Refactor switchable experiment, analysis, and display categories

[AndrewSazonov]

This PR it refactors the experiment, analysis, and project category architecture around explicit switchable categories, updates related calculator and CIF serialization behavior, and refreshes tutorials/docs to match the redesigned API.

Changes

• Updated the analysis workflow with a clearer fit category API, replacing the old fit_mode interface.
• Added new experiment calculation and project display settings for more explicit project configuration.
• Improved time-of-flight support, including TOF peak profile handling and CrysFML integration.
• Refreshed tutorials and user guide examples to match the redesigned API.
• Added a new BEER at ESS tutorial.
• Improved CIF output formatting for cleaner numeric values and uncertainties.
• Updated dependencies and expanded test coverage.

[codecov]

Codecov Report

❌ Patch coverage is 82.00000% with 90 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.30%. Comparing base (883c384) to head (59fc5b0).
⚠️ Report is 56 commits behind head on develop.

Files with missing lines	Patch %	Lines
...easydiffraction/analysis/categories/fit/default.py	71.26%	22 Missing and 3 partials ⚠️
...rc/easydiffraction/analysis/calculators/crysfml.py	55.81%	13 Missing and 6 partials ⚠️
...locks/experiment/categories/calculation/default.py	82.75%	6 Missing and 4 partials ⚠️
...n/datablocks/experiment/categories/peak/factory.py	76.31%	8 Missing and 1 partial ⚠️
src/easydiffraction/analysis/calculators/cryspy.py	20.00%	3 Missing and 5 partials ⚠️
...ydiffraction/project/categories/display/default.py	90.32%	3 Missing and 3 partials ⚠️
...easydiffraction/datablocks/experiment/item/base.py	92.18%	2 Missing and 3 partials ⚠️
src/easydiffraction/io/cif/serialize.py	86.48%	2 Missing and 3 partials ⚠️
...c/easydiffraction/analysis/categories/fit/enums.py	0.00%	1 Missing ⚠️
...asydiffraction/datablocks/experiment/item/enums.py	95.65%	0 Missing and 1 partial ⚠️
... and 1 more

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #157      +/-   ##
===========================================
+ Coverage    82.26%   88.30%   +6.04%     
===========================================
  Files           88      151      +63     
  Lines         5451     8698    +3247     
  Branches       454      891     +437     
===========================================
+ Hits          4484     7681    +3197     
+ Misses         802      722      -80     
- Partials       165      295     +130     

Flag	Coverage Δ
integration	74.91% <75.20%> (+4.96%)	⬆️
unittests	79.24% <75.20%> (+6.80%)	⬆️

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[Copilot]

Pull request overview

This PR refactors EasyDiffraction’s experiment/project/analysis architecture around explicit switchable categories (notably analysis.fit, experiment calculation, and project-level display), updates CIF serialization accordingly, and refreshes tests/tutorials to match the new API surface.

Changes:

• Replace the legacy analysis fit_mode / current_minimizer surface with a unified analysis.fit category (mode + minimizer + callable fit entry-point).
• Introduce explicit switchable categories for experiment calculation selection (experiment.calculation) and project display configuration (project.display), persisted via CIF.
• Update CIF numeric formatting (more readable values + uncertainty formatting) and refresh unit/integration tests + docs/tutorials to match.

