Release notes

3.3.1

Added:

Add regex parsing ability in PDFParser for file headers that do not have the structure output by xPDFsuite and PDFgetX.

3.3.0

Added:

Added add_parameter_set method to replace deprecated FitRecipe.addParameterSet.
Added add_parameter_set method to replace deprecated ParameterSet.addParameterSet.
Added diffpy.structure back to the requirements and run the test
Added add_constraint method to RecipeOrganizer.
Added remove_constraint method to RecipeOrganizer.
Added add_soft_bounds method to RecipeOrganizer.
Added remove_soft_bounds method to RecipeOrganizer.
Added register_soft_bounds method to RecipeOrganizer.
Added clear_all_soft_bounds method to RecipeOrganizer.
Added get_equation_from_string method to RecipeOrganizer.
Add parse_file method to ProfileParser to parse a file directly with load_data from diffpy.utils.
Add _parse_metadata and _parse_data hooks to ProfileParser, which subclasses override to support a new data format. parse_file is a template method that calls them.
Add get_num_banks method to ProfileParser to replace getNumBanks.
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_metadata method to ProfileParser to replace getMetaData.
Added get_equation method to BaseBuilder.
Added get_equation method to FitContribution.
Add plot_recipe method to FitRecipe.
Added initialize_recipe_with_results to FitRecipe.
Added iterate_over_parameters method.
Added register_calculator method.
Added register_function method.
Added register_string_function method.
Added evaluate_equation method.
Added is_constrained method.
Added get_constrained_parameters method.
Added clear_all_constraints method.
Added add_profile_generator to replace deprecated function.
Added is_constant method to Parameter.
Added bound_range method to Parameter.
Added bound_window method to Parameter.
Added set_weight method to FitRecipe to replace setWeight.
Added get_fit_hooks method to FitRecipe to replace getFitHooks.
Added clear_fit_hooks method to FitRecipe to replace clearFitHooks.
Added pop_fit_hook method to FitRecipe to replace popFitHook.
Added push_fit_hook method to FitRecipe to replace pushFitHook.
Add spherical_particle, spheroidal_particle, lognormal_spherical_particle, sheet_particle, and shell_particle to diffpy.srfit.pdf.characteristicfunctions, replacing sphericalCF, spheroidalCF, lognormalSphericalCF, sheetCF, and shellCF.
Add constrain_as_space_group to diffpy.srfit.structure.sgconstraints, replacing constrainAsSpaceGroup.
Added get_residual_equation method to FitContribution.
Added set_residual_equation method to FitContribution.
Added set_value method to diffpy.srfit.fitbase.Parameter.
Added save_results method to FitResults.
Added print_results method to FitResults.
Added get_results_string method to FitResults.
Added create_new_variable method to FitRecipe.
Added delete_variable method to FitRecipe.
Added add_variable method to FitRecipe.
Added scalar_residual method to FitRecipe.
Added remove_parameter_set method to FitRecipe.
Added test for remove_parameter_set method in FitRecipe.
Added initialize_recipe_from_recipe to FitRecipe.
Added convert_bounds_to_restraints method to FitRecipe.
Added get_bounds_pairs method to FitRecipe.
Added get_bounds_array method to FitRecipe.
Added get_names method to FitRecipe and RecipeContainer.
Added get_values method to FitRecipe and RecipeContainer.
Added is_free method to FitRecipe.
Added set_equation method to replace setEquation.
Added FitResults.get_results_dictionary in replace of resultsDictionary.
Added add_contribution in replace of addContribution.
Support for Python 3.14
Added load_parsed_data in replace of loadParsedData in Profile and SimpleRecipe.
Added set_observed_profile in replace of setObservedProfile in Profile and SimpleRecipe.
Added set_calculation_range in replace of setCalculationRange in Profile and SimpleRecipe.
Added set_calculation_points in replace of setCalculationPoints in Profile and SimpleRecipe.

