}', please choose one."
                 )
         return values
 

From 2b2a2811938ae2db2230a206d4407e99cabf0874 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:43:55 -0400
Subject: [PATCH 36/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index 1157bcbb5..ec92946a1 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -255,7 +255,7 @@ def check_outcome_type(cls, values):
         source_present = values.get('source') is not None
 
         if sum_present and source_present:
-            raise ValueError("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("Error in outcome: Neither 'sum' nor 'source' is present. Choose one.")
         return values

From 76b5adfebff88d86f492fdca3b365112198d20c6 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:44:12 -0400
Subject: [PATCH 37/48] Update
 flepimop/gempyor_pkg/src/gempyor/initial_conditions.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/initial_conditions.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
index 3e5b67490..17b43b859 100644
--- a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
+++ b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
@@ -271,7 +271,7 @@ def read_initial_condition_from_seir_output(ic_df, modinf, allow_missing_subpops
             if pl in ic_df.columns:
                 y0[comp_idx, pl_idx] = float(ic_df_compartment[pl].iloc[0])
             elif allow_missing_subpops:
-                raise ValueError("There is a bug; report this message. Past implemenation was buggy")
+                raise RuntimeError("There is a bug; report this message. Past implemenation was buggy")
                 # TODO this should set the full subpop, not just the 0th commpartment
                 logger.critical(
                     f"No initial conditions for for subpop {pl}, assuming everyone (n={modinf.subpop_pop[pl_idx]}) in the first metacompartments ({modinf.compartments.compartments['name'].iloc[0]})"

From a0ae5e35b7a03bc73d40d270fba727c21aabdd1f Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:44:30 -0400
Subject: [PATCH 38/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index ec92946a1..4bdafb035 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -257,7 +257,7 @@ def check_outcome_type(cls, values):
         if sum_present and source_present:
             raise ValueError("Both 'sum' and 'source' are present, please choose one.")
         elif not sum_present and not source_present:
-            raise ValueError("Error in outcome: Neither 'sum' nor 'source' is present. Choose one.")
+            raise ValueError("Neither 'sum' nor 'source' is present, please choose one.")
         return values
 
 class OutcomesConfig(BaseModel):

From 0c14d668fd8ebff8db11264046fe6d0e144a42a7 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:44:58 -0400
Subject: [PATCH 39/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index 4bdafb035..01f449dd4 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -272,7 +272,7 @@ 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("Error in outcome: `param_subpop_file` is required when `param_from_file` is 'True'.")
+            raise ValueError("A `param_subpop_file` is required when `param_from_file` is 'True'.")
         return values
 
 class ResampleConfig(BaseModel):

From 9a6ba69d5fb02fbbe68246349774e8c0e762e815 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:48:08 -0400
Subject: [PATCH 40/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index 01f449dd4..ff4a73edc 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -336,8 +336,7 @@ 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. Please provide groundtruth dates."
-            )
+            raise ValueError("Inference mode is enabled, but no groundtruth dates are provided. Please provide groundtruth dates.")
         elif start_date_groundtruth and not inference_present:
             raise ValueError(
                 f"Groundtruth dates are provided, but inference mode is not enabled. Please enable inference mode."

From 4ca01af67cabf5480556fdcf68aca7adebcebbd3 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:48:53 -0400
Subject: [PATCH 41/48] Update
 flepimop/gempyor_pkg/src/gempyor/config_validator.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/config_validator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index ff4a73edc..9b43692b1 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -339,7 +339,7 @@ def verify_inference(cls, values):
             raise ValueError("Inference mode is enabled, but no groundtruth dates are provided. Please provide groundtruth dates.")
         elif start_date_groundtruth and not inference_present:
             raise ValueError(
-                f"Groundtruth dates are provided, but inference mode is not enabled. Please enable inference mode."
+                "Groundtruth dates are provided, but inference mode is not enabled. Please enable inference mode."
             )
         return values
     

From 88e310db1fc7bfd34a28496779a6015ca4445a45 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Fri, 18 Oct 2024 12:49:22 -0400
Subject: [PATCH 42/48] Update flepimop/gempyor_pkg/src/gempyor/inference.py

Co-authored-by: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
---
 flepimop/gempyor_pkg/src/gempyor/inference.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/inference.py b/flepimop/gempyor_pkg/src/gempyor/inference.py
index fa28991de..36287f8ce 100644
--- a/flepimop/gempyor_pkg/src/gempyor/inference.py
+++ b/flepimop/gempyor_pkg/src/gempyor/inference.py
@@ -268,8 +268,8 @@ def autodetect_scenarios(config):
 
     if len(seir_modifiers_scenarios) != 1 or len(outcome_modifiers_scenarios) != 1:
         raise ValueError(
-            f"Inference only supports configuration files with one scenario, recieved:\n"
-            f"SEIR modifiers: '{seir_modifiers_scenarios}'."
+            f"Inference only supports configuration files with one scenario, recieved "
+            f"SEIR modifiers: '{seir_modifiers_scenarios}', and "
             f"Outcomes modifiers: '{outcome_modifiers_scenarios}'."
         )
 

From 01d11a7dfd05c980ce6bbdfd4a5625fc8223476b Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 18 Oct 2024 14:42:19 -0400
Subject: [PATCH 43/48] Update parameters.py and test_parameters_class.py

---
 flepimop/gempyor_pkg/src/gempyor/initial_conditions.py    | 8 ++++----
 flepimop/gempyor_pkg/src/gempyor/parameters.py            | 6 ++++--
 .../gempyor_pkg/tests/parameters/test_parameters_class.py | 6 +++---
 3 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
index 17b43b859..eff95b6b8 100644
--- a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
+++ b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
@@ -123,9 +123,9 @@ def check_population(y0, modinf, ignore_population_checks=False):
         if abs(n_y0 - n_pop) > 1:
             error = True
             warnings.warn(
-                f"ERROR: subpop_names {pl} (idx: plx_idx) has a population from  initial condition of {n_y0} "
-                f"while population geodata is {n_pop}. "
-                f"(absolute difference should be <1, here is {abs(n_y0-n_pop)})."
+                f"`subpop_names` '{pl}' (idx: plx_idx) has a population from  initial condition of '{n_y0}' "
+                f"while population geodata is '{n_pop}'. "
+                f"(absolute difference should be <1, here is '{abs(n_y0-n_pop)}')."
             )
 
