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Merge pull request #313 from emprzy/gempyor_error_improvements
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Improving readability/consistency of errors/exceptions in `gempyor`.
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@emprzy
emprzy authored Nov 8, 2024
2 parents b541e1e + 7b4f6e8 commit 7af554e
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Showing 8 changed files with 129 additions and 129 deletions.
90 changes: 46 additions & 44 deletions flepimop/gempyor_pkg/src/gempyor/compartments.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ def __init__(
self.times_set += 1

if self.times_set == 0:
raise ValueError("Compartments object not set, no config or file provided")
raise ValueError("Compartments object not set, no config or file provided.")
return

def constructFromConfig(self, seir_config, compartment_config):
Expand Down Expand Up @@ -153,15 +153,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
except Exception as e:
print(f"Error {e}:")
print(
f">>> in expand_transition_elements for `source:` at index {it.multi_index}"
f">>> in expand_transition_elements for `source:` at index '{it.multi_index}'"
)
print(
f">>> this transition source is: {single_transition_config['source']}"
f">>> this transition source is: '{single_transition_config['source']}'"
)
print(
f">>> this transition destination is: {single_transition_config['destination']}"
f">>> this transition destination is: '{single_transition_config['destination']}'"
)
print(f"transition_dimension: {problem_dimension}")
print(f"transition_dimension: '{problem_dimension}'")
raise e

try:
Expand All @@ -175,15 +175,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
except Exception as e:
print(f"Error {e}:")
print(
f">>> in expand_transition_elements for `destination:` at index {it.multi_index}"
f">>> in expand_transition_elements for `destination:` at index '{it.multi_index}'"
)
print(
f">>> this transition source is: {single_transition_config['source']}"
f">>> this transition source is: '{single_transition_config['source']}'"
)
print(
f">>> this transition destination is: {single_transition_config['destination']}"
f">>> this transition destination is: '{single_transition_config['destination']}'"
)
print(f"transition_dimension: {problem_dimension}")
print(f"transition_dimension: '{problem_dimension}'")
raise e

try:
Expand All @@ -197,15 +197,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
except Exception as e:
print(f"Error {e}:")
print(
f">>> in expand_transition_elements for `rate:` at index {it.multi_index}"
f">>> in expand_transition_elements for `rate:` at index '{it.multi_index}'"
)
print(
f">>> this transition source is: {single_transition_config['source']}"
f">>> this transition source is: '{single_transition_config['source']}'"
)
print(
f">>> this transition destination is: {single_transition_config['destination']}"
f">>> this transition destination is: '{single_transition_config['destination']}'"
)
print(f"transition_dimension: {problem_dimension}")
print(f"transition_dimension: '{problem_dimension}'")
raise e

try:
Expand All @@ -225,15 +225,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
except Exception as e:
print(f"Error {e}:")
print(
f">>> in expand_transition_elements for `proportional_to:` at index {it.multi_index}"
f">>> in expand_transition_elements for `proportional_to:` at index '{it.multi_index}'"
)
print(
f">>> this transition source is: {single_transition_config['source']}"
f">>> this transition source is: '{single_transition_config['source']}'"
)
print(
f">>> this transition destination is: {single_transition_config['destination']}"
f">>> this transition destination is: '{single_transition_config['destination']}'"
)
print(f"transition_dimension: {problem_dimension}")
print(f"transition_dimension: '{problem_dimension}'")
raise e

if (
Expand All @@ -260,15 +260,15 @@ def expand_transition_elements(self, single_transition_config, problem_dimension
except Exception as e:
print(f"Error {e}:")
print(
f">>> in expand_transition_elements for `proportion_exponent:` at index {it.multi_index}"
f">>> in expand_transition_elements for `proportion_exponent:` at index '{it.multi_index}'"
)
print(
f">>> this transition source is: {single_transition_config['source']}"
f">>> this transition source is: '{single_transition_config['source']}'"
)
print(
f">>> this transition destination is: {single_transition_config['destination']}"
f">>> this transition destination is: '{single_transition_config['destination']}'"
)
print(f"transition_dimension: {problem_dimension}")
print(f"transition_dimension: '{problem_dimension}'")
raise e
else:
new_transition_config["proportion_exponent"][it.multi_index] = [
Expand Down Expand Up @@ -379,7 +379,6 @@ def unformat_proportion_exponent(
def parse_single_transition(
self, seir_config, single_transition_config, fake_config=False
):

## This method relies on having run parse_compartments
if not fake_config:
single_transition_config = single_transition_config.get()
Expand Down Expand Up @@ -483,7 +482,9 @@ def get_comp_idx(self, comp_dict: dict, error_info: str = "no information") -> i
comp_idx = self.compartments[mask].index.values
if len(comp_idx) != 1:
raise ValueError(
f"The provided dictionary does not allow to isolate a compartment: {comp_dict} isolate {self.compartments[mask]} from options {self.compartments}. The get_comp_idx function was called by'{error_info}'."
f"The provided dictionary does not allow an isolated compartment: '{comp_dict}'. "
f"Isolate '{self.compartments[mask]}'. "
f"The `get_comp_idx` function was called by '{error_info}'."
)
return comp_idx[0]

