Merge pull request #179 from MDAnalysis/fix-super

fixed initialization of DXClasses

Author: orbeckst

CHANGELOG

@@ -13,6 +13,16 @@ The rules for this file:
   * accompany each entry with github issue/PR number (Issue #xyz)
 
 -------------------------------------------------------------------------------
+MM/DD/2026 orbeckst
+
+  * 1.3.0
+
+  Changes
+
+  * update init signature for OpenDX.DXClass to include name and components
+    as optional kwargs to streamline init in child classes (PR #179)
+        
+        
 05/22/2026 orbeckst, spyke7
 
   * 1.2.0

gridData/OpenDX.py

@@ -202,6 +202,7 @@
    :members:
 
 """
+
 import numpy
 import re
 import gzip
@@ -229,12 +230,12 @@ def _gzip_open(filename, mode="rt"):
 class DXclass(object):
     """'class' object as defined by OpenDX"""
 
-    def __init__(self, classid):
+    def __init__(self, classid, name=None, component=None):
         """id is the object number"""
         self.id = classid  # serial number of the object
-        self.name = None  # name of the DXclass
-        self.component = None  # component type
-        self.D = None  # dimensions
+        self.name = name  # name of the DXclass
+        self.component = component  # component type
+        self.D = 3  # dimensions
 
     def write(self, stream, optstring="", quote=False):
         """write the 'object' line; additional args are packed in string"""
@@ -279,12 +280,11 @@ class gridpositions(DXclass):
     def __init__(self, classid, shape=None, origin=None, delta=None, **kwargs):
         if shape is None or origin is None or delta is None:
             raise ValueError("all keyword arguments are required")
-        self.id = classid
-        self.name = "gridpositions"
-        self.component = "positions"
+        super().__init__(classid, name="gridpositions", component="positions")
         self.shape = numpy.asarray(shape)  # D dimensional shape
         self.origin = numpy.asarray(origin)  # D vector
         self.rank = len(self.shape)  # D === rank
+        assert self.rank == self.D, "DXClass is only used for 3D arrays"
 
         self.delta = numpy.asarray(delta)  # DxD array of grid spacings
         # gridDataFormats  actually provides a simple 1D array with the deltas because only
@@ -301,9 +301,7 @@ def __init__(self, classid, shape=None, origin=None, delta=None, **kwargs):
             )
 
     def write(self, stream):
-        super(gridpositions, self).write(
-            stream, ("counts " + self.ndformat(" %d")) % tuple(self.shape)
-        )
+        super().write(stream, ("counts " + self.ndformat(" %d")) % tuple(self.shape))
         self._write_line(stream, "origin %f %f %f\n" % tuple(self.origin))
         for delta in self.delta:
             self._write_line(
@@ -329,9 +327,7 @@ class gridconnections(DXclass):
     def __init__(self, classid, shape=None, **kwargs):
         if shape is None:
             raise ValueError("all keyword arguments are required")
-        self.id = classid
-        self.name = "gridconnections"
-        self.component = "connections"
+        super().__init__(classid, name="gridconnections", component="connections")
         self.shape = numpy.asarray(shape)  # D dimensional shape
 
     def write(self, stream):
@@ -410,9 +406,7 @@ def __init__(self, classid, array=None, type=None, typequote='"', **kwargs):
         """
         if array is None:
             raise ValueError("array keyword argument is required")
-        self.id = classid
-        self.name = "array"
-        self.component = "data"
+        super().__init__(classid, name="array", component="data")
         # detect type https://github.com/MDAnalysis/GridDataFormats/issues/35
         if type is None:
             self.array = numpy.asarray(array)
@@ -464,7 +458,7 @@ def write(self, stream):
                 ).format(self.type, list(self.dx_types.keys()))
             )
         typelabel = self.typequote + self.type + self.typequote
-        super(array, self).write(
+        super().write(
             stream,
             "type {0} rank 0 items {1} data follows".format(typelabel, self.array.size),
         )
@@ -544,6 +538,11 @@ def __init__(self, classid="0", components=None, comments=None):
            dx = OpenDX.field('density',[gridpoints,gridconnections,array])
 
         """
+        super().__init__(
+            classid,  # can be an arbitrary string
+            name="field",
+            component=None,  # cannot be a component of a field
+        )
         if components is None:
             components = dict(positions=None, connections=None, data=None)
         if comments is None:
@@ -553,9 +552,6 @@ def __init__(self, classid="0", components=None, comments=None):
             ]
         elif type(comments) is not list:
             comments = [str(comments)]
-        self.id = classid  # can be an arbitrary string
-        self.name = "field"
-        self.component = None  # cannot be a component of a field
         self.components = components
         self.comments = comments
 
@@ -584,8 +580,8 @@ def from_grid(cls, grid, type=None, typequote='"', **kwargs):
         -------
         field
             OpenDX field wrapper
-            
-            
+
+
         .. versionadded:: 1.2.0
         """
         comments = [
@@ -612,10 +608,10 @@ def from_grid(cls, grid, type=None, typequote='"', **kwargs):
     @property
     def native(self):
         """Return native object
-        
+
         The "native" object is the :class:`gridData.OpenDX.field` itself.
-            
-        
+
+
         .. versionadded:: 1.2.0
         """
         return self
@@ -647,7 +643,7 @@ def write(self, filename):
             for component, object in self.sorted_components():
                 object.write(outfile)
             # the field object itself
-            super(field, self).write(outfile, quote=True)
+            super().write(outfile, quote=True)
             for component, object in self.sorted_components():
                 self._write_line(
                     outfile, 'component "%s" value %s\n' % (component, str(object.id))
@@ -683,9 +679,11 @@ def read(self, stream):
         except (UnicodeDecodeError, RecursionError) as err:
             # parser got confused, likely not a valid file
             # (RecursionError was only observed on Windows)
-            raise ValueError("DX file could not be read. "
-                             "The original error was\n"
-                             f"   {err.__class__.__name__}: {err}")
+            raise ValueError(
+                "DX file could not be read. "
+                "The original error was\n"
+                f"   {err.__class__.__name__}: {err}"
+            )
 
     def add(self, component, DXobj):
         """add a component to the field"""