From f67d3bcca083579382aafd48546da7da6402e760 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 1 Nov 2024 11:26:04 -0400
Subject: [PATCH 01/56] Improving errors in another set of `gempyor` files

Includes model_info.py, outcomes.py, seeding.py, seir.py, and simulation_component.py (this last one didn't require any edits).
---
 .../gempyor_pkg/src/gempyor/model_info.py     | 33 ++++++++-----------
 flepimop/gempyor_pkg/src/gempyor/outcomes.py  | 22 +++++++------
 flepimop/gempyor_pkg/src/gempyor/seeding.py   |  8 ++---
 flepimop/gempyor_pkg/src/gempyor/seir.py      | 12 +++----
 4 files changed, 35 insertions(+), 40 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/model_info.py b/flepimop/gempyor_pkg/src/gempyor/model_info.py
index 54f981d8f..e28c22e02 100644
--- a/flepimop/gempyor_pkg/src/gempyor/model_info.py
+++ b/flepimop/gempyor_pkg/src/gempyor/model_info.py
@@ -11,7 +11,7 @@ def __init__(self, config: confuse.ConfigView):
         self.ti = config["start_date"].as_date()
         self.tf = config["end_date"].as_date()
         if self.tf <= self.ti:
-            raise ValueError("tf (time to finish) is less than or equal to ti (time to start)")
+            raise ValueError("`tf` (time to finish) is less than or equal to `ti` (time to start).")
         self.n_days = (self.tf - self.ti).days + 1
         self.dates = pd.date_range(start=self.ti, end=self.tf, freq="D")
 
@@ -67,9 +67,8 @@ def __init__(
         # Auto-detect old config
         if config["interventions"].exists():
             raise ValueError(
-                """This config has an intervention section, and has been written for a previous version of flepiMoP/COVIDScenarioPipeline \
-                             Please use flepiMoP Version 1.1 (Commit SHA: 0c30c23937dd496d33c2b9fa7c6edb198ad80dac) to run this config. \
-                             (use git checkout v1.1 inside the flepiMoP directory)"""
+                "This config has an intervention section, which is only compatible with a previous version of flepiMoP/COVIDScenarioPipeline. "
+                "Please use flepiMoP Version 1.1 to run this config."
             )
 
         # 1. Create a setup name that contains every scenario.
@@ -94,7 +93,7 @@ def __init__(
         # 3. What about subpopulations
         subpop_config = config["subpop_setup"]
         if "data_path" in config:
-            raise ValueError("The config has a data_path section. This is no longer supported.")
+            raise ValueError("The config has a `data_path` section. This is no longer supported.")
         self.path_prefix = pathlib.Path(path_prefix)
 
         self.subpop_struct = subpopulation_structure.SubpopulationStructure(
@@ -148,16 +147,14 @@ def __init__(
                     self.seir_modifiers_library = config["seir_modifiers"]["modifiers"].get()
                 else:
                     self.seir_modifiers_library = config["seir_modifiers"]["modifiers"].get()
-                    raise ValueError("Not implemented yet")  # TODO create a Stacked from all
+                    raise ValueError("This feature has not been implemented yet.")  # TODO create a Stacked from all
             elif self.seir_modifiers_scenario is not None:
-                raise ValueError(
-                    "An seir modifiers scenario was provided to ModelInfo but no 'seir_modifiers' sections in config"
-                )
+                raise ValueError("A seir modifiers scenario was provided to `ModelInfo` but there is no `seir_modifiers` sections in config.")
             else:
-                logging.info("Running ModelInfo with seir but without SEIR Modifiers")
+                logging.info("Running `ModelInfo` with seir but without SEIR Modifiers")
 
         elif self.seir_modifiers_scenario is not None:
-            raise ValueError("A seir modifiers scenario was provided to ModelInfo but no 'seir:' sections in config")
+            raise ValueError("A seir modifiers scenario was provided to `ModelInfo` but there is no `seir_modifiers` sections in config.")
         else:
             logging.critical("Running ModelInfo without SEIR")
 
@@ -171,24 +168,20 @@ def __init__(
                     self.outcome_modifiers_library = config["outcome_modifiers"]["modifiers"].get()
                 else:
                     self.outcome_modifiers_library = config["outcome_modifiers"]["modifiers"].get()
-                    raise ValueError("Not implemented yet")  # TODO create a Stacked from all
+                    raise ValueError("This feature has not been implemented yet.")  # TODO create a Stacked from all
 
             ## NEED TO IMPLEMENT THIS -- CURRENTLY CANNOT USE outcome modifiers
             elif self.outcome_modifiers_scenario is not None:
                 if config["outcome_modifiers"].exists():
-                    raise ValueError(
-                        "An outcome modifiers scenario was provided to ModelInfo but no 'outcome_modifiers' sections in config"
-                    )
+                    raise ValueError("An outcome modifiers scenario was provided to `ModelInfo` but there is no `outcome_modifiers` sections in config.")
                 else:
                     self.outcome_modifiers_scenario = None
             else:
-                logging.info("Running ModelInfo with outcomes but without Outcomes Modifiers")
+                logging.info("Running `ModelInfo` with outcomes but without Outcomes Modifiers")
         elif self.outcome_modifiers_scenario is not None:
-            raise ValueError(
-                "An outcome modifiers scenario was provided to ModelInfo but no 'outcomes:' sections in config"
-            )
+            raise ValueError("An outcome modifiers scenario was provided to `ModelInfo` but there is no `outcome_modifiers` sections in config.")
         else:
-            logging.info("Running ModelInfo without Outcomes")
+            logging.info("Running `ModelInfo` without Outcomes")
 
         # 6. Inputs and outputs
         if in_run_id is None:
diff --git a/flepimop/gempyor_pkg/src/gempyor/outcomes.py b/flepimop/gempyor_pkg/src/gempyor/outcomes.py
index 5563f4d85..cae19c275 100644
--- a/flepimop/gempyor_pkg/src/gempyor/outcomes.py
+++ b/flepimop/gempyor_pkg/src/gempyor/outcomes.py
@@ -133,7 +133,7 @@ def read_parameters_from_config(modinf: model_info.ModelInfo):
                 branching_data = pa.parquet.read_table(branching_file).to_pandas()
                 if "relative_probability" not in list(branching_data["quantity"]):
                     raise ValueError(
-                        f"No 'relative_probability' quantity in {branching_file}, therefor making it useless"
+                        f"There is no `relative_probability` quantity in '{branching_file}'."
                     )
 
                 print(
@@ -151,7 +151,7 @@ def read_parameters_from_config(modinf: model_info.ModelInfo):
 
                 if len(branching_data.subpop.unique()) != len(modinf.subpop_struct.subpop_names):
                     raise ValueError(
-                        f"Places in seir input files does not correspond to subpops in outcome probability file {branching_file}"
+                        f"SEIR input files do not have subpops that match those in outcome probability file '{branching_file}'."
                     )
 
         parameters = {}
@@ -167,7 +167,9 @@ def read_parameters_from_config(modinf: model_info.ModelInfo):
 
                 else:
                     raise ValueError(
-                        f"unsure how to read outcome {new_comp}: not a str, nor an incidence or prevalence: {src_name}"
+                        f"Unable to read outcome '{new_comp}': "
+                        f"expected a string or dictionary containing `incidence` or `prevalence`. " 
+                        f"Recieved: '{src_name}'." 
                     )
 
                 parameters[new_comp]["probability"] = outcomes_config[new_comp]["probability"]["value"]
@@ -248,7 +250,7 @@ def read_parameters_from_config(modinf: model_info.ModelInfo):
                 parameters[new_comp] = {}
                 parameters[new_comp]["sum"] = outcomes_config[new_comp]["sum"].get()
             else:
-                raise ValueError(f"No 'source' or 'sum' specified for comp {new_comp}")
+                raise ValueError(f"No `source` or `sum` specified for comp '{new_comp}'.")
 
     return parameters
 
@@ -348,14 +350,14 @@ def compute_all_multioutcomes(
                         outcome_name=new_comp,
                     )
                 else:
-                    raise ValueError(f"Unknown type for seir simulation provided, got f{type(seir_sim)}")
+                    raise ValueError(f"Unknown type provided for seir simulation, received '{type(seir_sim)}'.")
                 # we don't keep source in this cases
             else:  # already defined outcomes
                 if source_name in all_data:
                     source_array = all_data[source_name]
                 else:
                     raise ValueError(
-                        f"ERROR with outcome {new_comp}: the specified source {source_name} is not a dictionnary (for seir outcome) nor an existing pre-identified outcomes."
+                        f"Issue with outcome '{new_comp}'; the specified source '{source_name}' is neither a dictionnary (for seir outcome) nor an existing pre-identified outcome."
                     )
 
             if (loaded_values is not None) and (new_comp in loaded_values["outcome"].values):
@@ -510,7 +512,7 @@ def filter_seir_df(diffI, dates, subpops, filters, outcome_name) -> np.ndarray:
         vtype = "prevalence"
     else:
         raise ValueError(
-            f"Cannot distinguish the source of outcome {outcome_name}: it is not another previously defined outcome and there is no 'incidence:' or 'prevalence:'."
+            f"Cannot discern the source of outcome '{outcome_name}'; it is not a previously defined outcome and there is no `incidence` or `prevalence`."
         )
 
     diffI = diffI[diffI["mc_value_type"] == vtype]
@@ -539,7 +541,7 @@ def filter_seir_xr(diffI, dates, subpops, filters, outcome_name) -> np.ndarray:
         vtype = "prevalence"
     else:
         raise ValueError(
-            f"Cannot distinguish the source of outcome {outcome_name}: it is not another previously defined outcome and there is no 'incidence:' or 'prevalence:'."
+            f"Cannot discern the source of outcome '{outcome_name}'; it is not a previously defined outcome and there is no `incidence` or `prevalence`."
         )
     # Filter the data
     filters = filters[vtype]
@@ -587,7 +589,7 @@ def multishiftee(arr, shifts, stoch_delay_flag=True):
     result = np.zeros_like(arr)
 
     if stoch_delay_flag:
-        raise ValueError("NOT SUPPORTED YET")
+        raise ValueError("`stoch_delay_flag` not supported yet.")
         # for i, row in reversed(enumerate(np.rows(arr))):
         #    for j,elem in reversed(enumerate(row)):
         ## This function takes in :
@@ -613,7 +615,7 @@ def multishift(arr, shifts, stoch_delay_flag=True):
     result = np.zeros_like(arr)
 
     if stoch_delay_flag:
-        raise ValueError("NOT SUPPORTED YET")
+        raise ValueError("`stoch_delay_flag` not supported yet.")
         # for i, row in reversed(enumerate(np.rows(arr))):
         #    for j,elem in reversed(enumerate(row)):
         ## This function takes in :
diff --git a/flepimop/gempyor_pkg/src/gempyor/seeding.py b/flepimop/gempyor_pkg/src/gempyor/seeding.py
index fe58657c0..bb774e0b5 100644
--- a/flepimop/gempyor_pkg/src/gempyor/seeding.py
+++ b/flepimop/gempyor_pkg/src/gempyor/seeding.py
@@ -17,7 +17,7 @@
 
 def _DataFrame2NumbaDict(df, amounts, modinf) -> nb.typed.Dict:
     if not df["date"].is_monotonic_increasing:
-        raise ValueError("_DataFrame2NumbaDict got an unsorted dataframe, exposing itself to non-sense")
+        raise ValueError("`_DataFrame2NumbaDict` got an unsorted dataframe.")
 
     cmp_grp_names = [col for col in modinf.compartments.compartments.columns if col != "name"]
     seeding_dict: nb.typed.Dict = nb.typed.Dict.empty(
@@ -97,7 +97,7 @@ def get_from_config(self, sim_id: int, modinf) -> nb.typed.Dict:
             )
             dupes = seeding[seeding.duplicated(["subpop", "date"])].index + 1
             if not dupes.empty:
-                raise ValueError(f"Repeated subpop-date in rows {dupes.tolist()} of seeding::lambda_file.")
+                raise ValueError(f"There are repeating subpop-date in rows '{dupes.tolist()}' of `seeding::lambda_file`.")
         elif method == "FolderDraw":
             seeding = pd.read_csv(
                 self.path_prefix
@@ -121,7 +121,7 @@ def get_from_config(self, sim_id: int, modinf) -> nb.typed.Dict:
             seeding = pd.DataFrame(columns=["date", "subpop"])
             return _DataFrame2NumbaDict(df=seeding, amounts=[], modinf=modinf)
         else:
-            raise NotImplementedError(f"unknown seeding method [got: {method}]")
+            raise NotImplementedError(f"Unknown seeding method [received: '{method}'].")
 
