Adding Logging Support for Caught Exceptions (#1701)

* Added Logging Support to Debug for Caught Exceptions

* Removed \n\t formatting from Exception Messages

tardis/base.py

@@ -1,5 +1,10 @@
 # functions that are important for the general usage of TARDIS
 
+import logging
+
+
+logger = logging.getLogger(__name__)
+
 
 def run_tardis(
     config,
@@ -44,6 +49,9 @@ def run_tardis(
         try:
             tardis_config = Configuration.from_yaml(config)
         except TypeError:
+            logger.debug(
+                "TARDIS Config not available via YAML. Reading through TARDIS Config Dictionary"
+            )
             tardis_config = Configuration.from_config_dict(config)
 
     logging_state(log_state, tardis_config, specific)
@@ -52,6 +60,9 @@ def run_tardis(
         try:
             atom_data = AtomData.from_hdf(atom_data)
         except TypeError:
+            logger.debug(
+                "Atom Data Cannot be Read from HDF. Setting to Default Atom Data"
+            )
             atom_data = atom_data
 
     simulation = Simulation.from_config(

tardis/io/atom_data/base.py

@@ -164,33 +164,45 @@ def from_hdf(cls, fname=None):
                 try:
                     dataframes[name] = store[name]
                 except KeyError:
+                    logger.debug("Dataframe does not contain NAME column")
                     nonavailable.append(name)
 
             atom_data = cls(**dataframes)
 
             try:
                 atom_data.uuid1 = store.root._v_attrs["uuid1"].decode("ascii")
             except KeyError:
+                logger.debug(
+                    "UUID not available for Atom Data. Setting value to None"
+                )
                 atom_data.uuid1 = None
 
             try:
                 atom_data.md5 = store.root._v_attrs["md5"].decode("ascii")
             except KeyError:
+                logger.debug(
+                    "MD5 not available for Atom Data. Setting value to None"
+                )
                 atom_data.md5 = None
 
             try:
                 atom_data.version = store.root._v_attrs["database_version"]
             except KeyError:
+                logger.debug(
+                    "VERSION not available for Atom Data. Setting value to None"
+                )
                 atom_data.version = None
 
             # ToDo: strore data sources as attributes in carsus
 
             logger.info(
-                f"\n\tReading Atom Data with:\n\tUUID = {atom_data.uuid1}\n\tMD5  = {atom_data.md5} "
+                f"Reading Atom Data with: UUID = {atom_data.uuid1} MD5  = {atom_data.md5} "
             )
             if nonavailable:
                 logger.info(
-                    f'\n\tNon provided atomic data:\n\t{", ".join(nonavailable)}'
+                    "Non provided Atomic Data: {0}".format(
+                        ", ".join(nonavailable)
+                    )
                 )
 
         return atom_data

tardis/io/parsers/csvy.py

@@ -1,9 +1,12 @@
+import logging
 import yaml
 import pandas as pd
 from tardis.io.util import YAMLLoader
 
 YAML_DELIMITER = "---"
 
+logger = logging.getLogger(__name__)
+
 
 def load_csvy(fname):
     """
@@ -17,7 +20,7 @@ def load_csvy(fname):
     yaml_dict : dictionary
                 YAML part of the csvy file
     data : pandas.dataframe
-           csv data from csvy file
+            csv data from csvy file
     """
     with open(fname) as fh:
         yaml_lines = []
@@ -37,6 +40,7 @@ def load_csvy(fname):
         try:
             data = pd.read_csv(fname, skiprows=yaml_end_ind + 1)
         except pd.errors.EmptyDataError as e:
+            logger.debug(f"Could not Read CSV. Setting Dataframe to None")
             data = None
 
     return yaml_dict, data

tardis/io/util.py

@@ -248,6 +248,9 @@ def to_hdf_util(
             except TypeError as e:
                 if e.message == "Expected bytes, got HDFStore":
                     # when path_or_buf is an HDFStore buffer instead
+                    logger.debug(
+                        "Expected bytes, got HDFStore. Changing path to HDF buffer"
+                    )
                     buf = path_or_buf
                 else:
                     raise e
@@ -269,13 +272,19 @@ def to_hdf_util(
                     try:
                         pd.Series(value).to_hdf(buf, os.path.join(path, key))
                     except NotImplementedError:
+                        logger.debug(
+                            "Could not convert SERIES to HDF. Converting DATAFRAME to HDF"
+                        )
                         pd.DataFrame(value).to_hdf(buf, os.path.join(path, key))
                 else:
                     pd.DataFrame(value).to_hdf(buf, os.path.join(path, key))
             else:  # value is a TARDIS object like model, runner or plasma
                 try:
                     value.to_hdf(buf, path, name=key, overwrite=overwrite)
                 except AttributeError:
+                    logger.debug(
+                        "Could not convert VALUE to HDF. Converting DATA (Dataframe) to HDF"
+                    )
                     data = pd.DataFrame([value])
                     data.to_hdf(buf, os.path.join(path, key))
 