Reviewed changes

Copilot reviewed 130 out of 132 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
tests/unit/easydiffraction/test___main__.py	Updates CLI fit test expectations for the new display API and removed summary call.
tests/unit/easydiffraction/summary/test_summary_details.py	Adapts summary tests to new analysis/experiment configuration locations.
tests/unit/easydiffraction/summary/test_summary.py	Updates minimizer access pattern to analysis.fit.minimizer_type.
tests/unit/easydiffraction/project/test_project_load.py	Verifies round-tripping of fit config and new display configuration.
tests/unit/easydiffraction/project/categories/display/test_factory.py	Adds unit tests for the new DisplayFactory.
tests/unit/easydiffraction/project/categories/display/test_default.py	Adds unit tests for default project Display category behavior and CIF restore.
tests/unit/easydiffraction/io/cif/test_serialize_more.py	Adjusts serialization expectations for new numeric formatting + fit CIF keys.
tests/unit/easydiffraction/io/cif/test_serialize.py	Adds/updates tests for parameter formatting, including uncertainty rendering.
tests/unit/easydiffraction/datablocks/structure/categories/test_atom_site_aniso.py	Updates aniso ADP sync/CIF expectations (omit iso atoms from aniso loop).
tests/unit/easydiffraction/datablocks/experiment/test_collection.py	Updates experiment dummy type to include scattering_type.
tests/unit/easydiffraction/datablocks/experiment/item/test_enums_coverage.py	Updates peak-profile enum coverage for canonical tags and TOF additions.
tests/unit/easydiffraction/datablocks/experiment/item/test_bragg_sc_coverage.py	Adjusts extinction “show” API naming and expectations.
tests/unit/easydiffraction/datablocks/experiment/item/test_base_coverage.py	Updates calculator/peak-profile “show” API calls and calculation access.
tests/unit/easydiffraction/datablocks/experiment/categories/peak/test_tof.py	Adds enum-description consistency assertions for TOF peak classes.
tests/unit/easydiffraction/datablocks/experiment/categories/peak/test_factory.py	Updates peak factory tests for canonical tags + context-local aliasing.
tests/unit/easydiffraction/datablocks/experiment/categories/instrument/test_tof.py	Updates expected default TOF quadratic correction value.
tests/unit/easydiffraction/datablocks/experiment/categories/calculation/test_factory.py	Adds unit tests for new experiment CalculationFactory.
tests/unit/easydiffraction/datablocks/experiment/categories/calculation/test_default.py	Adds unit tests for Calculation category delegation + CIF restore.
tests/unit/easydiffraction/datablocks/experiment/categories/background/test_base.py	Updates background CIF numeric formatting expectations.
tests/unit/easydiffraction/core/test_parameters.py	Updates expected CIF string rendering for uncertainty formatting.
tests/unit/easydiffraction/analysis/test_analysis_coverage.py	Updates coverage tests to use analysis.fit.minimizer_type.
tests/unit/easydiffraction/analysis/test_analysis.py	Updates analysis tests to new analysis.fit API and help output.
tests/unit/easydiffraction/analysis/categories/test_fit_mode.py	Removes tests for the deleted fit_mode category.
tests/unit/easydiffraction/analysis/categories/test_fit.py	Adds unit tests for the new fit category (mode + minimizer).
tests/unit/easydiffraction/analysis/calculators/test_cryspy.py	Adds a TOF pseudo-Voigt CIF-section test for Cryspy integration.
tests/integration/scipp-analysis/dream/test_package_import.py	Makes version-check integration test resilient to newer upstream releases.
tests/integration/fitting/test_switch-calculator.py	Updates calculator switching to the new experiment.calculation surface.
tests/integration/fitting/test_project_load.py	Updates fit-config round-trip assertions to analysis.fit.
tests/integration/fitting/test_powder-diffraction_time-of-flight.py	Updates minimizer configuration to analysis.fit.minimizer_type.
tests/integration/fitting/test_powder-diffraction_joint-fit.py	Updates joint-fit mode/minimizer configuration to analysis.fit.
tests/integration/fitting/test_powder-diffraction_constant-wavelength.py	Updates minimizer configuration to analysis.fit.minimizer_type.
tests/integration/fitting/test_plotting.py	Updates plotting entry point to project.display.plotter.
tests/integration/fitting/test_multi.py	Updates multi-workflow integration tests to new fit + calculation API.
tests/integration/fitting/test_exploration_help.py	Updates switchable-category “show” APIs and calculation access paths.
