Add sample-displacement/transparency corrections and standardize the FullProf verification suite by AndrewSazonov · Pull Request #197 · easyscience/diffraction-lib

AndrewSazonov · 2026-06-09T17:14:00Z

No description provided.

Mirrors fit() as the non-fitting trigger that refreshes structures and experiments so experiment.data.intensity_calc reflects current params. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Loaders take (project_dir, file) and hide bundled_reference_dir; add load_fullprof_calc_profile for .prf Icalc minus real .bac background, handling both .bac layouts (two-column and header+flat-array). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Proposes a dirty-flag + compute-once-per-change lazy recompute of the calculated pattern so explicit calculate() becomes optional. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Zero all refinement codes (and remove VARY/BKG auto-refine keywords) so fp2k recomputes at fixed values; regenerate .prf/.bac/.sub references. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Per-engine sections with constants read from the frozen .pcr, Load reference after Define-structure, explicit project.analysis.calculate(), engine-specific profiles (SyCos/SySin, TCH-FCJ) in their own sections. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Constants from frozen .pcr, per-engine sections, fit both engines for the TOF scale convention with after-fit agreement. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

codecov · 2026-06-09T17:16:23Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.37%. Comparing base (2a6c0e1) to head (938e1df).
⚠️ Report is 1 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #197      +/-   ##
===========================================
- Coverage    90.66%   90.37%   -0.30%     
===========================================
  Files          265      265              
  Lines        22494    22625     +131     
  Branches      2612     2635      +23     
===========================================
+ Hits         20394    20447      +53     
- Misses        1577     1647      +70     
- Partials       523      531       +8

Flag	Coverage Δ
unittests	`90.37% <ø> (-0.30%)`	⬇️

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

Files with missing lines	Coverage Δ
src/easydiffraction/analysis/analysis.py	`93.18% <ø> (-0.27%)`	⬇️
...rc/easydiffraction/analysis/calculators/crysfml.py	`40.40% <ø> (+0.82%)`	⬆️
src/easydiffraction/analysis/calculators/cryspy.py	`33.91% <ø> (+3.66%)`	⬆️
src/easydiffraction/analysis/verification.py	`61.64% <ø> (-28.07%)`	⬇️
...datablocks/experiment/categories/instrument/cwl.py	`100.00% <ø> (ø)`
src/easydiffraction/display/plotters/plotly.py	`94.04% <ø> (+<0.01%)`	⬆️

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❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

AndrewSazonov and others added 30 commits June 8, 2026 18:57

Add cwl-sample-displacement-transparency implementation plan

35849c2

Add CWL sample displacement and transparency parameters

4870140

Emit SyCos/SySin offsets in cryspy CWL instrument CIF

ee0b833

Update cryspy dict with SyCos/SySin offsets

0679b4f

Note crysfml lacks SyCos/SySin instrument corrections

4466338

Enable SyCos/SySin corrections in LaB6 verification page

a66bd3f

Reach Phase 1 review gate

6dac9a1

Strip isotope number from atom symbol for crysfml

996efc6

Refine SyCos/SySin and use 11B in LaB6 verification page

0d39492

Restructure LaB6 page: compare engines, then refine cryspy

22c6ea0

Drop Zero offset from LaB6 page to match other pages

8570ce6

Add public Analysis.calculate() method

570a8e4

Mirrors fit() as the non-fitting trigger that refreshes structures and experiments so experiment.data.intensity_calc reflects current params. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Add lazy pattern recalculation ADR suggestion

55d70d0

Proposes a dirty-flag + compute-once-per-change lazy recompute of the calculated pattern so explicit calculate() becomes optional. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Freeze FullProf .pcr files and regenerate bundled references

7c7a4a8

Zero all refinement codes (and remove VARY/BKG auto-refine keywords) so fp2k recomputes at fixed values; regenerate .prf/.bac/.sub references. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Record sample-absorption modelling gap in open issues

cd7c3aa

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Rework TOF Si verification notebooks to canonical structure

a1b21e2

Constants from frozen .pcr, per-engine sections, fit both engines for the TOF scale convention with after-fit agreement. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Replace NCAF reference with single-pattern FullProf data

125127c

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Rework remaining verification notebooks to canonical structure

fb1e5ae

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Show fit results and drop redundant calls in verification pages

6a5c95e

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Apply formatting and lint fixes to analysis modules

0bc5419

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Register verification pages in nav and refine skip list

9325cbb

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Reflow SyCos correction comment to line-length limit

132e85e

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Refactor FullProf loaders to satisfy complexity and lint

bdbf73d

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Apply pixi run fix auto-fixes

1d745a0

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Update verification loader tests to project-dir API

9f3d3e3

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Test CWL sample displacement/transparency parameters

eaa2ed4

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Test cryspy SyCos/SySin CIF and dict mapping

d6c6156

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Skip NCAF verification page (tabulated IRF mismatch)

76e68dd

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

AndrewSazonov and others added 3 commits June 9, 2026 18:39

Remove implemented cwl-sample-displacement-transparency plan

54a5934

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Remove implemented test-suite-and-validation plan

a04eb97

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Comment out cryspy develop branch

ed3d498

AndrewSazonov added the [scope] maintenance Code/tooling cleanup, no feature or bugfix (major.minor.PATCH) label Jun 9, 2026

Add Jorgensen Si verification page to docs nav

fc2e423

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

AndrewSazonov and others added 7 commits June 9, 2026 19:32

Update verification index for canonical pages

c8523c8

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Re-theme metrics box background on dark-theme switch

11dd697

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Generalize refinement wording in verification index

2813ae2

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Split nightly tests into per-tier steps with output checks

a209ef3

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Align pypi-test concurrency group with nightly

fb370e8

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Drop dead env vars and report all tiers in pypi-test

1158516

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Rename nightly.yml to nightly-test.yml

938e1df

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

AndrewSazonov merged commit 6711fba into develop Jun 9, 2026
15 of 16 checks passed

AndrewSazonov deleted the cwl-sample-displacement-transparency branch June 9, 2026 18:14

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Add sample-displacement/transparency corrections and standardize the FullProf verification suite#197

Add sample-displacement/transparency corrections and standardize the FullProf verification suite#197
AndrewSazonov merged 41 commits into
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cwl-sample-displacement-transparency

AndrewSazonov commented Jun 9, 2026

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AndrewSazonov commented Jun 9, 2026

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codecov Bot commented Jun 9, 2026 •

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