Merge pull request #2 from cadenmyers13/migrate-changes

deprecated: Migrate changes made from srfit deprecation and change function names in `pdf` module

Author: sbillinge

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
@@ -21,45 +21,45 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 26.3.1
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.3.0
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 8.0.1
     hooks:
       - id: isort
         args: ["--profile", "black"]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.9.1
     hooks:
       - id: nbstripout
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       - id: no-commit-to-branch
         name: Prevent Commit to Main Branch
         args: ["--branch", "main"]
         stages: [pre-commit]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.2
     hooks:
       - id: codespell
         additional_dependencies:
           - tomli
   # prettier - multi formatter for .json, .yml, and .md files
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         additional_dependencies:
           - "prettier@^3.2.4"
   # docformatter - PEP 257 compliant docstring formatter
-  - repo: https://github.com/s-weigand/docformatter
-    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.7
     hooks:
       - id: docformatter
         additional_dependencies: [tomli]

news/migrate-changes.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added: updated all functions to be snake_case.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

requirements/conda.txt

@@ -1,3 +1,4 @@
 numpy
+diffpy.srreal
 diffpy.srfit
 diffpy.structure

requirements/pip.txt

@@ -1 +1,4 @@
 numpy
+diffpy.srreal
+diffpy.srfit
+diffpy.structure

src/diffpy/cmipdf/basepdfgenerator.py

@@ -46,7 +46,7 @@ class BasePDFGenerator(ProfileGenerator):
         the PDF.
     _phase
         The structure ParameterSet used to calculate the profile.
-    stru
+    structure
         The structure objected adapted by _phase.
     _lastr
         The last value of r over which the PDF was calculated. This is
@@ -72,15 +72,15 @@ class BasePDFGenerator(ProfileGenerator):
 
     Usable Metadata
     ---------------
-    stype
+    stype : str
         The scattering type "X" for x-ray, "N" for neutron (see
-        'setScatteringType').
+        'set_scattering_type').
     qmax
         The maximum scattering vector used to generate the PDF (see
-        setQmax).
+        set_qmax).
     qmin
         The minimum scattering vector used to generate the PDF (see
-        setQmin).
+        set_qmin).
     scale
         See Managed Parameters.
     delta1
@@ -98,7 +98,7 @@ def __init__(self, name="pdf"):
         ProfileGenerator.__init__(self, name)
 
         self._phase = None
-        self.stru = None
+        self.structure = None
         self.meta = {}
         self._lastr = numpy.empty(0)
         self._calc = None
@@ -109,7 +109,7 @@ def __init__(self, name="pdf"):
 
     _parnames = ["delta1", "delta2", "qbroad", "scale", "qdamp"]
 
-    def _setCalculator(self, calc):
+    def _set_calculator(self, calc):
         """Set the SrReal calculator instance.
 
         Setting the calculator creates Parameters from the variable
@@ -118,13 +118,13 @@ def _setCalculator(self, calc):
         self._calc = calc
         for pname in self.__class__._parnames:
             self.addParameter(ParameterAdapter(pname, self._calc, attr=pname))
-        self.processMetaData()
+        self._process_metadata()
         return
 
     def parallel(self, ncpu, mapfunc=None):
         """Run calculation in parallel.
 
-        Attributes
+        Parameters
         ----------
         ncpu
             Number of parallel processes.  Revert to serial mode when 1.
@@ -155,130 +155,159 @@ def parallel(self, ncpu, mapfunc=None):
         self._calc = createParallelCalculator(calc_serial, ncpu, mapfunc)
         return
 
-    def processMetaData(self):
+    def _process_metadata(self):
         """Process the metadata once it gets set."""
-        ProfileGenerator.processMetaData(self)
+        ProfileGenerator._process_metadata(self)
 
         stype = self.meta.get("stype")
         if stype is not None:
-            self.setScatteringType(stype)
+            self.set_scattering_type(stype)
 
         qmax = self.meta.get("qmax")
         if qmax is not None:
-            self.setQmax(qmax)
+            self.set_qmax(qmax)
 
         qmin = self.meta.get("qmin")
         if qmin is not None:
-            self.setQmin(qmin)
+            self.set_qmin(qmin)
 
         for name in self.__class__._parnames:
             val = self.meta.get(name)
             if val is not None:
                 par = self.get(name)
-                par.setValue(val)
+                par.set_value(val)
 
         return
 
-    def setScatteringType(self, stype="X"):
+    def set_scattering_type(self, stype="X"):
         """Set the scattering type.
 
-        Attributes
+        Parameters
         ----------
-        stype
-            "X" for x-ray, "N" for neutron, "E" for electrons,
+        stype : str, optional
+            The scattering type. Default is `"X"`.
+            `"X"` for x-ray, `"N"` for neutron, `"E"` for electrons,
             or any registered type from diffpy.srreal from
             ScatteringFactorTable.getRegisteredTypes().
 