tests/integration/fitting/test_aniso_adp_fitting.py	Updates expectation: iso atoms omitted (not ?) from aniso CIF loop.
tests/integration/fitting/test_analysis_display.py	Updates minimizer “show” calls to analysis.fit.show_minimizer_types.
tests/integration/fitting/conftest.py	Updates fitted-project fixture to set minimizer via analysis.fit.
tests/functional/test_switchable_categories.py	Updates functional expectations for analysis.fit and calculation accessor.
tests/functional/test_adp_switching.py	Updates CIF expectation: mixed ADP excludes iso atoms from aniso loop.
src/easydiffraction/utils/utils.py	Updates the external data index ref + hash.
src/easydiffraction/summary/summary.py	Updates summary rendering to pull calculator/minimizer from new categories.
src/easydiffraction/project/project.py	Introduces project-level display category and persists it in project.cif.
src/easydiffraction/project/categories/display/factory.py	Adds factory for project display categories.
src/easydiffraction/project/categories/display/default.py	Implements default project display category with plotter/tabler selection + CIF IO.
src/easydiffraction/project/categories/display/init.py	Exposes Display and DisplayFactory for registration/import.
src/easydiffraction/project/categories/init.py	Adds project categories package marker.
src/easydiffraction/io/cif/serialize.py	Updates numeric formatting, adds project config CIF (incl. display), and refactors analysis CIF to _fit.*.
src/easydiffraction/datablocks/structure/item/base.py	Changes aniso sync to include only anisotropic atoms and remove iso entries.
src/easydiffraction/datablocks/structure/categories/atom_sites/default.py	Triggers aniso sync when switching ADP type from anisotropic to isotropic.
src/easydiffraction/datablocks/structure/categories/atom_site_aniso/default.py	Removes legacy “question-mark rows for iso atoms” CIF behavior.
src/easydiffraction/datablocks/experiment/item/factory.py	Normalizes switchable type descriptors after CIF loading.
src/easydiffraction/datablocks/experiment/item/enums.py	Renames peak-profile enum tags to canonical, mode-specific values and adds TOF pV.
src/easydiffraction/datablocks/experiment/item/bragg_pd.py	Updates background support filtering and show method to use calculation category and new table rendering.
src/easydiffraction/datablocks/experiment/item/base.py	Introduces experiment calculation category, CIF restore, and updated show APIs.
src/easydiffraction/datablocks/experiment/categories/peak/total.py	Aligns total-scattering peak metadata with canonical peak-profile enum tags.
src/easydiffraction/datablocks/experiment/categories/peak/tof.py	Adds TOF pseudo-Voigt profile and aligns TOF peak tags/descriptions with enums.
src/easydiffraction/datablocks/experiment/categories/peak/factory.py	Adds context-local aliasing and enhanced supported-type printing.
src/easydiffraction/datablocks/experiment/categories/peak/cwl_mixins.py	Adjusts FCJ asymmetry defaults.
src/easydiffraction/datablocks/experiment/categories/peak/cwl.py	Aligns CWL peak tags/descriptions with canonical peak-profile enum values.
src/easydiffraction/datablocks/experiment/categories/peak/init.py	Exports the new TOF pseudo-Voigt peak class.
src/easydiffraction/datablocks/experiment/categories/instrument/tof.py	Changes default TOF quadratic correction to 0.0.
src/easydiffraction/datablocks/experiment/categories/data/total_pd.py	Updates calculator access to experiment.calculation.calculator.
src/easydiffraction/datablocks/experiment/categories/data/bragg_sc.py	Updates calculator access to experiment.calculation.calculator.
src/easydiffraction/datablocks/experiment/categories/data/bragg_pd.py	Updates calculator access to experiment.calculation.calculator.
src/easydiffraction/datablocks/experiment/categories/calculation/factory.py	Adds factory for experiment calculation categories.
src/easydiffraction/datablocks/experiment/categories/calculation/default.py	Implements calculation category (calculator type + delegation to parent).
src/easydiffraction/datablocks/experiment/categories/calculation/init.py	Exposes Calculation and CalculationFactory.
src/easydiffraction/analysis/sequential.py	Updates sequential fitting template to read minimizer/calculator from new categories.
src/easydiffraction/analysis/categories/fit_mode/fit_mode.py	Removes legacy fit-mode category implementation.
src/easydiffraction/analysis/categories/fit_mode/init.py	Removes legacy fit-mode exports.
src/easydiffraction/analysis/categories/fit/factory.py	Renames/replaces fit-mode factory with FitFactory.