     if error and not ignore_population_checks:
@@ -133,7 +133,7 @@ def check_population(y0, modinf, ignore_population_checks=False):
         )
     elif error and ignore_population_checks:
         warnings.warn(
-        "WARNING: Population mismatch errors ignored because `ignore_population_checks` is set to `True`. "
+        "Population mismatch errors ignored because `ignore_population_checks` is set to `True`. "
         "Execution will continue, but this is not recommended.",
         UserWarning
         )
diff --git a/flepimop/gempyor_pkg/src/gempyor/parameters.py b/flepimop/gempyor_pkg/src/gempyor/parameters.py
index 450a3638a..35526084c 100644
--- a/flepimop/gempyor_pkg/src/gempyor/parameters.py
+++ b/flepimop/gempyor_pkg/src/gempyor/parameters.py
@@ -134,14 +134,16 @@ def __init__(
                     print("loaded dates:", df.index)
                     raise ValueError(
                         f"Issue loading file '{fn_name}' for parameter '{pn}': " 
-                        f"The 'date' entries of the provided file do not include all the days specified to be modeled by the config."
+                        f"Provided file dates span '{str(df.index[0])}' to '{str(df.index[-1])}', "
+                        f"but the config dates span '{ti}' to '{tf}'."
                     )
                 if not (pd.date_range(ti, tf) == df.index).all():
                     print("config dates:", pd.date_range(ti, tf))
                     print("loaded dates:", df.index)
                     raise ValueError(
                         f"Issue loading file '{fn_name}' for parameter '{pn}': "
-                        f"the 'date' entries of the provided file do not include all the days specified to be modeled by the config."
+                        f"Provided file dates span '{str(df.index[0])}' to '{str(df.index[-1])}', "
+                        f"but the config dates span '{ti}' to '{tf}'."
                     )
 
                 self.pdata[pn]["ts"] = df
diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index 377bb800e..09b278914 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -282,9 +282,9 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
         with pytest.raises(
             ValueError,
             match=(
-                f"Issue loading file '{tmp_file}' for parameter 'sigma': The 'date' "
-                "entries of the provided file do not include all the days specified to "
-                f"be modeled by the config.$"
+                f"Issue loading file '{tmp_file}' for parameter 'sigma': "
+                f"Provided file dates span '{timeseries_start_date}( 00\:00\:00)?' to '{timeseries_end_date}( 00\:00\:00)?', "
+                f"but the config dates span '{mock_inputs.ti}' to '{mock_inputs.tf}'.$"
             ),
         ):
             mock_inputs.create_parameters_instance()

From 7096ef1df77149d3f6f5216e90306d3d7be2d2bd Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 4 Nov 2024 15:13:46 -0500
Subject: [PATCH 44/48] Updated compartments.py, config_validaor.py,
 inference.py, parameters.py, and one regex in test_ic.py

---
 .../gempyor_pkg/src/gempyor/compartments.py     | 12 ++++++------
 .../gempyor_pkg/src/gempyor/config_validator.py | 17 ++++-------------
 flepimop/gempyor_pkg/src/gempyor/inference.py   |  4 ++--
 flepimop/gempyor_pkg/src/gempyor/parameters.py  | 14 +++++++++-----
 flepimop/gempyor_pkg/tests/seir/test_ic.py      |  2 +-
 5 files changed, 22 insertions(+), 27 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/compartments.py b/flepimop/gempyor_pkg/src/gempyor/compartments.py
index 35b907c25..cff807559 100644
--- a/flepimop/gempyor_pkg/src/gempyor/compartments.py
+++ b/flepimop/gempyor_pkg/src/gempyor/compartments.py
@@ -375,9 +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 an isolated compartment: '{comp_dict}' "
+                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}'."
+                f"The `get_comp_idx` function was called by '{error_info}'."
             )
         return comp_idx[0]
 
@@ -496,8 +496,8 @@ def get_transition_array(self):
                                 rc = compartment
                         if rc == -1:
                             raise ValueError(
-                                f"Could not find proportional_to {elem3} in compartments. "
-                                f"Available compartments: {self.compartments}."
+                                f"Could not find `proportional_to` '{elem3}' in compartments. "
+                                f"Available compartments: '{self.compartments}'."
                             )
 
                         proportion_array[proportion_index] = rc
@@ -611,8 +611,8 @@ def parse_parameter_strings_to_numpy_arrays(
         ):  # 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}'. " 
-                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"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}'."
             )
 
diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index 9b43692b1..93aa4d6ff 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -70,20 +70,11 @@ 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"A `lambda_file` is required when method is '{method}', "
-                f"was given '{lambda_file}'."
-            )
+            raise ValueError("A `lambda_file` is required when method is 'PoissonDistributed'.")
         if method == 'FolderDraw' and not seeding_file_type:
-            raise ValueError(
-                f"A `seeding_file_type` is required when method is 'FolderDraw', "
-                f"was given '{seeding_file_type}'."
-            )
+            raise ValueError("A `seeding_file_type` is required when method is 'FolderDraw'.")
         if method == 'FromFile' and not seeding_file:
-            raise ValueError(
-                f"A `seeding_file` is required when method is 'FromFile', "
-                f"was given '{seeding_file}'."
-            )
+            raise ValueError("A `seeding_file` is required when method is 'FromFile'.")
         return values
     
     @model_validator(mode='before')
@@ -358,7 +349,7 @@ def check_dates(cls, values):
     def init_or_seed(cls, values):
         init = values.get('initial_conditions')
         seed = values.get('seeding')
-        if not init or seed:
+        if not (init or seed):
             raise ValueError(
                 f"At least one of `initial_conditions` or `seeding` must be provided."
                 )
diff --git a/flepimop/gempyor_pkg/src/gempyor/inference.py b/flepimop/gempyor_pkg/src/gempyor/inference.py
index 36287f8ce..25289349d 100644
--- a/flepimop/gempyor_pkg/src/gempyor/inference.py
+++ b/flepimop/gempyor_pkg/src/gempyor/inference.py
@@ -268,7 +268,7 @@ def autodetect_scenarios(config):
 
     if len(seir_modifiers_scenarios) != 1 or len(outcome_modifiers_scenarios) != 1:
         raise ValueError(
-            f"Inference only supports configuration files with one scenario, recieved "
+            f"Inference only supports configuration files with one scenario, received "
             f"SEIR modifiers: '{seir_modifiers_scenarios}', and "
             f"Outcomes modifiers: '{outcome_modifiers_scenarios}'."
         )
@@ -417,7 +417,7 @@ def get_all_sim_arguments(self):
     def get_logloss(self, proposal):
         if not self.inferpar.check_in_bound(proposal=proposal):
             if not self.silent:
-                print("OUT OF BOUNDS!!")
+                print("`llik` is -inf (out of bound proposal)")
             return -np.inf, -np.inf, -np.inf
 
