Merge pull request #171 from cadenmyers13/profileparser_dep

deprecate: Deprecate function in `ProfileParser` and deprecate `PDFParser`

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
@@ -21,46 +21,47 @@ 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
+        language_version: python3.13
         additional_dependencies: [tomli]
         args: [--in-place, --config, ./pyproject.toml]

docs/examples/coreshellnp.py

@@ -29,8 +29,9 @@
     FitRecipe,
     FitResults,
     Profile,
+    ProfileParser,
 )
-from diffpy.srfit.pdf import PDFGenerator, PDFParser
+from diffpy.srfit.pdf import PDFGenerator
 
 # Example Code
 
@@ -42,7 +43,7 @@ def makeRecipe(stru1, stru2, datname):
     profile = Profile()
 
     # Load data and add it to the profile
-    parser = PDFParser()
+    parser = ProfileParser()
     parser.parseFile(datname)
     profile.load_parsed_data(parser)
     profile.set_calculation_range(xmin=1.5, xmax=45, dx=0.1)

docs/examples/crystalpdf.py

@@ -32,8 +32,9 @@
     FitRecipe,
     FitResults,
     Profile,
+    ProfileParser,
 )
-from diffpy.srfit.pdf import PDFGenerator, PDFParser
+from diffpy.srfit.pdf import PDFGenerator
 from diffpy.structure import Structure
 
 ######
@@ -48,12 +49,12 @@ def makeRecipe(ciffile, datname):
     profile = Profile()
 
     # Load data and add it to the Profile. Unlike in other examples, we use a
-    # class (PDFParser) to help us load the data. This class will read the data
-    # and relevant metadata from a two- to four-column data file generated
+    # class (ProfileParser) to help us load the data. This class will read the
+    # data and relevant metadata from a two- to four-column data file generated
     # with PDFGetX2 or PDFGetN. The metadata will be passed to the PDFGenerator
     # when they are associated in the FitContribution, which saves some
     # configuration steps.
-    parser = PDFParser()
+    parser = ProfileParser()
     parser.parseFile(datname)
     profile.load_parsed_data(parser)
     profile.set_calculation_range(xmax=20)
@@ -62,7 +63,8 @@ def makeRecipe(ciffile, datname):
     # The PDFGenerator is for configuring and calculating a PDF profile. Here,
     # we want to refine a Structure object from diffpy.structure. We tell the
     # PDFGenerator that with the 'setStructure' method. All other configuration
-    # options will be inferred from the metadata that is read by the PDFParser.
+    # options will be inferred from the metadata that is read by the
+    # ProfileParser.
     # In particular, this will set the scattering type (x-ray or neutron), the
     # Qmax value, as well as initial values for the non-structural Parameters.
     generator = PDFGenerator("G")

docs/examples/crystalpdfall.py

@@ -27,8 +27,9 @@
     FitRecipe,
     FitResults,
     Profile,
+    ProfileParser,
 )
-from diffpy.srfit.pdf import PDFGenerator, PDFParser
+from diffpy.srfit.pdf import PDFGenerator
 
 ######
 #  Example Code
@@ -37,7 +38,7 @@
 def makeProfile(datafile):
     """Make an place data within a Profile."""
     profile = Profile()
-    parser = PDFParser()
+    parser = ProfileParser()
     parser.parseFile(datafile)
     profile.load_parsed_data(parser)
     profile.set_calculation_range(xmax=20)

docs/examples/crystalpdfobjcryst.py

@@ -28,8 +28,9 @@
     FitRecipe,
     FitResults,
     Profile,
+    ProfileParser,
 )
-from diffpy.srfit.pdf import PDFGenerator, PDFParser
+from diffpy.srfit.pdf import PDFGenerator
 
 ######
 #  Example Code
@@ -42,11 +43,11 @@ def makeRecipe(ciffile, datname):
     # This will be used to store the observed and calculated PDF profile.
     profile = Profile()
 