Changed:

Change PDFParser to inherit _parse_metadata and _parse_data unchanged from ProfileParser, since PDFgetX and PDFgetN headers are now plain name = value pairs. PDFParser.parse_file returns the same data and metadata that PDFParser.parseFile did.
Change ProfileParser.parse_file to accept the keyword arguments of load_data, such as usecols, delimiter and comments. Use usecols to select columns from a file with more than four of them.
Change PDFContribution.loadData to take a file name only.
Change the headers of the si-q27r60-xray.gr and ni-q27r100-neutron.gr test files to the modern diffpy.pdfgetx and xPDFsuite configuration formats, replacing the 2008-era PDFgetX2/PDFgetN headers. The data values are unchanged.
Change spheroidalCF2 and shellCF2 in diffpy.srfit.pdf.characteristicfunctions to be deprecated aliases that convert their arguments and call spheroidal_particle and shell_particle, instead of separate implementations.
Change the current characteristic functions in diffpy.srfit.pdf.characteristicfunctions (spherical_particle, spheroidal_particle, lognormal_spherical_particle, sheet_particle and shell_particle) to emit a RuntimeWarning when a non-physical shape parameter makes them return zero, since a zero return flattens the fit residual and stalls a refinement without any other sign to the user. The warning is issued once per process for each distinct problem so a refinement loop does not repeat it. The deprecated camel-case functions forward to these functions directly, so they emit the same warning and return the same result for non-physical input.
Change lognormal_spherical_particle in diffpy.srfit.pdf.characteristicfunctions to return zero for a negative particle_diameter_sigma instead of silently returning spherical_particle. A particle_diameter_sigma of zero is still the sphere limit.
Change sheet_particle in diffpy.srfit.pdf.characteristicfunctions to return an array of zeros for a non-positive sheet_thickness when r is an array, instead of a scalar zero.
Change ProfileParser.parse_file to set unavailable dx/dy uncertainties to None instead of 0, matching the format-specific parsers.
Change Profile.set_observed_profile to leave dyobs as None when no uncertainties are observed, instead of silently replacing them with an array of ones. The calculated dy still defaults to 1 at every calculation point, so unweighted fits refine exactly as before.
Change Profile._validate to accept a None dyobs, since observed uncertainties are optional. x, y, dy, xobs and yobs are still required.
Changed iterPars method to match all equal-type atoms to have same ADPs

Deprecated:

Deprecated addParameterSet method in FitRecipe.
Deprecate addParameterSet method in ParameterSet.
Deprecated constrain method of RecipeOrganizer. Use add_constraint instead.
Deprecated unconstrain method of RecipeOrganizer. Use remove_constraint instead.
Deprecated restrain method of RecipeOrganizer. Use add_soft_bounds instead.
Deprecated unrestrain methods of RecipeOrganizer. Use remove_soft_bounds instead.
Deprecated addRestraint method of RecipeOrganizer. Use register_soft_bounds instead.
Deprecate clearRestraints method of RecipeOrganizer. Use clear_all_soft_bounds instead.
Deprecated equationFromString method of RecipeOrganizer. Use get_equation_from_string instead.
Deprecate getNumBanks, selectBank, getFormat, getData, and getMetaData in ProfileParser.
Deprecate ProfileParser.parseFile, which now delegates to parse_file. Use parse_file instead.
Deprecated BaseBuilder.getEquation method for removal in 4.0.0.
Deprecated FitContributution.getEquation method for removal in 4.0.0.
Deprecated iterPars method. Use iterate_over_parameters instead.
Deprecated registerCalculator method. Use register_calculator instead.
Deprecated registerFunction method. Use register_function instead.
Deprecated registerStringFunction method. Use register_string_function instead.
Deprecated evaluateEquation method. Use evaluate_equation instead.
Deprecated isConstrained method. Use is_constrained instead.
Deprecated getConstrainedPars method. Use get_constrained_parameters instead.
Deprecated clearConstraints method. Use clear_all_constraints instead.
Deprecate setProfile for removal in version 4.0.0.
Deprecated addProfileGenerator for removal in 4.0.0.
Deprecated isConst method of Parameter. Use is_constant instead.
Deprecated boundRange method of Parameter. Use bound_range instead.
Deprecated boundWindow method of Parameter. Use bound_window instead.
Deprecated setWeight in FitRecipe for removal in 4.0.0.
Deprecated getFitHooks in FitRecipe for removal in 4.0.0.
Deprecated clearFitHooks in FitRecipe for removal in 4.0.0.
Deprecated popFitHook in FitRecipe for removal in 4.0.0.
Deprecated pushFitHook in FitRecipe for removal in 4.0.0.
Deprecate sphericalCF, spheroidalCF, spheroidalCF2, lognormalSphericalCF, sheetCF, shellCF, and shellCF2 in diffpy.srfit.pdf.characteristicfunctions.
Deprecate constrainAsSpaceGroup in diffpy.srfit.structure.sgconstraints.
Deprecated getResidualEquation method of FitContribution for removal in 4.0.0.
Deprecated setResidualEquation method of FitContribution for removal in 4.0.0.
Deprecated setValue method in diffpy.srfit.fitbase.Parameter for removal in 4.0.0.
Deprecated saveResults method for removal in 4.0.0.
Deprecated printResults method for removal in 4.0.0.
Deprecated formatResults method for removal in 4.0.0.
Deprecated newVar method for removal in 4.0.0.
Deprecated delVar method for removal in 4.0.0.
Deprecated addVar method for removal in 4.0.0.
Deprecated scalarResidual method for removal in 4.0.0.
Deprecated removeParameterSet method for removal in 4.0.0.
Deprecated boundsToRestraints method for removal in 4.0.0.
Deprecated getBounds method for removal in 4.0.0.
Deprecated getBounds2 method for removal in 4.0.0.
Deprecated getNames method for removal in 4.0.0.
Deprecated getValues method for removal in 4.0.0.
Deprecated isFree method for removal in 4.0.0.
Deprecated setEquation for removal in 4.0.0.
Deprecated resultsDictionary for removal in 4.0.0.
Deprecated addContribution for removal in 4.0.0.
Deprecated loadParsedData in Profile and SimpleRecipe for removal in 4.0.0.
Deprecated setObservedProfile in Profile and SimpleRecipe for removal in 4.0.0.
Deprecated setCalculationRange in Profile and SimpleRecipe for removal in 4.0.0.
Deprecated setCalculationPoints in Profile and SimpleRecipe for removal in 4.0.0.