         snpi_df_mod, hnpi_df_mod = self.inferpar.inject_proposal(
diff --git a/flepimop/gempyor_pkg/src/gempyor/parameters.py b/flepimop/gempyor_pkg/src/gempyor/parameters.py
index 35526084c..c013d7388 100644
--- a/flepimop/gempyor_pkg/src/gempyor/parameters.py
+++ b/flepimop/gempyor_pkg/src/gempyor/parameters.py
@@ -133,17 +133,21 @@ def __init__(
                     print("config dates:", pd.date_range(ti, tf))
                     print("loaded dates:", df.index)
                     raise ValueError(
-                        f"Issue loading file '{fn_name}' for parameter '{pn}': " 
-                        f"Provided file dates span '{str(df.index[0])}' to '{str(df.index[-1])}', "
-                        f"but the config dates span '{ti}' to '{tf}'."
+                        f"Issue loading file '{fn_name}' for parameter '{pn}': "
+                        f"the 'date' entries of the provided file do not include all the days specified to be modeled by "
+                        f"the config. The provided file includes '{len(df.index)}' days between '{str(df.index[0])}' and '{str(df.index[-1])}', " 
+                        f"while there are '{len(pd.date_range(ti, tf))}' days in the config time span of '{ti}' to '{tf}'. "
+                        f"The file must contain entries for the exact start and end dates from the config."
                     )
                 if not (pd.date_range(ti, tf) == df.index).all():
                     print("config dates:", pd.date_range(ti, tf))
                     print("loaded dates:", df.index)
                     raise ValueError(
                         f"Issue loading file '{fn_name}' for parameter '{pn}': "
-                        f"Provided file dates span '{str(df.index[0])}' to '{str(df.index[-1])}', "
-                        f"but the config dates span '{ti}' to '{tf}'."
+                        f"the 'date' entries of the provided file do not include all the days specified to be modeled by "
+                        f"the config. The provided file includes '{len(df.index)}' days between '{str(df.index[0])}' and '{str(df.index[-1])}', " 
+                        f"while there are '{len(pd.date_range(ti, tf))}' days in the config time span of '{ti}' to '{tf}'. "
+                        f"The file must contain entries for the exact start and end dates from the config."
                     )
 
                 self.pdata[pn]["ts"] = df
diff --git a/flepimop/gempyor_pkg/tests/seir/test_ic.py b/flepimop/gempyor_pkg/tests/seir/test_ic.py
index a24f141ea..b4cd240ee 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_ic.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_ic.py
@@ -44,7 +44,7 @@ def test_IC_allow_missing_node_compartments_success(self):
         sic.get_from_config(sim_id=100, modinf=s)
 
     def test_IC_IC_notImplemented_fail(self):
-        with pytest.raises(NotImplementedError, match=r"^Unknown initial conditions method \[received: .*?\]\.$"):
+        with pytest.raises(NotImplementedError, match=r".*unknown.*initial.*conditions.*"):
             config.clear()
             config.read(user=False)
             config.set_file(f"{DATA_DIR}/config.yml")

From 99b4aec107a13180cf565b3313b98dd4dba65b43 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 6 Nov 2024 13:52:42 -0500
Subject: [PATCH 45/48] Update parameters.py

Updating an error message to be more streamlined, and also match the RegEx in test_parameters_class.py
---
 flepimop/gempyor_pkg/src/gempyor/parameters.py | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/parameters.py b/flepimop/gempyor_pkg/src/gempyor/parameters.py
index 0a45883cb..7ab0de151 100644
--- a/flepimop/gempyor_pkg/src/gempyor/parameters.py
+++ b/flepimop/gempyor_pkg/src/gempyor/parameters.py
@@ -128,20 +128,16 @@ def __init__(
                     print("loaded dates:", df.index)
                     raise ValueError(
                         f"Issue loading file '{fn_name}' for parameter '{pn}': "
-                        f"the 'date' entries of the provided file do not include all the days specified to be modeled by "
-                        f"the config. The provided file includes '{len(df.index)}' days between '{str(df.index[0])}' and '{str(df.index[-1])}', " 
-                        f"while there are '{len(pd.date_range(ti, tf))}' days in the config time span of '{ti}' to '{tf}'. "
-                        f"The file must contain entries for the exact start and end dates from the config."
+                        f"Provided file dates span '{str(df.index[0])}' to '{str(df.index[-1])}', "
+                        f"but the config dates span '{ti}' to '{tf}'."
                     )
                 if not (pd.date_range(ti, tf) == df.index).all():
                     print("config dates:", pd.date_range(ti, tf))
                     print("loaded dates:", df.index)
                     raise ValueError(
                         f"Issue loading file '{fn_name}' for parameter '{pn}': "
-                        f"the 'date' entries of the provided file do not include all the days specified to be modeled by "
-                        f"the config. The provided file includes '{len(df.index)}' days between '{str(df.index[0])}' and '{str(df.index[-1])}', " 
-                        f"while there are '{len(pd.date_range(ti, tf))}' days in the config time span of '{ti}' to '{tf}'. "
-                        f"The file must contain entries for the exact start and end dates from the config."
+                        f"Provided file dates span '{str(df.index[0])}' to '{str(df.index[-1])}', "
+                        f"but the config dates span '{ti}' to '{tf}'."
                     )
 
                 self.pdata[pn]["ts"] = df

From d2f8cc28ba02ffde86b0fb03bd73e10ac2ba6b77 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 6 Nov 2024 14:58:19 -0500
Subject: [PATCH 46/48] Applying `black` to this branch