@@ -319,6 +328,9 @@ def to_hdf(self, file_path_or_buf, path="", name=None, overwrite=False):
                 name = self.hdf_name
             except AttributeError:
                 name = self.convert_to_snake_case(self.__class__.__name__)
+                logger.debug(
+                    f"self.hdf_name not present, setting name to {name} for HDF"
+                )
 
         data = self.get_properties()
         buff_path = os.path.join(path, name)

tardis/plasma/properties/nlte.py

@@ -215,6 +215,9 @@ def calculate(
                         )
                     except:
                         number_density = 0.0
+                        logger.debug(
+                            f"Number Density could not be calculated. Setting Number Density to {number_density}"
+                        )
                     output_file.write(number_density)
 
             helium_lines = lines[lines["atomic_number"] == 2]

tardis/plasma/properties/partition_function.py

@@ -188,10 +188,16 @@ def _main_nlte_calculation(
                 j_blues_filtered = j_blues.iloc[lines_index]
             except AttributeError:
                 j_blues_filtered = j_blues
+                logger.debug(
+                    f"J Blues Filtered Value could not be calculated. Using j_blues_filtered = {j_blues_filtered}"
+                )
             try:
                 beta_sobolevs_filtered = beta_sobolevs.iloc[lines_index]
             except AttributeError:
                 beta_sobolevs_filtered = beta_sobolevs
+                logger.debug(
+                    f"Beta Sobolevs Filtered Value could not be calculated. Using beta_sobolevs_filtered = {beta_sobolevs}"
+                )
             A_uls = nlte_data.A_uls[species]
             B_uls = nlte_data.B_uls[species]
             B_lus = nlte_data.B_lus[species]

tardis/plasma/properties/radiative_properties.py

@@ -359,6 +359,9 @@ def _get_macro_atom_data(atomic_data):
         try:
             return atomic_data.macro_atom_data
         except:
+            logger.debug(
+                "Macro Atom Data was not found. Instead returning All Macro Atom Data"
+            )
             return atomic_data.macro_atom_data_all
 
 

tardis/simulation/base.py

@@ -513,6 +513,7 @@ def remove_callback(self, id):
             del self._callbacks[id]
             return True
         except KeyError:
+            logger.debug(f"Call Back was not found in {self._callbacks.keys()}")
             return False
 
     @classmethod

tardis/util/base.py

@@ -219,6 +219,9 @@ def create_synpp_yaml(radial1d_mdl, fname, shell_no=0, lines_db=None):
                 radial1d_mdl.plasma.tau_sobolevs[0].loc[value["line_id"]]
             )
         except KeyError:
+            logger.debug(
+                "Synpp Ref does not have valid KEY for ref_log_tau in Radial1D Model"
+            )
             pass
 
     relevant_synpp_refs = radial1d_mdl.atom_data.synpp_refs[
@@ -371,6 +374,9 @@ def species_string_to_tuple(species_string):
     try:
         ion_number = roman_to_int(ion_number_string)
     except ValueError:
+        logger.debug(
+            "Ion Number does not contain a Roman Numeral. Checking for integer value"
+        )
         try:
             ion_number = int(ion_number_string)
         except ValueError:
@@ -555,6 +561,9 @@ def is_notebook():
         # Trying to import the ZMQInteractiveShell for Jupyter based environments
         from ipykernel.zmqshell import ZMQInteractiveShell
     except NameError:
+        logger.debug(
+            "Cannot Import ipykernel.zmqshell. Not present inside Jupyter Environment"
+        )
         # If the class cannot be imported then we are automatically return False Value
         # Raised due to Name Error with the imported Class
         return False
@@ -563,6 +572,9 @@ def is_notebook():
         # Trying to import Interactive Terminal based IPython shell
         from IPython.core.interactiveshell import InteractiveShell
     except NameError:
+        logger.debug(
+            "Cannot Import IPython.core.interactiveshell. Not present in IPython shell"
+        )
         # If the class cannot be imported then we are automatically return False Value
         # Raised due to Name Error with the imported Class
         return False
@@ -571,6 +583,7 @@ def is_notebook():
         # Trying to get the value of the shell via the get_ipython() method
         shell = get_ipython()
     except NameError:
+        logger.debug("Cannot infer Shell Id")
         # Returns False if the shell name cannot be inferred correctly
         return False