Merge branch 'lowercase-structure-import'

* use lowercase import for diffpy.structure
* require diffpy.structure 3.0 or later

Close #40.

Author: pavoljuhas

README.rst

@@ -29,8 +29,8 @@ that are used by PDFgui and its components.
 * matplotlib   - Python 2D plotting library
 * diffpy.pdffit2 - computational engine for PDFgui,
   https://github.com/diffpy/diffpy.pdffit2
-* diffpy.Structure - simple storage and manipulation of atomic
-  structures, https://github.com/diffpy/diffpy.Structure
+* diffpy.structure - simple storage and manipulation of atomic
+  structures, https://github.com/diffpy/diffpy.structure
 * diffpy.utils - shared helper utilities for wx GUI,
   https://github.com/diffpy/diffpy.utils
 

conda-recipe/meta.yaml

@@ -39,7 +39,7 @@ requirements:
     - wxpython 4.*
     - menuinst                  [win]
     - diffpy.pdffit2
-    - diffpy.structure
+    - diffpy.structure >=3
     - diffpy.utils
 
 test:

setup.py

@@ -113,7 +113,7 @@ def dirglob(d, *patterns):
     # manual and tutorial files should not be zipped
     zip_safe = False,
     install_requires = [
-        'diffpy.structure',
+        'diffpy.structure>=3',
         'diffpy.pdffit2',
         'diffpy.utils',
     ],

src/diffpy/pdfgui/control/fitstructure.py

@@ -24,7 +24,7 @@
 from diffpy.pdfgui.control.constraint import Constraint
 from diffpy.pdfgui.control.parameter import Parameter
 from diffpy.pdfgui.control.controlerrors import ControlTypeError, ControlValueError
-from diffpy.Structure import Atom
+from diffpy.structure import Atom
 
 class FitStructure(PDFStructure):
     """FitStructure holds initial and refined structure and related fit
@@ -42,7 +42,7 @@ class FitStructure(PDFStructure):
                        Use setSelectedPairs() and getSelectedPairs() methods
                        to access its value.
         custom_spacegroup -- instance of SpaceGroup which has no equivalent
-                       in diffpy.Structure.SpaceGroups module.  This can happen
+                       in diffpy.structure.spacegroups module.  This can happen
                        after reading from a CIF file.  When equivalent space
                        group exists, custom_spacegroup is None.
 
@@ -366,7 +366,7 @@ def isSpaceGroupPossible(self, spacegroup):
 
         Return bool.
         """
-        from diffpy.Structure.SymmetryUtilities import isSpaceGroupLatPar
+        from diffpy.structure.symmetryutilities import isSpaceGroupLatPar
         return isSpaceGroupLatPar(spacegroup, *self.initial.lattice.abcABG())
 
 
@@ -376,7 +376,7 @@ def getSpaceGroupList(self):
         with custom_spacegroup.
         """
         if not FitStructure.sorted_standard_space_groups:
-            import diffpy.Structure.SpaceGroups as SG
+            import diffpy.structure.spacegroups as SG
             existing_names = {}
             unique_named_list = []
             for sg in SG.SpaceGroupList:
@@ -400,7 +400,7 @@ def getSpaceGroup(self, sgname):
         Raise ValueError if sgname cannot be found or when it is not present
         in getSpaceGroupList().
         """
-        import diffpy.Structure.SpaceGroups as SG
+        import diffpy.structure.spacegroups as SG
         # this should match the "CIF data" sgname
         sgmatch = [sg for sg in self.getSpaceGroupList()
                 if sg.short_name == sgname]
@@ -420,11 +420,11 @@ def expandAsymmetricUnit(self, spacegroup, indices, sgoffset=[0,0,0]):
         of the occupancy("occ".  Constraints of unaffected atoms are adjusted
         for new positions self.initial.
 
-        spacegroup  -- instance of Structure.SpaceGroup
+        spacegroup  -- instance of SpaceGroup from diffpy.structure
         indices     -- list of integer indices of atoms to be expanded
         sgoffset    -- optional offset of space group origin [0,0,0]
         """
-        from diffpy.Structure.SymmetryUtilities import ExpandAsymmetricUnit
+        from diffpy.structure.symmetryutilities import ExpandAsymmetricUnit
         acd = self._popAtomConstraints()
         # get unique, reverse sorted indices
         ruindices = dict.fromkeys(indices).keys()
@@ -470,15 +470,15 @@ def applySymmetryConstraints(self, spacegroup, indices, posflag, Uijflag,
         erased.  New parameter indices start at fist decade after the last
         used parameter.
 
