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Restructure PIPT and POPT around explicit schemes, analyses and optimizers - #166

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rolfjl merged 341 commits into

Python-Ensemble-Toolbox:mainfrom

MathiasMNilsen:pr/restructure-pipt-popt

Sep 21, 2026

Merged

Restructure PIPT and POPT around explicit schemes, analyses and optimizers#166
rolfjl merged 341 commits into
Python-Ensemble-Toolbox:mainfrom
MathiasMNilsen:pr/restructure-pipt-popt

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Commits on Jan 14, 2026
- Comment out log.info
  MathiasMNilsen
  committed
  f88fe0e
- Reorganize code with ensemble-matrix
  MathiasMNilsen
  committed
  c8ae932
- Fix small bug
  MathiasMNilsen
  committed
  c6ed492
Commits on Jan 15, 2026
- Fix bug relating to data_mismatch for multilevel
  MathiasMNilsen
  committed
  fc4668c
- Remove unused imports for multilevel
  MathiasMNilsen
  committed
  3cc09aa
- Add progbar_settings to multilevel
  MathiasMNilsen
  committed
  5f935aa
- Update popt/update_schemes/linesearch.py
  
  KriFos1
  and
  Copilot
  authored
  2950568
- Update pipt/update_schemes/update_methods_ns/hybrid_update.py
  
  KriFos1
  and
  Copilot
  authored
  542c51e
- Update pipt/misc_tools/extract_tools.py
  
