Feature/beartype exceptions

.github/workflows/pylint.yml

@@ -16,10 +16,19 @@ permissions:
 
 jobs:
   pylint:
+
     runs-on: ubuntu-latest
 
+    permissions:                # Job-level permissions configuration starts here
+      contents: write           # 'write' access to repository contents
+      pull-requests: write      # 'write' access to pull requests
+
     steps:
     - uses: actions/checkout@master
+      with:
+        persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token.
+        fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository.
+
     - name: Setup Python
       uses: actions/setup-python@v2
       with:
@@ -97,5 +106,11 @@ jobs:
 
         git add .github/.pylint_cache
         git commit -m "Add .github/.pylint_cache on push event"
-        git push
+
+    - name: Push changes
+      if: github.event_name == 'push'
+      uses: ad-m/github-push-action@master
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        branch: ${{ github.ref }}
 

PQAnalysis/__init__.py

@@ -14,12 +14,26 @@
 
 from PQAnalysis.utils.custom_logging import CustomLogger
 
-beartype_this_package()
-
 __base_path__ = Path(__file__).parent
-
 __package_name__ = __name__
 
+##################
+# BEARTYPE SETUP #
+##################
+
+# TODO: change the default level to "RELEASE" after all changes are implemented
+__beartype_default_level__ = "DEBUG"
+__beartype_level__ = os.getenv(
+    "PQANALYSIS_BEARTYPE_LEVEL", __beartype_default_level__
+)
+
+if __beartype_level__.upper() == "DEBUG":
+    beartype_this_package()
+
+#################
+# LOGGING SETUP #
+#################
+
 logging_env_var = os.getenv("PQANALYSIS_LOGGING_LEVEL")
 
 if logging_env_var and logging_env_var not in logging.getLevelNamesMapping():

PQAnalysis/analysis/rdf/api.py

@@ -5,33 +5,36 @@
 from PQAnalysis.io import TrajectoryReader, RestartFileReader, MoldescriptorReader
 from PQAnalysis.traj import MDEngineFormat
 from PQAnalysis.topology import Topology
+from PQAnalysis.type_checking import runtime_type_checking
 
 from .rdf import RDF
 from .rdf_input_file_reader import RDFInputFileReader
 from .rdf_output_file_writer import RDFDataWriter, RDFLogWriter
 
 
+@runtime_type_checking
 def rdf(input_file: str, md_format: MDEngineFormat | str = MDEngineFormat.PQ):
     """
     Calculates the radial distribution function (RDF) using a given input file.
 
     This is just a wrapper function combining the underlying classes and functions.
 
-    For more information on the input file keys please 
+    For more information on the input file keys please
     visit :py:mod:`~PQAnalysis.analysis.rdf.rdfInputFileReader`.
     For more information on the exact calculation of
     the RDF please visit :py:class:`~PQAnalysis.analysis.rdf.rdf.RDF`.
 
     Parameters
     ----------
     input_file : str
-        The input file. For more information on the input file 
+        The input file. For more information on the input file
         keys please visit :py:mod:`~PQAnalysis.analysis.rdf.rdfInputFileReader`.
     md_format : MDEngineFormat | str, optional
-        the format of the input trajectory. Default is "PQ". 
+        the format of the input trajectory. Default is "PQ".
         For more information on the supported formats please visit
         :py:class:`~PQAnalysis.traj.formats.MDEngineFormat`.
     """
+
     md_format = MDEngineFormat(md_format)
 
     input_reader = RDFInputFileReader(input_file)