Expand All @@ -503,9 +504,8 @@ def get_transition_array(self):
if self.compartments["name"][compartment] == elem:
rc = compartment
if rc == -1:
print(self.compartments)
raise ValueError(
f"Could not find {colname} defined by {elem} in compartments"
f"Could not find '{colname}' defined by '{elem}' in '{self.compartments}'."
)
transition_array[cit, it] = rc

Expand Down Expand Up @@ -539,8 +539,10 @@ def get_transition_array(self):
candidate = reduce(lambda a, b: a + "*" + b, elem)
candidate = candidate.replace(" ", "")
# candidate = candidate.replace("*1", "")
if not candidate in unique_strings:
raise ValueError("Something went wrong")
if candidate not in unique_strings:
raise ValueError(
f"Candidate '{candidate}' from 'rate' column is not in the list of unique strings: {unique_strings}."
)
rc = [it for it, x in enumerate(unique_strings) if x == candidate][0]
transition_array[2][it] = rc

Expand Down Expand Up @@ -583,8 +585,10 @@ def get_transition_array(self):
candidate = reduce(lambda a, b: a + "*" + b, y)
candidate = candidate.replace(" ", "")
# candidate = candidate.replace("*1", "")
if not candidate in unique_strings:
raise ValueError("Something went wrong")
if candidate not in unique_strings:
raise ValueError(
f"Proportion exponent '{candidate}' is not found in the list of unique strings: '{unique_strings}'."
)
rc = [it for it, x in enumerate(unique_strings) if x == candidate][0]
proportion_info[2][proportion_compartment_index] = rc
proportion_compartment_index += 1
Expand All @@ -610,7 +614,8 @@ def get_transition_array(self):
rc = compartment
if rc == -1:
raise ValueError(
f"Could not find proportional_to {elem3} in compartments"
f"Could not find `proportional_to` '{elem3}' in compartments. "
f"Available compartments: '{self.compartments}'."
)

proportion_array[proportion_index] = rc
Expand Down Expand Up @@ -682,7 +687,7 @@ def parse_parameter_strings_to_numpy_arrays_v2(
parsed_formulas.append(f)
except Exception as e:
print(
f"Cannot parse formula: '{formula}' from parameters {parameter_names}"
f"Cannot parse formula '{formula}' from parameters: '{parameter_names}'."
)
raise (e) # Print the error message for debugging

Expand Down Expand Up @@ -733,10 +738,10 @@ def parse_parameter_strings_to_numpy_arrays(
not operators
): # empty list means all have been tried. Usually there just remains one string in string_list at that time.
raise ValueError(
f"""Could not parse string {string_list}.
This usually mean that '{string_list[0]}' is a parameter name that is not defined
or that it contains an operator that is not in the list of supported operator: ^,*,/,+,-.
The defined parameters are {parameter_names}."""
f"Could not parse string '{string_list}'. "
f"This usually means that '{string_list[0]}' is a parameter name that is not defined "
f"or that it contains an operator that is not in the list of supported operators: '{operators}'. "
f"The defined parameters are '{parameter_names}'."
)

split_strings = [x.split(operators[0]) for x in string_list]
Expand Down Expand Up @@ -851,16 +856,13 @@ def list_access_element_safe(thing, idx, dimension=None, encapsulate_as_list=Fal
try:
return list_access_element(thing, idx, dimension, encapsulate_as_list)
except Exception as e:
print(f"Error {e}:")
print(f">>> in list_access_element_safe for {thing} at index {idx}")
print(
">>> This is often, but not always because the object above is a list (there are brackets around it)."
)
print(
">>> and in this case it is not broadcast, so if you want to it to be broadcasted, you need remove the brackets around it."
raise Exception(
f"Error {e}: "
f"in list_access_element_safe for '{thing}' at index '{idx}'. "
f"This is often, but not always because the object above is a list (there are brackets around it). "
f"and in this case it is not broadcast, so if you want to it to be broadcasted, you need remove the brackets around it. "
f"dimension: '{dimension}'."
)
print(f"dimension: {dimension}")
raise e


def list_access_element(thing, idx, dimension=None, encapsulate_as_list=False):
Expand Down
55 changes: 25 additions & 30 deletions flepimop/gempyor_pkg/src/gempyor/config_validator.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -70,14 +70,14 @@ def validate_initial_file_check(cls, values):
initial_file_type = values.get("initial_file_type")
if method in {"FromFile", "SetInitialConditions"} and not initial_conditions_file:
raise ValueError(
f"Error in InitialConditions: An initial_conditions_file is required when method is {method}"
f"An `initial_conditions_file` is required when method is '{method}'."
)
if (
method in {"InitialConditionsFolderDraw", "SetInitialConditionsFolderDraw"}
and not initial_file_type
):
raise ValueError(
f"Error in InitialConditions: initial_file_type is required when method is {method}"
f"An `initial_file_type` is required when method is '{method}'."
)
return values

