3.3.1

Added:

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

3.3.1-rc.0

What's Changed

• refactor and feat: Add parsing ability for NOMAD datafiles and breakout tests in test_pdf.py into respective files by @cadenmyers13 in #207
• update installation instructions by @sbillinge in #209

Full Changelog: 3.3.0...3.3.1-rc.0

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 ``FitRe...

3.3.0-rc.3

What's Changed

• fix: fix broken entrypoint by @cadenmyers13 in #205

Full Changelog: 3.3.0-rc.2...3.3.0-rc.3

3.3.0-rc.2

What's Changed

• fix: change camelcase to snakecase in all private functions by @cadenmyers13 in #138
• feat: add plot_recipe method to FitRecipe by @cadenmyers13 in #143
• deprecate: deprecate setProfile by @cadenmyers13 in #144
• Api doc rerender by @cadenmyers13 in #145
• build: Update Matrix testing to run on dispatch by @cadenmyers13 in #148
• fix: fix Qmax update after load new parsed data by @stevenhua0320 in #173
• build: add diffpy.structure back to requirement by @stevenhua0320 in #175
• chore: rebuild the documentation with proper metadata handling by @stevenhua0320 in #177
• chore: update pre-commit by @danielsirakov in #184
• release: add support for python 3.14 and remove for 3.11 by @danielsirakov in #187
• Merge v3.3.0 into main by @cadenmyers13 in #201
• remove caden as a maintainer by @cadenmyers13 in #203
• rm caden from workflow release and add back to pyproject.toml by @cadenmyers13 in #204

Full Changelog: 3.2.0...3.3.0-rc.2

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

3.2.0-rc.2

What's Changed

• chore: fix docstrings to generate API page. by @ycexiao in #132

Full Changelog: 3.2.0-rc.1...3.2.0-rc.2

3.2.0-rc.1

What's Changed

• chore: fix examples by @ycexiao in #131
• chore: sync conf.py extensions with docs dependencies listed in requirements folder by @zmx27 in #130

Full Changelog: 3.2.0-rc.0...3.2.0-rc.1

3.2.0-rc.0

What's Changed

• fix: license designation in pyproject.toml by @sbillinge in #122
• style: rename CODE_OF_CONDUCT to CODE-OF-CONDUCT by @sbillinge in #123
• style: use numpy docstring and fix documentation rendering by @ycexiao in #125
• test: use filename string instead of pathlib.Path to fix tests using diffpy.structure by @ycexiao in #128
• refactor: update sasview api for test_sas.py by @zmx27 in #126

New Contributors

• @ycexiao made their first contribution in #125
• @zmx27 made their first contribution in #126

Full Changelog: 3.1.0...3.2.0-rc.0

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.