Allowing black to reformat my code
---
 .../gempyor_pkg/src/gempyor/compartments.py   | 143 +++++++++++-------
 .../src/gempyor/config_validator.py           |  89 ++++++-----
 flepimop/gempyor_pkg/src/gempyor/dev/steps.py |   4 +-
 flepimop/gempyor_pkg/src/gempyor/inference.py |   7 +-
 .../src/gempyor/initial_conditions.py         |  26 ++--
 flepimop/gempyor_pkg/src/gempyor/seeding.py   |  16 +-
 .../gempyor_pkg/src/gempyor/steps_source.py   |   4 +-
 .../tests/parameters/test_parameters_class.py |   4 +-
 .../gempyor_pkg/tests/utils/test_utils.py     |   1 -
 9 files changed, 174 insertions(+), 120 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/compartments.py b/flepimop/gempyor_pkg/src/gempyor/compartments.py
index 445759cbc..e521edffc 100644
--- a/flepimop/gempyor_pkg/src/gempyor/compartments.py
+++ b/flepimop/gempyor_pkg/src/gempyor/compartments.py
@@ -143,50 +143,68 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
         )  # it is an iterator that will go through all the indexes of the array
         for x in it:
             try:
-                new_transition_config["source"][it.multi_index] = (
-                    list_recursive_convert_to_string(
-                        self.access_original_config_by_multi_index(
-                            single_transition_config["source"], it.multi_index
-                        )
+                new_transition_config["source"][
+                    it.multi_index
+                ] = list_recursive_convert_to_string(
+                    self.access_original_config_by_multi_index(
+                        single_transition_config["source"], it.multi_index
                     )
                 )
             except Exception as e:
                 print(f"Error {e}:")
-                print(f">>> in expand_transition_elements for `source:` at index '{it.multi_index}'")
-                print(f">>> this transition source is: '{single_transition_config['source']}'")
-                print(f">>> this transition destination is: '{single_transition_config['destination']}'")
+                print(
+                    f">>> in expand_transition_elements for `source:` at index '{it.multi_index}'"
+                )
+                print(
+                    f">>> this transition source is: '{single_transition_config['source']}'"
+                )
+                print(
+                    f">>> this transition destination is: '{single_transition_config['destination']}'"
+                )
                 print(f"transition_dimension: '{problem_dimension}'")
                 raise e
 
             try:
-                new_transition_config["destination"][it.multi_index] = (
-                    list_recursive_convert_to_string(
-                        self.access_original_config_by_multi_index(
-                            single_transition_config["destination"], it.multi_index
-                        )
+                new_transition_config["destination"][
+                    it.multi_index
+                ] = list_recursive_convert_to_string(
+                    self.access_original_config_by_multi_index(
+                        single_transition_config["destination"], it.multi_index
                     )
                 )
             except Exception as e:
                 print(f"Error {e}:")
-                print(f">>> in expand_transition_elements for `destination:` at index '{it.multi_index}'")
-                print(f">>> this transition source is: '{single_transition_config['source']}'")
-                print(f">>> this transition destination is: '{single_transition_config['destination']}'")
+                print(
+                    f">>> in expand_transition_elements for `destination:` at index '{it.multi_index}'"
+                )
+                print(
+                    f">>> this transition source is: '{single_transition_config['source']}'"
+                )
+                print(
+                    f">>> this transition destination is: '{single_transition_config['destination']}'"
+                )
                 print(f"transition_dimension: '{problem_dimension}'")
                 raise e
 
             try:
-                new_transition_config["rate"][it.multi_index] = (
-                    list_recursive_convert_to_string(
-                        self.access_original_config_by_multi_index(
-                            single_transition_config["rate"], it.multi_index
-                        )
+                new_transition_config["rate"][
+                    it.multi_index
+                ] = list_recursive_convert_to_string(
+                    self.access_original_config_by_multi_index(
+                        single_transition_config["rate"], it.multi_index
                     )
                 )
             except Exception as e:
                 print(f"Error {e}:")
-                print(f">>> in expand_transition_elements for `rate:` at index '{it.multi_index}'")
-                print(f">>> this transition source is: '{single_transition_config['source']}'")
-                print(f">>> this transition destination is: '{single_transition_config['destination']}'")
+                print(
+                    f">>> in expand_transition_elements for `rate:` at index '{it.multi_index}'"
+                )
+                print(
+                    f">>> this transition source is: '{single_transition_config['source']}'"
+                )
+                print(
+                    f">>> this transition destination is: '{single_transition_config['destination']}'"
+                )
                 print(f"transition_dimension: '{problem_dimension}'")
                 raise e
 
@@ -206,9 +224,15 @@ 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}'")
-                print(f">>> this transition source is: '{single_transition_config['source']}'")
-                print(f">>> this transition destination is: '{single_transition_config['destination']}'")
+                print(
+                    f">>> in expand_transition_elements for `proportional_to:` at index '{it.multi_index}'"
+                )
+                print(
+                    f">>> this transition source is: '{single_transition_config['source']}'"
+                )
+                print(
+                    f">>> this transition destination is: '{single_transition_config['destination']}'"
+                )
                 print(f"transition_dimension: '{problem_dimension}'")
                 raise e
 
@@ -221,23 +245,29 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
                         it.multi_index,
                         problem_dimension,
                     )
-                    new_transition_config["proportion_exponent"][it.multi_index] = (
-                        list_recursive_convert_to_string(
-                            [
-                                self.access_original_config_by_multi_index(
-                                    single_transition_config["proportion_exponent"][p_idx],
-                                    it.multi_index,
-                                    problem_dimension,
-                                )
-                                for p_idx in range(proportion_size)
-                            ]
-                        )
+                    new_transition_config["proportion_exponent"][
+                        it.multi_index
+                    ] = list_recursive_convert_to_string(
+                        [
+                            self.access_original_config_by_multi_index(
+                                single_transition_config["proportion_exponent"][p_idx],
+                                it.multi_index,
+                                problem_dimension,
+                            )
+                            for p_idx in range(proportion_size)
+                        ]
                     )
                 except Exception as e:
                     print(f"Error {e}:")
-                    print(f">>> in expand_transition_elements for `proportion_exponent:` at index '{it.multi_index}'")
-                    print(f">>> this transition source is: '{single_transition_config['source']}'")
-                    print(f">>> this transition destination is: '{single_transition_config['destination']}'")
+                    print(
+                        f">>> in expand_transition_elements for `proportion_exponent:` at index '{it.multi_index}'"
+                    )
+                    print(
+                        f">>> this transition source is: '{single_transition_config['source']}'"
+                    )
+                    print(
+                        f">>> this transition destination is: '{single_transition_config['destination']}'"
+                    )
                     print(f"transition_dimension: '{problem_dimension}'")
                     raise e
             else:
@@ -349,7 +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()
@@ -475,7 +504,9 @@ def get_transition_array(self):
                         if self.compartments["name"][compartment] == elem:
                             rc = compartment
                     if rc == -1:
-                        raise ValueError(f"Could not find '{colname}' defined by '{elem}' in '{self.compartments}'.")
+                        raise ValueError(
+                            f"Could not find '{colname}' defined by '{elem}' in '{self.compartments}'."
+                        )
                     transition_array[cit, it] = rc
 
