skpkg: line length fixes, GH workflow edits, and other small edits

[cadenmyers13]

It looks like a lot of edits were made here but its mostly just autofixes made by pre-commit.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Please upload report for BASE (migration@d47b719). Learn more about missing BASE report.

Additional details and impacted files

@@             Coverage Diff              @@
##             migration     #136   +/-   ##
============================================
  Coverage             ?   98.97%           
============================================
  Files                ?        6           
  Lines                ?     1267           
  Branches             ?        0           
============================================
  Hits                 ?     1254           
  Misses               ?       13           
  Partials             ?        0           

Files with missing lines	Coverage Δ
tests/test_exceptions.py	99.80% <100.00%> (ø)
tests/test_pdffit.py	99.76% <100.00%> (ø)
tests/test_phase_fractions.py	98.70% <100.00%> (ø)
tests/test_shape_factors.py	99.53% <100.00%> (ø)

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[sbillinge]

Thanks @cadenmyers13 . If it is all autofixes I can merge it. If it s "mostly" autofixes, please tell me the manual fixes and I will check them.

In general, we want the autofix PRs to be just autofixed.

[cadenmyers13]

@sbillinge the only manual fixes were changing the copyright dates (going from 2024-2025) so basically it's all autofixed

[sbillinge]

I merged this, but please can you confirm that numpy is a requirement? It seems odd that we would be adding this if it wasn't there before @cadenmyers13.

[cadenmyers13]

@sbillinge numpy is used in tests and its in doc/source/. The only use of it in src/ is in this function.

class EasyPDFPlotting(object):
.
.
.
    @staticmethod
    def _asarray(x, dtype=None):
        import numpy

        return numpy.asarray(x, dtype=dtype)

[sbillinge]

@sbillinge numpy is used in tests and its in doc/source/. The only use of it in src/ is in this function.

class EasyPDFPlotting(object):
.
.
.
    @staticmethod
    def _asarray(x, dtype=None):
        import numpy

        return numpy.asarray(x, dtype=dtype)

interesting. Is that class used anywhere? I don't think we had any complaints from people when it wasn't in conda.txt. For the uses in tests and docs we don't need it in conda.txt.

[cadenmyers13]

Is that class used anywhere?

@sbillinge when i cmd+F search for it its only found in the file it is located in which is src/diffpy/pdffit2/ipy_ext.py. So maybe its not needed as a dependency. There's a docstring at the top of the file saying what this module is for:

"""This module defines functions within IPython session to simulate the old
pdffit2 interactive session.

Usage: %load_ext diffpy.pdffit2.ipy_ext
"""

[sbillinge]

I am guessing that that was a Pavol testing thing. Let's remove numpy from conda.txt etc.

[cadenmyers13]

@sbillinge okay ill send a PR