chore: derepcate P_pdb method

[stevenhua0320]

@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.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.15%. Comparing base (810ef8a) to head (c89466c).
⚠️ Report is 3 commits behind head on v3.4.0.

Additional details and impacted files

@@           Coverage Diff           @@
##           v3.4.0     #177   +/-   ##
=======================================
  Coverage   99.15%   99.15%           
=======================================
  Files          14       14           
  Lines        2359     2359           
=======================================
  Hits         2339     2339           
  Misses         20       20           

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[sbillinge]

@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.

[stevenhua0320]

@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