  KriFos1
  and
  Copilot
  authored
  559c9ba
- Update pipt/loop/ensemble.py
  
  KriFos1
  and
  Copilot
  authored
  af200ca
- Update optimize.py
  rolfjl
  authored
  16ed42e
- Fix bugs
  MathiasMNilsen
  committed
  f8f1a74
- Merge branch 'main' of github.com:MathiasMNilsen/PET
  MathiasMNilsen
  committed
  e3cc78e
Commits on Jan 16, 2026
- Fix bugs
  MathiasMNilsen
  committed
  b52f83f
- Update linesearch.py
  MathiasMNilsen
  authored
  602bb6b
- Update ensemble_tools.py
  MathiasMNilsen
  authored
  fc8bd60
- Merge branch 'Python-Ensemble-Toolbox:main' into main
  MathiasMNilsen
  authored
  10ac754
Commits on Jan 21, 2026
- update TrustRegion
  MathiasMNilsen
  committed
  b227367
- Fix serious bug regarding scaling of enX for popt
  MathiasMNilsen
  committed
  32dfeab
- Merge branch 'main' of github.com:MathiasMNilsen/PET
  MathiasMNilsen
  committed
  1890720
Commits on Jan 22, 2026
- Remove one-liner
  MathiasMNilsen
  committed
  6673b4e
- Improve some logic for ensemble gradient
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  committed
  43eee87
Commits on Feb 3, 2026
- Include adjoints from simulator
  MathiasMNilsen
  committed
  bfc4ee1
- fix bug
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  committed
  903f262
Commits on Feb 4, 2026
- Fix iter bug for line-search
  MathiasMNilsen
  committed
  2d9b20d
- Maake line-search logger fancier
  MathiasMNilsen
  committed
  ea5b356
- Make line-search logger fancier
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  committed
  bc77354
Commits on Feb 10, 2026
- Update TrustRegion and Logger
  MathiasMNilsen
  committed
  6e2ee74
Commits on Feb 11, 2026
- Include adjoints for LM-EnRML
  MathiasMNilsen
  committed
  602846a
- Small fix
  MathiasMNilsen
  committed
  4da0778
- Merge branch 'main' into main
  rolfjl
  authored
  e0dee27
- Merge branch 'Python-Ensemble-Toolbox:main' into main
  MathiasMNilsen
  authored
  c9f3d74
Commits on Mar 3, 2026
- Update truncSVD
  MathiasMNilsen
  committed
  dd4cf6c
- Change order of log_update
  MathiasMNilsen
  committed
  6286664
Commits on Mar 4, 2026
- Fix ensemble size handling and staticvar import logic
  MathiasMNilsen
  committed
  fd9f528
- Fix bug
  MathiasMNilsen
  committed
  c915ef1
Commits on Mar 5, 2026
- Merge branch 'Python-Ensemble-Toolbox:main' into main
  MathiasMNilsen
  authored
  594f6f9
Commits on Mar 12, 2026
- Update adjoint handling
  MathiasMNilsen
  committed
  c941c2a
Commits on Mar 16, 2026
- Fix logic for logging in LM-EnRML
  MathiasMNilsen
  committed
  9fbdfdd
- Include ensemble_mistfit for LM-EnRML
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  committed
  af8e3c1
Commits on Mar 17, 2026
- Include enAdj for ESMDA
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  3e29201
- Fix logger table column centering
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  2c84fff
Commits on Mar 18, 2026
- Merge branch 'Python-Ensemble-Toolbox:main' into main
  MathiasMNilsen
  authored
  2866655
Commits on Mar 19, 2026
- Add PETDataFrame and PETStateArray data structures
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  committed
  d80dc61
- Use PETDataFrame for adjoint ensemble
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  38454fc
Commits on Mar 23, 2026
- Add sampling function to PETStateArray
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Commits on Mar 24, 2026
- Add tests for PET structures
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  committed
  b70d7ff
Commits on Mar 25, 2026
- Add CSV reader to PETDataFrame
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  f2dcb13
Commits on Mar 27, 2026
- Start to use PETDataFrame for data and predictions
  MathiasMNilsen
  committed
  ceae3aa
Commits on Apr 7, 2026
- Normalize yes/no key flags to boolean checks
  MathiasMNilsen
  committed
  5326dab
- Refactor PET matrix/data handling and update structure tests
  MathiasMNilsen
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  0ee2f28
Commits on Apr 8, 2026
- Preserve ensemble metadata in matrix-based update flow
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  committed
  fb2ae07
Commits on Apr 9, 2026
- Add DataReader class and some refactoring
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  0d67993
Commits on Apr 10, 2026
- Include some tests for DataReader
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  committed
  1cebb7b
Commits on Apr 13, 2026
- Fix popt and add tests
  MathiasMNilsen
  committed
  3d36d1b
- Merge branch 'main' into feature/pet_structures
  MathiasMNilsen
  committed
  c65105d
- Move structures package into src and remove stray test artifact
  MathiasMNilsen
  committed
  909b9b2
- Fix bug
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  committed
  4fd6b9e
- Update Rosenbrock test
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  31d6e7a
- Fix bug
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  committed
  b282f69
- Rename some input variable
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  e040a45
Commits on Apr 14, 2026
- Add adjoint to EnKF
  MathiasMNilsen
  committed
  4e8c83c
- Add tests for truncSVD
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  committed
  25d5da6
Commits on Apr 15, 2026
- Move remove_outliers to anlysis_tools
  MathiasMNilsen
  committed
  25a6c59
- Move remove_outliers to anlysis_tools
  MathiasMNilsen
  committed
  2386093
Commits on Apr 16, 2026
- Fix bugs
  MathiasMNilsen
  committed
  57f8927
- Fix prediction save
  MathiasMNilsen
  committed
  704203a
- Small fix
  MathiasMNilsen
  committed
  8289c00
Commits on Apr 17, 2026
- Update ML with PET structures
  MathiasMNilsen
  committed
  65112c9
- Fix small bugs
  MathiasMNilsen
  committed
  3cc273c
- Fix small bugs
  MathiasMNilsen
  committed
  375ff55
Commits on Apr 21, 2026
- Fix ML bugs
  MathiasMNilsen
  committed
  3e25b2e
Commits on Apr 22, 2026
- Add scaling methods for PETDataFrame
  MathiasMNilsen
  committed
  37761ec
- Add scaling methods for PETDataFrame
  MathiasMNilsen
  committed
  21bf9b2
- Include scaling in code
  MathiasMNilsen
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  722be26
Commits on Apr 28, 2026
- Update Gauss-Newton
  MathiasMNilsen
  committed
  9278a70
- Fix some bugs
  MathiasMNilsen
  committed
  ef6a055
Commits on May 5, 2026
- Small bugfix
  MathiasMNilsen
  committed
  9a1bfd9
- Add VanderPol simulator for testing
  MathiasMNilsen
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  779ba74
- Add tests data assimilation workflows
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  13b22ee
Commits on May 13, 2026
- Add adjoint in Approx update
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  committed
  5e8c158
Commits on May 21, 2026
- Refactor Assimilate with AI
  MathiasMNilsen
  committed
  78c3103
- Fox bugs for sparse data run
  MathiasMNilsen
  committed
  ae1cb8b
- Fix small bug
  MathiasMNilsen
  committed
  e96f6d2
- Remove old data-reader methods
  MathiasMNilsen
  committed
  c1e1ce3
- Save DataFrames as list of records in debug files
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  f1a3a70
Commits on May 22, 2026
- Add report-pont reader
  MathiasMNilsen
  committed
  ced3315
Commits on May 26, 2026
Commits on May 27, 2026
- Update tests
  MathiasMNilsen
  committed
  ef60115