-        Raises ValueError for unknown scattering type.
+        Raises
+        ------
+        ValueError
+            If the scattering type is unknown.
         """
         self._calc.setScatteringFactorTableByType(stype)
         # update the meta dictionary only if there was no exception
-        self.meta["stype"] = self.getScatteringType()
+        self.meta["stype"] = self.get_scattering_type()
         return
 
-    def getScatteringType(self):
+    def get_scattering_type(self):
         """Get the scattering type.
 
-        See 'setScatteringType'.
+        See 'set_scattering_type'.
         """
         return self._calc.getRadiationType()
 
-    def setQmax(self, qmax):
-        """Set the qmax value."""
+    def set_qmax(self, qmax):
+        """Set the qmax value.
+
+        Parameters
+        ----------
+        qmax : float
+            The maximum scattering vector used to generate the PDF.
+        """
         self._calc.qmax = qmax
-        self.meta["qmax"] = self.getQmax()
+        self.meta["qmax"] = self.get_qmax()
         return
 
-    def getQmax(self):
-        """Get the qmax value."""
+    def get_qmax(self):
+        """Get the qmax value.
+
+        Returns
+        -------
+        float
+             The maximum scattering vector used to generate the PDF.
+        """
         return self._calc.qmax
 
-    def setQmin(self, qmin):
-        """Set the qmin value."""
+    def set_qmin(self, qmin):
+        """Set the qmin value.
+
+        Parameters
+        ----------
+        qmin : float
+            The minimum scattering vector used to generate the PDF.
+        """
         self._calc.qmin = qmin
-        self.meta["qmin"] = self.getQmin()
+        self.meta["qmin"] = self.get_qmin()
         return
 
-    def getQmin(self):
-        """Get the qmin value."""
+    def get_qmin(self):
+        """Get the qmin value.
+
+        Returns
+        -------
+        float
+            The minimum scattering vector used to generate the PDF.
+        """
         return self._calc.qmin
 
-    def setStructure(self, stru, name="phase", periodic=True):
+    def set_structure(self, structure, name="phase", periodic=True):
         """Set the structure that will be used to calculate the PDF.
 
         This creates a DiffpyStructureParSet, ObjCrystCrystalParSet or
-        ObjCrystMoleculeParSet that adapts stru to a ParameterSet interface.
+        ObjCrystMoleculeParSet that adapts structure to a ParameterSet
+        interface.
         See those classes (located in diffpy.srfit.structure) for how they are
         used. The resulting ParameterSet will be managed by this generator.
 
-        Attributes
+        Parameters
         ----------
-        stru
-            diffpy.structure.Structure, pyobjcryst.crystal.Crystal or
-            pyobjcryst.molecule.Molecule instance.  Default None.
-        name
-            A name to give to the managed ParameterSet that adapts stru
+        structure : Structure or Crystal or Molecule
+            The diffpy.structure.Structure, pyobjcryst.crystal.Crystal or
+            pyobjcryst.molecule.Molecule instance.
+        name : str, optional
+            The name to give to the managed ParameterSet that adapts structure
             (default "phase").
-        periodic
+        periodic : bool, optional
             The structure should be treated as periodic (default
             True). Note that some structures do not support
             periodicity, in which case this will have no effect on the
             PDF calculation.
         """
 
         # Create the ParameterSet
-        parset = struToParameterSet(name, stru)
+        parset = struToParameterSet(name, structure)
 
         # Set the phase
-        self.setPhase(parset, periodic)
+        self.set_structure_from_parset(parset, periodic)
         return
 
-    def setPhase(self, parset, periodic=True):
+    def set_structure_from_parset(self, parset, periodic=True):
         """Set the phase that will be used to calculate the PDF.
 
         Set the phase directly with a DiffpyStructureParSet,
         ObjCrystCrystalParSet or ObjCrystMoleculeParSet that adapts a structure
         object (from diffpy or pyobjcryst).  The passed ParameterSet will be
         managed by this generator.
 
-        Attributes
+        Parameters
         ----------
-        parset
-            A SrRealParSet that holds the structural information.
+        parset : SrRealParSet
+            The SrRealParSet that holds the structural information.
             This can be used to share the phase between multiple
             BasePDFGenerators, and have the changes in one reflect in
             another.
-        periodic
+        periodic : bool, optional
             The structure should be treated as periodic (default True).
             Note that some structures do not support periodicity, in
             which case this will be ignored.
         """
         # Store the ParameterSet for easy access
         self._phase = parset
-        self.stru = self._phase.stru
+        self.structure = self._phase.stru
 
         # Put this ParameterSet in the ProfileGenerator.
-        self.addParameterSet(parset)
+        self.add_parameter_set(parset)
 
         # Set periodicity
         self._phase.useSymmetry(periodic)
@@ -321,7 +350,7 @@ def __call__(self, r):
         if not numpy.array_equal(r, self._lastr):
             self._prepare(r)
 
-        rcalc, y = self._calc(self._phase._getSrRealStructure())
+        rcalc, y = self._calc(self._phase._get_srreal_structure())
 
         if numpy.isnan(y).any():
             y = numpy.zeros_like(r)