         # Sorting by date is very important here for the seeding format necessary !!!!
         # print(seeding.shape)
@@ -142,7 +142,7 @@ def get_from_config(self, sim_id: int, modinf) -> nb.typed.Dict:
         elif method == "FolderDraw" or method == "FromFile":
             amounts = seeding["amount"]
         else:
-            raise ValueError(f"Unknown seeding method: {method}")
+            raise ValueError(f"Unknown seeding method [received: '{method}'].")
 
         return _DataFrame2NumbaDict(df=seeding, amounts=amounts, modinf=modinf)
 
diff --git a/flepimop/gempyor_pkg/src/gempyor/seir.py b/flepimop/gempyor_pkg/src/gempyor/seir.py
index 4e59761f2..80b8c1021 100644
--- a/flepimop/gempyor_pkg/src/gempyor/seir.py
+++ b/flepimop/gempyor_pkg/src/gempyor/seir.py
@@ -31,7 +31,7 @@ def build_step_source_arg(
             if integration_method == "rk4":
                 integration_method = "rk4.jit"
             if integration_method not in ["rk4.jit", "legacy"]:
-                raise ValueError(f"Unknown integration method {integration_method}.")
+                raise ValueError(f"Unknown integration method [received: '{integration_method}'].")
         if "dt" in modinf.seir_config["integration"].keys():
             dt = float(
                 eval(str(modinf.seir_config["integration"]["dt"].get()))
@@ -143,8 +143,8 @@ def steps_SEIR(
     elif integration_method == "rk4.jit":
         if modinf.stoch_traj_flag == True:
             raise ValueError(
-                f"with method {integration_method}, only deterministic "
-                f"integration is possible (got stoch_straj_flag={modinf.stoch_traj_flag}"
+                f"With method '{integration_method}', only deterministic "
+                f"integration is possible (received `stoch_straj_flag` = '{modinf.stoch_traj_flag}')."
             )
         seir_sim = steps_rk4.rk4_integration(**fnct_args, silent=True)
     else:
@@ -159,8 +159,8 @@ def steps_SEIR(
         ]:
             if modinf.stoch_traj_flag == True:
                 raise ValueError(
-                    f"with method {integration_method}, only deterministic "
-                    f"integration is possible (got stoch_straj_flag={modinf.stoch_traj_flag}"
+                    f"With method '{integration_method}', only deterministic "
+                    f"integration is possible (received `stoch_straj_flag` = '{modinf.stoch_traj_flag}')."
                 )
             seir_sim = steps_experimental.ode_integration(**fnct_args, integration_method=integration_method)
         elif integration_method == "rk4.jit1":
@@ -180,7 +180,7 @@ def steps_SEIR(
         elif integration_method == "rk4_aot":
             seir_sim = steps_experimental.rk4_aot(**fnct_args)
         else:
-            raise ValueError(f"Unknow integration scheme, got {integration_method}")
+            raise ValueError(f"Unknown integration method [received '{integration_method}'].")
 
     # We return an xarray instead of a ndarray now
     compartment_coords = {}

From 90b361819fe6f8918513ffbd40a8418e3e86b710 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 8 Nov 2024 14:08:13 -0500
Subject: [PATCH 02/56] Applied `black` linting to this branch

---
 .../gempyor_pkg/src/gempyor/compartments.py   | 68 +++++++++++++-----
 .../src/gempyor/config_validator.py           | 69 +++++++++++--------
 .../src/gempyor/initial_conditions.py         | 27 +++++---
 .../gempyor_pkg/src/gempyor/model_info.py     | 44 +++++++++---
 flepimop/gempyor_pkg/src/gempyor/outcomes.py  |  8 ++-
 .../gempyor_pkg/src/gempyor/parameters.py     |  2 +-
 flepimop/gempyor_pkg/src/gempyor/seeding.py   |  4 +-
 flepimop/gempyor_pkg/src/gempyor/seir.py      |  8 ++-
 .../tests/parameters/test_parameters_class.py |  4 +-
 flepimop/gempyor_pkg/tests/seir/test_ic.py    |  5 +-
 10 files changed, 164 insertions(+), 75 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/compartments.py b/flepimop/gempyor_pkg/src/gempyor/compartments.py
index 7f19e8508..a379781f8 100644
--- a/flepimop/gempyor_pkg/src/gempyor/compartments.py
+++ b/flepimop/gempyor_pkg/src/gempyor/compartments.py
@@ -152,9 +152,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
                 )
             except Exception as e:
                 print(f"Error {e}:")
-                print(f">>> in expand_transition_elements for `source:` at index '{it.multi_index}'")
-                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
 
@@ -168,9 +174,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
                 )
             except Exception as e:
                 print(f"Error {e}:")
-                print(f">>> in expand_transition_elements for `destination:` at index '{it.multi_index}'")
-                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
 
@@ -184,9 +196,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
                 )
             except Exception as e:
                 print(f"Error {e}:")
-                print(f">>> in expand_transition_elements for `rate:` at index '{it.multi_index}'")
-                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
 
@@ -235,9 +259,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
                     )
                 except Exception as e:
                     print(f"Error {e}:")
-                    print(f">>> in expand_transition_elements for `proportion_exponent:` at index '{it.multi_index}'")
-                    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:
@@ -475,7 +505,9 @@ 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 = []
@@ -557,7 +589,7 @@ 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 +739,7 @@ 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 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}'."
diff --git a/flepimop/gempyor_pkg/src/gempyor/config_validator.py b/flepimop/gempyor_pkg/src/gempyor/config_validator.py
index 3c105ba55..3803cae94 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
 
@@ -106,21 +113,21 @@ 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:
+        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(
                 f"A `lambda_file` is required when method is '{method}', "
                 f"was given '{lambda_file}'."
             )
-        if method == 'FolderDraw' and not seeding_file_type:
+        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}'."
             )
-        if method == 'FromFile' and not seeding_file:
+        if method == "FromFile" and not seeding_file:
             raise ValueError(
                 f"A `seeding_file` is required when method is 'FromFile', "
                 f"was given '{seeding_file}'."
@@ -129,9 +136,9 @@ def validate_seedingfile(cls, 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}'."
@@ -167,10 +174,14 @@ 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
 
@@ -348,7 +359,9 @@ 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
 
 
@@ -432,7 +445,9 @@ 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."
@@ -457,5 +472,5 @@ def init_or_seed(cls, values):
         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/initial_conditions.py b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
index cc40f1a82..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 +263,10 @@ 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))
 
     for comp_idx, comp_name in modinf.compartments.compartments["name"].items():
@@ -299,7 +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/model_info.py b/flepimop/gempyor_pkg/src/gempyor/model_info.py
index dc0008e1e..74df06669 100644
--- a/flepimop/gempyor_pkg/src/gempyor/model_info.py
+++ b/flepimop/gempyor_pkg/src/gempyor/model_info.py
@@ -18,7 +18,9 @@ def __init__(self, config: confuse.ConfigView):
         self.ti = config["start_date"].as_date()
         self.tf = config["end_date"].as_date()
         if self.tf <= self.ti:
-            raise ValueError("`tf` (time to finish) is less than or equal to `ti` (time to start).")
+            raise ValueError(
+                "`tf` (time to finish) is less than or equal to `ti` (time to start)."
+            )
         self.n_days = (self.tf - self.ti).days + 1
         self.dates = pd.date_range(start=self.ti, end=self.tf, freq="D")
 
@@ -100,7 +102,9 @@ def __init__(
         # 3. What about subpopulations
         subpop_config = config["subpop_setup"]
         if "data_path" in config:
-            raise ValueError("The config has a `data_path` section. This is no longer supported.")
+            raise ValueError(
+                "The config has a `data_path` section. This is no longer supported."
+            )
         self.path_prefix = pathlib.Path(path_prefix)
 
         self.subpop_struct = subpopulation_structure.SubpopulationStructure(
@@ -161,15 +165,23 @@ def __init__(
                         "modifiers"
                     ].get()
                 else:
-                    self.seir_modifiers_library = config["seir_modifiers"]["modifiers"].get()
-                    raise ValueError("This feature has not been implemented yet.")  # TODO create a Stacked from all
+                    self.seir_modifiers_library = config["seir_modifiers"][
+                        "modifiers"
+                    ].get()
+                    raise ValueError(
+                        "This feature has not been implemented yet."
+                    )  # TODO create a Stacked from all
             elif self.seir_modifiers_scenario is not None:
-                raise ValueError("A seir modifiers scenario was provided to `ModelInfo` but there is no `seir_modifiers` sections in config.")
+                raise ValueError(
+                    "A seir modifiers scenario was provided to `ModelInfo` but there is no `seir_modifiers` sections in config."
+                )
             else:
                 logging.info("Running `ModelInfo` with seir but without SEIR Modifiers")
 
         elif self.seir_modifiers_scenario is not None:
-            raise ValueError("A seir modifiers scenario was provided to `ModelInfo` but there is no `seir_modifiers` sections in config.")
+            raise ValueError(
+                "A seir modifiers scenario was provided to `ModelInfo` but there is no `seir_modifiers` sections in config."
+            )
         else:
             logging.critical("Running ModelInfo without SEIR")
 
@@ -186,19 +198,29 @@ def __init__(
                         "modifiers"
                     ].get()
                 else:
-                    self.outcome_modifiers_library = config["outcome_modifiers"]["modifiers"].get()
-                    raise ValueError("This feature has not been implemented yet.")  # TODO create a Stacked from all
+                    self.outcome_modifiers_library = config["outcome_modifiers"][
+                        "modifiers"
+                    ].get()
+                    raise ValueError(
+                        "This feature has not been implemented yet."
+                    )  # TODO create a Stacked from all
 
             ## NEED TO IMPLEMENT THIS -- CURRENTLY CANNOT USE outcome modifiers
             elif self.outcome_modifiers_scenario is not None:
                 if config["outcome_modifiers"].exists():
-                    raise ValueError("An outcome modifiers scenario was provided to `ModelInfo` but there is no `outcome_modifiers` sections in config.")
+                    raise ValueError(
+                        "An outcome modifiers scenario was provided to `ModelInfo` but there is no `outcome_modifiers` sections in config."
+                    )
                 else:
                     self.outcome_modifiers_scenario = None
             else:
-                logging.info("Running `ModelInfo` with outcomes but without Outcomes Modifiers")
+                logging.info(
+                    "Running `ModelInfo` with outcomes but without Outcomes Modifiers"
+                )
         elif self.outcome_modifiers_scenario is not None:
-            raise ValueError("An outcome modifiers scenario was provided to `ModelInfo` but there is no `outcome_modifiers` sections in config.")
+            raise ValueError(
+                "An outcome modifiers scenario was provided to `ModelInfo` but there is no `outcome_modifiers` sections in config."
+            )
         else:
             logging.info("Running `ModelInfo` without Outcomes")
 
diff --git a/flepimop/gempyor_pkg/src/gempyor/outcomes.py b/flepimop/gempyor_pkg/src/gempyor/outcomes.py
index 9429c589c..aeb7e0032 100644
--- a/flepimop/gempyor_pkg/src/gempyor/outcomes.py
+++ b/flepimop/gempyor_pkg/src/gempyor/outcomes.py
@@ -185,8 +185,8 @@ def read_parameters_from_config(modinf: model_info.ModelInfo):
                 else:
                     raise ValueError(
                         f"Unable to read outcome '{new_comp}': "
-                        f"expected a string or dictionary containing `incidence` or `prevalence`. " 
-                        f"Recieved: '{src_name}'." 
+                        f"expected a string or dictionary containing `incidence` or `prevalence`. "
+                        f"Recieved: '{src_name}'."
                     )
 
                 parameters[new_comp]["probability"] = outcomes_config[new_comp][
@@ -397,7 +397,9 @@ def compute_all_multioutcomes(
                         outcome_name=new_comp,
                     )
                 else:
-                    raise ValueError(f"Unknown type provided for seir simulation, received '{type(seir_sim)}'.")
+                    raise ValueError(
+                        f"Unknown type provided for seir simulation, received '{type(seir_sim)}'."
+                    )
                 # we don't keep source in this cases
             else:  # already defined outcomes
                 if source_name in all_data:
diff --git a/flepimop/gempyor_pkg/src/gempyor/parameters.py b/flepimop/gempyor_pkg/src/gempyor/parameters.py
index 2c2c37721..7ab0de151 100644
--- a/flepimop/gempyor_pkg/src/gempyor/parameters.py
+++ b/flepimop/gempyor_pkg/src/gempyor/parameters.py
@@ -127,7 +127,7 @@ 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"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}'."
                     )
diff --git a/flepimop/gempyor_pkg/src/gempyor/seeding.py b/flepimop/gempyor_pkg/src/gempyor/seeding.py
index 7fd8486af..5d0653d0e 100644
--- a/flepimop/gempyor_pkg/src/gempyor/seeding.py
+++ b/flepimop/gempyor_pkg/src/gempyor/seeding.py
@@ -108,7 +108,9 @@ def get_from_config(self, sim_id: int, modinf) -> nb.typed.Dict:
             )
             dupes = seeding[seeding.duplicated(["subpop", "date"])].index + 1
             if not dupes.empty:
-                raise ValueError(f"There are repeating subpop-date in rows '{dupes.tolist()}' of `seeding::lambda_file`.")
+                raise ValueError(
+                    f"There are repeating subpop-date in rows '{dupes.tolist()}' of `seeding::lambda_file`."
+                )
         elif method == "FolderDraw":
             seeding = pd.read_csv(
                 self.path_prefix
diff --git a/flepimop/gempyor_pkg/src/gempyor/seir.py b/flepimop/gempyor_pkg/src/gempyor/seir.py
index 5064231bc..bb06cdfa5 100644
--- a/flepimop/gempyor_pkg/src/gempyor/seir.py
+++ b/flepimop/gempyor_pkg/src/gempyor/seir.py
@@ -31,7 +31,9 @@ def build_step_source_arg(
             if integration_method == "rk4":
                 integration_method = "rk4.jit"
             if integration_method not in ["rk4.jit", "legacy"]:
-                raise ValueError(f"Unknown integration method [received: '{integration_method}'].")
+                raise ValueError(
+                    f"Unknown integration method [received: '{integration_method}']."
+                )
         if "dt" in modinf.seir_config["integration"].keys():
             dt = float(
                 eval(str(modinf.seir_config["integration"]["dt"].get()))
@@ -187,7 +189,9 @@ def steps_SEIR(
         elif integration_method == "rk4_aot":
             seir_sim = steps_experimental.rk4_aot(**fnct_args)
         else:
-            raise ValueError(f"Unknown integration method [received '{integration_method}'].")
+            raise ValueError(
+                f"Unknown integration method [received '{integration_method}']."
+            )
 
     # We return an xarray instead of a ndarray now
     compartment_coords = {}
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/seir/test_ic.py b/flepimop/gempyor_pkg/tests/seir/test_ic.py
index 0dc29f956..fc478efb9 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_ic.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_ic.py
@@ -48,7 +48,10 @@ 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 a6c358548585b85b7818aabcf798b84eb4221734 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 8 Nov 2024 14:34:09 -0500
Subject: [PATCH 03/56] Updating a RegEx in `test_model_info.py`