- Remove NPV function, it is relocated to SimulatorWraps
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Commits on Jul 3, 2026
- small fix
  MathiasMNilsen
  committed
  b419905
Commits on Jul 6, 2026
- Remove npv import
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  committed
  45d3d3b
Commits on Jul 7, 2026
- Add new base class for optimization loop
  MathiasMNilsen
  committed
  ce61785
- Remove scaling from POPT ensembles and cleaned them up.
  MathiasMNilsen
  committed
  765d637
- Update TrustRegion
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  a693852
- Small change in func wrapper
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  committed
  4a5c87f
- Fix bug
  MathiasMNilsen
  committed
  221584f
- Refactor Enopt and test
  MathiasMNilsen
  committed
  4e2cc8f
- Re-write SmcOpt with AI
  MathiasMNilsen
  committed
  c7f80f6
- small test fix
  MathiasMNilsen
  committed
  c048932
- Improve docstrings for EnOpt and TrustRegion
  MathiasMNilsen
  committed
  8d665f7
- Better name structure for PET ensemble
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  fbabf66
- Update install dependencies
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  d279997
- Fix install bug
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  01ddc69
- Fix install bug
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  15dca2c
- Replace row_stack (depricated)
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Commits on Aug 11, 2026
- refactor: introduce pipt.localization package and modernise update schemes
  MathiasMNilsen
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  63af4c0
- Small logic fix
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  14debe8
Commits on Aug 12, 2026
- fix(distance_loc): correct CSV field order, actnum+z_range, and import taper
  MathiasMNilsen
  committed
  fdc4f7f
- Improve localizations
  MathiasMNilsen
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  5c7959f
- Fix logic
  MathiasMNilsen
  committed
  b7cd6f7
Commits on Aug 13, 2026
- Modernize packaging, tooling, and CI
  claude
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  0ee6f4c
- Add pet CLI for validating and converting config files
  claude
  committed
  5cd9c6f
- Clean up lint findings and fix latent bugs across src
  claude
  committed
  b52d359
- Merge feature/refactor_loc: adopt pipt.localization package
  claude
  committed
  e0206d0
- Add AssimilationSchemeBase, the PIPT counterpart to popt's OptimizerBase
  claude
  committed
  adc2946
- Add AnalysisStrategy base, deduplicating the analysis-flavour helpers
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  751d2c0
- Replace importlib scheme dispatch with an explicit registry
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  8f0b602
- Add algorithm-level scheme constructors, flavour as an argument
  claude
  committed
  994af67
- Replace the daalg config key with scheme, and add `pet migrate`
  claude
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  3dba9c9
- Tidy repo root: relocate example CSV, drop stray artifact
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  b1ed4dd
- Add CHANGELOG documenting the breaking config change
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  52fd87e
Commits on Aug 14, 2026
- Add characterisation tests pinning current numerical output
  claude
  committed
  6dbfe0a
- Split pipt/loop/ensemble.py into a pipt/ensembles/ package
  claude
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  d6fb280
- Add Phase 8 handover document
  claude
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  a22162c
- Preserve formatting and comments in `pet migrate`
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  83e8855
- Move the forecast from the assimilation loop onto the ensemble
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- Add characterisation coverage for es before migrating it
  claude
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  ceff647
- Migrate esmda onto AssimilationSchemeBase
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  b4417ee
- Migrate lmenrml and gnenrml onto AssimilationSchemeBase
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Commits on Aug 17, 2026
- Fix enkf's dangling full_cov_data reference and characterise it
  claude
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  193a91a
- Fix ES discarding its own update
  claude
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  c17f93e
- Migrate es and enkf onto AssimilationSchemeBase
  claude
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  3dd91ac
- Delete Assimilate; schemes own their loop
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  3b56980
- Make Scheme.assimilate() take what the constructor takes
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  d18cc7c
- Stop the factory's default from overriding the config's analysis
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  d531e04
- Let an analysis strategy bind to a scheme instead of being mixed in
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- Write strategy attributes through to the bound scheme
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  20962dd
- Collapse the eighteen scheme classes into five
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  c02be5c
- Drive the characterisation cases through Scheme.assimilate()
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  b25625f
- Move the remaining tests onto the class entry points
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Commits on Aug 18, 2026
- Rewrite the scheme and assimilate() docstrings
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  bd00a6e
- Fix the multilevel scheme, which had never completed a run
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  a467472
- Reorganise update_schemes by concern
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  80e23d9
- Bring the documentation back in line with the code
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- Fix the pipt tutorial
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Commits on Aug 19, 2026
- Make the prior forecast's misfit available to the iteration-0 artifacts
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  0dc9b65
- Rename analysisdebug to savedata and its output to assimilation_result_{i}
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  545b87e
- Completed PIPT tutorial
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  275900a
- Rename the loop methods for the job they do, in both packages
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  1336345
- Remake the popt tutorial to match the pipt one
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  7987cf2
- Make the popt tutorial's run cells safe to re-execute
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  4b70346
- Stop popt swallowing TypeErrors raised inside the objective
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  8a4f2d5
- Clear En_<member> scratch folders before each prediction, not only at init
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  166a9b6
- Report an objective that fits neither call shape, rather than guessing
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Commits on Aug 20, 2026
- Collapse eighteen per-flavour scheme classes into COMPATIBLE_ANALYSES dicts
  
