chore: merge remaining main edits into v3.3.0 - #189
Merged
Conversation
fix: fix Qmax update after load new parsed data
build: add diffpy.structure back to requirement
chore: rebuild the documentation with proper metadata handling
* chore: update pre-commit * [pre-commit.ci] auto fixes from pre-commit hooks * chore: fix docformatter and black conflict * chore: run pre-commit for file I missed * [pre-commit.ci] auto fixes from pre-commit hooks * chore: add #FIXME workaround * chore: add #FIXME workaround * [pre-commit.ci] auto fixes from pre-commit hooks * chore: add another #FIXME workaround * chore: add another #FIXME workaround * [pre-commit.ci] auto fixes from pre-commit hooks * chore: moved import statement to the top of import modules * [pre-commit.ci] auto fixes from pre-commit hooks * chore: added try except workaround --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## v3.3.0 #189 +/- ##
==========================================
+ Coverage 79.08% 81.27% +2.19%
==========================================
Files 25 25
Lines 3821 3798 -23
==========================================
+ Hits 3022 3087 +65
+ Misses 799 711 -88
🚀 New features to boost your workflow:
|
Contributor
Author
|
@sbillinge ready for review |
sbillinge
added a commit
that referenced
this pull request
Aug 8, 2026
* deprecate addProfileGenerator * update api docs * mock utils and pyobjcryst for doc rendering * news * restore api docs * revert conf.py commit * deprecate addContribution and replace with add_contribution * news * deprecate setEquation and replace with set_equation * more set_equation replacements * news * reorder dep message to prevent merge conflicts * one final setEquation switch in tests * pushFitHook deprecation * popFitHook deprecation * popFitHook dep message * getFitHooks and clearFitHooks deprecation * setWeight deprecation * news * news pt2 * addParameterSet deprecation * news * docstring typo * deprecate getEquation in fitcontribution.py * deprecate getEquation from builder.BaseBuilder * news * news typo * deprecate SimpleRecipe.loadParsedData * deprecate Profile.loadParsedData * deprecate Profile.setObservedProfile and SimpleRecipe.setObservedProfile * news * setCalculationRange * setCalculationPoints * change rebinArray to rebin_array * make _rebin_array private * missed deprecation tag in SimpleRecipe * setResidualEquation deprecation * getResidualEquation deprecation * news * news again * add test for remove and add param_set * removeParameterSet deprecation * scalarResidual deprecation * addVar deprecation * delVar deprecation * newVar deprecation * news * news 2 * isFree deprecation * getValues deprecation * fix typo in base name * getNames deprecation * getBounds deprecation * getBounds2 deprecation * add test for boundsToRestraints * boundsToRestraints deprecation * make bounds to restraints docstring better * news * news 2 * make new test cleaner * remove minus sign typo causing tests to fail * formatResults deprecation * printResults deprecation * add tests for printResults and formatResults * write test for saveResults * test for the addition of a header to results * saveResults deprecation * news * set fixtures to scope=function * add constraints and restraints for more strict testing * add initialization test and method * news * remove accidental commit * add test for ValueError * AUTHORS.rst * CODE-OF-CONDUCT.rst * cookiecutter.json * LICENSE.rst * LICENSE.rst pt2 * MANIFEST.in * pyproject.toml * README.rst * release_checklist.md * build-and-publish-docs-on-dispatch.yml * build-wheel-release-upload.yml * matrix-and-codecov.yml * README.rst pt2 * conf.py * index.rst * license.rst * diffpy.srfit.rst * __init__.py * __init__.py * __init__.py * srfit_app.py * version.py * news * [pre-commit.ci] auto fixes from pre-commit hooks * resultsDictionary deprecation, added to FitResults * news * test for resultsDictionary * improve test * add comments describing tests * rm merge-to-main duplicate workflow * add __init__ header to README * pull PR to list branch to fix docformatter failure * [pre-commit.ci] auto fixes from pre-commit hooks * fix conftest fixture so it creates new recipe object on each call * update fixture initial values to be more different * update expected to accound for the slight difference now * feat: initialize FitRecipe from a results file or object * test: tests for the new feature * add utils objects to get dict from results object or file * news * fix accident in test_fitresults * use get_results_dictionary method