Fixed:

Fixed load new parsed data with updated Qmax attribute
Fix PDFParser.parse_file and PDFContribution.loadData discarding PDF metadata. They parsed PDFgetX and PDFgetN headers as generic name = value pairs, which dropped stype, qmin, qmax, qdamp and qbroad, so PDFGenerator silently fell back to its default scattering type and Q range.
Update codebase to scikit-package 0.3.0 standards.
Updated project to the latest scikit-package template
Fix shell_particle in diffpy.srfit.pdf.characteristicfunctions returning a smoothly varying branch of unphysical values, some below negative one, for a negative thickness or radius, which a refinement could mistake for a real solution. It now returns zero.
Fix shell_particle in diffpy.srfit.pdf.characteristicfunctions returning one at every r for a zero thickness, where the normalizing denominator vanishes. It now returns zero.
Fix spheroidal_particle in diffpy.srfit.pdf.characteristicfunctions raising ZeroDivisionError for a zero equatorial_radius. It now returns zero.
Fix ProfileParser.parse_file producing zero-valued uncertainties for absent or invalid dx/dy columns, which gave non-finite residuals for any file without usable uncertainties instead of falling back to an unweighted fit.
Fix Profile.dyobs reporting an array of ones for data that carries no uncertainties, which made an unweighted profile indistinguishable from one whose uncertainties were genuinely all 1.

Removed:

Remove parseString from ProfileParser, and PDFParser. Parsers read from a file, so a format is now supported by overriding the _parse_metadata and _parse_data hooks.
Remove support for passing a data string or an open file object to PDFContribution.loadData. Pass a file name instead.
Support for Python 3.11

3.2.0

Changed:

Temporarily removed support for SAS characteristic functions until we can migrate to the new sasview api.
doc/ -> docs/
requirements/test.txt -> requirements/tests.txt

Fixed:

Better license designation in pyproject.toml

3.1.0

Version 3.0.0 – 2019-03-14

Added:

Support for Python 3.7, 3.6, 3.5 in addition to 2.7.

Changed:

Always use lower-case imports from diffpy.structure.
Use numeric-value sort to order variables in PrintFitHook.

Deprecated:

Variable __gitsha__ in the version module renamed to __git_commit__.

Removed:

Optional upper and lower-bound arguments in Parameter.setValue. The bounds can be set with Parameter.boundRange instead.
Unused classes ListOperator, SetOperator.

Fixed:

Metadata retrieval from PDFContribution hierarchy.
Refresh PDFGenerator when its rgrid is changed in-place.
Zero division in the nppdfsas.py example.
Crash in ellipsoidsas.py example because of bug in Parameter.setValue.
Pickling of ProfileGenerator objects and of bound class methods.
Invalid escape sequences in string values.