Formatting Logging Output for Simulation (tardis-sn#1632)

* Formatting Logging Output for Simulation runs via Notebook

* Reverting removed import

* Fixing decimal precision for luminosity values

* Formatting changes for the Plasma Stratification values displayed

* Allowing pandas dataframe to be displayed in Notebook as well as Terminal

* Removing redundant pandas setting

* Adding import for get_ipython()

* Moving simulation environment checking to another PR & made appropriate changes

* Added some more formatting changes to other logging messages for consistency

* Renamed check_simulation_env() to is_notebook(), Added better conditional checks for the environment using isinstance()

* Formatting changed for Simulation message about no of iterations & time taken

* Added Tests for checking the logging done while running the simulation

tardis/io/atom_data/base.py

@@ -186,11 +186,11 @@ def from_hdf(cls, fname=None):
             # ToDo: strore data sources as attributes in carsus
 
             logger.info(
-                f"Read Atom Data with UUID={atom_data.uuid1} and MD5={atom_data.md5}."
+                f"\n\tReading Atom Data with:\n\tUUID = {atom_data.uuid1}\n\tMD5  = {atom_data.md5} "
             )
             if nonavailable:
                 logger.info(
-                    f'Non provided atomic data: {", ".join(nonavailable)}'
+                    f'\n\tNon provided atomic data:\n\t{", ".join(nonavailable)}'
                 )
 
         return atom_data

tardis/io/atom_data/util.py

@@ -31,7 +31,7 @@ def resolve_atom_data_fname(fname):
     fpath = os.path.join(os.path.join(get_data_dir(), fname))
     if os.path.exists(fpath):
         logger.info(
-            f"Atom Data {fname} not found in local path. Exists in TARDIS Data repo {fpath}"
+            f"\n\tAtom Data {fname} not found in local path.\n\tExists in TARDIS Data repo {fpath}"
         )
         return fpath
 

tardis/plasma/standard_plasmas.py

@@ -88,7 +88,7 @@ def assemble_plasma(config, model, atom_data=None):
         else:
             raise ValueError("No atom_data option found in the configuration.")
 
-        logger.info("Reading Atomic Data from %s", atom_data_fname)
+        logger.info(f"\n\tReading Atomic Data from {atom_data_fname}")
 
         try:
             atom_data = AtomData.from_hdf(atom_data_fname)

tardis/simulation/base.py

@@ -10,7 +10,9 @@
 from tardis.plasma.standard_plasmas import assemble_plasma
 from tardis.io.util import HDFWriterMixin
 from tardis.io.config_reader import ConfigurationError
+from tardis.util.base import is_notebook
 from tardis.montecarlo import montecarlo_configuration as mc_config_module
+from IPython.display import display
 
 # Adding logging support
 logger = logging.getLogger(__name__)
@@ -320,7 +322,7 @@ def advance_state(self):
 
     def iterate(self, no_of_packets, no_of_virtual_packets=0, last_run=False):
         logger.info(
-            f"Starting iteration {(self.iterations_executed + 1):d}/{self.iterations:d}"
+            f"\n\tStarting iteration {(self.iterations_executed + 1):d} of {self.iterations:d}"
         )
         self.runner.run(
             self.model,
@@ -348,6 +350,7 @@ def run(self):
         """
         run the simulation
         """
+
         start_time = time.time()
         while self.iterations_executed < self.iterations - 1:
             self.store_plasma_state(
@@ -378,8 +381,8 @@ def run(self):
         self.reshape_plasma_state_store(self.iterations_executed)
 
         logger.info(
-            f"Simulation finished in {self.iterations_executed:d} iterations "
-            f"and took {(time.time() - start_time):.2f} s"
+            f"\n\tSimulation finished in {self.iterations_executed:d} iterations "
+            f"\n\tSimulation took {(time.time() - start_time):.2f} s\n"
         )
         self._call_back()
 
@@ -421,23 +424,35 @@ def log_plasma_state(
         plasma_state_log["next_t_rad"] = next_t_rad
         plasma_state_log["w"] = w
         plasma_state_log["next_w"] = next_w
+        plasma_state_log.columns.name = "Shell No."
 