to get params_dict * initializeRecipe deprecation * add better docstrings to fitrecipe and fitresults * add 'The' to docstrings * do linspace with odd number of points * revert recipe fixture back, explicitly set scope to 'function', and add a new helper function that builds recipe for init testing * add assert recipes arent equal * add fixture that returns two identical recipes * add second recipe to fixture build_recipe_one_contribution * change fixture name to be plural (build_recipes_one_contribution) * rm deprecated six and other deprecated python2 objects * setValue deprecation * news * skip test_speed.py * ignore test_speed.py in codecov * iterPars deprecation * registerCalculator deprecation * registerFunction deprecation in EquationFactory and RecipeOrganizer * registerStringFunction deprecation * evaluateEquation deprecation * isConstrained deprecation * replace par with parameter * getConstrainedPars deprecation, and write a test for it :) * small fix * clearConstraints deprecation, and write small test * clean up and fix variable names in restrain and constrain methods * minor docstring typos * news * constrain and unconstrain deprecation * change name to register_restraint * restrain deprecation * unrestrain deprecation * clearRestraints deprecation * equationFromString deprecation * news * constrain_parameter --> add_constraint * unconstrain_parameter --> remove_constraint * add_restraint --> add_penalty * remove_restraint --> remove_penalty * register_restraint --> register_penalty * clear_all_restraints --> clear_all_penalties * change lb to lower_bound everywhere * change ub to upper_bound everywhere * add_penalty --> add_soft_bounds * remove_penalty --> remove_soft_bounds * register_penalty --> register_soft_bounds * clear_all_penalties --> clear_all_soft_bounds * add more to add_soft_bounds docstring * more to docstring * processMetaData --> _process_metadata * isConst --> is_constant * change Attributes --> Parameters in all docstrings * boundRange --> bound_range * boundWindow --> bound_window * write tests for bound_window and bound_range * news * minor docstring fix * deprecate PDFParser * build parse_file and deprecate getNumBank, selectBank, getFormat, getData, and getMetaData * add ProfileParser to __init__ so it can be imported from fitbase * add test files as conftest fixture * use ProfileParser in PDFContribution, replacing PDFParser * Use ProfileParser instead of PDFParser for fitrecipe testing * getData --> get_data, and getMetaData --> get_metadata in Profile * add set_parsed_profile test with ProfileParser * update examples with new parser * update test_pdf to reflect new parser * update old formatted test data to get parser to pass tests * add test for ProfileParser * update sas module and test to reflect new changes * news * rm comment * blank commit to fix pre-commit * run pre-commit autoupdate and run pre-commit * set python version to 3.13 to pin pre-commit CI * pin only docformatter to python3.13 * rm python3.13 pin on pre-commit-config for now * pip pre-commit docformatter to 3.13 * fix: fix iterpars behavior * [pre-commit.ci] auto fixes from pre-commit hooks * chore: rename par to parameter * chore: change docstring, refind test description and structure * [pre-commit.ci] auto fixes from pre-commit hooks * chore: change to if else statement in the logic * chore: refactor pytest fixtures and sync `pyproject.toml` and pre-commit file with main (#188) * sync pre-commit file and pyproject.toml with main * refactor pytest fixtures to remove use of triple quotes * chore: news * [pre-commit.ci] auto fixes from pre-commit hooks * fix docformatter and black conflicts * chore: news v2 * clean up ugly docstring formating * empty commit --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * chore: merge remaining `main` edits into `v3.3.0` (#189) * fix: fix Qmax update after load new parsed data * chore: add news item * chore: rename the private method * build: add diffpy.structure back to requirement * chore: rebuild the documentation with proper metadata handling * chore: update pre-commit (#184) * chore: update pre-commit * [pre-commit.ci] auto fixes from pre-commit hooks * chore: fix docformatter and black conflict * chore: run pre-commit for file I missed * [pre-commit.ci] auto fixes from pre-commit hooks * chore: add #FIXME workaround * chore: add #FIXME workaround * [pre-commit.ci] auto fixes from pre-commit hooks * chore: add another #FIXME workaround * chore: add another #FIXME workaround * [pre-commit.ci] auto