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Add SPODI refinement tutorial and improve fitting controls - #227

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AndrewSazonov merged 16 commits into
developfrom
more-minor-fixes
Sep 22, 2026
Merged

AndrewSazonov merged 16 commits into
developfrom
more-minor-fixes

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@AndrewSazonov

@AndrewSazonov AndrewSazonov commented Sep 22, 2026

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  • Adds a staged YAlO₃/Al₂O₃ refinement tutorial using SPODI data, with automatic background estimation, model-based background refinement, and a generated notebook.
  • Introduces readable, method-specific convergence tolerances with dynamic settings, backend mappings, documentation, and tests. Applicable tutorials use chi_square_change_tolerance = 1e-2 to reduce documentation build time.
  • Warns about unsupported ionic atom symbols, applies documented scattering-factor fallbacks, and keeps notebook warnings on one line.
  • Records free-parameter counts in tutorial baselines.

@AndrewSazonov AndrewSazonov added the [scope] enhancement Adds/improves features (major.MINOR.patch) label Sep 22, 2026
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Codecov Report

❌ Patch coverage is 93.77778% with 14 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.42%. Comparing base (5e3ea2a) to head (297f6e1).

Files with missing lines Patch % Lines
...ablocks/structure/categories/atom_sites/default.py 81.25% 4 Missing and 2 partials ⚠️
src/easydiffraction/analysis/minimizers/bumps.py 66.66% 1 Missing and 3 partials ⚠️
src/easydiffraction/analysis/calculators/cryspy.py 94.59% 1 Missing and 1 partial ⚠️
...fraction/analysis/categories/minimizer/lsq_base.py 97.14% 2 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #227      +/-   ##
===========================================
+ Coverage    90.39%   90.42%   +0.02%     
===========================================
  Files          284      284              
  Lines        24789    24992     +203     
  Branches      2909     2926      +17     
===========================================
+ Hits         22409    22600     +191     
- Misses        1754     1761       +7     
- Partials       626      631       +5     
Flag Coverage Δ
unittests 90.42% <93.77%> (+0.02%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines Coverage Δ
...rc/easydiffraction/analysis/calculators/crysfml.py 70.85% <100.00%> (+1.10%) ⬆️
...diffraction/analysis/categories/minimizer/bumps.py 100.00% <100.00%> (ø)
...tion/analysis/categories/minimizer/bumps_amoeba.py 100.00% <100.00%> (ø)
...fraction/analysis/categories/minimizer/bumps_de.py 100.00% <100.00%> (ø)
...fraction/analysis/categories/minimizer/bumps_lm.py 100.00% <100.00%> (ø)
...diffraction/analysis/categories/minimizer/dfols.py 100.00% <100.00%> (ø)
...diffraction/analysis/categories/minimizer/lmfit.py 100.00% <100.00%> (ø)
...alysis/categories/minimizer/lmfit_least_squares.py 100.00% <100.00%> (ø)
...ion/analysis/categories/minimizer/lmfit_leastsq.py 100.00% <100.00%> (ø)
...asydiffraction/analysis/minimizers/bumps_amoeba.py 100.00% <100.00%> (ø)
... and 12 more

... and 1 file with indirect coverage changes

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@AndrewSazonov AndrewSazonov changed the title Add SPODI YAP refinement tutorial and configurable minimizer tolerances Add SPODI refinement tutorial and improve fitting controls Sep 22, 2026
@AndrewSazonov
AndrewSazonov merged commit 7e415c8 into develop Sep 22, 2026
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