Bugfix/logger

PQAnalysis/traj/trajectory.py

@@ -184,8 +184,8 @@ def window(
         -------
         If not all frames are included in the windows, a warning is issued.
 
-        Returns
-        -------
+        Yields
+        ------
         Iterable[Trajectory]
             An iterable over the windows of the trajectory with the specified window size and gap.
         """
@@ -194,28 +194,32 @@ def window(
         if window_stop is None:
             window_stop = len(self)
 
-        # If window_start is less than 0 or greater than the length of the trajectory, raise an IndexError
+        # If window_start is less than 0 or greater than the
+        # length of the trajectory, raise an IndexError
         if window_start < 0 or window_start > len(self):
             self.logger.error(
                 "start index is less than 0 or greater than the length of the trajectory",
                 exception=IndexError,
             )
 
-        # If window_stop is less than 0 or greater than the length of the trajectory, raise an IndexError
+        # If window_stop is less than 0 or greater than the
+        # length of the trajectory, raise an IndexError
         if window_stop < 0 or window_stop > len(self):
             self.logger.error(
                 "stop index is less than 0 or greater than the length of the trajectory",
                 exception=IndexError,
             )
 
-        # If window_step is less than 1 or greater than the length of the trajectory, raise an IndexError
+        # If window_step is less than 1 or greater than
+        # the length of the trajectory, raise an IndexError
         if window_size < 1 or window_size > len(self):
             self.logger.error(
                 "window size can not be less than 1 or greater than the length of the trajectory",
                 exception=IndexError,
             )
 
-        # If window_gap is less than 1 or greater than the length of the trajectory, raise an IndexError
+        # If window_gap is less than 1 or greater than
+        # the length of the trajectory, raise an IndexError
         if window_gap < 1 or window_gap > len(self):
             self.logger.error(
                 "window gap can not be less than 1 or greater than the length of the trajectory",
@@ -245,7 +249,7 @@ def window(
 
         # generate the window of the trajectory
         for i in range(window_start, window_stop - window_size + 1, window_gap):
-            yield self[i : i + window_size]
+            yield self[i: i + window_size]
 
     def __contains__(self, item: AtomicSystem) -> bool:
         """

PQAnalysis/utils/custom_logging.py

@@ -107,10 +107,16 @@ def _log(self,   # pylint: disable=arguments-differ
             if the level is logging.ERROR or logging.CRITICAL and the logger
             is not enabled for logging.DEBUG.
         """
+        if exception is not None:
+            extra = {'custom_exception': exception}
+        else:
+            extra = None
+
         self._original_log(
             level,
             msg,
             args,
+            extra,
             **kwargs
         )
 
@@ -145,6 +151,7 @@ def _original_log(self,
                       level: Any,
                       msg: Any,
                       args: Any,
+                      extra=None,
                       **kwargs) -> None:
         """
         The original _log method of the logging.Logger class.
@@ -160,9 +167,11 @@ def _original_log(self,
             The message to log.
         args : Any
             The arguments of the log message.
+        extra : Any, optional
+            Additional information to log, by default None.
         """
 
-        super()._log(level, msg, args, **kwargs)
+        super()._log(level, msg, args, extra=extra, **kwargs)
 
     def error(self,
               msg: Any,
@@ -321,7 +330,14 @@ def format(self, record: logging.LogRecord) -> str:
         longest_level_key = max(level_keys, key=len)
 
         name = record.name
-        header = f'{formatted_level} {name}\n\n'
+
+        if hasattr(record, 'custom_exception'):
+            header = (
+                f'{formatted_level} {name} - '
+                f'{record.custom_exception.__qualname__}\n\n'
+            )
+        else:
+            header = f'{formatted_level} {name}\n\n'
 
         messages = message.split('\n')
         wrapper = textwrap.TextWrapper(

tests/conftest.py

@@ -88,23 +88,43 @@ def caplog_for_logger(caplog, logger_name, level):
     logger.removeHandler(caplog.handler)
 
 
-def assert_logging(caplog, logging_name, logging_level, message_to_test, function, *args, **kwargs):
+def assert_logging_with_exception(caplog, logging_name, logging_level, message_to_test, exception, function, *args, **kwargs):
     with caplog_for_logger(caplog, __package_name__ + "." + logging_name, logging_level):
         result = None
         try:
             result = function(*args, **kwargs)
         except SystemExit:
             pass
 
-        assert caplog.record_tuples[0][0] == __package_name__ + \
+        record = caplog.records[0]
+
+        assert record.name == __package_name__ + \
             "." + logging_name
-        assert caplog.record_tuples[0][1] == logging.getLevelName(
-            logging_level)
-        message = caplog.record_tuples[0][2]
+        assert record.levelno == logging.getLevelName(
+            logging_level
+        )
+
+        if exception is not None:
+            assert record.custom_exception == exception
+
+        message = record.msg
 
         messages = [message.strip() for message in message.split("\n")]
 
         for message in messages:
             assert message in message_to_test
 
         return result
+
+
+def assert_logging(caplog, logging_name, logging_level, message_to_test, function, *args, **kwargs):
+    return assert_logging_with_exception(
+        caplog,
+        logging_name,
+        logging_level,
+        message_to_test,
+        None,
+        function,
+        *args,
+        **kwargs
+    )

tests/topology/test_topology.py

@@ -147,17 +147,17 @@ def test_setup_residues(self, caplog):
         topology.reference_residues = reference_residues
 
