fix: validate box lengths and angles on Cell construction

PQAnalysis/core/__init__.py

@@ -17,6 +17,7 @@
     from .cell import Cell, Cells
     from .exceptions import (
         AtomError,
+        CellError,
         ElementNotFoundError,
         ResidueError,
         ResidueWarning,
@@ -28,6 +29,7 @@
     "ResidueError": ".exceptions",
     "ResidueWarning": ".exceptions",
     "AtomError": ".exceptions",
+    "CellError": ".exceptions",
     "Cell": ".cell",
     "Cells": ".cell",
     "Atom": ".atom",

PQAnalysis/core/cell/cell.py

@@ -2,6 +2,7 @@
 A module containing the Cell class.
 """
 
+import logging
 import sys
 import warnings
 
@@ -14,9 +15,12 @@
 
 from PQAnalysis.type_checking import runtime_type_checking
 from PQAnalysis.types import Np3x3NumberArray, Np2DNumberArray, NpnDNumberArray, PositiveReal, Bool
+from PQAnalysis.utils.custom_logging import setup_logger
 from PQAnalysis.utils.math import allclose_vectorized
+from PQAnalysis import __package_name__
 
 from ._standard_properties import _StandardPropertiesMixin
+from ..exceptions import CellError
 
 
 
@@ -26,6 +30,9 @@ class Cell(_StandardPropertiesMixin):
     Class for storing unit cell parameters.
     """
 
+    logger = logging.getLogger(__package_name__).getChild(__qualname__)
+    logger = setup_logger(logger)
+
     @runtime_type_checking
     def __init__(
         self,
@@ -72,7 +79,30 @@ def setup_box_matrix(self) -> Np3x3NumberArray:
         -------
         box matrix: Np3x3NumberArray
             The box matrix.
+
+        Raises
+        ------
+        CellError
+            If a box length is not positive, a box angle is not
+            within the interval (0, 180) or the box angles do not
+            define a valid unit cell.
         """
+        if not np.all(np.greater(self.box_lengths, 0)):
+            self.logger.error(
+                f"Box lengths must be positive, but got {self.box_lengths}.",
+                exception=CellError
+            )
+
+        if not (
+            np.all(np.greater(self.box_angles, 0)) and
+            np.all(np.less(self.box_angles, 180))
+        ):
+            self.logger.error(
+                "Box angles must be within the interval (0, 180) degrees, "
+                f"but got {self.box_angles}.",
+                exception=CellError
+            )
+
         matrix = np.array([[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]])
 
         alpha, beta, gamma = np.deg2rad(self.box_angles)
@@ -81,14 +111,23 @@ def setup_box_matrix(self) -> Np3x3NumberArray:
         sin_beta = np.sin(beta)
         x, y, z = self.box_lengths
 
+        radicand = (
+            sin_beta**2 - (cos_alpha - cos_beta * cos_gamma)**2 / sin_gamma**2
+        )
+
+        if not radicand > 0:
+            self.logger.error(
+                f"Box angles {self.box_angles} do not define a valid "
+                "unit cell.",
+                exception=CellError
+            )
+
         matrix[0][0] = x
         matrix[0][1] = y * cos_gamma
         matrix[0][2] = z * cos_beta
         matrix[1][1] = y * sin_gamma
         matrix[1][2] = z * (cos_alpha - cos_beta * cos_gamma) / sin_gamma
-        matrix[2][2] = z * np.sqrt(
-            sin_beta**2 - (cos_alpha - cos_beta * cos_gamma)**2 / sin_gamma**2
-        )
+        matrix[2][2] = z * np.sqrt(radicand)
 
         return matrix
 

PQAnalysis/core/exceptions.py

@@ -68,3 +68,11 @@ class AtomError(PQException):
     """
     Exception raised for errors related to the Atom class
     """
+
+
+
+class CellError(PQException):
+
+    """
+    Exception raised for errors related to the Cell class
+    """

tests/core/test_cell.py

@@ -2,8 +2,9 @@
 import pytest
 
 from . import pytestmark
+from ..conftest import assert_logging_with_exception
 
-from PQAnalysis.core import Cell
+from PQAnalysis.core import Cell, CellError
 
 
 
@@ -35,6 +36,67 @@ def test__init__(self):
             )
         )
 
+    def test__init__non_positive_box_lengths(self, caplog):
+        assert_logging_with_exception(
+            caplog,
+            Cell.__qualname__,
+            "ERROR",
+            "Box lengths must be positive, but got [0. 0. 0.].",
+            CellError,
+            Cell,
+            0.0,
+            0.0,
+            0.0
+        )
+
+    def test__init__box_angles_out_of_range(self, caplog):
+        assert_logging_with_exception(
+            caplog,
+            Cell.__qualname__,
+            "ERROR",
+            "Box angles must be within the interval (0, 180) degrees, "
+            "but got [190.  90.  90.].",
+            CellError,
+            Cell,
+            10.0,
+            10.0,
+            10.0,
+            190.0,
+            90.0,
+            90.0
+        )
+
+    def test__init__impossible_box_angles(self, caplog):
+        assert_logging_with_exception(
+            caplog,
+            Cell.__qualname__,
+            "ERROR",
+            "Box angles [170.  10.  10.] do not define a valid unit cell.",
+            CellError,
+            Cell,
+            10.0,
+            10.0,
+            10.0,
+            170.0,
+            10.0,
+            10.0
+        )
+
+    def test_set_box_lengths_non_positive(self, caplog):
+        cell = Cell(1, 2, 3)
+
+        def set_box_lengths():
+            cell.box_lengths = np.array([0.0, 2.0, 3.0])
+
+        assert_logging_with_exception(
+            caplog,
+            Cell.__qualname__,
+            "ERROR",
+            "Box lengths must be positive, but got [0. 2. 3.].",
+            CellError,
+            set_box_lengths
+        )
+
     def test_box_lengths(self):
         cell = Cell(1, 2, 3)
         assert np.allclose(cell.box_lengths, np.array([1, 2, 3]))