src/easydiffraction/analysis/categories/fit/enums.py	Updates fit-mode enum behavior (returns empty string for unknown).
src/easydiffraction/analysis/categories/fit/default.py	Adds Fit category: minimizer + mode + show helpers + callable run entry-point + CIF restore hook.
src/easydiffraction/analysis/categories/fit/init.py	Exposes new fit category components.
src/easydiffraction/analysis/calculators/cryspy.py	Updates TOF peak CIF rendering and peak-update logic; removes prior cryspy DWF monkey-patch.
src/easydiffraction/analysis/calculators/crysfml.py	Adds TOF calculation path, refactors experiment dict construction and mappings.
src/easydiffraction/analysis/analysis.py	Rewires analysis to use fit category and makes fit execution internal (_run_fit).
src/easydiffraction/main.py	Updates CLI to use project.display.plotter and comments out summary output.
pyproject.toml	Adds pytest-benchmark to dev dependencies.
docs/mkdocs.yml	Reorganizes tutorial navigation and adds BEER tutorial entry.
docs/docs/user-guide/first-steps.md	Updates examples to new calculation/display/minimizer APIs.
docs/docs/user-guide/analysis-workflow/project.md	Updates project/experiment/analysis CIF examples for new _display + _fit + _calculation keys.
docs/docs/user-guide/analysis-workflow/analysis.md	Updates analysis workflow docs for analysis.fit, calculation category, and display usage.
docs/docs/tutorials/index.md	Reorganizes tutorial index and adds a Simulated Data section.
docs/docs/tutorials/index.json	Adds tutorial metadata for new BEER tutorial.
docs/docs/tutorials/ed-9.py	Updates tutorial to use project.display.plotter and new show methods.
docs/docs/tutorials/ed-9.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-8.py	Updates tutorial to new show methods and analysis.fit API and display plotting.
docs/docs/tutorials/ed-8.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-7.py	Updates tutorial plotting/show methods to new display API.
docs/docs/tutorials/ed-7.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-6.py	Updates tutorial plotting/show methods to new display API.
docs/docs/tutorials/ed-6.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-5.py	Updates tutorial plotting/show methods to new display API.
docs/docs/tutorials/ed-5.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-4.py	Updates tutorial to analysis.fit API and display plotting.
docs/docs/tutorials/ed-4.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-3.py	Updates tutorial to new show methods, analysis.fit, and display plotting.
docs/docs/tutorials/ed-20.py	Adds new BEER-at-ESS tutorial (simulated TOF data workflow).
docs/docs/tutorials/ed-2.py	Updates tutorial to new minimizer/show/plotting APIs.
docs/docs/tutorials/ed-2.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-18.py	Updates plotting API usage to project.display.plotter.
docs/docs/tutorials/ed-18.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-17.py	Updates tutorial minimizer and plotting APIs to analysis.fit/display.
docs/docs/tutorials/ed-17.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-16.py	Updates tutorial to analysis.fit and display plotting API.
docs/docs/tutorials/ed-16.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-15.py	Updates tutorial to analysis.fit and display plotting API.
docs/docs/tutorials/ed-15.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-14.py	Updates tutorial to analysis.fit and display plotting API.
docs/docs/tutorials/ed-14.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-12.py	Updates tutorial plotting/show methods to new display API.
docs/docs/tutorials/ed-12.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-11.py	Updates tutorial plotting configuration to project.display.plotter.
docs/docs/tutorials/ed-11.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-10.py	Updates tutorial plotting to project.display.plotter.
docs/docs/tutorials/ed-10.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/docs/tutorials/ed-1.py	Updates tutorial plotting to project.display.plotter.
docs/docs/tutorials/ed-1.ipynb	Regenerated notebook reflecting updated tutorial API usage.
docs/architecture/package-structure-short.md	Updates documented package structure to include new categories.
docs/architecture/package-structure-full.md	Updates detailed package structure listing for new categories/classes.
docs/architecture/issues_open.md	Updates open-issues text to refer to new APIs and removes resolved calculator persistence item.
docs/architecture/issues_closed.md	Updates closed-issues log with calculator persistence + other historical notes.