         assert_logging(
-            caplog,
-            Topology.__qualname__,
-            "ERROR",
-            (
+            caplog=caplog,
+            logging_name=Topology.__qualname__,
+            logging_level="ERROR",
+            message_to_test=(
                 "The element of atom 0 is not set. If any reference residues are given the "
                 "program tries to automatically deduce the residues from the residue ids and "
                 "the reference residues. This means that any atom with an unknown element "
                 "raises an error. To avoid deducing residue information please set 'check_residues' "
                 "to False"
             ),
-            topology._setup_residues,
+            function=topology._setup_residues,
             residue_ids=residue_ids,
             atoms=atoms
         )
@@ -167,19 +167,20 @@ def test_setup_residues(self, caplog):
         topology.reference_residues = reference_residues
 
         residues, new_atoms = assert_logging(
-            caplog,
-            Topology.__qualname__,
-            "WARNING",
-            (
+            caplog=caplog,
+            logging_name=Topology.__qualname__,
+            logging_level="WARNING",
+            message_to_test=(
                 "The element of atom 1 (Element(c, 6, 12.0107)) does not match "
                 "the element of the reference residue ALA (Element(h, 1, 1.00794)). "
                 "Therefore the element type of the residue description will be used "
                 "within the topology format!"
             ),
-            topology._setup_residues,
+            function=topology._setup_residues,
             residue_ids=residue_ids,
             atoms=atoms,
         )
+
         assert len(residues) == 2
         assert new_atoms == atoms
         assert residues[0] == QMResidue(Element('C'))

tests/traj/test_trajectory.py

@@ -6,7 +6,7 @@
 import pytest
 import numpy as np
 
-from ..conftest import assert_logging
+from ..conftest import assert_logging, assert_logging_with_exception
 
 from PQAnalysis.traj import Trajectory
 from PQAnalysis.core import Cell, Atom
@@ -163,70 +163,90 @@ def test_window(self, caplog):
             traj.window(2, 2).__next__,
         )
 
-        assert_logging(
+        assert_logging_with_exception(
             caplog,
             Trajectory.__qualname__,
+            exception=IndexError,
             logging_level="ERROR",
             message_to_test=(
                 "window size can not be less than 1 or greater than the length of the trajectory"
             ),
             function=traj.window(0).__next__,
         )
 
-        assert_logging(
+        assert_logging_with_exception(
             caplog,
             Trajectory.__qualname__,
-            "ERROR",
-            "window size can not be less than 1 or greater than the length of the trajectory",
-            traj.window(4).__next__,
+            exception=IndexError,
+            logging_level="ERROR",
+            message_to_test=(
+                "window size can not be less than 1 or greater than the length of the trajectory"
+            ),
+            function=traj.window(4).__next__,
         )
 
-        assert_logging(
+        assert_logging_with_exception(
             caplog,
             Trajectory.__qualname__,
-            "ERROR",
-            "window gap can not be less than 1 or greater than the length of the trajectory",
-            traj.window(1, 0).__next__,
+            exception=IndexError,
+            logging_level="ERROR",
+            message_to_test=(
+                "window gap can not be less than 1 or greater than the length of the trajectory"
+            ),
+            function=traj.window(1, 0).__next__,
         )
 
-        assert_logging(
+        assert_logging_with_exception(
             caplog,
             Trajectory.__qualname__,
-            "ERROR",
-            "window gap can not be less than 1 or greater than the length of the trajectory",
-            traj.window(1, 4).__next__,
+            exception=IndexError,
+            logging_level="ERROR",
+            message_to_test=(
+                "window gap can not be less than 1 or greater than the length of the trajectory"
+            ),
+            function=traj.window(1, 4).__next__,
         )
 
-        assert_logging(
+        assert_logging_with_exception(
             caplog,
             Trajectory.__qualname__,
-            "ERROR",
-            "start index is less than 0 or greater than the length of the trajectory",
-            traj.window(1, 1, window_start=-1).__next__,
+            exception=IndexError,
+            logging_level="ERROR",
+            message_to_test=(
+                "start index is less than 0 or greater than the length of the trajectory"
+            ),
+            function=traj.window(1, 1, window_start=-1).__next__,
         )
 
-        assert_logging(
+        assert_logging_with_exception(
             caplog,
             Trajectory.__qualname__,
-            "ERROR",
-            "stop index is less than 0 or greater than the length of the trajectory",
-            traj.window(1, 1, window_stop=-1).__next__,
+            exception=IndexError,
+            logging_level="ERROR",
+            message_to_test=(
+                "stop index is less than 0 or greater than the length of the trajectory"
+            ),
+            function=traj.window(1, 1, window_stop=-1).__next__,
         )
 
-        assert_logging(
+        assert_logging_with_exception(
             caplog,
             Trajectory.__qualname__,
-            "ERROR",
-            "start index is greater than or equal to the stop index",
-            traj.window(1, 1, window_start=2, window_stop=1).__next__,
+            exception=IndexError,
+            logging_level="ERROR",
+            message_to_test=("start index is greater than or equal to the stop index"),
+            function=traj.window(1, 1, window_start=2, window_stop=1).__next__,
         )
 
-        assert_logging(
+        assert_logging_with_exception(
             caplog,
             Trajectory.__qualname__,
-            "ERROR",
-            "window size is greater than the window_stop - window_start",
-            traj.window(3, 1, window_start=1, window_stop=3).__next__,
+            exception=IndexError,
+            logging_level="ERROR",
+            message_to_test=(
+                "window size is greater than the window_stop - window_start"
+            ),
+            function=traj.window(3, 1, window_start=1, window_stop=3).__next__,
         )
 
     def test__iter__(self):