ditching the patched copy approach

Further details or things to look at:
2a48bf504e (note_12028)

python/damask/_result.py

@@ -1,9 +1,6 @@
 import re
 import fnmatch
 import os
-import sys
-import importlib
-import importlib.util
 import copy
 import datetime
 import xml.etree.ElementTree as ET                                                                  # noqa
@@ -28,27 +25,6 @@ from . import tensor
 from . import util
 from ._typehints import FloatSequence, IntSequence, DADF5Dataset
 
-h5py_module_list = ['h5py','h5py._hl','h5py._hl.attrs']
-module_dict = {}
-
-SPEC_H5PY = importlib.util.find_spec('h5py')
-h5py_modified = importlib.util.module_from_spec(SPEC_H5PY)
-SPEC_H5PY.loader.exec_module(h5py_modified)
-sys.modules['h5py_modified'] = h5py_modified
-
-SPEC_H5PY_HL = importlib.util.find_spec('h5py._hl')
-h5py_hl_modified = importlib.util.module_from_spec(SPEC_H5PY_HL)
-SPEC_H5PY_HL.loader.exec_module(h5py_hl_modified)
-sys.modules['h5py_hl_modified'] = h5py_hl_modified
-
-SPEC_H5PY_HL_attrs = importlib.util.find_spec('h5py._hl.attrs')
-h5py_hl_attrs_modified = importlib.util.module_from_spec(SPEC_H5PY_HL_attrs)
-SPEC_H5PY_HL_attrs.loader.exec_module(h5py_hl_attrs_modified)
-sys.modules['h5py_hl_attrs_modified'] = h5py_hl_attrs_modified
-
-h5py_hl_modified.__dict__['attrs'] = h5py_hl_attrs_modified
-h5py_modified.__dict__['_hl'] = h5py_hl_modified
-
 h5py3 = h5py.__version__[0] == '3'
 
 chunk_size = 1024**2//8                                                                             # for compression in HDF5
@@ -86,7 +62,7 @@ def _empty_like(dataset: np.ma.core.MaskedArray,
                     fill_value = fill_float if dataset.dtype in np.sctypes['float'] else fill_int,
                     mask = True)
 
-class AttributeManagerNullterm(h5py_modified.AttributeManager):
+class AttributeManagerNullterm(h5py.AttributeManager):
     """
     Attribute management for DREAM.3D hdf5 files.
 
@@ -107,7 +83,7 @@ class AttributeManagerNullterm(h5py_modified.AttributeManager):
         else:
             super().create(name=name,data=data,shape=shape,dtype=dtype)
 
-class ResetAttributeManager(h5py_modified.AttributeManager):
+class ResetAttributeManager(h5py.AttributeManager):
     """
     Reset the attribute management for DREAM.3D hdf5 files.
 
@@ -2007,13 +1983,14 @@ class Result:
             Directory to save DREAM3D files. Will be created if non-existent.
 
         """
-        h5py_modified._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch'
+        h5py._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch'
         if self.N_constituents != 1 or not self.structured:
             raise TypeError('DREAM3D output requires structured grid with single constituent.')
 
         N_digits = int(np.floor(np.log10(max(1,self.incs[-1]))))+1
 
-        Crystal_structure_types = {'Hexagonal': 0, 'Cubic': 1, 'Triclinic': 4, 'Monoclinic': 5, 'Orthorhombic': 6, 'Tetrogonal': 8}
+        Crystal_structure_types = {'Hexagonal': 0, 'Cubic': 1, 'Triclinic': 4, 'Monoclinic': 5, \
+                                                            'Orthorhombic': 6, 'Tetrogonal': 8}
         # crystal structure map according to Dream3D
 
         Phase_types = {'Primary': 0}
@@ -2048,7 +2025,7 @@ class Result:
                         phase_ID_array[at_cell_ph[c][label]] = count + 1
 
                 job_file_no_ext = self.fname.stem
-                o = h5py_modified.File(f'{dream_dir}/{job_file_no_ext}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}.dream3d','w')
+                o = h5py.File(f'{dream_dir}/{job_file_no_ext}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}.dream3d','w')
                 o.attrs['DADF5toDREAM3D'] = '1.0'
                 o.attrs['FileVersion']    = '7.0'
 
@@ -2105,15 +2082,16 @@ class Result:
                     elif lattice_dict[label] in ['tP','tI']:
                         crystal_structure = 'tetragonal'
                     crystal_structure_list.append(Crystal_structure_types[crystal_structure])
-                o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array(crystal_structure_list)).reshape((len(self.phases)+1,1))
+                o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array(crystal_structure_list)).reshape((len(self.phases)\
+                                                                     +1,1))
                 o[ensemble_label + '/PhaseTypes']        = np.uint32(np.array([999] + [Phase_types['Primary']]*len(self.phases)))\
                                                                                         .reshape((len(self.phases)+1,1))
                 phase_name_list = ['Unknown Phase Type']
                 phase_name_list.extend(i for i in self.visible['phases'])
-                tid = h5py_modified.h5t.C_S1.copy()
+                tid = h5py.h5t.C_S1.copy()
-                tid.set_size(h5py_modified.h5t.VARIABLE)
+                tid.set_size(h5py.h5t.VARIABLE)
-                tid.set_cset(h5py_modified.h5t.CSET_ASCII)
+                tid.set_cset(h5py.h5t.CSET_ASCII)
-                o[ensemble_label].create_dataset(name='PhaseName',data = phase_name_list, dtype=h5py_modified.Datatype(tid))
+                o[ensemble_label].create_dataset(name='PhaseName',data = phase_name_list, dtype=h5py.Datatype(tid))
 
                 # Attributes Ensemble Matrix
                 o[ensemble_label].attrs['AttributeMatrixType'] = np.array([11],np.uint32)
@@ -2145,7 +2123,7 @@ class Result:
                 o[geom_label].attrs['GeometryType']          = np.array([0],np.uint32)
                 o[geom_label].attrs['SpatialDimensionality'] = np.array([3],np.uint32)
                 o[geom_label].attrs['UnitDimensionality']    = np.array([3],np.uint32)
-        h5py_modified._hl.attrs.AttributeManager = ResetAttributeManager # Reset the attribute manager to original:
+        h5py._hl.attrs.AttributeManager = ResetAttributeManager # Reset the attribute manager to original:
 
 
     def export_DADF5(self,