Rewrite - #44

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beykyle wants to merge 76 commits into

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Commits on Sep 10, 2026

Clear the tree for the 1.0 rewrite
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7fe34bb
Move the harvested modules into the 1.0 layout
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1e94204
Bootstrap the 1.0 rewrite branch
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11208e5
Add Parameter: an identity-hashed declaration with optional marginal prior
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09e4973
Rewrite transforms to the 1.0 skeleton
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3d41641
Trim units to the registry, the constants and the angle-grid check
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8e3f4b6
Rewrite likelihood to the 1.0 skeleton
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53a5aad
Rewrite terms as stateless declarations with the factory helpers
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8c66754
Export terms from the package
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c5835e7
Drop pint: a fixed unit-label table replaces the registry
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5e31869
Add Dataset: pure data with reported systematics as inert metadata
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e8a1dd0
Add Model and Predictor with |, + and * composition
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72d0ff6
Add Comparison and Constraint: comparison space, masks, reported terms
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667e3c4
Export Comparison and Constraint from the package
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6bf6be6
Define the alpha+Ca error-model labels once, with a legend
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0bf5fb9
Add the structured (Woodbury) covariance
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086eb65
Export covariance from the package
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c7004bc
Define the error-model ladder in the recipes, not the tests
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6c11404
Add Problem: the compile step and the flat sampler interface
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99c39c9
Start the recipe acceptance suite: recipes 1-13
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86963b8
Recipes 16-24, joint-block hyperparameters, and an earlier singular check
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b5622d3
Recipes 25-38: the driver-loop and hierarchy recipes
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d47feb2
Recipe 27: pin the exact closed form of the data-built bias
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950ca9a

Commits on Sep 11, 2026

Rewrite the reaction models as Model subclasses that override bind
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5b68139
Add from_measurement: EXFOR measurements to datasets in internal units
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54b0aaa
Add recipe tests 3, 14, 15 and 37 for the reaction layer
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60dab9b
Give terms the block boundaries of a spanning support
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a58ddfa
Return a KernelTerm from kernel() so predictions can find the kernel
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3fd29de
Rewrite diagnostics on (problem, samples) with a conditional held-out score
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079f8c1
Rewrite the total predictive band to read everything from the problem
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7b7253a
Add recipe tests 7, 17, 18, 28, 30 and 31 for the analysis layer
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3ab41b0
Guard the recipe index: one test file per heading, and the legend too
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97e07eb
Wire the notebooks: gallery, index test, converged workflow; recipe 37 rewritten
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1fa734b
Add the linear_calibration notebook (recipes 1, 17)
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9a699cb
Add the error_models notebook (recipes 2, 4, 5, 19)
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29003a3
Add the normalization_and_covariance_structure notebook (recipes 3, 6, 27)
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b1efa73
Export the likelihood functionals from the package
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4651913
Add the correlated_observations and robust_likelihoods notebooks
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c83a497
Add the measurement_to_calibration notebook (recipes 12, 14, 15, 16, 21, 26)
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789f72e
Add the gp_discrepancy notebook (recipes 7, 8, 36)
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9a38cda
Silence the sparse-contour warning in the tempering figure
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75a2855
Add the hierarchical_calibration notebook (recipes 22, 24, 30, 35, 38)
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e1ca3fe
Add the alpha_ca_error_model_comparison notebook (recipes 10, 11, 13, 18)
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2841d68
Port the 0.x regression pins to the 1.0 spelling
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c582470
Write design.md from the plan of record and add the API reference
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9def154
Rewrite the README as the front door of 1.0
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6a374fd
Merge branch 'main' into rewrite
beykyle
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e561c3c
update readme
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5cc80f2
clean up examples
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39b7165
Fix the silent wrong answers found in the PR #44 review
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bb1f011
Word the install notes for 1.0 on main and guard the PyPI workflow
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b5ee8b6
Score the alpha-Ca held-out angles conditionally on the fit
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9c6e7b5
Fix the rest of the PR #44 review backlog
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0e7ddca

Commits on Sep 12, 2026

Restructure the examples: delete, rename, recipe 39, shared plot style
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c5634e9
Restyle linear_calibration for the notebook review
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7281e41
Split error_models and restyle both halves
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c385a68
Split robust_likelihoods and add the outlier-rejection loop
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1a3c233
Rework normalization_and_covariance_structure around five experiments
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7566187
Rework gp_discrepancy around mean-zero discrepancies
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fc147d7
Restyle alpha_ca and add predictive draws with coverage
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5f7bd96
Rebuild the optical-model notebook around a real measurement
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960bd7a
Format the LaTeX-escape guard with black
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5bf4969
Rework hierarchical_calibration: BDA3, smaller bumps, new plots
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39b34c1

Commits on Sep 14, 2026

Commits on Sep 22, 2026

Merge noise_fraction and model_error into proportional_error
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dab2052
Accept a plain dict in from_measurement
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34d5e26
Let a scalar reported normalisation travel to a new grid
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5ed280d
Tighten the linear_calibration prose and re-run it
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a955c87
Open error_models with where the Gaussian likelihood comes from
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b0819e7
Sample sharing_error_models with dynesty, one panel per error model
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f27876e
Add the tempering section to robust_likelihoods (recipe 12)
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cd5b4b2
Rebuild the two reaction notebooks on the jitr error model
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63a4416
Drop nbconvert's execution-timing metadata from two notebooks
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10637e2
Re-run error_models in order
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c2f1026
Finish the rewrite of normalization_and_covariance_structure
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cbcaae8