deprecate: Deprecate remaining methods of FitRecipe

[cadenmyers13]

deprecated,

• removeParameterSet
• scalarResidual
• addVar
• delVar
• newVar

I also added a test for remove_parameter_set since it didn't exist

[cadenmyers13]

@sbillinge ready for review

Also, this is where we are with deprecations in srfit, 40 functions deprecated!

tests/test_builder.py::testBuildEquation
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_builder.py:269: DeprecationWarning: 'diffpy.srfit.equation.builder.BaseBuilder.getEquation' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.equation.builder.BaseBuilder.get_equation' instead.
    eq4 = (3 * E(A, D) - 1).getEquation()

tests/test_contribution.py::TestContribution::testAddProfileGenerator
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_contribution.py:61: DeprecationWarning: 'diffpy.srfit.fitbase.FitContribution.addProfileGenerator' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitContribution.add_profile_generator' instead.
    fc.addProfileGenerator(gen, "gen")

tests/test_contribution.py::TestContribution::test_getResidualEquation
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_contribution.py:175: DeprecationWarning: 'diffpy.srfit.fitbase.FitContribution.getResidualEquation' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitContribution.get_residual_equation' instead.
    self.assertEqual("((eq - y) / dy)", fc.getResidualEquation())

tests/test_contribution.py::TestContribution::test_getResidualEquation
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_contribution.py:176: DeprecationWarning: 'diffpy.srfit.fitbase.FitContribution.setResidualEquation' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitContribution.set_residual_equation' instead.
    fc.setResidualEquation("2 * (eq - y)")

tests/test_contribution.py::TestContribution::testset_profile
  /opt/miniconda3/envs/srfit/lib/python3.13/unittest/case.py:238: DeprecationWarning: 'diffpy.srfit.fitbase.FitContribution.setProfile' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitContribution.set_profile' instead.
    callable_obj(*args, **kwargs)

tests/test_contribution.py::test_setEquation
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_contribution.py:299: DeprecationWarning: 'diffpy.srfit.fitbase.FitContribution.setEquation' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitContribution.set_equation' instead.
    fc.setEquation("x + 5")

tests/test_contribution.py::test_getEquation
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_contribution.py:329: DeprecationWarning: 'diffpy.srfit.fitbase.FitContribution.getEquation' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitContribution.get_equation' instead.
    assert "(A * sin((x + 5)))" == fc.getEquation()

tests/test_fitrecipe.py: 16 warnings
tests/test_fitresults.py: 3 warnings
tests/test_sgconstraints.py: 1 warning
  /opt/miniconda3/envs/srfit/lib/python3.13/site-packages/diffpy/srfit/fitbase/fitrecipe.py:192: DeprecationWarning: 'diffpy.srfit.fitbase.FitRecipe.pushFitHook' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitRecipe.push_fit_hook' instead.
    self.pushFitHook(PrintFitHook())

tests/test_fitrecipe.py::TestFitRecipe::testVars
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_fitrecipe.py:158: DeprecationWarning: 'diffpy.srfit.fitbase.FitRecipe.addVar' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitRecipe.add_variable' instead.
    recipe.addVar(con.c, 0)

tests/test_fitrecipe.py::TestFitRecipe::testVars
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_fitrecipe.py:159: DeprecationWarning: 'diffpy.srfit.fitbase.FitRecipe.newVar' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitRecipe.create_new_variable' instead.
    recipe.newVar("B", 0)

tests/test_fitrecipe.py::TestFitRecipe::testVars
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_fitrecipe.py:171: DeprecationWarning: 'diffpy.srfit.fitbase.FitRecipe.delVar' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitRecipe.delete_variable' instead.
    recipe.delVar(recipe.B)

tests/test_fitrecipe.py::testPrintFitHook
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_fitrecipe.py:319: DeprecationWarning: 'diffpy.srfit.fitbase.FitRecipe.addContribution' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitRecipe.add_contribution' instead.
    recipe.addContribution(fitcontribution)

