chore: Fix internal deprecated function usage

news/fix-internal-deps.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news needed: fix internal use of deprecated functions.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/structure/__init__.py

@@ -101,10 +101,10 @@ def load_structure(filename, fmt="auto", **kw):
         Path to the file to be loaded.
     fmt : str, Optional
         Format of the structure file such as 'cif' or 'xyz'. Must be
-        one of the formats listed by the `parsers.inputFormats` function.
+        one of the formats listed by the `parsers.input_formats` function.
         When 'auto', all supported formats are tried in a sequence.
     kw : Optional
-        Extra keyword arguments that are passed to `parsers.getParser`
+        Extra keyword arguments that are passed to `parsers.get_parser`
         function. These configure the dedicated Parser object that
         is used to read content in filename.
 

src/diffpy/structure/apps/anyeye.py

@@ -187,7 +187,7 @@ def convert_structure_file(pd):
     fmt = pd.get("format", "auto")
     stru = None
     if fmt == "auto":
-        stru, fmt = loadStructureFile(strufile)
+        stru, fmt = load_structure_file(strufile)
         pd["fmt"] = fmt
     # if fmt is recognized by the viewer, use as is
     if fmt in pd["formats"] and pd["formula"] is None:

src/diffpy/structure/lattice.py

@@ -159,8 +159,8 @@ class Lattice(object):
     Note
     ----
     The array attributes are read-only. They get updated by changing
-    some lattice parameters or by calling the `setLatPar()` or
-    `setLatBase()` methods.
+    some lattice parameters or by calling the `set_latt_parms()` or
+    `set_new_latt_base_vec()` methods.
 
     Examples
     --------
@@ -757,13 +757,13 @@ def __repr__(self):
         I3 = numpy.identity(3, dtype=float)
         rotbaseI3diff = max(numpy.reshape(numpy.fabs(self.baserot - I3), 9))
         cartlatpar = numpy.array([1.0, 1.0, 1.0, 90.0, 90.0, 90.0])
-        latpardiff = cartlatpar - self.abcABG()
+        latpardiff = cartlatpar - self.cell_parms()
         if rotbaseI3diff > self._epsilon:
             s = "Lattice(base=%r)" % self.base
         elif numpy.fabs(latpardiff).max() < self._epsilon:
             s = "Lattice()"
         else:
-            s = "Lattice(a=%g, b=%g, c=%g, alpha=%g, beta=%g, gamma=%g)" % self.abcABG()
+            s = "Lattice(a=%g, b=%g, c=%g, alpha=%g, beta=%g, gamma=%g)" % self.cell_parms()
         return s
 
 

src/diffpy/structure/parsers/__init__.py

@@ -16,7 +16,7 @@
 
 The recognized structure formats are defined by subclassing `StructureParser`,
 by convention these classes are named `P_<format>.py`. The parser classes should
-to override the `parseLines()` and `toLines()` methods of `StructureParser`.
+to override the `parse_lines()` and `to_lines()` methods of `StructureParser`.
 Any structure parser needs to be registered in `parser_index` module.
 
 For normal usage it should be sufficient to use the routines provided
@@ -25,9 +25,9 @@
 Content:
     * StructureParser: base class for a concrete Parser
     * parser_index: dictionary of known structure formats
-    * getParser: factory for Parser at given format
-    * inputFormats: list of available input formats
-    * outputFormats: list of available output formats
+    * get_parser: factory for Parser at given format
+    * input_formats: list of available input formats
+    * output_formats: list of available output formats
 """
 
 from diffpy.structure.parsers.parser_index_mod import parser_index

src/diffpy/structure/parsers/p_auto.py

@@ -14,7 +14,7 @@
 ##############################################################################
 """Parser for automatic file format detection.
 
-This Parser does not provide the the `toLines()` method.
+This Parser does not provide the the `to_lines()` method.
 """
 
 import os

src/diffpy/structure/parsers/p_cif.py

@@ -19,7 +19,7 @@
 rx_float : re.Pattern
     The constant regular expression for `leading_float()`.
 symvec : dict
-    The helper dictionary for `getSymOp()`.
+    The helper dictionary for `get_symop()`.
 
 Note
 ----
@@ -362,7 +362,6 @@ def parseLines(self, lines):
         """
         return self.parse_lines(lines)
 
-    @deprecated(parseLines_deprecation_msg)
     def parse_lines(self, lines):
         """Parse list of lines in CIF format.
 