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

diff --git a/flepimop/gempyor_pkg/tests/seir/test_model_info.py b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
index 3fbf21a75..28855f2f4 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_model_info.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
@@ -44,7 +44,7 @@ def test_ModelInfo_init_tf_is_ahead_of_ti_fail(self):
         config.read(user=False)
         config.set_file(f"{DATA_DIR}/config_test.yml")
         config["start_date"] = "2022-01-02"
-        with pytest.raises(ValueError, match=r"tf.*is less than or equal to ti.*"):
+        with pytest.raises(ValueError, match=r"`tf`\s?\(time to finish\)\s?is less than or equal to\s?`ti`\s?\(time to start\)\."):
             s = ModelInfo(
                 config=config,
                 seir_modifiers_scenario=None,

From e2a87c3f71fae83858f3269305e3139d15fdcc9b Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 8 Nov 2024 14:40:03 -0500
Subject: [PATCH 04/56] `black` linting and RegEx alteration

---
 flepimop/gempyor_pkg/tests/seir/test_model_info.py | 5 ++++-
 flepimop/gempyor_pkg/tests/seir/test_seir.py       | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/seir/test_model_info.py b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
index 28855f2f4..4790063eb 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_model_info.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
@@ -44,7 +44,10 @@ def test_ModelInfo_init_tf_is_ahead_of_ti_fail(self):
         config.read(user=False)
         config.set_file(f"{DATA_DIR}/config_test.yml")
         config["start_date"] = "2022-01-02"
-        with pytest.raises(ValueError, match=r"`tf`\s?\(time to finish\)\s?is less than or equal to\s?`ti`\s?\(time to start\)\."):
+        with pytest.raises(
+            ValueError,
+            match=r"`tf`\s?\(time to finish\)\s?is less than or equal to\s?`ti`\s?\(time to start\)\.",
+        ):
             s = ModelInfo(
                 config=config,
                 seir_modifiers_scenario=None,
diff --git a/flepimop/gempyor_pkg/tests/seir/test_seir.py b/flepimop/gempyor_pkg/tests/seir/test_seir.py
index d9d6d696f..8b772a689 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_seir.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_seir.py
@@ -128,7 +128,7 @@ def test_constant_population_legacy_integration():
 
 
 def test_constant_population_rk4jit_integration_fail():
-    with pytest.raises(ValueError, match=r".*with.*method.*integration.*"):
+    with pytest.raises(ValueError, match=r".*With.*method.*integration.*"):
         config.set_file(f"{DATA_DIR}/config.yml")
 
         first_sim_index = 1

From 17a4f384686b61ccc9cde171aac02f718c4ce3b7 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Wed, 13 Nov 2024 11:34:32 -0500
Subject: [PATCH 05/56] Update flepimop/gempyor_pkg/src/gempyor/seir.py

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

diff --git a/flepimop/gempyor_pkg/src/gempyor/seir.py b/flepimop/gempyor_pkg/src/gempyor/seir.py
index bb06cdfa5..182af3418 100644
--- a/flepimop/gempyor_pkg/src/gempyor/seir.py
+++ b/flepimop/gempyor_pkg/src/gempyor/seir.py
@@ -150,8 +150,7 @@ def steps_SEIR(
     elif integration_method == "rk4.jit":
         if modinf.stoch_traj_flag == True:
             raise ValueError(
-                f"With method '{integration_method}', only deterministic "
-                f"integration is possible (received `stoch_straj_flag` = '{modinf.stoch_traj_flag}')."
+                f"'{integration_method}' integration method only supports deterministic integration, but `stoch_straj_flag` is '{modinf.stoch_traj_flag}'."
             )
         seir_sim = steps_rk4.rk4_integration(**fnct_args, silent=True)
     else:

From 3acad126401cc13af08069e74752c230b3575e96 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <100221052+emprzy@users.noreply.github.com>
Date: Wed, 13 Nov 2024 11:35:37 -0500
Subject: [PATCH 06/56] Update flepimop/gempyor_pkg/src/gempyor/seir.py

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

diff --git a/flepimop/gempyor_pkg/src/gempyor/seir.py b/flepimop/gempyor_pkg/src/gempyor/seir.py
index 182af3418..da62c9101 100644
--- a/flepimop/gempyor_pkg/src/gempyor/seir.py
+++ b/flepimop/gempyor_pkg/src/gempyor/seir.py
@@ -165,8 +165,7 @@ def steps_SEIR(
         ]:
             if modinf.stoch_traj_flag == True:
                 raise ValueError(
-                    f"With method '{integration_method}', only deterministic "
-                    f"integration is possible (received `stoch_straj_flag` = '{modinf.stoch_traj_flag}')."
+                f"'{integration_method}' integration method only supports deterministic integration, but `stoch_straj_flag` is '{modinf.stoch_traj_flag}'."
                 )
             seir_sim = steps_experimental.ode_integration(
                 **fnct_args, integration_method=integration_method

From 44ccc848df6e64af5082abc52206582202838be1 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 13 Nov 2024 11:54:31 -0500
Subject: [PATCH 07/56] Implementing Tim's suggestions!

---
 .../gempyor_pkg/src/gempyor/model_info.py     | 19 ++++----
 flepimop/gempyor_pkg/src/gempyor/outcomes.py  |  9 ++--
 flepimop/gempyor_pkg/src/gempyor/seeding.py   |  4 +-
 .../gempyor_pkg/src/gempyor/statistics.py     | 18 ++++---
 flepimop/gempyor_pkg/src/gempyor/utils.py     | 47 +++++++++----------
 flepimop/gempyor_pkg/tests/seir/test_seir.py  |  2 +-
 6 files changed, 50 insertions(+), 49 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/model_info.py b/flepimop/gempyor_pkg/src/gempyor/model_info.py
index 74df06669..f22e16d1d 100644
--- a/flepimop/gempyor_pkg/src/gempyor/model_info.py
+++ b/flepimop/gempyor_pkg/src/gempyor/model_info.py
@@ -19,7 +19,7 @@ def __init__(self, config: confuse.ConfigView):
         self.tf = config["end_date"].as_date()
         if self.tf <= self.ti:
             raise ValueError(
-                "`tf` (time to finish) is less than or equal to `ti` (time to start)."
+                f"Time to finish ('{self.tf}') is less than or equal to ('{self.ti}')."
             )
         self.n_days = (self.tf - self.ti).days + 1
         self.dates = pd.date_range(start=self.ti, end=self.tf, freq="D")
@@ -76,8 +76,7 @@ def __init__(
         # Auto-detect old config
         if config["interventions"].exists():
             raise ValueError(
-                "This config has an intervention section, which is only compatible with a previous version of flepiMoP/COVIDScenarioPipeline. "
-                "Please use flepiMoP Version 1.1 to run this config."
+                "This config has an intervention section, which is only compatible with a previous version (1.1) of flepiMoP."
             )
 
         # 1. Create a setup name that contains every scenario.
@@ -168,19 +167,19 @@ def __init__(
                     self.seir_modifiers_library = config["seir_modifiers"][
                         "modifiers"
                     ].get()
-                    raise ValueError(
+                    raise NotImplementedError(
                         "This feature has not been implemented yet."
                     )  # TODO create a Stacked from all
             elif self.seir_modifiers_scenario is not None:
                 raise ValueError(
-                    "A seir modifiers scenario was provided to `ModelInfo` but there is no `seir_modifiers` sections in config."
+                    "A seir modifiers scenario was provided to `ModelInfo` but there is no `seir_modifiers` section in the config."
                 )
             else:
                 logging.info("Running `ModelInfo` with seir but without SEIR Modifiers")
 
         elif self.seir_modifiers_scenario is not None:
             raise ValueError(
-                "A seir modifiers scenario was provided to `ModelInfo` but there is no `seir_modifiers` sections in config."
+                "A seir modifiers scenario was provided to `ModelInfo` but there is no `seir_modifiers` section in the config."
             )
         else:
             logging.critical("Running ModelInfo without SEIR")
@@ -201,7 +200,7 @@ def __init__(
                     self.outcome_modifiers_library = config["outcome_modifiers"][
                         "modifiers"
                     ].get()
-                    raise ValueError(
+                    raise NotImplementedError(
                         "This feature has not been implemented yet."
                     )  # TODO create a Stacked from all
 
@@ -209,7 +208,7 @@ def __init__(
             elif self.outcome_modifiers_scenario is not None:
                 if config["outcome_modifiers"].exists():
                     raise ValueError(
-                        "An outcome modifiers scenario was provided to `ModelInfo` but there is no `outcome_modifiers` sections in config."
+                        "An outcome modifiers scenario was provided to `ModelInfo` but there is no `outcome_modifiers` section in the config."
                     )
                 else:
                     self.outcome_modifiers_scenario = None
@@ -219,10 +218,10 @@ def __init__(
                 )
         elif self.outcome_modifiers_scenario is not None:
             raise ValueError(
-                "An outcome modifiers scenario was provided to `ModelInfo` but there is no `outcome_modifiers` sections in config."
+                "An outcome modifiers scenario was provided to `ModelInfo` but there is no `outcome_modifiers` section in the config."
             )
         else:
-            logging.info("Running `ModelInfo` without Outcomes")
+            logging.info("Running `ModelInfo` without outcomes.")
 
         # 6. Inputs and outputs
         if in_run_id is None:
diff --git a/flepimop/gempyor_pkg/src/gempyor/outcomes.py b/flepimop/gempyor_pkg/src/gempyor/outcomes.py
index aeb7e0032..7141d0c58 100644
--- a/flepimop/gempyor_pkg/src/gempyor/outcomes.py
+++ b/flepimop/gempyor_pkg/src/gempyor/outcomes.py
@@ -184,9 +184,8 @@ def read_parameters_from_config(modinf: model_info.ModelInfo):
 
                 else:
                     raise ValueError(
-                        f"Unable to read outcome '{new_comp}': "
-                        f"expected a string or dictionary containing `incidence` or `prevalence`. "
-                        f"Recieved: '{src_name}'."
+                        f"Expected a `str` or `dict` containing `incidence` or `prevalence`. "
+                        f"Instead given '{src_name}' for outcome '{new_comp}'."
                     )
 
                 parameters[new_comp]["probability"] = outcomes_config[new_comp][
@@ -671,7 +670,7 @@ def multishiftee(arr, shifts, stoch_delay_flag=True):
     result = np.zeros_like(arr)
 
     if stoch_delay_flag:
-        raise ValueError("`stoch_delay_flag` not supported yet.")
+        raise NotImplementedError("`stoch_delay_flag` not supported yet.")
         # for i, row in reversed(enumerate(np.rows(arr))):
         #    for j,elem in reversed(enumerate(row)):
         ## This function takes in :
@@ -697,7 +696,7 @@ def multishift(arr, shifts, stoch_delay_flag=True):
     result = np.zeros_like(arr)
 
     if stoch_delay_flag:
-        raise ValueError("`stoch_delay_flag` not supported yet.")
+        raise NotImplementedError("`stoch_delay_flag` not supported yet.")
         # for i, row in reversed(enumerate(np.rows(arr))):
         #    for j,elem in reversed(enumerate(row)):
         ## This function takes in :
diff --git a/flepimop/gempyor_pkg/src/gempyor/seeding.py b/flepimop/gempyor_pkg/src/gempyor/seeding.py
index 5d0653d0e..e86f598c9 100644
--- a/flepimop/gempyor_pkg/src/gempyor/seeding.py
+++ b/flepimop/gempyor_pkg/src/gempyor/seeding.py
@@ -17,7 +17,7 @@
 
 def _DataFrame2NumbaDict(df, amounts, modinf) -> nb.typed.Dict:
     if not df["date"].is_monotonic_increasing:
-        raise ValueError("`_DataFrame2NumbaDict` got an unsorted dataframe.")
+        raise ValueError("The `df` given is not sorted by the 'date' column.")
 
     cmp_grp_names = [
         col for col in modinf.compartments.compartments.columns if col != "name"
@@ -134,7 +134,7 @@ def get_from_config(self, sim_id: int, modinf) -> nb.typed.Dict:
             seeding = pd.DataFrame(columns=["date", "subpop"])
             return _DataFrame2NumbaDict(df=seeding, amounts=[], modinf=modinf)
         else:
-            raise NotImplementedError(f"Unknown seeding method [received: '{method}'].")
+            raise ValueError(f"Unknown seeding method [received: '{method}'].")
 
         # Sorting by date is very important here for the seeding format necessary !!!!
         # print(seeding.shape)
diff --git a/flepimop/gempyor_pkg/src/gempyor/statistics.py b/flepimop/gempyor_pkg/src/gempyor/statistics.py
index ea10e7aa1..3208a6569 100644
--- a/flepimop/gempyor_pkg/src/gempyor/statistics.py
+++ b/flepimop/gempyor_pkg/src/gempyor/statistics.py
@@ -74,7 +74,10 @@ def __init__(self, name: str, statistic_config: confuse.ConfigView) -> None:
                 reg_name = reg_config["name"].get()
                 reg_func = getattr(self, f"_{reg_name}_regularize", None)
                 if reg_func is None:
-                    raise ValueError(f"Unsupported regularization: {reg_name}")
+                    raise ValueError(
+                        f"Unsupported regularization [received: '{reg_name}']. "
+                        f"Currently only `forecast` and `allsubpop` are supported."
+                    )
                 self.regularizations.append((reg_func, reg_config.get()))
 
         self.resample = False
@@ -253,7 +256,10 @@ def llik(self, model_data: xr.DataArray, gt_data: xr.DataArray) -> xr.DataArray:
             "absolute_error": lambda x, y: -np.log(np.nansum(np.abs(x - y))),
         }
         if self.dist not in dist_map:
-            raise ValueError(f"Invalid distribution specified: {self.dist}")
+            raise ValueError(
+                f"Invalid distribution specified [received: '{self.dist}']. "
+                f"Valid distributions: '{dist_map}'."
+            )
         if self.dist in ["pois", "nbinom"]:
             model_data = model_data.astype(int)
             gt_data = gt_data.astype(int)
@@ -295,11 +301,9 @@ def compute_logloss(
 
         if not model_data.shape == gt_data.shape:
             raise ValueError(
-                (
-                    f"{self.name} Statistic error: data and groundtruth do not have "
-                    f"the same shape: model_data.shape={model_data.shape} != "
-                    f"gt_data.shape={gt_data.shape}"
-                )
+                    f"`model_data` and `gt_data` do not have "
+                    f"the same shape: `model_data.shape` = '{model_data.shape}' != "
+                    f"`gt_data.shape` = '{gt_data.shape}'."
             )
 
         regularization = 0.0
diff --git a/flepimop/gempyor_pkg/src/gempyor/utils.py b/flepimop/gempyor_pkg/src/gempyor/utils.py
index 377dcdee5..7df96d1f4 100644
--- a/flepimop/gempyor_pkg/src/gempyor/utils.py
+++ b/flepimop/gempyor_pkg/src/gempyor/utils.py
@@ -47,7 +47,7 @@ def write_df(
         None
 
     Raises:
-        NotImplementedError: The given output extension is not supported yet.
+        ValueError: The given output extension is not supported yet.
     """
     # Decipher the path given
     fname = fname.decode() if isinstance(fname, bytes) else fname
@@ -57,8 +57,8 @@ def write_df(
         return df.to_csv(path, index=False)
     elif path.suffix == ".parquet":
         return df.to_parquet(path, index=False, engine="pyarrow")
-    raise NotImplementedError(
-        f"Invalid extension {path.suffix[1:]}. Must be 'csv' or 'parquet'."
+    raise ValueError(
+        f"Invalid extension provided: '{path.suffix[1:]}'. Supported extensions are `.csv` or `.parquet`."
     )
 
 
@@ -82,7 +82,7 @@ def read_df(
         A pandas DataFrame parsed from the file given.
 
