rm PDF generator functions, will put on another PR

Author: cadenmyers13

.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]

src/diffpy/cmipdf/debyepdfgenerator.py

@@ -23,11 +23,9 @@
 
 __all__ = ["DebyePDFGenerator"]
 
-from pathlib import Path
 
 from diffpy.cmipdf.basepdfgenerator import BasePDFGenerator
 from diffpy.srreal.pdfcalculator import DebyePDFCalculator
-from diffpy.structure import loadStructure
 
 
 class DebyePDFGenerator(BasePDFGenerator):
@@ -144,98 +142,6 @@ def __init__(self, name="pdf"):
         self._set_calculator(DebyePDFCalculator())
         return
 
-    def generate_pdf_from_structure(
-        self,
-        structure,
-        rmin=0,
-        rmax=30,
-        qmin=0.1,
-        qmax=25.0,
-        qdamp=0.03,
-        qbroad=0.0,
-        delta1=0.0,
-        delta2=0.0,
-        uiso=0.007,
-    ):
-        """Calculate the PDF from a structure and return G vs. r.
-
-        This is a convenience method that allows the user to calculate
-        the PDF from a
-        structure without having to set up the calculator and
-        structure ParameterSet
-        manually. The structure can be passed as a path to a
-        structure file or as a
-        `diffpy.structure.Structure` object.
-
-        Parameters
-        ----------
-        structure : Path, str, or diffpy.structure.Structure
-            The structure to calculate the PDF from. Can be a path
-            to a structure file or a diffpy.structure.Structure
-            object.
-        rmin : float, optional
-            The minimum r value in Angstroms for the PDF (default 0).
-        rmax : float, optional
-            The maximum r value in Angstroms for the PDF (default 30).
-        qmin : float, optional
-            The minimum scattering vector used to generate the PDF
-            (default 0.1).
-        qmax : float, optional
-            The maximum scattering vector used to generate the PDF
-            (default 25.0).
-        uiso : float, optional
-            The isotropic atomic displacement parameter to use for all
-            atoms in the structure (default 0.007).
-        qdamp : float, optional
-            The resolution dampening term to use in the PDF calculation
-            (default 0.03).
-        qbroad : float, optional
-            The resolution broadening term to use in the PDF calculation
-            (default 0.0).
-        delta1 : float, optional
-            The linear peak broadening term to use in the PDF calculation
-            (default 0.0).
-        delta2 : float, optional
-            The quadratic peak broadening term to use in the PDF calculation
-            (default 0.0).
-        uiso : float, optional
-            The isotropic atomic displacement parameter to use for all
-            atoms in the structure (default 0.007).
-
-        Returns
-        -------
-        r : numpy.ndarray
-            The r values for the PDF in units of Angstroms.
-        G : numpy.ndarray
-            The G values for the PDF in units of 1/Angstrom^2.
-
-        Example
-        -------
-        .. code-block:: python
-            xyz_path = "path/to/nanoparticle.xyz"
-            gen = PDFGenerator()
-            r, g = gen.generate_pdf_from_structure(xyz_path)
-        """
-        if isinstance(structure, Path):
-            structure = loadStructure(str(structure))
-        elif isinstance(structure, str):
-            structure = loadStructure(structure)
-        structure.Uisoequiv = uiso
-
-        calc = DebyePDFCalculator()
-        calc.qmin = qmin
-        calc.qmax = qmax
-        calc.rstep = 0.01
-        calc.rmin = rmin
-        calc.rmax = rmax
-        calc.qdamp = qdamp
-        calc.qbroad = qbroad
-        calc.delta1 = delta1
-        calc.delta2 = delta2
-
-        r, g = calc(structure)
-        return r, g
-
 
 # End class DebyePDFGenerator
 

src/diffpy/cmipdf/pdfgenerator.py

@@ -25,11 +25,9 @@
 
 __all__ = ["PDFGenerator"]
 
-from pathlib import Path
 
 from diffpy.cmipdf.basepdfgenerator import BasePDFGenerator
 from diffpy.srreal.pdfcalculator import PDFCalculator
-from diffpy.structure import loadStructure
 
 
 class PDFGenerator(BasePDFGenerator):
@@ -94,94 +92,5 @@ def __init__(self, name="pdf"):
         self._set_calculator(PDFCalculator())
         return
 
-    def generate_pdf_from_structure(
-        self,
-        structure,
-        rmin=0,
-        rmax=30,
-        qmin=0.1,
-        qmax=25.0,
-        qdamp=0.03,
-        qbroad=0.0,
-        delta1=0.0,
-        delta2=0.0,
-        uiso=0.007,
-    ):
-        """Calculate the PDF from a structure and return G vs. r.
-
-        This is a convenience method that allows the user to calculate
-        the PDF from a
-        structure without having to set up the calculator and
-        structure ParameterSet
-        manually. The structure can be passed as a path to a
-        structure file or as a
-        `diffpy.structure.Structure` object.
-
-        Parameters
-        ----------
-        structure : Path, str, or diffpy.structure.Structure
-            The structure to calculate the PDF from. Can be a path
-            to a structure file or a diffpy.structure.Structure
-            object.
-        rmin : float, optional
-            The minimum r value in Angstroms for the PDF (default 0).
-        rmax : float, optional
-            The maximum r value in Angstroms for the PDF (default 30).
-        qmin : float, optional
-            The minimum scattering vector used to generate the PDF
-            (default 0.1).
-        qmax : float, optional
-            The maximum scattering vector used to generate the PDF
-            (default 25.0).
-        qdamp : float, optional
-            The resolution dampening term to use in the PDF calculation
-            (default 0.03).
-        qbroad : float, optional
-            The resolution broadening term to use in the PDF calculation
-            (default 0.0).
-        delta1 : float, optional
-            The linear peak broadening term to use in the PDF calculation
-            (default 0.0).
-        delta2 : float, optional
-            The quadratic peak broadening term to use in the PDF calculation
-            (default 0.0).
-        uiso : float, optional
-            The isotropic atomic displacement parameter to use for all
-            atoms in the structure (default 0.007).
-
-        Returns
-        -------
-        r : numpy.ndarray
-            The r values for the PDF in units of Angstroms.
-        G : numpy.ndarray
-            The G values for the PDF in units of 1/Angstrom^2.
-
-        Example
-        -------
-        .. code-block:: python
-            cif_path = "path/to/ni.cif"
-            gen = PDFGenerator()
-            r, g = gen.generate_pdf_from_structure(cifpath)
-        """
-        if isinstance(structure, Path):
-            structure = loadStructure(str(structure))
-        elif isinstance(structure, str):
-            structure = loadStructure(structure)
-        structure.Uisoequiv = uiso
-
-        calc = PDFCalculator()
-        calc.qmin = qmin
-        calc.qmax = qmax
-        calc.rstep = 0.01
-        calc.rmin = rmin
-        calc.rmax = rmax
-        calc.qdamp = qdamp
-        calc.qbroad = qbroad
-        calc.delta1 = delta1
-        calc.delta2 = delta2
-
-        r, g = calc(structure)
-        return r, g
-
 
 # End class PDFGenerator