-    # Load data and add it to the Profile. As before we use a PDFParser. The
-    # metadata is still passed to the PDFGenerator later on. The interaction
-    # between the PDFGenerator and the metadata does not depend on type of
-    # structure being refined.
-    parser = PDFParser()
+    # Load data and add it to the Profile. As before we use a ProfileParser.
+    # The metadata is still passed to the PDFGenerator later on.
+    # The interaction between the PDFGenerator and the metadata does not
+    # depend on type of structure being refined.
+    parser = ProfileParser()
     parser.parseFile(datname)
     profile.load_parsed_data(parser)
     profile.set_calculation_range(xmax=20)

docs/examples/crystalpdftwodata.py

@@ -29,8 +29,9 @@
     FitRecipe,
     FitResults,
     Profile,
+    ProfileParser,
 )
-from diffpy.srfit.pdf import PDFGenerator, PDFParser
+from diffpy.srfit.pdf import PDFGenerator
 
 ######
 #  Example Code
@@ -46,12 +47,12 @@ def makeRecipe(ciffile, xdatname, ndatname):
     nprofile = Profile()
 
     # Load data and add it to the proper Profile.
-    parser = PDFParser()
+    parser = ProfileParser()
     parser.parseFile(xdatname)
     xprofile.load_parsed_data(parser)
     xprofile.set_calculation_range(xmax=20)
 
-    parser = PDFParser()
+    parser = ProfileParser()
     parser.parseFile(ndatname)
     nprofile.load_parsed_data(parser)
     nprofile.set_calculation_range(xmax=20)

docs/examples/crystalpdftwophase.py

@@ -29,8 +29,9 @@
     FitRecipe,
     FitResults,
     Profile,
+    ProfileParser,
 )
-from diffpy.srfit.pdf import PDFGenerator, PDFParser
+from diffpy.srfit.pdf import PDFGenerator
 
 ######
 #  Example Code
@@ -43,7 +44,7 @@ def makeRecipe(niciffile, siciffile, datname):
     profile = Profile()
 
     # Load data and add it to the profile
-    parser = PDFParser()
+    parser = ProfileParser()
     parser.parseFile(datname)
     profile.load_parsed_data(parser)
     profile.set_calculation_range(xmax=20)

docs/examples/nppdfcrystal.py

@@ -32,8 +32,9 @@
     FitRecipe,
     FitResults,
     Profile,
+    ProfileParser,
 )
-from diffpy.srfit.pdf import PDFGenerator, PDFParser
+from diffpy.srfit.pdf import PDFGenerator
 
 
 def makeRecipe(ciffile, grdata):
@@ -42,7 +43,7 @@ def makeRecipe(ciffile, grdata):
     # Set up a PDF fit as has been done in other examples.
     pdfprofile = Profile()
 
-    pdfparser = PDFParser()
+    pdfparser = ProfileParser()
     pdfparser.parseFile(grdata)
     pdfprofile.load_parsed_data(pdfparser)
     pdfprofile.set_calculation_range(xmin=0.1, xmax=20)

docs/examples/nppdfsas.py

@@ -31,8 +31,9 @@
     FitRecipe,
     FitResults,
     Profile,
+    ProfileParser,
 )
-from diffpy.srfit.pdf import PDFGenerator, PDFParser
+from diffpy.srfit.pdf import PDFGenerator
 from diffpy.srfit.pdf.characteristicfunctions import SASCF
 from diffpy.srfit.sas import SASGenerator, SASParser
 
@@ -47,7 +48,7 @@ def makeRecipe(ciffile, grdata, iqdata):
 
     # Create a PDF contribution as before
     pdfprofile = Profile()
-    pdfparser = PDFParser()
+    pdfparser = ProfileParser()
     pdfparser.parseFile(grdata)
     pdfprofile.load_parsed_data(pdfparser)
     pdfprofile.set_calculation_range(xmin=0.1, xmax=20)

news/profileparser_dep.rst

@@ -0,0 +1,29 @@
+**Added:**
+
+* Add ``parse_file`` method to ``ProfileParser`` to parse a file directly with ``load_data`` from ``diffpy.utils``.
+* Add ``get_num_bank`` method to ``ProfileParser`` to replace ``getNumBank``.
+* Add ``select_bank`` method to ``ProfileParser`` to replace ``selectBank``.
+* Add ``get_format`` method to ``ProfileParser`` to replace ``getFormat``.
+* Add ``get_data`` method to ``ProfileParser`` to replace ``getData``.
+* Add ``get_meta_data`` method to ``ProfileParser`` to replace ``getMetaData``.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* Deprecate ``PDFParser``. Use ``ProfileParser`` instead.
+* Deprecate ``getNumBank``, ``selectBank``, ``getFormat``, ``getData``, and ``getMetaData`` in ``ProfileParser``.
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>