     Raises:
-        NotImplementedError: The given output extension is not supported yet.
+        ValueError: The given output extension is not supported yet.
     """
     # Decipher the path given
     fname = fname.decode() if isinstance(fname, bytes) else fname
@@ -94,8 +94,8 @@ def read_df(
         )
     elif path.suffix == ".parquet":
         return pd.read_parquet(path, engine="pyarrow")
-    raise NotImplementedError(
-        f"Invalid extension {path.suffix[1:]}. Must be 'csv' or 'parquet'."
+    raise ValueError(
+        f"Invalid extension provided: '{path.suffix[1:]}'. Supported extensions are `.csv` or `.parquet`."
     )
 
 
@@ -114,7 +114,7 @@ def command_safe_run(
         As a tuple; the return code, the standard output, and standard error from running the command.
 
     Raises:
-        Exception: If fail_on_fail=True and the command fails, an exception will be thrown.
+        RuntimeError: If fail_on_fail=True and the command fails, an error will be thrown.
     """
     import subprocess
     import shlex  # using shlex to split the command because it's not obvious https://docs.python.org/3/library/subprocess.html#subprocess.Popen
@@ -124,8 +124,8 @@ def command_safe_run(
     )
     (stdout, stderr) = sr.communicate()
     if sr.returncode != 0:
-        print(f"{command_name} failed failed with returncode {sr.returncode}")
-        print(f"{command_name}:  {command}")
+        print(f"'{command_name}' failed failed with returncode '{sr.returncode}'")
+        print(f"'{command_name}': '{command}'")
         print("{command_name} command failed with stdout and stderr:")
 
         print("{command_name} stdout >>>>>>")
@@ -136,7 +136,7 @@ def command_safe_run(
         print(stderr.decode())
         print("{command_name} stderr <<<<<<")
         if fail_on_fail:
-            raise Exception(f"{command_name} command failed")
+            raise RuntimeError(f"The '{command_name}' command failed.")
 
     return sr.returncode, stdout, stderr
 
@@ -362,7 +362,7 @@ def as_evaled_expression(self):
         except TypeError as e:
             raise ValueError(e) from e
     else:
-        raise ValueError(f"expected numeric or string expression [got: {value}]")
+        raise ValueError(f"Expected numeric or string expression [received: '{value}'].")
 
 
 def get_truncated_normal(
@@ -484,7 +484,7 @@ def random_distribution_sampler(
     elif distribution == "binomial":
         p = kwargs.get("p")
         if not (0 < p < 1):
-            raise ValueError(f"p value {p} is out of range [0,1]")
+            raise ValueError(f"Invalid `p-value`: '{p}' is out of range [0,1].")
         return functools.partial(np.random.binomial, kwargs.get("n"), p)
     elif distribution == "truncnorm":
         # Truncated normal with mean, sd on interval [a, b]
@@ -497,7 +497,7 @@ def random_distribution_sampler(
     elif distribution == "lognorm":
         # Lognormal distribution with meanlog, sdlog
         return get_log_normal(kwargs.get("meanlog"), kwargs.get("sdlog")).rvs
-    raise NotImplementedError(f"unknown distribution [got: {distribution}]")
+    raise NotImplementedError(f"Unkown distribution [received: '{distribution}'].")
 
 
 @add_method(confuse.ConfigView)
@@ -556,7 +556,7 @@ def as_random_distribution(self):
         elif dist == "binomial":
             p = self["p"].as_evaled_expression()
             if (p < 0) or (p > 1):
-                raise ValueError(f"""p value { p } is out of range [0,1]""")
+                raise ValueError(f"Invalid `p-value`: '{p}' is out of range [0,1].")
                 # if (self["p"] < 0) or (self["p"] > 1):
                 #    raise ValueError(f"""p value { self["p"] } is out of range [0,1]""")
             return functools.partial(
@@ -578,7 +578,7 @@ def as_random_distribution(self):
                 sdlog=self["sdlog"].as_evaled_expression(),
             ).rvs
         else:
-            raise NotImplementedError(f"unknown distribution [got: {dist}]")
+            raise NotImplementedError(f"Unkown distribution [received: '{dist}'].")
     else:
         # we allow a fixed value specified directly:
         return functools.partial(
@@ -716,13 +716,13 @@ def bash(command: str) -> str:
         f"shutil.disk_usage: {total_bytes/ 1000000} Mb total, {used_bytes / 1000000} Mb used, {free_bytes / 1000000} Mb free..."
     )
     print("------------")
-    print(f"df -hT: {bash('df -hT')}")
+    print(f"df -hT: '{bash('df -hT')}'")
     print("------------")
-    print(f"df -i: {bash('df -i')}")
+    print(f"df -i: '{bash('df -i')}'")
     print("------------")
-    print(f"free -h: {bash('free -h')}")
+    print(f"free -h: '{bash('free -h')}'")
     print("------------")
-    print(f"lsblk: {bash('lsblk')}")
+    print(f"lsblk: '{bash('lsblk')}'")
     print("END AWS DIAGNOSIS ================================")
 
 
@@ -1004,8 +1004,8 @@ def download_file_from_s3(name_map: dict[str, str]) -> None:
     except ModuleNotFoundError:
         raise ModuleNotFoundError(
             (
-                "No module named 'boto3', which is required for "
-                "gempyor.utils.download_file_from_s3. Please install the aws target."
+                "No module named `boto3` found, which is required for "
+                "`gempyor.utils.download_file_from_s3`. Please install the aws target."
             )
         )
     s3 = boto3.client("s3")
@@ -1020,10 +1020,9 @@ def download_file_from_s3(name_map: dict[str, str]) -> None:
                 object = s3_uri[len(bucket) + 6 :]
                 s3.download_file(bucket, object, name_map[s3_uri])
             else:
-                raise ValueError(f"Invalid S3 URI format {s3_uri}")
+                raise ValueError(f"Invalid S3 URI format [received: '{s3_uri}'].")
         except ClientError as e:
-            print(f"An error occurred: {e}")
-            print("Could not download file from s3")
+            raise Exception(f"'{e}': could not download filefrom S3.")
 
 
 def move_file_at_local(name_map: dict[str, str]) -> None:
diff --git a/flepimop/gempyor_pkg/tests/seir/test_seir.py b/flepimop/gempyor_pkg/tests/seir/test_seir.py
index 8b772a689..b14767115 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_seir.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_seir.py
@@ -128,7 +128,7 @@ def test_constant_population_legacy_integration():
 
 
 def test_constant_population_rk4jit_integration_fail():
-    with pytest.raises(ValueError, match=r".*With.*method.*integration.*"):
+    with pytest.raises(ValueError, match=r".*integration method only supports deterministic integration.*"):
         config.set_file(f"{DATA_DIR}/config.yml")
 
         first_sim_index = 1

From b32c64e392e15deb675543026be3554979dc768b Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 13 Nov 2024 12:13:48 -0500
Subject: [PATCH 08/56] Regex adjustment

---
 flepimop/gempyor_pkg/src/gempyor/model_info.py     | 2 +-
 flepimop/gempyor_pkg/tests/seir/test_model_info.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/model_info.py b/flepimop/gempyor_pkg/src/gempyor/model_info.py
index f22e16d1d..82956dd9e 100644
--- a/flepimop/gempyor_pkg/src/gempyor/model_info.py
+++ b/flepimop/gempyor_pkg/src/gempyor/model_info.py
@@ -19,7 +19,7 @@ def __init__(self, config: confuse.ConfigView):
         self.tf = config["end_date"].as_date()
         if self.tf <= self.ti:
             raise ValueError(
-                f"Time to finish ('{self.tf}') is less than or equal to ('{self.ti}')."
+                f"Time to finish ('{self.tf}') is less than or equal to time to start ('{self.ti}')."
             )
         self.n_days = (self.tf - self.ti).days + 1
         self.dates = pd.date_range(start=self.ti, end=self.tf, freq="D")
diff --git a/flepimop/gempyor_pkg/tests/seir/test_model_info.py b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
index 4790063eb..81cf69492 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_model_info.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
@@ -46,7 +46,7 @@ def test_ModelInfo_init_tf_is_ahead_of_ti_fail(self):
         config["start_date"] = "2022-01-02"
         with pytest.raises(
             ValueError,
-            match=r"`tf`\s?\(time to finish\)\s?is less than or equal to\s?`ti`\s?\(time to start\)\.",
+            match=r"Time to finish \('\{self\.tf\}'\) is less than or equal to time to start \('\{self\.ti\}'\)\.",
         ):
             s = ModelInfo(
                 config=config,

From d844ced1d806e8047f4ad3a2b94d294c4186b00f Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 13 Nov 2024 12:24:53 -0500
Subject: [PATCH 09/56] Regex update

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

diff --git a/flepimop/gempyor_pkg/tests/seir/test_model_info.py b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
index 81cf69492..baad036b4 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_model_info.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
@@ -46,7 +46,7 @@ def test_ModelInfo_init_tf_is_ahead_of_ti_fail(self):
         config["start_date"] = "2022-01-02"
         with pytest.raises(
             ValueError,
-            match=r"Time to finish \('\{self\.tf\}'\) is less than or equal to time to start \('\{self\.ti\}'\)\.",
+            match=r"Time to finish.*is less than or equal to time to start.*",
         ):
             s = ModelInfo(
                 config=config,

From 2cbf2ed375ce464c3e375c7bf5a7dba92e20d68e Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 13 Nov 2024 16:06:51 -0500
Subject: [PATCH 10/56] Implementing Tim's suggestions

---
 flepimop/gempyor_pkg/src/gempyor/seeding.py | 4 ++--
 flepimop/gempyor_pkg/src/gempyor/seir.py    | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/seeding.py b/flepimop/gempyor_pkg/src/gempyor/seeding.py
index e86f598c9..c341ed93c 100644
--- a/flepimop/gempyor_pkg/src/gempyor/seeding.py
+++ b/flepimop/gempyor_pkg/src/gempyor/seeding.py
@@ -134,7 +134,7 @@ def get_from_config(self, sim_id: int, modinf) -> nb.typed.Dict:
             seeding = pd.DataFrame(columns=["date", "subpop"])
             return _DataFrame2NumbaDict(df=seeding, amounts=[], modinf=modinf)
         else:
-            raise ValueError(f"Unknown seeding method [received: '{method}'].")
+            raise ValueError(f"Unknown seeding method given, '{method}'.")
 
         # Sorting by date is very important here for the seeding format necessary !!!!
         # print(seeding.shape)
@@ -159,7 +159,7 @@ def get_from_config(self, sim_id: int, modinf) -> nb.typed.Dict:
         elif method == "FolderDraw" or method == "FromFile":
             amounts = seeding["amount"]
         else:
-            raise ValueError(f"Unknown seeding method [received: '{method}'].")
+            raise ValueError(f"Unknown seeding method given, '{method}'.")
 
         return _DataFrame2NumbaDict(df=seeding, amounts=amounts, modinf=modinf)
 
diff --git a/flepimop/gempyor_pkg/src/gempyor/seir.py b/flepimop/gempyor_pkg/src/gempyor/seir.py
index da62c9101..7bbf6995c 100644
--- a/flepimop/gempyor_pkg/src/gempyor/seir.py
+++ b/flepimop/gempyor_pkg/src/gempyor/seir.py
@@ -32,7 +32,7 @@ def build_step_source_arg(
                 integration_method = "rk4.jit"
             if integration_method not in ["rk4.jit", "legacy"]:
                 raise ValueError(
-                    f"Unknown integration method [received: '{integration_method}']."
+                    f"Unknown integration method given, '{integration_method}'."
                 )
         if "dt" in modinf.seir_config["integration"].keys():
             dt = float(
@@ -188,7 +188,7 @@ def steps_SEIR(
             seir_sim = steps_experimental.rk4_aot(**fnct_args)
         else:
             raise ValueError(
-                f"Unknown integration method [received '{integration_method}']."
+                f"Unknown integration method given, '{integration_method}'."
             )
 
     # We return an xarray instead of a ndarray now

From a1692a159e09ab44602a37f5f839fed286b85f17 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 18 Nov 2024 13:03:19 -0500
Subject: [PATCH 11/56] Regex update in test_statistic_class.py

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

diff --git a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
index 4843986c1..614a63d67 100644
--- a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
+++ b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
@@ -249,7 +249,7 @@ def test_unsupported_regularizations_value_error(
             if reg_name not in ["forecast", "allsubpop"]
         )
         with pytest.raises(
-            ValueError, match=rf"^Unsupported regularization\: {unsupported_name}$"
+            ValueError, match=r"^Unsupported regularization \[received:.*$"
         ):
             mock_inputs.create_statistic_instance()
 

