now possible to check also for logger exception types

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

@@ -107,12 +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.
         """
-        self.custom_exception = exception
+        if exception is not None:
+            extra = {'custom_exception': exception}
+        else:
+            extra = None
 
         self._original_log(
             level,
             msg,
             args,
+            extra,
             **kwargs
         )
 
@@ -147,6 +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.
@@ -162,22 +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)
-
-    def makeRecord(self, name, level, fn, lno, msg, args, exc_info,
-                   func=None, extra=None, sinfo=None):
-        """
-        This method creates a log record.
-        """
-
-        record = super().makeRecord(name, level, fn, lno, msg, args, exc_info,
-                                    func=func, extra=extra, sinfo=sinfo)
-        if hasattr(self, 'custom_exception'):
-            setattr(record, 'custom_exception', self.custom_exception)
-
-        return record
+        super()._log(level, msg, args, extra=extra, **kwargs)
 
     def error(self,
               msg: Any,
@@ -338,7 +332,10 @@ def format(self, record: logging.LogRecord) -> str:
         name = record.name
 
         if hasattr(record, 'custom_exception'):
-            header = f'{formatted_level} {name} - {record.custom_exception}\n\n'
+            header = (
+                f'{formatted_level} {name} - '
+                f'{record.custom_exception.__qualname__}\n\n'
+            )
         else:
             header = f'{formatted_level} {name}\n\n'
 

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'))