             unique_strings = []
@@ -543,9 +574,9 @@ def get_transition_array(self):
                     proportion_info[0][
                         current_proportion_sum_it
                     ] = current_proportion_sum_start
-                    proportion_info[1][current_proportion_sum_it] = (
-                        current_proportion_sum_start + len(elem_tmp)
-                    )
+                    proportion_info[1][
+                        current_proportion_sum_it
+                    ] = current_proportion_sum_start + len(elem_tmp)
                     current_proportion_sum_it += 1
                     current_proportion_sum_start += len(elem_tmp)
             proportion_compartment_index = 0
@@ -557,7 +588,7 @@ def get_transition_array(self):
                     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
@@ -707,7 +738,7 @@ 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}'. " 
+                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}'."
@@ -730,14 +761,14 @@ def parse_parameter_strings_to_numpy_arrays(
             if not is_totally_resolvable:
                 not_resolvable_indices = [it for it, x in enumerate(is_resolvable) if not x]
 
-                tmp_rc[not_resolvable_indices] = (
-                    self.parse_parameter_strings_to_numpy_arrays(
-                        parameters,
-                        parameter_names,
-                        [string[not is_resolvable]],
-                        operator_reduce_lambdas,
-                        operators[1:],
-                    )
+                tmp_rc[
+                    not_resolvable_indices
+                ] = self.parse_parameter_strings_to_numpy_arrays(
+                    parameters,
+                    parameter_names,
+                    [string[not is_resolvable]],
+                    operator_reduce_lambdas,
+                    operators[1:],
                 )
             for numeric_index in [x for x in range(len(is_numeric)) if is_numeric[x]]:
                 tmp_rc[numeric_index] = parameters[0] * 0 + float(string[numeric_index])
diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index 74909631c..128fbc6b8 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -65,20 +65,27 @@ class InitialConditionsConfig(BaseModel):
 
     @model_validator(mode="before")
     def validate_initial_file_check(cls, values):
-        method = values.get('method')
-        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"An `initial_conditions_file` is required when method is '{method}'.")
-        if method in {'InitialConditionsFolderDraw','SetInitialConditionsFolderDraw'} and not initial_file_type:
-            raise ValueError(f"An `initial_file_type` is required when method is '{method}'.")
+        method = values.get("method")
+        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"An `initial_conditions_file` is required when method is '{method}'."
+            )
+        if (
+            method in {"InitialConditionsFolderDraw", "SetInitialConditionsFolderDraw"}
+            and not initial_file_type
+        ):
+            raise ValueError(
+                f"An `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:
+        method = values.get("method")
+        plugin_file_path = values.get("plugin_file_path")
+        if method == "plugin" and not plugin_file_path:
             raise ValueError("A plugin file path is required when method is plugin.")
         return values
 
@@ -106,23 +113,27 @@ class SeedingConfig(BaseModel):
 
     @model_validator(mode="before")
     def validate_seedingfile(cls, values):
-        method = values.get('method')
-        lambda_file = values.get('lambda_file')
-        seeding_file_type = values.get('seeding_file_type')        
-        seeding_file = values.get('seeding_file')        
-        if method == 'PoissonDistributed' and not lambda_file:
-            raise ValueError("A `lambda_file` is required when method is 'PoissonDistributed'.")
-        if method == 'FolderDraw' and not seeding_file_type:
-            raise ValueError("A `seeding_file_type` is required when method is 'FolderDraw'.")
-        if method == 'FromFile' and not seeding_file:
+        method = values.get("method")
+        lambda_file = values.get("lambda_file")
+        seeding_file_type = values.get("seeding_file_type")
+        seeding_file = values.get("seeding_file")
+        if method == "PoissonDistributed" and not lambda_file:
+            raise ValueError(
+                "A `lambda_file` is required when method is 'PoissonDistributed'."
+            )
+        if method == "FolderDraw" and not seeding_file_type:
+            raise ValueError(
+                "A `seeding_file_type` is required when method is 'FolderDraw'."
+            )
+        if method == "FromFile" and not seeding_file:
             raise ValueError("A `seeding_file` is required when method is 'FromFile'.")
         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:
+        method = values.get("method")
+        plugin_file_path = values.get("plugin_file_path")
+        if method == "plugin" and not plugin_file_path:
             raise ValueError(
                 f"A plugin file path is required when method is 'plugin', "
                 f"was given '{plugin_file_path!r}'."
@@ -158,10 +169,14 @@ def check_distr(cls, values):
         b = values.get("b")
         if distr != "fixed":
             if not mean and not sd:
-                raise ValueError("Mean and sd must be provided for non-fixed distributions.")
-            if distr == 'truncnorm' and not a and not b:
-                raise ValueError("a and b must be provided for truncated normal distributions.")
-        if distr == 'fixed' and not value:
+                raise ValueError(
+                    "Mean and sd must be provided for non-fixed distributions."
+                )
+            if distr == "truncnorm" and not a and not b:
+                raise ValueError(
+                    "a and b must be provided for truncated normal distributions."
+                )
+        if distr == "fixed" and not value:
             raise ValueError("Value must be provided for fixed distributions.")
         return values
 
@@ -169,9 +184,9 @@ def check_distr(cls, values):
 class BaseParameterConfig(BaseModel):
     value: Optional[ValueConfig] = None
     modifier_parameter: Optional[str] = None
-    name: Optional[str] = (
-        None  # this is only for outcomes, to build outcome_prevalence_name (how to restrict this?)
-    )
+    name: Optional[
+        str
+    ] = None  # this is only for outcomes, to build outcome_prevalence_name (how to restrict this?)
 
 
 class SeirParameterConfig(BaseParameterConfig):
@@ -282,7 +297,7 @@ def which_source(cls, values):
         if incidence and prevalence:
             raise ValueError(
                 f"Parsed a source with both an incidence, '{values.get('incidence')!r}', and prevalence, '{values.get('prevalence')!r}', please choose one."
-                )
+            )
         return values
 
     # @model_validator(mode='before') # DOES NOT WORK
@@ -339,7 +354,9 @@ 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("A `param_subpop_file` is required when `param_from_file` is 'True'.")
+            raise ValueError(
+                "A `param_subpop_file` is required when `param_from_file` is 'True'."
+            )
         return values
 
 
@@ -423,7 +440,9 @@ 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. Please provide groundtruth dates.")
+            raise ValueError(
+                "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. Please enable inference mode."
@@ -443,10 +462,10 @@ def check_dates(cls, values):
 