From 759795fdeeb282ec892c06ec8cc578df31a39f85 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 18 Nov 2024 13:17:13 -0500
Subject: [PATCH 12/56] Regex update in `test_statistic_class.py`

---
 flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
index 614a63d67..d9d4270e4 100644
--- a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
+++ b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
@@ -523,9 +523,7 @@ def test_compute_logloss_data_misshape_value_error(
         model_rows, model_cols = mock_inputs.model_data[mock_inputs.config["sim_var"]].shape
         gt_rows, gt_cols = mock_inputs.gt_data[mock_inputs.config["data_var"]].shape
         expected_match = (
-            rf"^{mock_inputs.name} Statistic error\: data and groundtruth do not have "
-            rf"the same shape\: model\_data\.shape\=\({model_rows}\, {model_cols}\) "
-            rf"\!\= gt\_data\.shape\=\({gt_rows}\, {gt_cols}\)$"
+            rf".*do not have the same shape:.*"
         )
         with pytest.raises(ValueError, match=expected_match):
             statistic.compute_logloss(mock_inputs.model_data, mock_inputs.gt_data)

From df784d59d86277a1574a5d70dceb0765ab55342d Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 18 Nov 2024 15:19:11 -0500
Subject: [PATCH 13/56] Regex adjusment in
 `test_random_distribution_sampler.py`

---
 flepimop/gempyor_pkg/src/gempyor/utils.py                       | 2 +-
 .../gempyor_pkg/tests/utils/test_random_distribution_sampler.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/utils.py b/flepimop/gempyor_pkg/src/gempyor/utils.py
index 7df96d1f4..8ad0d940e 100644
--- a/flepimop/gempyor_pkg/src/gempyor/utils.py
+++ b/flepimop/gempyor_pkg/src/gempyor/utils.py
@@ -578,7 +578,7 @@ def as_random_distribution(self):
                 sdlog=self["sdlog"].as_evaled_expression(),
             ).rvs
         else:
-            raise NotImplementedError(f"Unkown distribution [received: '{dist}'].")
+            raise NotImplementedError(f"Unknown distribution [received: '{dist}'].")
     else:
         # we allow a fixed value specified directly:
         return functools.partial(
diff --git a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
index 4ca9c0ac7..41846a632 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
@@ -14,7 +14,7 @@ class TestRandomDistributionSampler:
     def test_not_implemented_error_exception(self, distribution: str) -> None:
         with pytest.raises(
             NotImplementedError,
-            match=rf"^unknown distribution \[got\: {distribution}\]$",
+            match=rf"^Unknown distribution \[received.*",
         ):
             random_distribution_sampler(distribution)
 

From 8ec6c0578b9ffc36cfd82d67b0abfe817df2689f Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 18 Nov 2024 15:42:51 -0500
Subject: [PATCH 14/56] Fixing typo in `utils.py`

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

diff --git a/flepimop/gempyor_pkg/src/gempyor/utils.py b/flepimop/gempyor_pkg/src/gempyor/utils.py
index 8ad0d940e..8c76ffb5e 100644
--- a/flepimop/gempyor_pkg/src/gempyor/utils.py
+++ b/flepimop/gempyor_pkg/src/gempyor/utils.py
@@ -497,7 +497,7 @@ def random_distribution_sampler(
     elif distribution == "lognorm":
         # Lognormal distribution with meanlog, sdlog
         return get_log_normal(kwargs.get("meanlog"), kwargs.get("sdlog")).rvs
-    raise NotImplementedError(f"Unkown distribution [received: '{distribution}'].")
+    raise NotImplementedError(f"Unknown distribution [received: '{distribution}'].")
 
 
 @add_method(confuse.ConfigView)

From d760ddc8ed821e0da0c232240fe1a14205b38852 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 18 Nov 2024 16:27:07 -0500
Subject: [PATCH 15/56] Regex update in `test_random_distribution_sampler.py`

---
 .../gempyor_pkg/tests/utils/test_random_distribution_sampler.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
index 41846a632..5283babbc 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
@@ -22,7 +22,7 @@ def test_not_implemented_error_exception(self, distribution: str) -> None:
     def test_binomial_p_value_error(self, p: float) -> None:
         with pytest.raises(
             ValueError,
-            match=rf"^p value {p} is out of range \[0\,1\]$",
+            match=r"^Invalid\s`p-value`.*\s'is\sout\sof\srange.*'",
         ):
             random_distribution_sampler("binomial", n=100, p=p)
 

From 7e19700eb57302ee527d012422c5edf191a82237 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 18 Nov 2024 16:53:58 -0500
Subject: [PATCH 16/56] Regex update in `test_random_distribution_sampler.py`

---
 .../gempyor_pkg/tests/utils/test_random_distribution_sampler.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
index 5283babbc..596d296c1 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
@@ -22,7 +22,7 @@ def test_not_implemented_error_exception(self, distribution: str) -> None:
     def test_binomial_p_value_error(self, p: float) -> None:
         with pytest.raises(
             ValueError,
-            match=r"^Invalid\s`p-value`.*\s'is\sout\sof\srange.*'",
+            match=r"^Invalid\s`p-value`.*\sis\sout\sof\srange.*$",
         ):
             random_distribution_sampler("binomial", n=100, p=p)
 

From 452ddbbdba62481eb79c40aac0bca7aa5aa8250d Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 20 Nov 2024 10:16:06 -0500
Subject: [PATCH 17/56] Update utils.py

the function `test_raises_not_implemented_error()` in test file `test_read_df.py` on account that it was receiving a `ValueError` when it expected a `NotImplementedError`. I switched the error within `utils.py:read_df()` to be an expected `NotImplementedError`.
---
 flepimop/gempyor_pkg/src/gempyor/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/utils.py b/flepimop/gempyor_pkg/src/gempyor/utils.py
index 8c76ffb5e..397bd0909 100644
--- a/flepimop/gempyor_pkg/src/gempyor/utils.py
+++ b/flepimop/gempyor_pkg/src/gempyor/utils.py
@@ -94,7 +94,7 @@ def read_df(
         )
     elif path.suffix == ".parquet":
         return pd.read_parquet(path, engine="pyarrow")
-    raise ValueError(
+    raise NotImplementedError(
         f"Invalid extension provided: '{path.suffix[1:]}'. Supported extensions are `.csv` or `.parquet`."
     )
 

From 99d2f36cc1976b9d3c4da194f2b02c9aad234baf Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 20 Nov 2024 10:42:51 -0500
Subject: [PATCH 18/56] Regex update in `test_read_df.py`

---
 flepimop/gempyor_pkg/tests/utils/test_read_df.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_read_df.py b/flepimop/gempyor_pkg/tests/utils/test_read_df.py
index 48f05dbd5..34d05708a 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_read_df.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_read_df.py
@@ -38,13 +38,13 @@ def test_raises_not_implemented_error(self) -> None:
         """
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match="Invalid extension txt. Must be 'csv' or 'parquet'.",
+            match=".*Supported extensions are \.`csv`\s+or\s+\.`parquet`\.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 read_df(fname=temp_file.name)
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match="Invalid extension txt. Must be 'csv' or 'parquet'.",
+            match=".*Supported extensions are \.`csv`\s+or\s+\.`parquet`\.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 fname = temp_file.name[:-4]

From 47514d574e9d96dcb34df2315b87b95629c9feea Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 20 Nov 2024 11:10:06 -0500
Subject: [PATCH 19/56] Regex update in `test_read_df.py`

---
 flepimop/gempyor_pkg/tests/utils/test_read_df.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_read_df.py b/flepimop/gempyor_pkg/tests/utils/test_read_df.py
index 34d05708a..48ac4e770 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_read_df.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_read_df.py
@@ -38,13 +38,13 @@ def test_raises_not_implemented_error(self) -> None:
         """
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match=".*Supported extensions are \.`csv`\s+or\s+\.`parquet`\.",
+            match=r".*Supported extensions are \.`csv`\s+or\s+\.`parquet`\.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 read_df(fname=temp_file.name)
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match=".*Supported extensions are \.`csv`\s+or\s+\.`parquet`\.",
+            match=r".*Supported extensions are \.`csv`\s+or\s+\.`parquet`\.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 fname = temp_file.name[:-4]

From 97d39960ffca3244bf2238ae2af39840c1df6bb1 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 20 Nov 2024 11:45:45 -0500
Subject: [PATCH 20/56] Regex update in `test_read_df.py`

---
 flepimop/gempyor_pkg/tests/utils/test_read_df.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_read_df.py b/flepimop/gempyor_pkg/tests/utils/test_read_df.py
index 48ac4e770..676f5d699 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_read_df.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_read_df.py
@@ -38,13 +38,13 @@ def test_raises_not_implemented_error(self) -> None:
         """
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match=r".*Supported extensions are \.`csv`\s+or\s+\.`parquet`\.",
+            match=r".*Supported extensions are `.csv` or `.parquet`.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 read_df(fname=temp_file.name)
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match=r".*Supported extensions are \.`csv`\s+or\s+\.`parquet`\.",
+            match=r".*Supported extensions are `.csv` or `.parquet`.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 fname = temp_file.name[:-4]

From 918ebc793032f796cc0ec8affe02c79d1ec0ea6b Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 20 Nov 2024 11:57:12 -0500
Subject: [PATCH 21/56] Updating a unit test in `test_utils.py`

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

diff --git a/flepimop/gempyor_pkg/tests/utils/test_utils.py b/flepimop/gempyor_pkg/tests/utils/test_utils.py
index 87e7c4fbb..5a434d299 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_utils.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_utils.py
@@ -37,7 +37,7 @@ def test_read_df_and_write_success(fname, extension):
     ("fname", "extension"), [("mobility", "csv"), ("usa-geoid-params-output", "parquet")]
 )
 def test_read_df_and_write_fail(fname, extension):
-    with pytest.raises(NotImplementedError, match=r".*Invalid.*extension.*Must.*"):
+    with pytest.raises(ValueError, match=r".*Invalid.*extension.*Must.*"):
         os.chdir(tmp_path)
         os.makedirs("data", exist_ok=True)
         os.chdir("data")

From 764c4b2c73c2a02e57b2ac902acbd4297f3f6845 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 20 Nov 2024 12:07:45 -0500
Subject: [PATCH 22/56] Regex update in `test_utils.py` and error type
 agreement with `utils.py`

---
 flepimop/gempyor_pkg/src/gempyor/utils.py      | 2 +-
 flepimop/gempyor_pkg/tests/utils/test_utils.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/utils.py b/flepimop/gempyor_pkg/src/gempyor/utils.py
index 397bd0909..5178d19a9 100644
--- a/flepimop/gempyor_pkg/src/gempyor/utils.py
+++ b/flepimop/gempyor_pkg/src/gempyor/utils.py
@@ -57,7 +57,7 @@ def write_df(
         return df.to_csv(path, index=False)
     elif path.suffix == ".parquet":
         return df.to_parquet(path, index=False, engine="pyarrow")
-    raise ValueError(
+    raise NotImplementedError(
         f"Invalid extension provided: '{path.suffix[1:]}'. Supported extensions are `.csv` or `.parquet`."
     )
 
diff --git a/flepimop/gempyor_pkg/tests/utils/test_utils.py b/flepimop/gempyor_pkg/tests/utils/test_utils.py
index 5a434d299..942d79588 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_utils.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_utils.py
@@ -37,7 +37,7 @@ def test_read_df_and_write_success(fname, extension):
     ("fname", "extension"), [("mobility", "csv"), ("usa-geoid-params-output", "parquet")]
 )
 def test_read_df_and_write_fail(fname, extension):
-    with pytest.raises(ValueError, match=r".*Invalid.*extension.*Must.*"):
+    with pytest.raises(NotImplementedError, match=r".*Supported extensions are `.csv` or `.parquet`."):
         os.chdir(tmp_path)
         os.makedirs("data", exist_ok=True)
         os.chdir("data")

From c1e79c2c0ed24f6b3cf9e79d311f4e7570660493 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 20 Nov 2024 12:16:30 -0500
Subject: [PATCH 23/56] Regex update in `test_write_df.py`

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

diff --git a/flepimop/gempyor_pkg/tests/utils/test_write_df.py b/flepimop/gempyor_pkg/tests/utils/test_write_df.py
index b13e0b948..314c24152 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_write_df.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_write_df.py
@@ -30,7 +30,7 @@ def test_raises_not_implemented_error(self) -> None:
         """
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match="Invalid extension txt. Must be 'csv' or 'parquet'.",
+            match=r".*Supported extensions are `.csv` or `.parquet`.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 write_df(fname=temp_file.name, df=self.sample_df)

From 4fd1b116f40d776988cbe3c667700c9d53a83ab9 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 20 Nov 2024 12:23:50 -0500
Subject: [PATCH 24/56] Regex update in `test-write_df.py`

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

diff --git a/flepimop/gempyor_pkg/tests/utils/test_write_df.py b/flepimop/gempyor_pkg/tests/utils/test_write_df.py
index 314c24152..8f4e18baf 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_write_df.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_write_df.py
@@ -36,7 +36,7 @@ def test_raises_not_implemented_error(self) -> None:
                 write_df(fname=temp_file.name, df=self.sample_df)
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match="Invalid extension txt. Must be 'csv' or 'parquet'.",
+            match=r".*Supported extensions are `.csv` or `.parquet`.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 fname = temp_file.name[:-4]

From 2e62ae35147ab85e2b7c723fb2fc2cb6156b51b7 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 20 Nov 2024 12:37:45 -0500
Subject: [PATCH 25/56] Removing deprecated style of `\` to escape colons

---
 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 f82cf2a27..9801a6193 100644
--- a/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
+++ b/flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
@@ -283,7 +283,7 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
             ValueError,
             match=(
                 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"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}'.$"
             ),
         ):

From e5772c79b242a2ff4f839313d0c2cec75191fac0 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 20 Nov 2024 12:56:03 -0500
Subject: [PATCH 26/56] linting with `black`

---
 flepimop/gempyor_pkg/src/gempyor/seir.py                  | 6 ++----
 flepimop/gempyor_pkg/src/gempyor/statistics.py            | 6 +++---
 flepimop/gempyor_pkg/tests/seir/test_seir.py              | 4 +++-
 .../gempyor_pkg/tests/statistics/test_statistic_class.py  | 8 ++------
 flepimop/gempyor_pkg/tests/utils/test_utils.py            | 4 +++-
 5 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/seir.py b/flepimop/gempyor_pkg/src/gempyor/seir.py
index 7bbf6995c..b5742efad 100644
--- a/flepimop/gempyor_pkg/src/gempyor/seir.py
+++ b/flepimop/gempyor_pkg/src/gempyor/seir.py
@@ -165,7 +165,7 @@ def steps_SEIR(
         ]:
             if modinf.stoch_traj_flag == True:
                 raise ValueError(
-                f"'{integration_method}' integration method only supports deterministic integration, but `stoch_straj_flag` is '{modinf.stoch_traj_flag}'."
+                    f"'{integration_method}' integration method only supports deterministic integration, but `stoch_straj_flag` is '{modinf.stoch_traj_flag}'."
                 )
             seir_sim = steps_experimental.ode_integration(
                 **fnct_args, integration_method=integration_method
@@ -187,9 +187,7 @@ def steps_SEIR(
         elif integration_method == "rk4_aot":
             seir_sim = steps_experimental.rk4_aot(**fnct_args)
         else:
-            raise ValueError(
-                f"Unknown integration method given, '{integration_method}'."
-            )
+            raise ValueError(f"Unknown integration method given, '{integration_method}'.")
 
