Merge branch 'release/0.4.0'

PQAnalysis/core/atom.py

@@ -28,13 +28,11 @@
 
 """
 
-import numpy as np
-
 from multimethod import multimethod
 from beartype.typing import Any, Tuple
 from numbers import Real
 
-from PQAnalysis.utils.exceptions import ElementNotFoundError
+from PQAnalysis.exceptions import ElementNotFoundError
 
 
 def guess_element(id: int | str) -> Tuple[str, int, Real]:

PQAnalysis/core/atomicSystem.py

@@ -23,7 +23,7 @@
 
 from .atom import Atom
 from .cell import Cell
-from ..utils.mytypes import Numpy2DFloatArray, Numpy1DFloatArray
+from ..types import Numpy2DFloatArray, Numpy1DFloatArray
 
 
 def check_atoms_pos(func):

PQAnalysis/core/cell.py

@@ -16,7 +16,7 @@
 from beartype.typing import Any
 from numbers import Real
 
-from ..utils.mytypes import Numpy3x3FloatArray, Numpy2DFloatArray, Numpy1DFloatArray
+from ..types import Numpy3x3FloatArray, Numpy2DFloatArray, Numpy1DFloatArray
 
 
 class Cell:

PQAnalysis/exceptions.py

@@ -0,0 +1,70 @@
+"""
+A module containing different exceptions which could be useful.
+
+...
+
+Classes
+-------
+PQException
+    Base class for exceptions in this module.
+ElementNotFoundError
+    Exception raised if the given element id is not valid
+TrajectoryFormatError
+    Exception raised if the given enum is not valid
+"""
+
+from beartype.typing import Any
+
+
+class PQException(Exception):
+    """
+    Base class for exceptions in this module.
+    """
+
+    def __init__(self, message: str) -> None:
+        self.message = message
+        super().__init__(self.message)
+
+
+class ElementNotFoundError(PQException):
+    """
+    Exception raised if the given element id is not valid
+    """
+
+    def __init__(self, id: Any) -> None:
+        self.id = id
+        self.message = f"""Id {self.id} is not a valid element identifier."""
+        super().__init__(self.message)
+
+
+class FormatEnumError(PQException):
+    """
+    Exception raised if the given enum is not valid
+    """
+
+    def __init__(self, value: object, enum: object) -> None:
+        self.enum = enum
+        self.value = value
+        self.message = f"""
+'{self.value}' is not a valid {enum.__name__}.
+Possible values are: {enum.member_repr()}
+or their case insensitive string representation: {enum.value_repr()}"""
+        super().__init__(self.message)
+
+
+class TrajectoryFormatError(FormatEnumError):
+    """
+    Exception raised if the given enum is not valid
+    """
+
+    def __init__(self, value: object, enum: object) -> None:
+        super().__init__(value, enum)
+
+
+class MDEngineFormatError(FormatEnumError):
+    """
+    Exception raised if the given enum is not valid
+    """
+
+    def __init__(self, value: object, enum: object) -> None:
+        super().__init__(value, enum)

PQAnalysis/io/energyFileReader.py

@@ -15,6 +15,7 @@
 from .base import BaseReader
 from .infoFileReader import InfoFileReader
 from ..physicalData.energy import Energy
+from ..traj.formats import MDEngineFormat
 
 
 class EnergyFileReader(BaseReader):
@@ -34,15 +35,15 @@ class EnergyFileReader(BaseReader):
         The name of the info file to read from.
     withInfoFile : bool
         If True, the info file was found.
+    format : MDEngineFormat
+        The format of the file. Default is MDEngineFormat.PIMD_QMCF.
     """
 
-    formats = ["pimd-qmcf", "qmcfc"]
-
     def __init__(self,
                  filename: str,
                  info_filename: str | None = None,
                  use_info_file: bool = True,
-                 format: str = "pimd-qmcf"
+                 format: MDEngineFormat | str = MDEngineFormat.PIMD_QMCF
                  ) -> None:
         """
         Initializes the EnergyFileReader with the given filename.
@@ -61,13 +62,8 @@ def __init__(self,
             The name of the info file to read from, by default None
         use_info_file : bool, optional
             If True, the info file is searched for, by default True
-        format : str, optional
-            The format of the info file, by default "pimd-qmcf"
-
-        Raises
-        ------
-        ValueError
-            If the format is not supported.
+        format : MDEngineFormat | str, optional
+            The format of the file, by default MDEngineFormat.PIMD_QMCF
         """
         super().__init__(filename)
         self.info_filename = info_filename
@@ -77,11 +73,7 @@ def __init__(self,
         else:
             self.withInfoFile = False
 
-        if format not in self.formats:
-            raise ValueError(
-                f"Format {format} is not supported. Supported formats are {self.formats}.")
-
-        self.format = format
+        self.format = MDEngineFormat(format)
 
     def read(self) -> Energy:
         """