-        plasma_state_log.index.name = "Shell"
-
-        plasma_state_log = str(plasma_state_log[::log_sampling])
+        if is_notebook():
+            logger.info("\n\tPlasma stratification:")
+            logger.info(
+                display(
+                    plasma_state_log.iloc[::log_sampling].style.format("{:.3g}")
+                )
+            )
+        else:
+            output_df = ""
+            plasma_output = plasma_state_log.iloc[::log_sampling].to_string(
+                float_format=lambda x: "{:.3g}".format(x),
+                justify="center",
+            )
+            for value in plasma_output.split("\n"):
+                output_df = output_df + "\t{}\n".format(value)
+            logger.info("\n\tPlasma stratification:")
+            logger.info(f"\n{output_df}")
 
-        plasma_state_log = "".join(
-            ["\t%s\n" % item for item in plasma_state_log.split("\n")]
+        logger.info(
+            f"\n\tCurrent t_inner = {t_inner:.3f}\n\tExpected t_inner for next iteration = {next_t_inner:.3f}\n"
         )
 
-        logger.info("Plasma stratification:\n%s\n", plasma_state_log)
-        logger.info(f"t_inner {t_inner:.3f} -- next t_inner {next_t_inner:.3f}")
-
     def log_run_results(self, emitted_luminosity, absorbed_luminosity):
         logger.info(
-            f"Luminosity emitted = {emitted_luminosity:.5e} "
-            f"Luminosity absorbed = {absorbed_luminosity:.5e} "
-            f"Luminosity requested = {self.luminosity_requested:.5e}"
+            f"\n\tLuminosity emitted   = {emitted_luminosity:.3e}\n"
+            f"\tLuminosity absorbed  = {absorbed_luminosity:.3e}\n"
+            f"\tLuminosity requested = {self.luminosity_requested:.3e}\n"
         )
 
     def _call_back(self):

tardis/simulation/tests/test_simulation.py

@@ -1,6 +1,8 @@
 import os
 
 import pytest
+import logging
+
 from tardis.io.config_reader import Configuration
 from tardis.simulation import Simulation
 
@@ -153,3 +155,20 @@ def test_plasma_state_storer_reshape(
 
 #     assert_quantity_allclose(
 #             t_rad, simulation_compare_data['test1/t_rad'] * u.Unit('K'), atol=0.0 * u.Unit('K'))
+
+
+def test_logging_simulation(atomic_data_fname, caplog):
+    """
+    Testing the logs for simulations runs
+    """
+    config = Configuration.from_yaml(
+        "tardis/io/tests/data/tardis_configv1_verysimple.yml"
+    )
+    config["atom_data"] = atomic_data_fname
+
+    simulation = Simulation.from_config(config)
+
+    simulation.run()
+
+    for record in caplog.records:
+        assert record.levelno >= logging.INFO

tardis/util/base.py

@@ -542,23 +542,44 @@ def convert_abundances_format(fname, delimiter=r"\s+"):
     return df
 
 
-def check_simulation_env():
+def is_notebook():
     """
-    Checking the environment where the simulation is run
+    Checking the shell environment where the simulation is run is Jupyter based
 
     Returns
     -------
-    True : if the environment is IPython Based
-    False : if the environment is Terminal or anything else
+    True : if the shell environment is IPython Based
+    False : if the shell environment is Terminal or anything else
     """
     try:
-        shell = get_ipython().__class__.__name__
+        # Trying to import the ZMQInteractiveShell for Jupyter based environments
+        from ipykernel.zmqshell import ZMQInteractiveShell
     except NameError:
+        # If the class cannot be imported then we are automatically return False Value
+        # Raised due to Name Error with the imported Class
         return False
 
-    if shell == "ZMQInteractiveShell":
+    try:
+        # Trying to import Interactive Terminal based IPython shell
+        from IPython.core.interactiveshell import InteractiveShell
+    except NameError:
+        # If the class cannot be imported then we are automatically return False Value
+        # Raised due to Name Error with the imported Class
+        return False
+
+    try:
+        # Trying to get the value of the shell via the get_ipython() method
+        shell = get_ipython()
+    except NameError:
+        # Returns False if the shell name cannot be inferred correctly
+        return False
+
+    # Checking if the shell instance is Jupyter based & if True, returning True
+    if isinstance(shell, ZMQInteractiveShell):
         return True
-    elif shell == "TerminalInteractiveShell":
+    # Checking if the shell instance is Terminal IPython based & if True, returning False
+    elif isinstance(shell, InteractiveShell):
         return False
+    # All other shell instances are returned False
     else:
         return False