runtime type checking decorator implemented and tested for rdf api

PQAnalysis/type_checking.py

@@ -37,8 +37,8 @@ def runtime_type_checking(func, *args, **kwargs):
                 logger.error(
                     _get_type_error_message(
                         arg_name,
+                        arg_value,
                         type_hints[arg_name],
-                        type(arg_value)
                     ),
                     exception=TypeError,
                 )
@@ -50,8 +50,8 @@ def runtime_type_checking(func, *args, **kwargs):
                 logger.error(
                     _get_type_error_message(
                         kwarg_name,
+                        kwarg_value,
                         type_hints[kwarg_name],
-                        type(kwarg_value)
                     ),
                     exception=TypeError,
                 )
@@ -60,14 +60,16 @@ def runtime_type_checking(func, *args, **kwargs):
     return func(*args, **kwargs)
 
 
-def _get_type_error_message(arg_name, expected_type, actual_type):
+def _get_type_error_message(arg_name, value, expected_type):
     """
     Get the error message for a type error.
     """
 
+    actual_type = type(value)
+
     header = (
-        f"Argument '{arg_name}' should be of type {expected_type}, "
-        f"but got {actual_type}."
+        f"Argument '{arg_name}' with {value=} should be "
+        f"of type {expected_type}, but got {actual_type}."
     )
 
     if expected_type is Np1DIntArray:

PQAnalysis/utils/custom_logging.py

@@ -121,15 +121,15 @@ def _log(self,   # pylint: disable=arguments-differ
         )
 
         if level in [logging.CRITICAL, logging.ERROR]:
+
+            exception = exception or Exception
+
             if self.isEnabledFor(logging.DEBUG):
                 back_tb = None
 
                 try:
-                    if exception is not None:
-                        raise exception
-
-                    raise Exception  # pylint: disable=broad-exception-raised
-                except Exception:  # pylint: disable=broad-except
+                    raise exception  # pylint: disable=broad-exception-raised
+                except exception:  # pylint: disable=broad-except
                     traceback = sys.exc_info()[2]
                     back_frame = traceback.tb_frame.f_back
 
@@ -140,12 +140,21 @@ def _log(self,   # pylint: disable=arguments-differ
                         tb_lineno=back_frame.f_lineno
                     )
 
-                if exception is not None:
-                    raise Exception(msg).with_traceback(back_tb)
-
                 raise exception(msg).with_traceback(back_tb)
 
-            sys.exit(1)
+            class DevNull:
+                """
+                Dummy class to redirect the sys.stderr to /dev/null.
+                """
+
+                def write(self, _):
+                    """
+                    Dummy write method.
+                    """
+
+            sys.stderr = DevNull()
+
+            raise exception(msg)  # pylint: disable=raise-missing-from
 
     def _original_log(self,
                       level: Any,

tests/__init__.py

@@ -0,0 +1,3 @@
+import os
+
+os.environ['PQANALYSIS_BEARTYPE_LEVEL'] = "RELEASE"

tests/analysis/rdf/test_api.py

@@ -1,18 +1,22 @@
 import pytest
 
 from PQAnalysis.analysis.rdf.api import rdf
+from PQAnalysis.type_checking import _get_type_error_message
 
 from .. import pytestmark  # pylint: disable=unused-import
-from ...conftest import assert_logging
+from ...conftest import assert_logging_with_exception
 
 
 class TestRDFAPI:
     def test_wrong_param_types(self, caplog):
-        assert_logging(
+        assert_logging_with_exception(
             caplog=caplog,
-            logging_name=rdf.__name__,
+            logging_name="TypeChecking",
             logging_level="ERROR",
-            message_to_test="Input file must be a string",
+            message_to_test=_get_type_error_message(
+                "input_file", 1, str,
+            ),
+            exception=TypeError,
             function=rdf,
             input_file=1,
         )

tests/conftest.py

@@ -93,7 +93,7 @@ def assert_logging_with_exception(caplog, logging_name, logging_level, message_t
         result = None
         try:
             result = function(*args, **kwargs)
-        except SystemExit:
+        except:
             pass
 
         record = caplog.records[0]

tests/io/test_frameReader.py

@@ -1,17 +1,15 @@
 import pytest
 import numpy as np
 
-from beartype.roar import BeartypeException
-
-from . import pytestmark
-
 from PQAnalysis.io import FrameReader
 from PQAnalysis.io.traj_file.exceptions import FrameReaderError
 from PQAnalysis.core import Cell, Atom
 from PQAnalysis.traj.exceptions import TrajectoryFormatError
 from PQAnalysis.traj import TrajectoryFormat
 from PQAnalysis.topology import Topology
 
+from . import pytestmark
+
 
 class TestFrameReader:
 
@@ -67,9 +65,6 @@ def test__read_scalar(self):
     def test_read(self):
         reader = FrameReader()
 
-        with pytest.raises(BeartypeException):
-            reader.read(["tmp"])
-
         frame = reader.read(
             "2 2.0 3.0 4.0 5.0 6.0 7.0\n\nh 1.0 2.0 3.0\no 2.0 2.0 2.0")
         assert frame.n_atoms == 2

tests/io/test_infoFileReader.py

@@ -1,24 +1,18 @@
 import pytest
 
-from beartype.roar import BeartypeException
-
-from . import pytestmark
-
 from PQAnalysis.io import InfoFileReader
 from PQAnalysis.traj import MDEngineFormat
 from PQAnalysis.traj.exceptions import MDEngineFormatError
 
+from . import pytestmark
+
 
 @pytest.mark.parametrize("example_dir", ["readInfoFile"], indirect=False)
 def test__init__(test_with_data_dir):
     with pytest.raises(FileNotFoundError) as exception:
         InfoFileReader("tmp")
     assert str(exception.value) == "File tmp not found."
 
-    with pytest.raises(BeartypeException) as exception:
-        InfoFileReader(
-            "md-01.info", engine_format=None)
-
     with pytest.raises(MDEngineFormatError) as exception:
         InfoFileReader(
             "md-01.info", engine_format="tmp")

tests/physicalData/test_energy.py

@@ -1,32 +1,20 @@
-import pytest
-import numpy as np
 
 from collections import defaultdict
-from beartype.roar import BeartypeException
+
+import pytest
+import numpy as np
 
 from PQAnalysis.physical_data import Energy, EnergyError
 
 
 class TestEnergy:
     def test__init__(self):
-        with pytest.raises(BeartypeException):
-            Energy(1)
-
-        with pytest.raises(BeartypeException):
-            Energy([[[1]]])
-
         data = np.array([1, 2, 3])
         energy = Energy(data)
 
         assert np.allclose(energy.data, [data])
 
     def test__setup_info_dictionary(self):
-        with pytest.raises(BeartypeException):
-            Energy(np.array([1]), info=1)
-
-        with pytest.raises(BeartypeException):
-            Energy(np.array([1]), units=1)
-
         data = np.array([[1], [2]])
         info = {1: 0, 2: 1}
         units = {1: "a", 2: "b"}