fixes from pre-commit hooks * chore: moved import statement to the top of import modules * [pre-commit.ci] auto fixes from pre-commit hooks * chore: added try except workaround --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * release: add support for python 3.14 and remove for 3.11 (#187) * chore: news * chore: remove duplicate FIXME line * chore: fix improperly merged method in ProfileGenerator --------- Co-authored-by: stevenhua0320 <r.hua@mail.utoronto.ca> Co-authored-by: Simon Billinge <sbillinge@users.noreply.github.com> Co-authored-by: Daniel Sirakov <danielsirakov73@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * skpkg: update project to latest scikit-package template (#190) * skpkg: update project to latest scikit-package template * Reorganize update message in changelog Moved the update of the project template from 'Changed' to 'Fixed' section. --------- Co-authored-by: Simon Billinge <sbillinge@users.noreply.github.com> * change: Handle uncertainties as `None` rather than `1`s (#193) * fix: return None instead of 0 for unavailable dx/dy uncertainties * test: update and add tests for None uncertainty behavior * chore: add news entry for uncertainty None fix * test: add tests to ensure new handling of uncertainties doesn't break refinements * change: update profile.set_observed_profile() to not convert dy to ones if dy is None * chore: update news file * Update tests to make it easier to not use a testdata file for interpretability * add as_list as a fixture * add comment about how the fixture is used in test * add three_column case * use as_list as a fixture * Fix: Restore extensibility of `ProfileParser` and use `load_data` from `diffpy.utils` (#196) * Update examples to use the correct parser and add description of how to create your own parser in docs * update old metadata format to new xPDFsuite and pdfgetx headers. One testdata file for each * add test for new parser behavior * change how ProfileParsers work by allowing user to create their own parsers for metadata and the data itself * update the pre-existing news file with these changes * Make PDFParser identical to ProfileParser now that ProfileParser defaults to load_data * update old data metadata formats in testdata files to mirror xPDFsuite (neutron data) and pdfgetx (xray data) * updated expected metadata in test * fix docs description of ProfileParser * update news * minor docstring fix * tests for adding metadata upon parsing a file with ProfileParser * feat: allow user to append metadata when parsing a file with profileparser * doc: Update docstrings across `fitbase/` and `pdf/` to group standards (#198) * Update docstrings in fitbase to numpy/group standards * update docstrings in pdf to np/group standards * update docstrings in interface and structure to group standards * news * use recipe.plot_recipe() to plot fits in examples * remove plot_results in favor of recipe.plot_recipe() method * Change plot_recipe to display the contribution name as the title * add tests for the new plot_recipe behavior * rm accidentally commited output file * tidy a test up * empty commit for CI * dep: Deprecate characteristic functions containing camel case (#197) * Deprecate characteristic function camel case names * Change cf names in example scripts * add tests for characteristic functions * news * deprecate constrainAsSpaceGroup * update news * change: emit a warning if a characteristic function goes to a negative value during refinement. The output goes to zero * Add tests for new CF behavior for non-physical input parameters * cf news * empty commit for CI * change: update how the deprecated characteristic functions handle the signature changes (#199) * revert parameters in old function signatures to prevent errors when the name is specified in the signature * Change how the deprecated characteristic functions handle the signature change * Add test cases for the deprecated functions signature changes * news --------- Co-authored-by: Simon Billinge <sbillinge@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: stevenhua0320 <r.hua@mail.utoronto.ca> Co-authored-by: Daniel Sirakov <danielsirakov73@gmail.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
4 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Per the commits found on this PR, this is mostly edits that were made into
main(instead ofv3.3.0) by @danielsirakov and @stevenhua0320. I dealt with only a few minor merge conflicts (like docstring differences) otherwise everything seems to be working good.