chore: derepcate P_pdb method - #177
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sbillinge merged 1 commit intoMar 6, 2026
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Codecov Report✅ All modified and coverable lines are covered by tests. @@ Coverage Diff @@
## v3.4.0 #177 +/- ##
=======================================
Coverage 99.15% 99.15%
=======================================
Files 14 14
Lines 2359 2359
=======================================
Hits 2339 2339
Misses 20 20
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sbillinge
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Mar 6, 2026
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src/diffpy/structure/parsers/p_pdffit.py
| return stru | ||
|
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||
| def toLines(self, stru): | ||
| """Convert `Structure` stru to a list of lines in PDFfit format. |
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@stevenhua0320 this is a lot of lines being deleted. Normally, this would be the new function. Please can you check that everything is ok here and confirm before I merge this? Thanks.
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@sbillinge I have checked this. This is because in the previous PR I forgot to replace the old function with the new function call. Originally I have created the new function but forgot to replace it. This is the current code in this branch. I also run the pytest and everything is right.
def toLines(self, stru):
"""This function has been deprecated and will be removed in
version 4.0.0.
Please use diffpy.structure.P_pdffit.toLines instead.
"""
return self.to_lines(stru)
def to_lines(self, stru):
"""Convert `Structure` stru to a list of lines in PDFfit format.
Parameters
----------
stru : Structure
Structure to be converted.
Returns
-------
list of str
List of lines in PDFfit format.
"""
# build the stru_pdffit dictionary initialized from the defaults
# in PDFFitStructure
stru_pdffit = PDFFitStructure().pdffit
if stru.pdffit:
stru_pdffit.update(stru.pdffit)
lines = []
# default values of standard deviations
d_sigxyz = numpy.zeros(3, dtype=float)
d_sigo = 0.0
d_sigU = numpy.zeros((3, 3), dtype=float)
# here we can start
line = "title " + stru.title
lines.append(line.strip())
lines.append("format pdffit")
lines.append("scale %9.6f" % stru_pdffit["scale"])
lines.append(
"sharp %9.6f, %9.6f, %9.6f, %9.6f"
% (
stru_pdffit["delta2"],
stru_pdffit["delta1"],
stru_pdffit["sratio"],
stru_pdffit["rcut"],
)
)
lines.append("spcgr " + stru_pdffit["spcgr"])
if stru_pdffit.get("spdiameter", 0.0) > 0.0:
line = "shape sphere, %g" % stru_pdffit["spdiameter"]
lines.append(line)
if stru_pdffit.get("stepcut", 0.0) > 0.0:
line = "shape stepcut, %g" % stru_pdffit["stepcut"]
lines.append(line)
lat = stru.lattice
lines.append(
"cell %9.6f, %9.6f, %9.6f, %9.6f, %9.6f, %9.6f"
% (lat.a, lat.b, lat.c, lat.alpha, lat.beta, lat.gamma)
)
lines.append("dcell %9.6f, %9.6f, %9.6f, %9.6f, %9.6f, %9.6f" % tuple(stru_pdffit["dcell"]))
lines.append("ncell %9i, %9i, %9i, %9i" % (1, 1, 1, len(stru)))
lines.append("atoms")
for a in stru:
ad = a.__dict__
lines.append(
"%-4s %17.8f %17.8f %17.8f %12.4f"
% (
a.element.upper(),
a.xyz[0],
a.xyz[1],
a.xyz[2],
a.occupancy,
)
)
sigmas = numpy.concatenate((ad.get("sigxyz", d_sigxyz), [ad.get("sigo", d_sigo)]))
lines.append(" %18.8f %17.8f %17.8f %12.4f" % tuple(sigmas))
sigU = ad.get("sigU", d_sigU)
Uii = (a.U[0][0], a.U[1][1], a.U[2][2])
Uij = (a.U[0][1], a.U[0][2], a.U[1][2])
sigUii = (sigU[0][0], sigU[1][1], sigU[2][2])
sigUij = (sigU[0][1], sigU[0][2], sigU[1][2])
lines.append(" %18.8f %17.8f %17.8f" % Uii)
lines.append(" %18.8f %17.8f %17.8f" % sigUii)
lines.append(" %18.8f %17.8f %17.8f" % Uij)
lines.append(" %18.8f %17.8f %17.8f" % sigUij)
return lines
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@sbillinge ready to review. Note that I realized in the previous getParser and toLines process I missed to replace the deprecation docstring for all of the getParser and one of the function replacement to to_lines call. In this PR I also supplement that.