Refactor switchable experiment, analysis, and display categories by AndrewSazonov · Pull Request #157 · easyscience/diffraction-lib

AndrewSazonov · 2026-04-27T11:30:22Z

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 · 2026-04-27T11:32:08Z

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.

AndrewSazonov added 30 commits April 25, 2026 14:02

Add pycrysfml tests

cbd5e93

Change default FCJ asymmetry values

62fa5a2

Add pytest-benchmark dependency

8e6eb0e

Add simple non-convoluted pseudo-Voigt TOF profile

c676646

Fix and extend crysfml wrapper with TOF

9c379a1

Remove cryspy monkey patch for DWF aniso

7b1dd6f

Add tests

4bfd073

Add BEER tutorial

9d2eb7a

Update data index hash

a8cdde9

Fix formatting

53370e0

Refactor crysfml

9b283ff

Fix formatting

67138a2

Update package structure

b3c1bdc

Make profile names more clear

2bc95f5

Add canonical peak profile tags with local aliases

3974045

Update BEER tutorial

e17c468

Update unit tests

e26523c

Update BEER tutorial

1ed833c

Only keep anisotropic atoms in atom_site_aniso collection

b4b2771

Unify selector naming and add concise show type APIs

c48cd33

Update tests and docs for unified selector type APIs

74a2d66

Round CIF uncertainties to 2 significant digits

4d9b35f

Strip trailing zeros from CIF float output

27b783d

Update tutorials

ba351f9

Rename analysis CIF keys to match API names

8c7d5a5

Add refactor plan

d38a023

Replace fit_mode with fit category

08585ab

Add experiment calculation category

004b19e

Add project display category

5d99ebd

Redesign fit, calculation, and display categories

b768b9c

AndrewSazonov added 16 commits April 26, 2026 23:29

Update integration test command to disable benchmarking

c608dad

Move pycrysfml tests out of edl

20c081a

Remove temporary tutorials

5cfb906

Migrate ed-8/ed-17 tutorials to fit category API

586e753

Update user guide to fit category selector API

c46ea18

Fold selector-family taxonomy into architecture

03b5349

Fold selector-family taxonomy into architecture

1b92679

Remove leftover fit_mode package directory

6399859

Remove merged fit/selector refactor plan

4e23e92

Remove benchmark-disable flag

4f926f8

Update tutorials

b185f93

Set d_to_tof_quad to zero

489d139

Update tutorial

3e94df3

Bump dependencies

7ef164f

Fix tests

74bcc58

Add new tutorial: BEER at ESS

59fc5b0

AndrewSazonov requested a review from Copilot April 27, 2026 11:30

AndrewSazonov self-assigned this Apr 27, 2026

AndrewSazonov added the [scope] enhancement Adds/improves features (major.MINOR.patch) label Apr 27, 2026

Copilot started reviewing on behalf of AndrewSazonov April 27, 2026 11:30 View session

Copilot AI reviewed Apr 27, 2026

View reviewed changes

Minor fixes [ci skip]

4b447d9

AndrewSazonov merged commit 6bf3deb into develop Apr 27, 2026
2 checks passed

AndrewSazonov deleted the redesign branch April 27, 2026 11:54

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Refactor switchable experiment, analysis, and display categories#157

Refactor switchable experiment, analysis, and display categories#157
AndrewSazonov merged 47 commits intodevelopfrom
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AndrewSazonov commented Apr 27, 2026

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codecov Bot commented Apr 27, 2026 •

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