src/diffpy/structure/parsers/p_discus.py

@@ -140,7 +140,7 @@ def parseLines(self, lines):
                 raise StructureFormatError(emsg)
             # take care of superlattice
             if self.stru.pdffit["ncell"][:3] != [1, 1, 1]:
-                latpars = list(self.stru.lattice.abcABG())
+                latpars = list(self.stru.lattice.cell_parms())
                 superlatpars = [latpars[i] * self.stru.pdffit["ncell"][i] for i in range(3)] + latpars[3:]
                 superlattice = Lattice(*superlatpars)
                 self.stru.place_in_lattice(superlattice)
@@ -215,7 +215,7 @@ def parse_lines(self, lines):
                 raise StructureFormatError(emsg)
             # take care of superlattice
             if self.stru.pdffit["ncell"][:3] != [1, 1, 1]:
-                latpars = list(self.stru.lattice.abcABG())
+                latpars = list(self.stru.lattice.cell_parms())
                 superlatpars = [latpars[i] * self.stru.pdffit["ncell"][i] for i in range(3)] + latpars[3:]
                 superlattice = Lattice(*superlatpars)
                 self.stru.place_in_lattice(superlattice)
@@ -268,7 +268,7 @@ def to_lines(self, stru):
         if stru_pdffit.get("stepcut", 0.0) > 0.0:
             line = "shape   stepcut, %g" % stru_pdffit["stepcut"]
             lines.append(line)
-        lines.append("cell   %9.6f, %9.6f, %9.6f, %9.6f, %9.6f, %9.6f" % self.stru.lattice.abcABG())
+        lines.append("cell   %9.6f, %9.6f, %9.6f, %9.6f, %9.6f, %9.6f" % self.stru.lattice.cell_parms())
         lines.append("ncell  %9i, %9i, %9i, %9i" % (1, 1, 1, len(self.stru)))
         lines.append("atoms")
         for a in self.stru:

src/diffpy/structure/parsers/p_pdb.py

@@ -215,9 +215,9 @@ def parse_lines(self, lines):
                     sc[2, :] = [float(x) for x in line[10:40].split()]
                     scaleU[2] = float(line[45:55])
                     base = numpy.transpose(numpy.linalg.inv(sc))
-                    abcABGcryst = numpy.array(stru.lattice.abcABG())
+                    abcABGcryst = numpy.array(stru.lattice.cell_parms())
                     stru.lattice.set_new_latt_base_vec(base)
-                    abcABGscale = numpy.array(stru.lattice.abcABG())
+                    abcABGscale = numpy.array(stru.lattice.cell_parms())
                     reldiff = numpy.fabs(1.0 - abcABGscale / abcABGcryst)
                     if not numpy.all(reldiff < 1.0e-4):
                         emsg = "%d: " % p_nl + "SCALE and CRYST1 are not consistent."

src/diffpy/structure/parsers/p_vesta.py

@@ -184,7 +184,7 @@ def parse_lines(self, lines):
                 emsg = "VESTA file is missing STRUC lattice parameters"
                 raise StructureFormatError(emsg)
 
-            stru.lattice.setLatPar(
+            stru.lattice.set_latt_parms(
                 a=latt_abc[0],
                 b=latt_abc[1],
                 c=latt_abc[2],

src/diffpy/structure/parsers/structureparser.py

@@ -98,7 +98,7 @@ def to_lines(self, stru):
     def parse(self, s):
         """Create `Structure` instance from a string."""
         lines = s.rstrip("\r\n").split("\n")
-        stru = self.parseLines(lines)
+        stru = self.parse_lines(lines)
         return stru
 
     def tostring(self, stru):

src/diffpy/structure/pdffitstructure.py

@@ -98,10 +98,10 @@ def readStr(self, s, format="auto"):
         return self.read_structure(s, format)
 
     def read_structure(self, s, format="auto"):
-        """Same as `Structure.readStr`, but update `spcgr` value in
-        `self.pdffit` when parser can get spacegroup.
+        """Same as `Structure.read_structure`, but update `spcgr` value
+        in `self.pdffit` when parser can get spacegroup.
 
-        See `Structure.readStr()` for more info.
+        See `Structure.read_structure()` for more info.
 
         Parameters
         ----------

src/diffpy/structure/spacegroups.py

@@ -748,7 +748,7 @@ def is_space_group_identifier(sgid):
     bool
     """
     try:
-        GetSpaceGroup(sgid)
+        get_space_group(sgid)
         rv = True
     except ValueError:
         rv = False

src/diffpy/structure/symmetryutilities.py

@@ -602,7 +602,7 @@ def __init__(
         self.pparameters = []
         self.Uparameters = []
         # fill in the values
-        sites, ops, mult = expandPosition(spacegroup, xyz, sgoffset, eps)
+        sites, ops, mult = expand_position(spacegroup, xyz, sgoffset, eps)
         invariants = _find_invariants(ops)
         # shift self.xyz exactly to the special position
         if mult > 1:
@@ -613,7 +613,7 @@ def __init__(
             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)
+                sites, ops, mult = expand_position(spacegroup, self.xyz, self.sgoffset, eps)
                 invariants = _find_invariants(ops)
         # self.xyz, sites, ops are all adjusted here
         self.eqxyz = sites
@@ -1322,7 +1322,7 @@ def position_formulas_pruned(self, xyzsymbols=None):
 
         See also
         --------
-        positionFormulas()
+        position_formulas()
 
         Parameters
         ----------
@@ -1429,7 +1429,7 @@ def u_formulas_pruned(self, Usymbols=None):
 
         See Also
         --------
-        UFormulas()
+        u_formulas()
 
         Parameters
         ----------
@@ -1459,7 +1459,7 @@ def u_formulas_pruned(self, Usymbols=None):
     g = GeneratorSite(sg100, site, Uij=Uij)
     fm100 = g.position_formula(site)
     print("g = GeneratorSite(sg100, %r)" % site)
-    print("g.positionFormula(%r) = %s" % (site, fm100))
+    print("g.position_formula(%r) = %s" % (site, fm100))
     print("g.pparameters =", g.pparameters)
     print("g.Uparameters =", g.Uparameters)
-    print("g.UFormula(%r) =" % site, g.u_formula(site))
+    print("g.u_formula(%r) =" % site, g.u_formula(site))