tests/test_fitrecipe.py::testPrintFitHook
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_fitrecipe.py:323: DeprecationWarning: 'diffpy.srfit.fitbase.FitRecipe.getFitHooks' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitRecipe.get_fit_hooks' instead.
    (pfh,) = recipe.getFitHooks()

tests/test_fitrecipe.py::testPrintFitHook
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/conftest.py:141: DeprecationWarning: 'diffpy.srfit.fitbase.FitRecipe.scalarResidual' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitRecipe.scalar_residual' instead.
    f(*args, **kwargs)

tests/test_fitrecipe.py::test_add_and_remove_ParameterSet
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_fitrecipe.py:346: DeprecationWarning: 'diffpy.srfit.fitbase.FitRecipe.addParameterSet' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitRecipe.add_parameter_set' instead.
    recipe.addParameterSet(parameter_to_add)

tests/test_fitrecipe.py::test_add_and_remove_ParameterSet
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_fitrecipe.py:351: DeprecationWarning: 'diffpy.srfit.fitbase.FitRecipe.removeParameterSet' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.FitRecipe.remove_parameter_set' instead.
    recipe.removeParameterSet(parameter_to_add)

tests/test_fitrecipe.py::test_plot_recipe_labels_from_gr_file_overwrite_deprecated
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_fitrecipe.py:469: DeprecationWarning: 'diffpy.srfit.fitbase.profile.Profile.loadParsedData' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.profile.Profile.load_parsed_data' instead.
    profile.loadParsedData(parser)

tests/test_parameterset.py::TestParameterSet::testAddParameterSet
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_parameterset.py:38: DeprecationWarning: 'diffpy.srfit.fitbase.parameterset.ParameterSet.addParameterSet' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.parameterset.ParameterSet.add_parameter_set' instead.
    self.parset.addParameterSet(parset2)

tests/test_profile.py::TestProfile::testSetCalculationPoints
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_profile.py:251: DeprecationWarning: 'diffpy.srfit.fitbase.profile.Profile.setCalculationPoints' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.profile.Profile.set_calculation_points' instead.
    prof.setCalculationPoints(xcalc)

tests/test_profile.py::TestProfile::testSetCalculationRange
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_profile.py:213: DeprecationWarning: 'diffpy.srfit.fitbase.profile.Profile.setCalculationRange' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.profile.Profile.set_calculation_range' instead.
    prof.setCalculationRange()

tests/test_profile.py::TestProfile::testSetObservedProfile
  /Users/cadenmyers/billingelab/dev/diffpy.srfit/tests/test_profile.py:102: DeprecationWarning: 'diffpy.srfit.fitbase.profile.Profile.setObservedProfile' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.srfit.fitbase.profile.Profile.set_observed_profile' instead.
    self.profile.setObservedProfile(x, y, dy)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

[cadenmyers13]

A similar test for this exists in test_parameterset, but no test existed for the FitRecipe.removeParameterSet.

[codecov]

Codecov Report

❌ Patch coverage is 98.93617% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 71.06%. Comparing base (1a3aa78) to head (644cc97).
⚠️ Report is 10 commits behind head on v3.3.0.

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

Additional details and impacted files

@@            Coverage Diff             @@
##           v3.3.0     #157      +/-   ##
==========================================
+ Coverage   70.63%   71.06%   +0.43%     
==========================================
  Files          25       25              
  Lines        3606     3660      +54     
==========================================
+ Hits         2547     2601      +54     
  Misses       1059     1059              

Files with missing lines	Coverage Δ
tests/conftest.py	91.48% <100.00%> (ø)
tests/test_fitrecipe.py	99.81% <100.00%> (+0.02%)	⬆️
tests/test_fitresults.py	98.41% <100.00%> (ø)
tests/test_sgconstraints.py	10.06% <0.00%> (ø)

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[sbillinge]

This is amazing. I love the new function names and appreciate the tests