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Improve analysis reliability and expand refinement workflows - #218

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AndrewSazonov merged 34 commits into
developfrom
fullprof-occupancy-notation
Aug 17, 2026
Merged

Improve analysis reliability and expand refinement workflows#218
AndrewSazonov merged 34 commits into
developfrom
fullprof-occupancy-notation

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@AndrewSazonov

@AndrewSazonov AndrewSazonov commented Jul 2, 2026

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  • Adds LaM7O3 P02.1 synchrotron X-ray and LMO ECHIDNA neutron refinement tutorials with automatic backgrounds, constraints, absorption, site mixing, and oxygen-position refinement.
  • Adds a Bayesian exercise notebook using BUMPS DREAM to explore correlations, credible intervals, and posterior predictions.
  • Calculates CrysFML constant-wavelength patterns at exact measurement coordinates, improving irregular-grid and position-correction handling.
  • Enables Chebyshev backgrounds for CrysFML and verifies its FCJ asymmetry against FullProf.
  • Makes automatic line-segment background estimation honor excluded regions and pending exclusion changes.
  • Fixes interactive Plotly rendering in Google Colab with version-matched assets and visible retry errors.
  • Corrects FullProf occupancy and scale references, enabling direct intensity comparisons without artificial scale fitting in matching examples.
  • Renames TOF size/strain parameters and CIF tags by removing redundant _g and _l suffixes.
  • Shows a clear error and lowercase suggestion when structure or experiment datablock names contain uppercase letters, preventing later calculation failures.

@AndrewSazonov AndrewSazonov added the [scope] bug Bug report or fix (major.minor.PATCH) label Jul 2, 2026
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.34%. Comparing base (883c384) to head (bd5204e).
⚠️ Report is 127 commits behind head on develop.

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@@             Coverage Diff             @@
##           develop     #218      +/-   ##
===========================================
+ Coverage    82.26%   90.34%   +8.08%     
===========================================
  Files           88      284     +196     
  Lines         5451    24783   +19332     
  Branches       454     2912    +2458     
===========================================
+ Hits          4484    22390   +17906     
- Misses         802     1761     +959     
- Partials       165      632     +467     
Flag Coverage Δ
integration ?
unittests 90.34% <ø> (+17.89%) ⬆️

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 69.19% <ø> (+21.05%) ⬆️
src/easydiffraction/analysis/calculators/cryspy.py 55.04% <ø> (-34.30%) ⬇️
...tion/analysis/categories/sequential_fit/default.py 100.00% <ø> (ø)
src/easydiffraction/analysis/minimizers/bumps.py 85.50% <ø> (ø)
src/easydiffraction/core/category.py 95.12% <ø> (-4.88%) ⬇️
src/easydiffraction/core/datablock.py 82.14% <ø> (-3.80%) ⬇️
src/easydiffraction/core/guard.py 87.50% <ø> (+4.40%) ⬆️
src/easydiffraction/core/validation.py 94.16% <ø> (+4.60%) ⬆️
src/easydiffraction/core/variable.py 92.90% <ø> (ø)
...ocks/experiment/categories/background/chebyshev.py 81.94% <ø> (ø)
... and 19 more

... and 300 files with indirect coverage changes

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@AndrewSazonov AndrewSazonov changed the title Improve FullProf verification intensity agreement Improve analysis reliability and expand refinement workflows Aug 17, 2026
@AndrewSazonov AndrewSazonov added [scope] enhancement Adds/improves features (major.MINOR.patch) and removed [scope] bug Bug report or fix (major.minor.PATCH) labels Aug 17, 2026
@AndrewSazonov
AndrewSazonov merged commit a46feb9 into develop Aug 17, 2026
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