     # We return an xarray instead of a ndarray now
     compartment_coords = {}
diff --git a/flepimop/gempyor_pkg/src/gempyor/statistics.py b/flepimop/gempyor_pkg/src/gempyor/statistics.py
index 3208a6569..b6ced5e6d 100644
--- a/flepimop/gempyor_pkg/src/gempyor/statistics.py
+++ b/flepimop/gempyor_pkg/src/gempyor/statistics.py
@@ -301,9 +301,9 @@ def compute_logloss(
 
         if not model_data.shape == gt_data.shape:
             raise ValueError(
-                    f"`model_data` and `gt_data` do not have "
-                    f"the same shape: `model_data.shape` = '{model_data.shape}' != "
-                    f"`gt_data.shape` = '{gt_data.shape}'."
+                f"`model_data` and `gt_data` do not have "
+                f"the same shape: `model_data.shape` = '{model_data.shape}' != "
+                f"`gt_data.shape` = '{gt_data.shape}'."
             )
 
         regularization = 0.0
diff --git a/flepimop/gempyor_pkg/tests/seir/test_seir.py b/flepimop/gempyor_pkg/tests/seir/test_seir.py
index b14767115..9cf89032e 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_seir.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_seir.py
@@ -128,7 +128,9 @@ def test_constant_population_legacy_integration():
 
 
 def test_constant_population_rk4jit_integration_fail():
-    with pytest.raises(ValueError, match=r".*integration method only supports deterministic integration.*"):
+    with pytest.raises(
+        ValueError, match=r".*integration method only supports deterministic integration.*"
+    ):
         config.set_file(f"{DATA_DIR}/config.yml")
 
         first_sim_index = 1
diff --git a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
index d9d4270e4..5ec48ba76 100644
--- a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
+++ b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
@@ -248,9 +248,7 @@ def test_unsupported_regularizations_value_error(
             ]
             if reg_name not in ["forecast", "allsubpop"]
         )
-        with pytest.raises(
-            ValueError, match=r"^Unsupported regularization \[received:.*$"
-        ):
+        with pytest.raises(ValueError, match=r"^Unsupported regularization \[received:.*$"):
             mock_inputs.create_statistic_instance()
 
     @pytest.mark.parametrize("factory", all_valid_factories)
@@ -522,9 +520,7 @@ def test_compute_logloss_data_misshape_value_error(
 
         model_rows, model_cols = mock_inputs.model_data[mock_inputs.config["sim_var"]].shape
         gt_rows, gt_cols = mock_inputs.gt_data[mock_inputs.config["data_var"]].shape
-        expected_match = (
-            rf".*do not have the same shape:.*"
-        )
+        expected_match = rf".*do not have the same shape:.*"
         with pytest.raises(ValueError, match=expected_match):
             statistic.compute_logloss(mock_inputs.model_data, mock_inputs.gt_data)
 
diff --git a/flepimop/gempyor_pkg/tests/utils/test_utils.py b/flepimop/gempyor_pkg/tests/utils/test_utils.py
index 942d79588..c57ac900e 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_utils.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_utils.py
@@ -37,7 +37,9 @@ def test_read_df_and_write_success(fname, extension):
     ("fname", "extension"), [("mobility", "csv"), ("usa-geoid-params-output", "parquet")]
 )
 def test_read_df_and_write_fail(fname, extension):
-    with pytest.raises(NotImplementedError, match=r".*Supported extensions are `.csv` or `.parquet`."):
+    with pytest.raises(
+        NotImplementedError, match=r".*Supported extensions are `.csv` or `.parquet`."
+    ):
         os.chdir(tmp_path)
         os.makedirs("data", exist_ok=True)
         os.chdir("data")

From 8fe918aea488736f89eaf378a9f2d768867d96ec Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 20 Nov 2024 13:14:35 -0500
Subject: [PATCH 27/56] Updating `steps_source.py` and `utils.py`

There were not that many changes in the final batch of error improvements, so I went ahead and lumped them in with batch two.
---
 flepimop/gempyor_pkg/src/gempyor/steps_source.py | 7 +++++--
 flepimop/gempyor_pkg/src/gempyor/utils.py        | 4 ++--
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/steps_source.py b/flepimop/gempyor_pkg/src/gempyor/steps_source.py
index ea6f7ad21..7da7c393d 100644
--- a/flepimop/gempyor_pkg/src/gempyor/steps_source.py
+++ b/flepimop/gempyor_pkg/src/gempyor/steps_source.py
@@ -278,8 +278,11 @@ def steps_SEIR_nb(
                 print("  ", states_current[comp].max())
 
         if (states_current.min() < 0) or (states_current.max() > 10**10):
-            print((states_current.min() < 0), (states_current.max() > 10**10))
-            raise ValueError(f"Overflow error. Too small ?. Too large ?")
+            raise ValueError(
+                f"State values are outside the valid range. "
+                f"Minimum value: '{states_current.min()}', Maximum value: '{states_current.max()}'. "
+                f"Valid range is between 0 and {10**10}."
+            )
 
     return states, states_daily_incid
 
diff --git a/flepimop/gempyor_pkg/src/gempyor/utils.py b/flepimop/gempyor_pkg/src/gempyor/utils.py
index 5178d19a9..a937b53b4 100644
--- a/flepimop/gempyor_pkg/src/gempyor/utils.py
+++ b/flepimop/gempyor_pkg/src/gempyor/utils.py
@@ -47,7 +47,7 @@ def write_df(
         None
 
     Raises:
-        ValueError: The given output extension is not supported yet.
+        NotImplementedError: The given output extension is not supported yet.
     """
     # Decipher the path given
     fname = fname.decode() if isinstance(fname, bytes) else fname
@@ -82,7 +82,7 @@ def read_df(
         A pandas DataFrame parsed from the file given.
 
     Raises:
-        ValueError: The given output extension is not supported yet.
+        NotImplementedError: The given output extension is not supported yet.
     """
     # Decipher the path given
     fname = fname.decode() if isinstance(fname, bytes) else fname

From f7e53a70b5f66e8b4be0b2b4eda67226c1a99d53 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 22 Nov 2024 14:35:06 -0500
Subject: [PATCH 28/56] Implementing Carl's suggestions

Awaiting regex error kickback to adjust the test files.
---
 flepimop/gempyor_pkg/src/gempyor/model_info.py | 12 ++++++------
 flepimop/gempyor_pkg/src/gempyor/seeding.py    |  2 --
 flepimop/gempyor_pkg/src/gempyor/statistics.py |  4 ++--
 3 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/model_info.py b/flepimop/gempyor_pkg/src/gempyor/model_info.py
index 82956dd9e..3ba989cf3 100644
--- a/flepimop/gempyor_pkg/src/gempyor/model_info.py
+++ b/flepimop/gempyor_pkg/src/gempyor/model_info.py
@@ -19,7 +19,7 @@ def __init__(self, config: confuse.ConfigView):
         self.tf = config["end_date"].as_date()
         if self.tf <= self.ti:
             raise ValueError(
-                f"Time to finish ('{self.tf}') is less than or equal to time to start ('{self.ti}')."
+                f"Final time ('{self.tf}') is less than or equal to initial time('{self.ti}')."
             )
         self.n_days = (self.tf - self.ti).days + 1
         self.dates = pd.date_range(start=self.ti, end=self.tf, freq="D")
@@ -76,7 +76,7 @@ def __init__(
         # Auto-detect old config
         if config["interventions"].exists():
             raise ValueError(
-                "This config has an intervention section, which is only compatible with a previous version (1.1) of flepiMoP."
+                "This config has an intervention section, which is only compatible with a previous version (v1.1) of flepiMoP. "
             )
 
         # 1. Create a setup name that contains every scenario.
@@ -172,14 +172,14 @@ def __init__(
                     )  # TODO create a Stacked from all
             elif self.seir_modifiers_scenario is not None:
                 raise ValueError(
-                    "A seir modifiers scenario was provided to `ModelInfo` but there is no `seir_modifiers` section in the config."
+                    "A `seir_modifiers_scenario` argument was provided to `ModelInfo` but there is no `seir_modifiers` section in the config."
                 )
             else:
                 logging.info("Running `ModelInfo` with seir but without SEIR Modifiers")
 
         elif self.seir_modifiers_scenario is not None:
             raise ValueError(
-                "A seir modifiers scenario was provided to `ModelInfo` but there is no `seir_modifiers` section in the config."
+                "A `seir_modifiers_scenario` argument was provided to `ModelInfo` but there is no `seir` section in the config."
             )
         else:
             logging.critical("Running ModelInfo without SEIR")
@@ -208,7 +208,7 @@ def __init__(
             elif self.outcome_modifiers_scenario is not None:
                 if config["outcome_modifiers"].exists():
                     raise ValueError(
-                        "An outcome modifiers scenario was provided to `ModelInfo` but there is no `outcome_modifiers` section in the config."
+                        "A `outcome_modifiers_scenario` argument was provided to `ModelInfo` but there is no `outcome_modifiers` section in the config."
                     )
                 else:
                     self.outcome_modifiers_scenario = None
@@ -218,7 +218,7 @@ def __init__(
                 )
         elif self.outcome_modifiers_scenario is not None:
             raise ValueError(
-                "An outcome modifiers scenario was provided to `ModelInfo` but there is no `outcome_modifiers` section in the config."
+                "A `outcome_modifiers_scenario` argument was provided to `ModelInfo` but there is no `outcomes` section in the config."
             )
         else:
             logging.info("Running `ModelInfo` without outcomes.")
diff --git a/flepimop/gempyor_pkg/src/gempyor/seeding.py b/flepimop/gempyor_pkg/src/gempyor/seeding.py
index c341ed93c..a2ae8bb88 100644
--- a/flepimop/gempyor_pkg/src/gempyor/seeding.py
+++ b/flepimop/gempyor_pkg/src/gempyor/seeding.py
@@ -158,8 +158,6 @@ def get_from_config(self, sim_id: int, modinf) -> nb.typed.Dict:
             )
         elif method == "FolderDraw" or method == "FromFile":
             amounts = seeding["amount"]
-        else:
-            raise ValueError(f"Unknown seeding method given, '{method}'.")
 
         return _DataFrame2NumbaDict(df=seeding, amounts=amounts, modinf=modinf)
 
diff --git a/flepimop/gempyor_pkg/src/gempyor/statistics.py b/flepimop/gempyor_pkg/src/gempyor/statistics.py
index b6ced5e6d..180dbe80e 100644
--- a/flepimop/gempyor_pkg/src/gempyor/statistics.py
+++ b/flepimop/gempyor_pkg/src/gempyor/statistics.py
@@ -257,8 +257,8 @@ def llik(self, model_data: xr.DataArray, gt_data: xr.DataArray) -> xr.DataArray:
         }
         if self.dist not in dist_map:
             raise ValueError(
-                f"Invalid distribution specified [received: '{self.dist}']. "
-                f"Valid distributions: '{dist_map}'."
+                f"Invalid distribution specified: '{self.dist}'. "
+                f"Valid distributions: '{dist_map.keys()}'."
             )
         if self.dist in ["pois", "nbinom"]:
             model_data = model_data.astype(int)

From d5fe360a5f0854a3006a2967e6958b562a46323d Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Fri, 22 Nov 2024 16:06:52 -0500
Subject: [PATCH 29/56] Regex update in `test_model_info.py`

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

diff --git a/flepimop/gempyor_pkg/tests/seir/test_model_info.py b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
index baad036b4..7cfc78d4e 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_model_info.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
@@ -46,7 +46,7 @@ def test_ModelInfo_init_tf_is_ahead_of_ti_fail(self):
         config["start_date"] = "2022-01-02"
         with pytest.raises(
             ValueError,
-            match=r"Time to finish.*is less than or equal to time to start.*",
+            match=r"Final time.*is less than or equal to initial time.*",
         ):
             s = ModelInfo(
                 config=config,

From 9c6e1f1f102b11382c50a0b1e738a2ceda72e6bf Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Tue, 26 Nov 2024 17:13:57 -0500
Subject: [PATCH 30/56] Regex update in `test_model_info.py`

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

diff --git a/flepimop/gempyor_pkg/tests/seir/test_model_info.py b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
index 7cfc78d4e..25c3c00c8 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_model_info.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
@@ -46,7 +46,7 @@ def test_ModelInfo_init_tf_is_ahead_of_ti_fail(self):
         config["start_date"] = "2022-01-02"
         with pytest.raises(
             ValueError,
-            match=r"Final time.*is less than or equal to initial time.*",
+            match=rf"Final time ('{config["end_date"]}') is less than or equal to initial time ('{config["start_date"]}').",
         ):
             s = ModelInfo(
                 config=config,

