deprecate: Deprecate function in ProfileParser and deprecate PDFParser

[cadenmyers13]

As I was working on deprecation, I felt as if we could centralize the parser to one place and use load_data from diffpy.utils instead of having separate parsers.

The PDFParser was designed for older data formats too so it doesn't capture as much info as shown here:

PDFParser metadata: for data.gr

{'bank': 0,
 'filename': PosixPath('data.gr'),
 'nbanks': 1,
 'qmax': 25.0,
 'qmin': 0.1,
 'stype': 'X'}

ProfileParser metadata: for data.gr

{'backgroundfile': 'Xiaoyu_empty_kapton_PDF_20251021-124540_f33625_sum.iq',
 'backgroundfilefull': '/Users/cadenmyers/billingelab/BNL/oct2025_beamtime/data/Xiaoyu/iq/Xiaoyu_empty_kapton_PDF_20251021-124540_f33625_sum.iq',
 'bank': 0,
 'bgscale': 1.0,
 'composition': 'TiSe2',
 'dataformat': 'QA',
 'filename': 'data.gr',
 'inputdir': '/Users/cadenmyers/billingelab/BNL/oct2025_beamtime/data/Xiaoyu/iq',
 'inputfile': 'TiSe2_RT_XS2_intercalated_PDF_20251021-124651_85419c_sum.iq',
 'mode': 'xray',
 'nbanks': 1,
 'outputtype': 'gr',
 'qmax': 25.0,
 'qmaxinst': 25.0,
 'qmin': 0.1,
 'rmax': 140.0,
 'rmin': 0.0,
 'rpoly': 0.7,
 'rstep': 0.01,
 'savedir': '/Users/cadenmyers/billingelab/BNL/oct2025_beamtime/data/Xiaoyu/gr',
 'wavelength': 0.1}

The work here deprecates PDFParser in favor of ProfileParser, a more general approach to parsing data. I've included tests for this too. This also centralizes some parsing functionality which will hopefully make it easier to dev on and easier for users. Im open to discussion if you'd prefer a different route though.

From what i inferred from the code, it seems like ProfileParser was designed so people can build their own parsers for their specific data formats and PDFParser is one example that does this.

[cadenmyers13]

Here in the docstring describes the default behavior, users can change this depending on their data format

[cadenmyers13]

@sbillinge ready for review. It looks like precommit is failing because of some python 3.14 thing

[codecov]

Codecov Report

❌ Patch coverage is 98.41270% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 78.89%. Comparing base (ec2b2af) to head (ab44228).
⚠️ Report is 1 commits behind head on v3.3.0.

Files with missing lines	Patch %	Lines
tests/test_sas.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           v3.3.0     #171      +/-   ##
==========================================
+ Coverage   78.60%   78.89%   +0.29%     
==========================================
  Files          24       25       +1     
  Lines        3734     3786      +52     
==========================================
+ Hits         2935     2987      +52     
  Misses        799      799              

Files with missing lines	Coverage Δ
tests/conftest.py	92.89% <100.00%> (+0.49%)	⬆️
tests/test_contribution.py	99.58% <ø> (ø)
tests/test_fitrecipe.py	99.85% <100.00%> (ø)
tests/test_pdf.py	43.58% <100.00%> (+0.29%)	⬆️
tests/test_profile.py	99.52% <100.00%> (+0.03%)	⬆️
tests/test_profileparser.py	100.00% <100.00%> (ø)
tests/test_weakrefcallable.py	98.91% <ø> (ø)
tests/test_sas.py	15.78% <0.00%> (ø)

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[cadenmyers13]

@sbillinge I figured out the pre-commit issue. its failing because docformatter is not compatible with python3.14 yet and pre-commit.ci is already running on python3.14. The way we can fix this is by pinning language_version: python3.13 in docformatter,

  - 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]

This will have to be removed in the future or we can just let pre-commit fail for now until docformatter is up to 3.14 standards.

It fails because some .s attribute was deprecated and now removed in favor of .value. Looks like this issue is already addressed here : scikit-package/scikit-package#640