Internal call to deprecated function should be replaced · Issue #200 · diffpy/diffpy.structure · GitHub

Problem

Hi all!

In orix, I can silence all sources of deprecation warnings from 3.4.0 but one: two calls to expandPosition() inside diffpy.structure itself:

diffpy.structure/src/diffpy/structure/symmetryutilities.py

Lines 604 to 615 in 2e5530d

    
           sites, ops, mult = expandPosition(spacegroup, xyz, sgoffset, eps) 
        
           invariants = _find_invariants(ops) 
        
           # shift self.xyz exactly to the special position 
        
           if mult > 1: 
        
               xyzdups = numpy.array([op(xyz + self.sgoffset) - self.sgoffset for op in invariants]) 
        
               dxyz = xyzdups - xyz 
        
               dxyz = numpy.mean(dxyz - dxyz.round(), axis=0) 
        
               # recalculate if needed 
        
               if numpy.any(dxyz != 0.0): 
        
                   self.xyz = xyz + dxyz 
        
                   self.xyz[numpy.fabs(self.xyz) < self.eps] = 0.0 
        
                   sites, ops, mult = expandPosition(spacegroup, self.xyz, self.sgoffset, eps)

Proposed solution

I propose to replace those two calls with expand_position().

closed by #201

Internal call to deprecated function should be replaced · Issue #200 · diffpy/diffpy.structure · GitHub

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Internal call to deprecated function should be replaced #200

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	sites, ops, mult = expandPosition(spacegroup, xyz, sgoffset, eps)
	invariants = _find_invariants(ops)
	# shift self.xyz exactly to the special position
	if mult > 1:
	xyzdups = numpy.array([op(xyz + self.sgoffset) - self.sgoffset for op in invariants])
	dxyz = xyzdups - xyz
	dxyz = numpy.mean(dxyz - dxyz.round(), axis=0)
	# recalculate if needed
	if numpy.any(dxyz != 0.0):
	self.xyz = xyz + dxyz
	self.xyz[numpy.fabs(self.xyz) < self.eps] = 0.0
	sites, ops, mult = expandPosition(spacegroup, self.xyz, self.sgoffset, eps)

Internal call to deprecated function should be replaced · Issue #200 · diffpy/diffpy.structure · GitHub

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Internal call to deprecated function should be replaced #200

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sbillinge commented on Aug 21, 2026

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