From f7c1ad08f832a42d7e5b007aea3473ecc11b87ae Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Tue, 26 Nov 2024 17:17:26 -0500
Subject: [PATCH 31/56] Regex update in `test_model_info.py`

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

diff --git a/flepimop/gempyor_pkg/tests/seir/test_model_info.py b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
index 25c3c00c8..714763204 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_model_info.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
@@ -46,7 +46,7 @@ def test_ModelInfo_init_tf_is_ahead_of_ti_fail(self):
         config["start_date"] = "2022-01-02"
         with pytest.raises(
             ValueError,
-            match=rf"Final time ('{config["end_date"]}') is less than or equal to initial time ('{config["start_date"]}').",
+            match=rf"Final time ('{config['end_date']}') is less than or equal to initial time ('{config['start_date']}').",
         ):
             s = ModelInfo(
                 config=config,

From ebe2ebcfb36a546cd9d86d5c0a5404e3742923f7 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 27 Nov 2024 08:11:42 -0500
Subject: [PATCH 32/56] Typo in `model_info.py`

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

diff --git a/flepimop/gempyor_pkg/src/gempyor/model_info.py b/flepimop/gempyor_pkg/src/gempyor/model_info.py
index 3ba989cf3..3b6cf5afc 100644
--- a/flepimop/gempyor_pkg/src/gempyor/model_info.py
+++ b/flepimop/gempyor_pkg/src/gempyor/model_info.py
@@ -19,7 +19,7 @@ def __init__(self, config: confuse.ConfigView):
         self.tf = config["end_date"].as_date()
         if self.tf <= self.ti:
             raise ValueError(
-                f"Final time ('{self.tf}') is less than or equal to initial time('{self.ti}')."
+                f"Final time ('{self.tf}') is less than or equal to initial time ('{self.ti}')."
             )
         self.n_days = (self.tf - self.ti).days + 1
         self.dates = pd.date_range(start=self.ti, end=self.tf, freq="D")

From 57240be501036c8ce13f74066f50310348429e34 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Wed, 27 Nov 2024 08:19:15 -0500
Subject: [PATCH 33/56] Using `re.escape()` to escape non-alphanumeric
 characters in the regex

---
 flepimop/gempyor_pkg/tests/seir/test_model_info.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/seir/test_model_info.py b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
index 714763204..b241ba263 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_model_info.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_model_info.py
@@ -4,6 +4,7 @@
 import pandas as pd
 import pytest
 import confuse
+import re
 
 from gempyor.model_info import ModelInfo, subpopulation_structure
 
@@ -46,7 +47,7 @@ def test_ModelInfo_init_tf_is_ahead_of_ti_fail(self):
         config["start_date"] = "2022-01-02"
         with pytest.raises(
             ValueError,
-            match=rf"Final time ('{config['end_date']}') is less than or equal to initial time ('{config['start_date']}').",
+            match=re.escape(rf"Final time ('{config['end_date']}') is less than or equal to initial time ('{config['start_date']}')."),
         ):
             s = ModelInfo(
                 config=config,

From cc52fb7ad803a938fcd2160c4c15f1f9d3fda7fc Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 08:41:39 -0500
Subject: [PATCH 34/56] Regex update in `test_seir.py`

Updating a regex to match on a specific value rather than arbitrary wording of error message.
---
 flepimop/gempyor_pkg/tests/seir/test_seir.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/seir/test_seir.py b/flepimop/gempyor_pkg/tests/seir/test_seir.py
index 9cf89032e..c81dea883 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_seir.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_seir.py
@@ -129,7 +129,7 @@ def test_constant_population_legacy_integration():
 
 def test_constant_population_rk4jit_integration_fail():
     with pytest.raises(
-        ValueError, match=r".*integration method only supports deterministic integration.*"
+        ValueError, match=rf"'{modinf.seir_config["integration"]["method"].get()}' integration method only supports deterministic integration.*"
     ):
         config.set_file(f"{DATA_DIR}/config.yml")
 

From 328dacfd0de8ac7079bc93e500e5a464b85d85f2 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 09:09:02 -0500
Subject: [PATCH 35/56] Syntax update in `test_seir.py`

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

diff --git a/flepimop/gempyor_pkg/tests/seir/test_seir.py b/flepimop/gempyor_pkg/tests/seir/test_seir.py
index c81dea883..a9e3db633 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_seir.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_seir.py
@@ -129,7 +129,7 @@ def test_constant_population_legacy_integration():
 
 def test_constant_population_rk4jit_integration_fail():
     with pytest.raises(
-        ValueError, match=rf"'{modinf.seir_config["integration"]["method"].get()}' integration method only supports deterministic integration.*"
+        ValueError, match=rf"'{modinf.seir_config['integration']['method'].get()}' integration method only supports deterministic integration.*"
     ):
         config.set_file(f"{DATA_DIR}/config.yml")
 

From e7621d93fe65ef7f3ba1c70e449a3a8166451b55 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 09:32:01 -0500
Subject: [PATCH 36/56] Update test_seir.py

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

diff --git a/flepimop/gempyor_pkg/tests/seir/test_seir.py b/flepimop/gempyor_pkg/tests/seir/test_seir.py
index a9e3db633..eeb04fff8 100644
--- a/flepimop/gempyor_pkg/tests/seir/test_seir.py
+++ b/flepimop/gempyor_pkg/tests/seir/test_seir.py
@@ -129,7 +129,7 @@ def test_constant_population_legacy_integration():
 
 def test_constant_population_rk4jit_integration_fail():
     with pytest.raises(
-        ValueError, match=rf"'{modinf.seir_config['integration']['method'].get()}' integration method only supports deterministic integration.*"
+        ValueError, match=r"'rk4.jit' integration method only supports deterministic integration.*"
     ):
         config.set_file(f"{DATA_DIR}/config.yml")
 

From d74a214b6ef93aa0d72a7d6be7e5d679fb13e13a Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 11:19:05 -0500
Subject: [PATCH 37/56] Regex update in `test_statistic_class.py`

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

diff --git a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
index 5ec48ba76..31b752ded 100644
--- a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
+++ b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
@@ -248,7 +248,7 @@ def test_unsupported_regularizations_value_error(
             ]
             if reg_name not in ["forecast", "allsubpop"]
         )
-        with pytest.raises(ValueError, match=r"^Unsupported regularization \[received:.*$"):
+        with pytest.raises(ValueError, match=rf"^Unsupported regularization \[received: '{mock_inputs.config.get('regularize', [])}'\]"):
             mock_inputs.create_statistic_instance()
 
     @pytest.mark.parametrize("factory", all_valid_factories)

From d5087931e56d17a4e977e59fbb6d186593522c6d Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 11:26:22 -0500
Subject: [PATCH 38/56] Regex update in `test_statistic_class.py`

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

diff --git a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
index 31b752ded..fa6964a7f 100644
--- a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
+++ b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
@@ -248,7 +248,7 @@ def test_unsupported_regularizations_value_error(
             ]
             if reg_name not in ["forecast", "allsubpop"]
         )
-        with pytest.raises(ValueError, match=rf"^Unsupported regularization \[received: '{mock_inputs.config.get('regularize', [])}'\]"):
+        with pytest.raises(ValueError, match=rf"^Unsupported regularization \[received: 'invalid'\]"):
             mock_inputs.create_statistic_instance()
 
     @pytest.mark.parametrize("factory", all_valid_factories)

From 6fc2a5a6b2a41c9a6499148631cf88be518022d6 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 13:51:03 -0500
Subject: [PATCH 39/56] Regex update in `test_statistic_class.py`

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

diff --git a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
index fa6964a7f..268b9ce21 100644
--- a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
+++ b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
@@ -520,7 +520,7 @@ def test_compute_logloss_data_misshape_value_error(
 
         model_rows, model_cols = mock_inputs.model_data[mock_inputs.config["sim_var"]].shape
         gt_rows, gt_cols = mock_inputs.gt_data[mock_inputs.config["data_var"]].shape
-        expected_match = rf".*do not have the same shape:.*"
+        expected_match = rf".*'{mock_inputs.model_data[mock_inputs.config["sim_var"]].shape}' !=.*'{mock_inputs.gt_data[mock_inputs.config["data_var"]].shape}'"
         with pytest.raises(ValueError, match=expected_match):
             statistic.compute_logloss(mock_inputs.model_data, mock_inputs.gt_data)
 

From f8b9dc31cf05e7517b99604b121905e8de1c0686 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 13:56:06 -0500
Subject: [PATCH 40/56] Syntax change in `test_statistic_class.py`

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

diff --git a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
index 268b9ce21..4531d5490 100644
--- a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
+++ b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
@@ -520,7 +520,7 @@ def test_compute_logloss_data_misshape_value_error(
 
         model_rows, model_cols = mock_inputs.model_data[mock_inputs.config["sim_var"]].shape
         gt_rows, gt_cols = mock_inputs.gt_data[mock_inputs.config["data_var"]].shape
-        expected_match = rf".*'{mock_inputs.model_data[mock_inputs.config["sim_var"]].shape}' !=.*'{mock_inputs.gt_data[mock_inputs.config["data_var"]].shape}'"
+        expected_match = rf".*'{mock_inputs.model_data[mock_inputs.config['sim_var']].shape}' !=.*'{mock_inputs.gt_data[mock_inputs.config['data_var']].shape}'"
         with pytest.raises(ValueError, match=expected_match):
             statistic.compute_logloss(mock_inputs.model_data, mock_inputs.gt_data)
 

From ad623ab86386f2ae573993e919c289051aaa087c Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 14:12:25 -0500
Subject: [PATCH 41/56] Regex update in `test_statistic_class.py`

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

diff --git a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
index 4531d5490..18a5e94b0 100644
--- a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
+++ b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
@@ -520,7 +520,7 @@ def test_compute_logloss_data_misshape_value_error(
 
         model_rows, model_cols = mock_inputs.model_data[mock_inputs.config["sim_var"]].shape
         gt_rows, gt_cols = mock_inputs.gt_data[mock_inputs.config["data_var"]].shape
-        expected_match = rf".*'{mock_inputs.model_data[mock_inputs.config['sim_var']].shape}' !=.*'{mock_inputs.gt_data[mock_inputs.config['data_var']].shape}'"
+        expected_match = rf".*'{mock_inputs.model_data[mock_inputs.config['sim_var']].shape}'.*'{mock_inputs.gt_data[mock_inputs.config['data_var']].shape}'"
         with pytest.raises(ValueError, match=expected_match):
             statistic.compute_logloss(mock_inputs.model_data, mock_inputs.gt_data)
 

From a3b5f621d6d0400cf8594574ede4e7a837c98fac Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 14:26:29 -0500
Subject: [PATCH 42/56] Testing a regex in `test_statistic_class.py`

---
 .../gempyor_pkg/tests/statistics/test_statistic_class.py    | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
index 18a5e94b0..274a344bf 100644
--- a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
+++ b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
@@ -520,7 +520,11 @@ def test_compute_logloss_data_misshape_value_error(
 
         model_rows, model_cols = mock_inputs.model_data[mock_inputs.config["sim_var"]].shape
         gt_rows, gt_cols = mock_inputs.gt_data[mock_inputs.config["data_var"]].shape
-        expected_match = rf".*'{mock_inputs.model_data[mock_inputs.config['sim_var']].shape}'.*'{mock_inputs.gt_data[mock_inputs.config['data_var']].shape}'"
+        expected_match = (
+            rf"`model_data` and `gt_data` do not have the same shape: "
+            rf"`model_data.shape` = '{mock_inputs.model_data[mock_inputs.config['sim_var']].shape}' "
+            rf"!= `gt_data.shape` = '{mock_inputs.gt_data[mock_inputs.config['data_var']].shape}'."
+        )
         with pytest.raises(ValueError, match=expected_match):
             statistic.compute_logloss(mock_inputs.model_data, mock_inputs.gt_data)
 

From 1daed72da55c2a9f09880bb75064221e3503a0f3 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 14:41:03 -0500
Subject: [PATCH 43/56] Using re.escape() to escape non-alphanumeric characters
 in the regex

---
 flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
index 274a344bf..bc2007270 100644
--- a/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
+++ b/flepimop/gempyor_pkg/tests/statistics/test_statistic_class.py
@@ -8,6 +8,7 @@
 import pytest
 import scipy
 import xarray as xr
+import re
 
 from gempyor.statistics import Statistic
 from gempyor.testing import create_confuse_configview_from_dict
@@ -520,7 +521,7 @@ def test_compute_logloss_data_misshape_value_error(
 
         model_rows, model_cols = mock_inputs.model_data[mock_inputs.config["sim_var"]].shape
         gt_rows, gt_cols = mock_inputs.gt_data[mock_inputs.config["data_var"]].shape
-        expected_match = (
+        expected_match = re.escape(
             rf"`model_data` and `gt_data` do not have the same shape: "
             rf"`model_data.shape` = '{mock_inputs.model_data[mock_inputs.config['sim_var']].shape}' "
             rf"!= `gt_data.shape` = '{mock_inputs.gt_data[mock_inputs.config['data_var']].shape}'."