Expand All @@ -86,9 +86,7 @@ def plugin_filecheck(cls, values):
method = values.get("method")
plugin_file_path = values.get("plugin_file_path")
if method == "plugin" and not plugin_file_path:
raise ValueError(
"Error in InitialConditions: a plugin file path is required when method is plugin"
)
raise ValueError("A plugin file path is required when method is plugin.")
return values


Expand Down Expand Up @@ -121,16 +119,14 @@ def validate_seedingfile(cls, values):
seeding_file = values.get("seeding_file")
if method == "PoissonDistributed" and not lambda_file:
raise ValueError(
f"Error in Seeding: A lambda_file is required when method is {method}"
"A `lambda_file` is required when method is 'PoissonDistributed'."
)
if method == "FolderDraw" and not seeding_file_type:
raise ValueError(
"Error in Seeding: A seeding_file_type is required when method is FolderDraw"
"A `seeding_file_type` is required when method is 'FolderDraw'."
)
if method == "FromFile" and not seeding_file:
raise ValueError(
"Error in Seeding: A seeding_file is required when method is FromFile"
)
raise ValueError("A `seeding_file` is required when method is 'FromFile'.")
return values

@model_validator(mode="before")
Expand All @@ -139,7 +135,8 @@ def plugin_filecheck(cls, values):
plugin_file_path = values.get("plugin_file_path")
if method == "plugin" and not plugin_file_path:
raise ValueError(
"Error in Seeding: a plugin file path is required when method is plugin"
f"A plugin file path is required when method is 'plugin', "
f"was given '{plugin_file_path!r}'."
)
return values

Expand Down Expand Up @@ -173,16 +170,14 @@ def check_distr(cls, values):
if distr != "fixed":
if not mean and not sd:
raise ValueError(
"Error in value: mean and sd must be provided for non-fixed distributions"
"Mean and sd must be provided for non-fixed distributions."
)
if distr == "truncnorm" and not a and not b:
raise ValueError(
"Error in value: a and b must be provided for truncated normal distributions"
"a and b must be provided for truncated normal distributions."
)
if distr == "fixed" and not value:
raise ValueError(
"Error in value: value must be provided for fixed distributions"
)
raise ValueError("Value must be provided for fixed distributions.")
return values


Expand Down Expand Up @@ -211,7 +206,7 @@ def which_value(cls, values):
timeseries = values.get("timeseries") is not None
if value and timeseries:
raise ValueError(
"Error in seir::parameters: your parameter is both a timeseries and a value, please choose one"
f"Parsed a parameter with both a timeseries, '{values.get('timeseries')!r}', and a value, '{values.get('value')!r}', please choose one."
)
return values

Expand Down Expand Up @@ -301,7 +296,7 @@ def which_source(cls, values):
prevalence = values.get("prevalence")
if incidence and prevalence:
raise ValueError(
"Error in outcomes::source. Can only be incidence or prevalence, not both."
f"Parsed a source with both an incidence, '{values.get('incidence')!r}', and prevalence, '{values.get('prevalence')!r}', please choose one."
)
return values

Expand Down Expand Up @@ -339,13 +334,9 @@ def check_outcome_type(cls, values):
source_present = values.get("source") is not None

if sum_present and source_present:
raise ValueError(
f"Error in outcome: Both 'sum' and 'source' are present. Choose one."
)
raise ValueError("Both 'sum' and 'source' are present, please choose one.")
elif not sum_present and not source_present:
raise ValueError(
f"Error in outcome: Neither 'sum' nor 'source' is present. Choose one."
)
raise ValueError("Neither 'sum' nor 'source' is present, please choose one.")
return values


Expand All @@ -364,7 +355,7 @@ def check_paramfromfile_type(cls, values):

if param_from_file and not param_subpop_file:
raise ValueError(
f"Error in outcome: 'param_subpop_file' is required when 'param_from_file' is True"
"A `param_subpop_file` is required when `param_from_file` is 'True'."
)
return values

Expand Down Expand Up @@ -450,11 +441,11 @@ def verify_inference(cls, values):
start_date_groundtruth = values.get("start_date_groundtruth") is not None
if inference_present and not start_date_groundtruth:
raise ValueError(
"Inference mode is enabled but no groundtruth dates are provided"
"Inference mode is enabled, but no groundtruth dates are provided. Please provide groundtruth dates."
)
elif start_date_groundtruth and not inference_present:
raise ValueError(
"Groundtruth dates are provided but inference mode is not enabled"
"Groundtruth dates are provided, but inference mode is not enabled. Please enable inference mode."
)
return values

Expand All @@ -464,13 +455,17 @@ def check_dates(cls, values):
end_date = values.get("end_date")
if start_date and end_date:
if end_date <= start_date:
raise ValueError("end_date must be greater than start_date")
raise ValueError(
f"`end_date` ('{end_date}') must be later than `start_date` ('{start_date}'))."
)
return values

@model_validator(mode="before")
def init_or_seed(cls, values):
init = values.get("initial_conditions")
seed = values.get("seeding")
if not init or seed:
raise ValueError("either initial_conditions or seeding must be provided")
if not (init or seed):
raise ValueError(
f"At least one of `initial_conditions` or `seeding` must be provided."
)
return values
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