PQAnalysis/type_checking.py

@@ -0,0 +1,92 @@
+"""
+A module for type checking of arguments passed to functions at runtime.
+"""
+
+import logging
+
+from decorator import decorator
+from beartype.door import is_bearable
+
+from PQAnalysis.utils.custom_logging import setup_logger
+from .types import (
+    Np1DIntArray,
+    Np2DIntArray,
+    Np1DNumberArray,
+    Np2DNumberArray,
+    Np3x3NumberArray,
+    NpnDNumberArray,
+)
+
+__logger_name__ = "PQAnalysis.TypeChecking"
+
+if not logging.getLogger(__logger_name__).handlers:
+    logger = setup_logger(logging.getLogger(__logger_name__))
+else:
+    logger = logging.getLogger(__logger_name__)
+
+
+@decorator
+def runtime_type_checking(func, *args, **kwargs):
+    """
+    A decorator to check the type of the arguments passed to a function at runtime.
+    """
+
+    # Get the type hints of the function
+    type_hints = func.__annotations__
+
+    # Check the type of each argument
+    for arg_name, arg_value in zip(func.__code__.co_varnames, args):
+        if arg_name in type_hints:
+            if not is_bearable(arg_value, type_hints[arg_name]):
+                logger.error(
+                    _get_type_error_message(
+                        arg_name,
+                        arg_value,
+                        type_hints[arg_name],
+                    ),
+                    exception=TypeError,
+                )
+
+    # Check the type of each keyword argument
+    for kwarg_name, kwarg_value in kwargs.items():
+        if kwarg_name in type_hints:
+            if not is_bearable(kwarg_value, type_hints[kwarg_name]):
+                logger.error(
+                    _get_type_error_message(
+                        kwarg_name,
+                        kwarg_value,
+                        type_hints[kwarg_name],
+                    ),
+                    exception=TypeError,
+                )
+
+    # Call the function
+    return func(*args, **kwargs)
+
+
+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}' with {value=} should be "
+        f"of type {expected_type}, but got {actual_type}."
+    )
+
+    if expected_type is Np1DIntArray:
+        header += " Expected a 1D numpy integer array."
+    elif expected_type is Np2DIntArray:
+        header += " Expected a 2D numpy integer array."
+    elif expected_type is Np1DNumberArray:
+        header += " Expected a 1D numpy number array."
+    elif expected_type is Np2DNumberArray:
+        header += " Expected a 2D numpy number array."
+    elif expected_type is Np3x3NumberArray:
+        header += " Expected a 3x3 numpy number array."
+    elif expected_type is NpnDNumberArray:
+        header += " Expected an n-dimensional numpy number array."
+
+    return header

PQAnalysis/utils/custom_logging.py

@@ -121,15 +121,15 @@
         )
 
         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 @@
                         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,

pytest.ini

@@ -5,6 +5,7 @@ markers =
     topology
     traj
     io
+    analysis
 
 testpaths = 
     tests

tests/__init__.py

@@ -0,0 +1,7 @@
+"""
+Unit tests for the PQAnalysis package.
+"""
+
+import os
+
+os.environ['PQANALYSIS_BEARTYPE_LEVEL'] = "RELEASE"

tests/analysis/__init__.py

@@ -0,0 +1,3 @@
+import pytest
+
+pytestmark = pytest.mark.analysis

tests/analysis/rdf/test_api.py

@@ -0,0 +1,26 @@
+"""
+A module to test the RDF API.
+"""
+
+import pytest  # pylint: disable=unused-import
+
+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_with_exception
+
+
+class TestRDFAPI:
+    def test_wrong_param_types(self, caplog):
+        assert_logging_with_exception(
+            caplog=caplog,
+            logging_name="TypeChecking",
+            logging_level="ERROR",
+            message_to_test=_get_type_error_message(
+                "input_file", 1, str,
+            ),
+            exception=TypeError,
+            function=rdf,
+            input_file=1,
+        )

tests/analysis/rdf/test_rdfInputFileReader.py

@@ -3,6 +3,10 @@
 from PQAnalysis.analysis.rdf.rdf_input_file_reader import RDFInputFileReader
 from PQAnalysis.io.input_file_reader.exceptions import InputFileError
 
+# import topology marker
+from .. import pytestmark  # pylint: disable=unused-import
+from ...conftest import assert_logging
+
 
 class TestRDFInputFileReader:
     @pytest.mark.parametrize("example_dir", ["rdf"], indirect=False)

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")