From 239f5a0bc63988204c3d57d4a502b4b3a68acf7a Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 14:50:16 -0500
Subject: [PATCH 44/56] Regex update in `test_random_distribution_sampler.py`

---
 .../gempyor_pkg/tests/utils/test_random_distribution_sampler.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
index 596d296c1..f4e26115d 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
@@ -14,7 +14,7 @@ class TestRandomDistributionSampler:
     def test_not_implemented_error_exception(self, distribution: str) -> None:
         with pytest.raises(
             NotImplementedError,
-            match=rf"^Unknown distribution \[received.*",
+            match=rf"^Unknown distribution \[received '{distribution}'\]",
         ):
             random_distribution_sampler(distribution)
 

From 50b91ce36c10dc4b1adcb10183a7d0738046996e Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 15:04:16 -0500
Subject: [PATCH 45/56] Regex update in `test_random_distribution_sampler.py`

---
 .../tests/utils/test_random_distribution_sampler.py           | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
index f4e26115d..f3fe2c899 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
@@ -14,7 +14,7 @@ class TestRandomDistributionSampler:
     def test_not_implemented_error_exception(self, distribution: str) -> None:
         with pytest.raises(
             NotImplementedError,
-            match=rf"^Unknown distribution \[received '{distribution}'\]",
+            match=rf"Unknown distribution [received '{distribution}']",
         ):
             random_distribution_sampler(distribution)
 
@@ -22,7 +22,7 @@ def test_not_implemented_error_exception(self, distribution: str) -> None:
     def test_binomial_p_value_error(self, p: float) -> None:
         with pytest.raises(
             ValueError,
-            match=r"^Invalid\s`p-value`.*\sis\sout\sof\srange.*$",
+            match=rf"Invalid `p-value`: '{p}' is out of range [0,1].",
         ):
             random_distribution_sampler("binomial", n=100, p=p)
 

From 84fb06796feed2137af1b66a82fca33f82b1cc5d Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 15:13:41 -0500
Subject: [PATCH 46/56] Update test_random_distribution_sampler.py

---
 .../gempyor_pkg/tests/utils/test_random_distribution_sampler.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
index f3fe2c899..148686996 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
@@ -14,7 +14,7 @@ class TestRandomDistributionSampler:
     def test_not_implemented_error_exception(self, distribution: str) -> None:
         with pytest.raises(
             NotImplementedError,
-            match=rf"Unknown distribution [received '{distribution}']",
+            match=rf"Unknown distribution [received: '{distribution}']",
         ):
             random_distribution_sampler(distribution)
 

From 4bf61fb4dad446a63fa85d8011f9db29c4bd1bb2 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 15:23:13 -0500
Subject: [PATCH 47/56] Update test_random_distribution_sampler.py

---
 .../gempyor_pkg/tests/utils/test_random_distribution_sampler.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
index 148686996..0d94c0456 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
@@ -14,7 +14,7 @@ class TestRandomDistributionSampler:
     def test_not_implemented_error_exception(self, distribution: str) -> None:
         with pytest.raises(
             NotImplementedError,
-            match=rf"Unknown distribution [received: '{distribution}']",
+            match=rf"Unknown distribution [received: '{distribution}'].",
         ):
             random_distribution_sampler(distribution)
 

From 660795fbbd280533d5772ae058ba2df2cb8501fd Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 15:29:30 -0500
Subject: [PATCH 48/56] Using `re.escape()` in regexs

---
 .../tests/utils/test_random_distribution_sampler.py          | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
index 0d94c0456..0dcd110fb 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_random_distribution_sampler.py
@@ -4,6 +4,7 @@
 
 import numpy as np
 import pytest
+import re
 
 from gempyor.testing import partials_are_similar
 from gempyor.utils import random_distribution_sampler
@@ -14,7 +15,7 @@ class TestRandomDistributionSampler:
     def test_not_implemented_error_exception(self, distribution: str) -> None:
         with pytest.raises(
             NotImplementedError,
-            match=rf"Unknown distribution [received: '{distribution}'].",
+            match=re.escape(rf"Unknown distribution [received: '{distribution}']."),
         ):
             random_distribution_sampler(distribution)
 
@@ -22,7 +23,7 @@ def test_not_implemented_error_exception(self, distribution: str) -> None:
     def test_binomial_p_value_error(self, p: float) -> None:
         with pytest.raises(
             ValueError,
-            match=rf"Invalid `p-value`: '{p}' is out of range [0,1].",
+            match=re.escape(rf"Invalid `p-value`: '{p}' is out of range [0,1]."),
         ):
             random_distribution_sampler("binomial", n=100, p=p)
 

From 00120cf2019efd0d273865ef16acf5fa1c91dfa0 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 15:40:12 -0500
Subject: [PATCH 49/56] Regex update in `test_read_df.py`

---
 flepimop/gempyor_pkg/tests/utils/test_read_df.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_read_df.py b/flepimop/gempyor_pkg/tests/utils/test_read_df.py
index 676f5d699..0ed485852 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_read_df.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_read_df.py
@@ -38,13 +38,13 @@ def test_raises_not_implemented_error(self) -> None:
         """
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match=r".*Supported extensions are `.csv` or `.parquet`.",
+            match=rf"Invalid extension provided: '.txt'. Supported extensions are `.csv` or `.parquet`.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 read_df(fname=temp_file.name)
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match=r".*Supported extensions are `.csv` or `.parquet`.",
+            match=rf"Invalid extension provided: '.txt'. Supported extensions are `.csv` or `.parquet`.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 fname = temp_file.name[:-4]

From 0a05cb546e3bb29c11cd934060d56235d4875700 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Mon, 2 Dec 2024 15:46:49 -0500
Subject: [PATCH 50/56] Update utils.py

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

diff --git a/flepimop/gempyor_pkg/src/gempyor/utils.py b/flepimop/gempyor_pkg/src/gempyor/utils.py
index a937b53b4..f8852e17a 100644
--- a/flepimop/gempyor_pkg/src/gempyor/utils.py
+++ b/flepimop/gempyor_pkg/src/gempyor/utils.py
@@ -95,7 +95,7 @@ def read_df(
     elif path.suffix == ".parquet":
         return pd.read_parquet(path, engine="pyarrow")
     raise NotImplementedError(
-        f"Invalid extension provided: '{path.suffix[1:]}'. Supported extensions are `.csv` or `.parquet`."
+        f"Invalid extension provided: '.{path.suffix[1:]}'. Supported extensions are `.csv` or `.parquet`."
     )
 
 

From 190c4839b8efd21959ff6d9fd30168fb46e6eb18 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Tue, 3 Dec 2024 15:11:23 -0500
Subject: [PATCH 51/56] Regex update in `test_utils.py`

---
 flepimop/gempyor_pkg/tests/utils/test_read_df.py | 4 ++--
 flepimop/gempyor_pkg/tests/utils/test_utils.py   | 5 ++---
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_read_df.py b/flepimop/gempyor_pkg/tests/utils/test_read_df.py
index 0ed485852..b591aecd9 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_read_df.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_read_df.py
@@ -38,13 +38,13 @@ def test_raises_not_implemented_error(self) -> None:
         """
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match=rf"Invalid extension provided: '.txt'. Supported extensions are `.csv` or `.parquet`.",
+            match=r"Invalid extension provided: '.txt'. Supported extensions are `.csv` or `.parquet`.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 read_df(fname=temp_file.name)
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match=rf"Invalid extension provided: '.txt'. Supported extensions are `.csv` or `.parquet`.",
+            match=r"Invalid extension provided: '.txt'. Supported extensions are `.csv` or `.parquet`.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 fname = temp_file.name[:-4]
diff --git a/flepimop/gempyor_pkg/tests/utils/test_utils.py b/flepimop/gempyor_pkg/tests/utils/test_utils.py
index c57ac900e..384cae617 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_utils.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_utils.py
@@ -38,8 +38,7 @@ def test_read_df_and_write_success(fname, extension):
 )
 def test_read_df_and_write_fail(fname, extension):
     with pytest.raises(
-        NotImplementedError, match=r".*Supported extensions are `.csv` or `.parquet`."
-    ):
+        NotImplementedError, match=rf"Invalid extension provided: '{extension}'. Supported extensions are `.csv` or `.parquet`."):
         os.chdir(tmp_path)
         os.makedirs("data", exist_ok=True)
         os.chdir("data")
@@ -58,7 +57,7 @@ def test_read_df_and_write_fail(fname, extension):
 
 @pytest.mark.parametrize(("fname", "extension"), [("mobility", "")])
 def test_read_df_fail(fname, extension):
-    with pytest.raises(NotImplementedError, match=r".*Invalid.*extension.*"):
+    with pytest.raises(NotImplementedError, match=rf"Invalid extension provided: '{extension}'. Supported extensions are `.csv` or `.parquet`."):
         os.chdir(tmp_path)
         utils.read_df(fname=f"{DATA_DIR}/" + fname, extension=extension)
 

From fb6c9ed967bd63c6afbc40c29475be2d11f2adeb Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Tue, 3 Dec 2024 15:33:48 -0500
Subject: [PATCH 52/56] Regex update in `test_utils.py`

---
 flepimop/gempyor_pkg/tests/utils/test_utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_utils.py b/flepimop/gempyor_pkg/tests/utils/test_utils.py
index 384cae617..817b8db55 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_utils.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_utils.py
@@ -38,7 +38,7 @@ def test_read_df_and_write_success(fname, extension):
 )
 def test_read_df_and_write_fail(fname, extension):
     with pytest.raises(
-        NotImplementedError, match=rf"Invalid extension provided: '{extension}'. Supported extensions are `.csv` or `.parquet`."):
+        NotImplementedError, match=r"Invalid extension provided: ''. Supported extensions are `.csv` or `.parquet`."):
         os.chdir(tmp_path)
         os.makedirs("data", exist_ok=True)
         os.chdir("data")
@@ -57,7 +57,7 @@ def test_read_df_and_write_fail(fname, extension):
 
 @pytest.mark.parametrize(("fname", "extension"), [("mobility", "")])
 def test_read_df_fail(fname, extension):
-    with pytest.raises(NotImplementedError, match=rf"Invalid extension provided: '{extension}'. Supported extensions are `.csv` or `.parquet`."):
+    with pytest.raises(NotImplementedError, match=r"Invalid extension provided: ''. Supported extensions are `.csv` or `.parquet`."):
         os.chdir(tmp_path)
         utils.read_df(fname=f"{DATA_DIR}/" + fname, extension=extension)
 

From 8255da25ae91c077d233b6ca9b5347d2c4518aed Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Tue, 3 Dec 2024 16:00:52 -0500
Subject: [PATCH 53/56] Update test_utils.py

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

diff --git a/flepimop/gempyor_pkg/tests/utils/test_utils.py b/flepimop/gempyor_pkg/tests/utils/test_utils.py
index 817b8db55..d83bc04e8 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_utils.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_utils.py
@@ -57,7 +57,7 @@ def test_read_df_and_write_fail(fname, extension):
 
 @pytest.mark.parametrize(("fname", "extension"), [("mobility", "")])
 def test_read_df_fail(fname, extension):
-    with pytest.raises(NotImplementedError, match=r"Invalid extension provided: ''. Supported extensions are `.csv` or `.parquet`."):
+    with pytest.raises(NotImplementedError, match=r"Invalid extension provided: '.'. Supported extensions are `.csv` or `.parquet`."):
         os.chdir(tmp_path)
         utils.read_df(fname=f"{DATA_DIR}/" + fname, extension=extension)
 

From 8a5e772939d5e1d7261480252ab88e3cd9bc6455 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Tue, 3 Dec 2024 16:17:48 -0500
Subject: [PATCH 54/56] Regex update in `test_write_df.py`

---
 flepimop/gempyor_pkg/tests/utils/test_write_df.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/flepimop/gempyor_pkg/tests/utils/test_write_df.py b/flepimop/gempyor_pkg/tests/utils/test_write_df.py
index 8f4e18baf..e63afa2e5 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_write_df.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_write_df.py
@@ -30,13 +30,13 @@ def test_raises_not_implemented_error(self) -> None:
         """
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match=r".*Supported extensions are `.csv` or `.parquet`.",
+            match=r"Invalid extension provided: '.txt'. Supported extensions are `.csv` or `.parquet`.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 write_df(fname=temp_file.name, df=self.sample_df)
         with pytest.raises(
             expected_exception=NotImplementedError,
-            match=r".*Supported extensions are `.csv` or `.parquet`.",
+            match=r"Invalid extension provided: '.txt'. Supported extensions are `.csv` or `.parquet`.",
         ) as _:
             with NamedTemporaryFile(suffix=".txt") as temp_file:
                 fname = temp_file.name[:-4]

From 6ce17606aa0644fa8dcb54b36ccf13b5e5ca9023 Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Tue, 3 Dec 2024 16:25:40 -0500
Subject: [PATCH 55/56] Update utils.py

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

diff --git a/flepimop/gempyor_pkg/src/gempyor/utils.py b/flepimop/gempyor_pkg/src/gempyor/utils.py
index f8852e17a..9732d70c2 100644
--- a/flepimop/gempyor_pkg/src/gempyor/utils.py
+++ b/flepimop/gempyor_pkg/src/gempyor/utils.py
@@ -58,7 +58,7 @@ def write_df(
     elif path.suffix == ".parquet":
         return df.to_parquet(path, index=False, engine="pyarrow")
     raise NotImplementedError(
-        f"Invalid extension provided: '{path.suffix[1:]}'. Supported extensions are `.csv` or `.parquet`."
+        f"Invalid extension provided: '.{path.suffix[1:]}'. Supported extensions are `.csv` or `.parquet`."
     )
 
 

From 178861a38184c248ee9e7651fc86a25065e4775d Mon Sep 17 00:00:00 2001
From: Emily Przykucki <emily.przykucki@gmail.com>
Date: Tue, 3 Dec 2024 16:38:41 -0500
Subject: [PATCH 56/56] Update test_utils.py

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

diff --git a/flepimop/gempyor_pkg/tests/utils/test_utils.py b/flepimop/gempyor_pkg/tests/utils/test_utils.py
index d83bc04e8..7b6606166 100644
--- a/flepimop/gempyor_pkg/tests/utils/test_utils.py
+++ b/flepimop/gempyor_pkg/tests/utils/test_utils.py
@@ -38,7 +38,7 @@ def test_read_df_and_write_success(fname, extension):
 )
 def test_read_df_and_write_fail(fname, extension):
     with pytest.raises(
-        NotImplementedError, match=r"Invalid extension provided: ''. Supported extensions are `.csv` or `.parquet`."):
+        NotImplementedError, match=r"Invalid extension provided: '.'. Supported extensions are `.csv` or `.parquet`."):
         os.chdir(tmp_path)
         os.makedirs("data", exist_ok=True)
         os.chdir("data")