     @model_validator(mode="before")
     def init_or_seed(cls, values):
-        init = values.get('initial_conditions')
-        seed = values.get('seeding')
+        init = values.get("initial_conditions")
+        seed = values.get("seeding")
         if not (init or seed):
             raise ValueError(
                 f"At least one of `initial_conditions` or `seeding` must be provided."
-                )
+            )
         return values
diff --git a/flepimop/gempyor_pkg/src/gempyor/dev/steps.py b/flepimop/gempyor_pkg/src/gempyor/dev/steps.py
index 1bbf5b207..3ddde56ee 100644
--- a/flepimop/gempyor_pkg/src/gempyor/dev/steps.py
+++ b/flepimop/gempyor_pkg/src/gempyor/dev/steps.py
@@ -1693,9 +1693,7 @@ def rk4_integrate(today, x):
     ## Return
     "UniTuple(float64[:, :, :], 2) ("  ## return states and cumlative states, both [ ndays x ncompartments x nspatial_nodes ]
     ## Dimensions
-    "int32,"
-    "int32,"
-    "int32,"  ## ncompartments  ## nspatial_nodes  ## Number of days
+    "int32," "int32," "int32,"  ## ncompartments  ## nspatial_nodes  ## Number of days
     ## Parameters
     "float64[:, :, :],"
     "float64,"  ## Parameters [ nparameters x ndays x nspatial_nodes]  ## dt
diff --git a/flepimop/gempyor_pkg/src/gempyor/inference.py b/flepimop/gempyor_pkg/src/gempyor/inference.py
index aae76eaff..823ba52b3 100644
--- a/flepimop/gempyor_pkg/src/gempyor/inference.py
+++ b/flepimop/gempyor_pkg/src/gempyor/inference.py
@@ -353,9 +353,10 @@ def __init__(
 
         config.set_file(os.path.join(path_prefix, config_filepath))
 
-        self.seir_modifiers_scenario, self.outcome_modifiers_scenario = (
-            autodetect_scenarios(config)
-        )
+        (
+            self.seir_modifiers_scenario,
+            self.outcome_modifiers_scenario,
+        ) = autodetect_scenarios(config)
 
         if run_id is None:
             run_id = file_paths.run_id()
diff --git a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
index b86226cca..1926b5513 100644
--- a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
+++ b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
@@ -116,7 +116,9 @@ def get_from_config(self, sim_id: int, modinf) -> np.ndarray:
                 allow_missing_subpops=self.allow_missing_subpops,
             )
         else:
-            raise NotImplementedError(f"Unknown initial conditions method [received: '{method}'].")
+            raise NotImplementedError(
+                f"Unknown initial conditions method [received: '{method}']."
+            )
 
         # check that the inputed values sums to the subpop population:
         check_population(
@@ -147,13 +149,14 @@ def check_population(y0, modinf, ignore_population_checks=False):
             )
 
     if error and not ignore_population_checks:
-        raise ValueError("Geodata and initial condition do not agree on population size. Use `ignore_population_checks: True` to ignore."
+        raise ValueError(
+            "Geodata and initial condition do not agree on population size. Use `ignore_population_checks: True` to ignore."
         )
     elif error and ignore_population_checks:
         warnings.warn(
-        "Population mismatch errors ignored because `ignore_population_checks` is set to `True`. "
-        "Execution will continue, but this is not recommended.",
-        UserWarning
+            "Population mismatch errors ignored because `ignore_population_checks` is set to `True`. "
+            "Execution will continue, but this is not recommended.",
+            UserWarning,
         )
 
 
@@ -201,7 +204,9 @@ def read_initial_condition_from_tidydataframe(
             logger.critical(
                 f"No initial conditions for for subpop {pl}, assuming everyone (n={modinf.subpop_pop[pl_idx]}) in the first metacompartment ({modinf.compartments.compartments['name'].iloc[0]})"
             )
-            raise RuntimeError("There is a bug; report this message. Past implemenation was buggy.")
+            raise RuntimeError(
+                "There is a bug; report this message. Past implemenation was buggy."
+            )
             # TODO: this is probably ok but highlighting for consistency
             if "proportional" in self.initial_conditions_config.keys():
                 if self.initial_conditions_config["proportional"].get():
@@ -258,8 +263,9 @@ def read_initial_condition_from_seir_output(
         (ic_df["date"] == str(modinf.ti)) & (ic_df["mc_value_type"] == "prevalence")
     ]
     if ic_df.empty:
-        raise ValueError(f"No entry provided for initial time `ti` in the `initial_conditions::states_file.` "
-                         f"`ti`: '{modinf.ti}'."
+        raise ValueError(
+            f"No entry provided for initial time `ti` in the `initial_conditions::states_file.` "
+            f"`ti`: '{modinf.ti}'."
         )
     y0 = np.zeros((modinf.compartments.compartments.shape[0], modinf.nsubpops))
 
