Decorator logging function (#232)

* Logging function name where error occurs

* updated text

src/pyciemss/PetriNetODE/interfaces.py

@@ -40,12 +40,14 @@
     StaticParameterInterventionEvent,
 )
 
+from pyciemss.custom_decorators import pyciemss_logging_wrappper
+
 # TODO: These interfaces should probably be just in terms of JSON-like objects.
 
 PetriSolution = dict[str, torch.Tensor]
 PetriInferredParameters = pyro.nn.PyroModule
 
-
+@pyciemss_logging_wrappper
 def load_and_sample_petri_model(
     petri_model_or_path: Union[str, mira.metamodel.TemplateModel, mira.modeling.Model],
     num_samples: int,
@@ -122,7 +124,7 @@ def load_and_sample_petri_model(
 
     return processed_samples
 
-
+@pyciemss_logging_wrappper
 def load_and_calibrate_and_sample_petri_model(
     petri_model_or_path: Union[str, mira.metamodel.TemplateModel, mira.modeling.Model],
     data_path: str,
@@ -233,7 +235,7 @@ def load_and_calibrate_and_sample_petri_model(
 
 ##############################################################################
 # Internal Interfaces Below - TA4 above
-
+@pyciemss_logging_wrappper
 def load_petri_model(
     petri_model_or_path: Union[str, mira.metamodel.TemplateModel, mira.modeling.Model],
     add_uncertainty=True,
@@ -243,7 +245,6 @@ def load_petri_model(
     """
     Load a petri net from a file and compile it into a probabilistic program.
     """
-
     if add_uncertainty:
         model = ScaledBetaNoisePetriNetODESystem.from_askenet(petri_model_or_path, compile_rate_law_p=compile_rate_law_p)
         model.pseudocount = torch.tensor(pseudocount)
@@ -253,6 +254,7 @@ def load_petri_model(
 
 
 @setup_model.register
+@pyciemss_logging_wrappper
 def setup_petri_model(
     petri: PetriNetODESystem,
     start_time: float,
@@ -269,6 +271,7 @@ def setup_petri_model(
 
 
 @reset_model.register
+@pyciemss_logging_wrappper
 def reset_petri_model(petri: PetriNetODESystem) -> PetriNetODESystem:
     """
     Reset a model to its initial state.
@@ -280,6 +283,7 @@ def reset_petri_model(petri: PetriNetODESystem) -> PetriNetODESystem:
 
 
 @intervene.register
+@pyciemss_logging_wrappper
 def intervene_petri_model(
     petri: PetriNetODESystem, interventions: Iterable[Tuple[float, str, float]]
 ) -> PetriNetODESystem:
@@ -297,6 +301,7 @@ def intervene_petri_model(
 
 
 @calibrate.register
+@pyciemss_logging_wrappper
 def calibrate_petri(
     petri: PetriNetODESystem,
     data: Iterable[Tuple[float, dict[str, float]]],
@@ -340,6 +345,7 @@ def calibrate_petri(
 
 
 @sample.register
+@pyciemss_logging_wrappper
 def sample_petri(
     petri: PetriNetODESystem,
     timepoints: Iterable[float],
@@ -366,6 +372,7 @@ def sample_petri(
 
 
 @optimize.register
+@pyciemss_logging_wrappper
 def optimize_petri(
     petri: PetriNetODESystem,
     timepoints: Iterable,

src/pyciemss/custom_decorators.py

@@ -0,0 +1,32 @@
+import logging
+import time
+import functools
+
+def pyciemss_logging_wrappper( function):
+    def wrapped(*args, **kwargs):
+        try:
+            start_time = time.perf_counter()
+            result = function(*args, **kwargs)
+            end_time = time.perf_counter()
+            logging.info(
+                f"Elapsed time for {function.__name__}:",
+                end_time - start_time
+                )
+            return result
+        except Exception as e:
+
+            log_message = f"""
+                ###############################
+
+                There was an exception in pyciemss
+                
+                Error occured in function: {function.__name__}
+
+                Function docs : {function.__doc__}
+
+                ################################
+            """
+            logging.exception(log_message)
+            raise e
+    functools.update_wrapper(wrapped, function)
+    return wrapped