-        spacegroup  -- instance of Structure.SpaceGroup
+        spacegroup  -- instance of SpaceGroup from diffpy.structure
         indices     -- list of integer indices of atoms to be expanded
         posflag     -- required bool flag for constraining positions
         Uijflag     -- required bool flag for Uij constrainment
         sgoffset    -- optional offset of space group origin [0,0,0]
         """
         if not posflag and not Uijflag:     return
         # need to do something
-        from diffpy.Structure.SymmetryUtilities import SymmetryConstraints
+        from diffpy.structure.symmetryutilities import SymmetryConstraints
         # get unique sorted indices
         tobeconstrained = dict.fromkeys(indices)
         uindices = tobeconstrained.keys()

src/diffpy/pdfgui/control/pdfstructure.py

@@ -16,7 +16,7 @@
 import copy
 import re
 
-from diffpy.Structure import PDFFitStructure
+from diffpy.structure import PDFFitStructure
 from diffpy.pdfgui.control.pdfcomponent import PDFComponent
 from diffpy.pdfgui.control.controlerrors import \
         ControlKeyError, ControlFileError
@@ -48,7 +48,7 @@ def read(self, filename, format='auto'):
         Return instance of StructureParser used to load the data.
         See Structure.read() for more info.
         """
-        from diffpy.Structure import StructureFormatError
+        from diffpy.structure import StructureFormatError
         try:
             p = PDFFitStructure.read(self, filename, format)
         except StructureFormatError, err:

src/diffpy/pdfgui/control/structureviewer.py

@@ -51,7 +51,7 @@ class StructureViewer(object):
                   quoting.  Instances of '%s' in the string are replaced with
                   temporary structure file.  By default '%s'
     fileformat -- structure format that can be loaded by the viewer.
-                  Must be one of output formats supported by diffpy.Structure
+                  Must be one of output formats supported by diffpy.structure
                   package.  By default 'pdb'.
     _tmpdir    -- Temporary directory for structure files opened by the viewer.
                   tmpdir is None before the first call to plot.  The directory
@@ -71,7 +71,7 @@ def __init__(self, executable=None, argstr=None, fileformat=None):
         argstr     -- argument string for the viewer program, it can use
                       shell quoting.  Instances of '%s' are replaced with
                       temporary structure file.
-        fileformat -- structure format supported by diffpy.Structure package.
+        fileformat -- structure format supported by diffpy.structure package.
         """
         # declare instance data
         self.executable = ''
@@ -119,15 +119,15 @@ def setConfig(self, cfg):
     def getFileFormats():
         """Return list of valid values for the fileformat attribute.
         """
-        from diffpy.Structure.Parsers import outputFormats
+        from diffpy.structure.parsers import outputFormats
         return outputFormats()
     getFileFormats = staticmethod(getFileFormats)
 
 
     def plot(self, stru):
         """Launch new structure viewer and open a temporary copy of stru.
 
-        stru    -- instance of Structure class from diffpy.Structure
+        stru    -- instance of Structure class from diffpy.structure
 
         No return value.
         Raise ControlConfigError if structure viewer could not be launched.
@@ -203,7 +203,7 @@ def _writeTemporaryStructure(self, stru):
         Return full path to the temporary file.
         """
         # get extension preferred by fileformat
-        from diffpy.Structure.Parsers import parser_index
+        from diffpy.structure.parsers import parser_index
         ffext = parser_index[self.fileformat]['file_extension']
         d = self._createTemporaryDirectory()
         # Use a simple file name to avoid naming errors. It is common to put

src/diffpy/pdfgui/gui/phaseconfigurepanel.py

@@ -18,7 +18,7 @@
 
 import wx
 import wx.grid
-from diffpy.Structure import Atom
+from diffpy.structure import Atom
 from diffpy.pdffit2 import is_element
 from diffpy.pdfgui.gui.insertrowsdialog import InsertRowsDialog
 from diffpy.pdfgui.gui.pdfpanel import PDFPanel

src/diffpy/pdfgui/gui/sgstructuredialog.py

@@ -163,7 +163,7 @@ def updateWidgets(self):
             self.offset[i] = val
 
         # find how many new atoms would be generated
-        from diffpy.Structure.SymmetryUtilities import ExpandAsymmetricUnit
+        from diffpy.structure.symmetryutilities import ExpandAsymmetricUnit
         corepos = [ self.structure[i].xyz for i in self.indices ]
         symposeps = self.structure.symposeps
         eau = ExpandAsymmetricUnit(self.spacegroup, corepos,

src/diffpy/pdfgui/tests/TestFitStructure.py

@@ -151,7 +151,7 @@ def test_changeParameterIndex(self):
     def test_insertAtoms(self):
         """check FitStructure.insertAtoms()
         """
-        from diffpy.Structure import Atom
+        from diffpy.structure import Atom
         stru = self.stru
         stru.read(datafile('Ni.stru'), format='pdffit')
         cns = Constraint('@1')

src/diffpy/pdfgui/tests/TestPDFStructure.py

@@ -92,7 +92,7 @@ def test_setvar(self):
     def test_getvar(self):
         """check PDFStructure.getvar()
         """
-        from diffpy.Structure import Atom
+        from diffpy.structure import Atom
         stru = self.stru
         abcABG = (3.0, 4.0, 5.0, 81, 82, 83)
         stru.lattice.setLatPar(*abcABG)