@@ -300,7 +306,9 @@ def read_initial_condition_from_seir_output(
             if pl in ic_df.columns:
                 y0[comp_idx, pl_idx] = float(ic_df_compartment[pl].iloc[0])
             elif allow_missing_subpops:
-                raise RuntimeError("There is a bug; report this message. Past implemenation was buggy")
+                raise RuntimeError(
+                    "There is a bug; report this message. Past implemenation was buggy"
+                )
                 # TODO this should set the full subpop, not just the 0th commpartment
                 logger.critical(
                     f"No initial conditions for for subpop {pl}, assuming everyone (n={modinf.subpop_pop[pl_idx]}) in the first metacompartments ({modinf.compartments.compartments['name'].iloc[0]})"
diff --git a/flepimop/gempyor_pkg/src/gempyor/seeding.py b/flepimop/gempyor_pkg/src/gempyor/seeding.py
index 53b81c8dc..885c446ba 100644
--- a/flepimop/gempyor_pkg/src/gempyor/seeding.py
+++ b/flepimop/gempyor_pkg/src/gempyor/seeding.py
@@ -59,15 +59,15 @@ def _DataFrame2NumbaDict(df, amounts, modinf) -> nb.typed.Dict:
                     source_dict,
                     error_info=f"(seeding source at idx={idx}, row_index={row_index}, row=>>{row}<<)",
                 )
-                seeding_dict["seeding_destinations"][idx] = (
-                    modinf.compartments.get_comp_idx(
-                        destination_dict,
-                        error_info=f"(seeding destination at idx={idx}, row_index={row_index}, row=>>{row}<<)",
-                    )
-                )
-                seeding_dict["seeding_subpops"][idx] = (
-                    modinf.subpop_struct.subpop_names.index(row["subpop"])
+                seeding_dict["seeding_destinations"][
+                    idx
+                ] = modinf.compartments.get_comp_idx(
+                    destination_dict,
+                    error_info=f"(seeding destination at idx={idx}, row_index={row_index}, row=>>{row}<<)",
                 )
+                seeding_dict["seeding_subpops"][
+                    idx
+                ] = modinf.subpop_struct.subpop_names.index(row["subpop"])
                 seeding_amounts[idx] = amounts[idx]
                 # id_seed+=1
             else:
diff --git a/flepimop/gempyor_pkg/src/gempyor/steps_source.py b/flepimop/gempyor_pkg/src/gempyor/steps_source.py
index ea6f7ad21..13d5a7ed5 100644
--- a/flepimop/gempyor_pkg/src/gempyor/steps_source.py
+++ b/flepimop/gempyor_pkg/src/gempyor/steps_source.py
@@ -30,9 +30,7 @@
     ## Return
     "UniTuple(float64[:, :, :], 2) ("  ## return states and cumlative states, both [ ndays x ncompartments x nspatial_nodes ]
     ## Dimensions
-    "int32,"
-    "int32,"
-    "int32,"  ## ncompartments  ## nspatial_nodes  ## Number of days
+    "int32," "int32," "int32,"  ## ncompartments  ## nspatial_nodes  ## Number of days
     ## Parameters
     "float64[:, :, :],"
     "float64,"  ## Parameters [ nparameters x ndays x nspatial_nodes]  ## dt
diff --git a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
index e18cdaca2..f82cf2a27 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -237,8 +237,8 @@ def test_timeseries_parameter_has_insufficient_columns_value_error(
         with pytest.raises(
             ValueError,
             match=(
-                rf"^Issue loading file '{tmp_file}' for parameter 'sigma': " 
-                rf"the number of non-'date' columns is '{actual_columns}', expected '{mock_inputs.number_of_subpops()}' " 
+                rf"^Issue loading file '{tmp_file}' for parameter 'sigma': "
+                rf"the number of non-'date' columns is '{actual_columns}', expected '{mock_inputs.number_of_subpops()}' "
                 rf"\(number of subpopulations\) or one\.$"
             ),
         ):
diff --git a/flepimop/gempyor_pkg/tests/utils/test_utils.py b/flepimop/gempyor_pkg/tests/utils/test_utils.py
index 058e2401b..87e7c4fbb 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_utils.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_utils.py
@@ -115,7 +115,6 @@ def test_create_resume_out_filename():
 
 
 def test_create_resume_input_filename():
-
     result = utils.create_resume_input_filename(
         flepi_slot_index="2",
         resume_run_index="321",

From cde6acbcb20eaf313dfcc1a7e3e2c702cdb6b59b Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 8 Nov 2024 11:07:11 -0500
Subject: [PATCH 47/48] linting my code with `black`

---
 .../gempyor_pkg/src/gempyor/compartments.py   | 74 +++++++++----------
 .../src/gempyor/config_validator.py           |  6 +-
 flepimop/gempyor_pkg/src/gempyor/dev/steps.py |  4 +-
 flepimop/gempyor_pkg/src/gempyor/seeding.py   | 16 ++--
 .../gempyor_pkg/src/gempyor/steps_source.py   |  4 +-
 5 files changed, 54 insertions(+), 50 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/compartments.py b/flepimop/gempyor_pkg/src/gempyor/compartments.py
index e521edffc..da503357f 100644
--- a/flepimop/gempyor_pkg/src/gempyor/compartments.py
+++ b/flepimop/gempyor_pkg/src/gempyor/compartments.py
@@ -143,11 +143,11 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
         )  # it is an iterator that will go through all the indexes of the array
         for x in it:
             try:
-                new_transition_config["source"][
-                    it.multi_index
-                ] = list_recursive_convert_to_string(
-                    self.access_original_config_by_multi_index(
-                        single_transition_config["source"], it.multi_index
+                new_transition_config["source"][it.multi_index] = (
+                    list_recursive_convert_to_string(
+                        self.access_original_config_by_multi_index(
+                            single_transition_config["source"], it.multi_index
+                        )
                     )
                 )
             except Exception as e:
@@ -165,11 +165,11 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
                 raise e
 
             try:
-                new_transition_config["destination"][
-                    it.multi_index
-                ] = list_recursive_convert_to_string(
-                    self.access_original_config_by_multi_index(
-                        single_transition_config["destination"], it.multi_index
+                new_transition_config["destination"][it.multi_index] = (
+                    list_recursive_convert_to_string(
+                        self.access_original_config_by_multi_index(
+                            single_transition_config["destination"], it.multi_index
+                        )
                     )
                 )
             except Exception as e:
@@ -187,11 +187,11 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
                 raise e
 
             try:
-                new_transition_config["rate"][
-                    it.multi_index
-                ] = list_recursive_convert_to_string(
-                    self.access_original_config_by_multi_index(
-                        single_transition_config["rate"], it.multi_index
+                new_transition_config["rate"][it.multi_index] = (
+                    list_recursive_convert_to_string(
+                        self.access_original_config_by_multi_index(
+                            single_transition_config["rate"], it.multi_index
+                        )
                     )
                 )
             except Exception as e:
@@ -245,17 +245,17 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
                         it.multi_index,
                         problem_dimension,
                     )
-                    new_transition_config["proportion_exponent"][
-                        it.multi_index
-                    ] = list_recursive_convert_to_string(
-                        [
-                            self.access_original_config_by_multi_index(
-                                single_transition_config["proportion_exponent"][p_idx],
-                                it.multi_index,
-                                problem_dimension,
-                            )
-                            for p_idx in range(proportion_size)
-                        ]
+                    new_transition_config["proportion_exponent"][it.multi_index] = (
+                        list_recursive_convert_to_string(
+                            [
+                                self.access_original_config_by_multi_index(
+                                    single_transition_config["proportion_exponent"][p_idx],
+                                    it.multi_index,
+                                    problem_dimension,
+                                )
+                                for p_idx in range(proportion_size)
+                            ]
+                        )
                     )
                 except Exception as e:
                     print(f"Error {e}:")
@@ -574,9 +574,9 @@ def get_transition_array(self):
                     proportion_info[0][
                         current_proportion_sum_it
                     ] = current_proportion_sum_start
-                    proportion_info[1][
-                        current_proportion_sum_it
-                    ] = current_proportion_sum_start + len(elem_tmp)
+                    proportion_info[1][current_proportion_sum_it] = (
+                        current_proportion_sum_start + len(elem_tmp)
+                    )
                     current_proportion_sum_it += 1
                     current_proportion_sum_start += len(elem_tmp)
             proportion_compartment_index = 0
@@ -761,14 +761,14 @@ def parse_parameter_strings_to_numpy_arrays(
             if not is_totally_resolvable:
                 not_resolvable_indices = [it for it, x in enumerate(is_resolvable) if not x]
 
-                tmp_rc[
-                    not_resolvable_indices
-                ] = self.parse_parameter_strings_to_numpy_arrays(
-                    parameters,
-                    parameter_names,
-                    [string[not is_resolvable]],
-                    operator_reduce_lambdas,
-                    operators[1:],
+                tmp_rc[not_resolvable_indices] = (
+                    self.parse_parameter_strings_to_numpy_arrays(
+                        parameters,
+                        parameter_names,
+                        [string[not is_resolvable]],
+                        operator_reduce_lambdas,
+                        operators[1:],
+                    )
                 )
             for numeric_index in [x for x in range(len(is_numeric)) if is_numeric[x]]:
                 tmp_rc[numeric_index] = parameters[0] * 0 + float(string[numeric_index])
diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index 128fbc6b8..37e749c6d 100644
--- a/flepimop/gempyor_pkg/src/gempyor/config_validator.py
+++ b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
@@ -184,9 +184,9 @@ def check_distr(cls, values):
 class BaseParameterConfig(BaseModel):
     value: Optional[ValueConfig] = None
     modifier_parameter: Optional[str] = None
-    name: Optional[
-        str
-    ] = None  # this is only for outcomes, to build outcome_prevalence_name (how to restrict this?)
+    name: Optional[str] = (
+        None  # this is only for outcomes, to build outcome_prevalence_name (how to restrict this?)
+    )
 
 
 class SeirParameterConfig(BaseParameterConfig):
diff --git a/flepimop/gempyor_pkg/src/gempyor/dev/steps.py b/flepimop/gempyor_pkg/src/gempyor/dev/steps.py
index 3ddde56ee..1bbf5b207 100644
--- a/flepimop/gempyor_pkg/src/gempyor/dev/steps.py
+++ b/flepimop/gempyor_pkg/src/gempyor/dev/steps.py
@@ -1693,7 +1693,9 @@ def rk4_integrate(today, x):
     ## Return
     "UniTuple(float64[:, :, :], 2) ("  ## return states and cumlative states, both [ ndays x ncompartments x nspatial_nodes ]
     ## Dimensions
-    "int32," "int32," "int32,"  ## ncompartments  ## nspatial_nodes  ## Number of days
+    "int32,"
+    "int32,"
+    "int32,"  ## ncompartments  ## nspatial_nodes  ## Number of days
     ## Parameters
     "float64[:, :, :],"
     "float64,"  ## Parameters [ nparameters x ndays x nspatial_nodes]  ## dt
diff --git a/flepimop/gempyor_pkg/src/gempyor/seeding.py b/flepimop/gempyor_pkg/src/gempyor/seeding.py
index 885c446ba..53b81c8dc 100644
--- a/flepimop/gempyor_pkg/src/gempyor/seeding.py
+++ b/flepimop/gempyor_pkg/src/gempyor/seeding.py
@@ -59,15 +59,15 @@ def _DataFrame2NumbaDict(df, amounts, modinf) -> nb.typed.Dict:
                     source_dict,
                     error_info=f"(seeding source at idx={idx}, row_index={row_index}, row=>>{row}<<)",
                 )
-                seeding_dict["seeding_destinations"][
-                    idx
-                ] = modinf.compartments.get_comp_idx(
-                    destination_dict,
-                    error_info=f"(seeding destination at idx={idx}, row_index={row_index}, row=>>{row}<<)",
+                seeding_dict["seeding_destinations"][idx] = (
+                    modinf.compartments.get_comp_idx(
+                        destination_dict,
+                        error_info=f"(seeding destination at idx={idx}, row_index={row_index}, row=>>{row}<<)",
+                    )
+                )
+                seeding_dict["seeding_subpops"][idx] = (
+                    modinf.subpop_struct.subpop_names.index(row["subpop"])
                 )
-                seeding_dict["seeding_subpops"][
-                    idx
-                ] = modinf.subpop_struct.subpop_names.index(row["subpop"])
                 seeding_amounts[idx] = amounts[idx]
                 # id_seed+=1
             else:
diff --git a/flepimop/gempyor_pkg/src/gempyor/steps_source.py b/flepimop/gempyor_pkg/src/gempyor/steps_source.py
index 13d5a7ed5..ea6f7ad21 100644
--- a/flepimop/gempyor_pkg/src/gempyor/steps_source.py
+++ b/flepimop/gempyor_pkg/src/gempyor/steps_source.py
@@ -30,7 +30,9 @@
     ## Return
     "UniTuple(float64[:, :, :], 2) ("  ## return states and cumlative states, both [ ndays x ncompartments x nspatial_nodes ]
     ## Dimensions
-    "int32," "int32," "int32,"  ## ncompartments  ## nspatial_nodes  ## Number of days
+    "int32,"
+    "int32,"
+    "int32,"  ## ncompartments  ## nspatial_nodes  ## Number of days
     ## Parameters
     "float64[:, :, :],"
     "float64,"  ## Parameters [ nparameters x ndays x nspatial_nodes]  ## dt

From 7b4f6e8ecc8ef4bf113e0dc5442dbdab16aa7dab Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 8 Nov 2024 12:17:02 -0500
Subject: [PATCH 48/48] Capitalization correct in a RegEx in `test_ic.py`

---
 flepimop/gempyor_pkg/tests/seir/test_ic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/seir/test_ic.py b/flepimop/gempyor_pkg/tests/seir/test_ic.py
index e9c275347..6d39a8ad6 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_ic.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_ic.py
@@ -48,7 +48,7 @@ def test_IC_allow_missing_node_compartments_success(self):
         sic.get_from_config(sim_id=100, modinf=s)
 
     def test_IC_IC_notImplemented_fail(self):
-        with pytest.raises(NotImplementedError, match=r".*unknown.*initial.*conditions.*"):
+        with pytest.raises(NotImplementedError, match=r".*Unknown.*initial.*conditions.*"):
             config.clear()
             config.read(user=False)
             config.set_file(f"{DATA_DIR}/config.yml")