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  ad595a8
- Check convergence after every attempt, not only accepted iterations
  
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- Replace the popt 3WELL tutorial with a 5SpotLineSearch walkthrough
  
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- Move the pipt tutorial into TinyBox/, add a GN-EnRML/margis example
  
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  008d37f
- Remove stale Phase 8 handover doc
  
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Commits on Aug 24, 2026
- Make logit/logger_name real options, defaulting to ASSIM.log
  
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  c16df9a
- Replace scheme->ensemble __getattr__ with declared properties; unify naming
  
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  ab20d4c
- Report the criterion that stopped a converged EnRML run; fix lint
  
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  dff6dc1
- Finish check_state_convergence: snapshot enX_old in the loop
  
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- Trim inline commentary in scheme_base to the load-bearing parts
  
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  b945dcd
- Assign step_accepted directly from update_step()
  
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- add localization tutorials
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- Add tutorials for writing a new analysis and a new scheme
  
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  9c05db8
- Move after_analysis off the scheme base
  
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- Replace the optional-hooks table with the actual call order
  
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  40931ed
- Document what update_step() must leave behind
  
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  b15df91
- Return a StepReport from update_step() instead of a bool
  
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  b249dce
- Rename data_misfit to data_misfit_mean on the schemes
  
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  838c11d
- Fix a docstring the data_misfit_mean rename missed
  
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  f684b0c
- Move the state commit into StepReport and the loop
  
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  6b87184
- Say why enX_temp is cleared, and drop an import the change orphaned
  
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  5166c49
- Pass the state to forecast instead of parking it in enX_temp
  
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  0ac5454
- Update the scheme tutorial's prose for the forecast(state) change
  
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  9de972b
- Add the state field to the tutorial's StepReport snippet
  
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- Move the shared log_update row to the scheme base
  
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  a5440d4
- Give the scheme tutorial a config it actually reads
  
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  a2a173c
- Bring the scheme checklist in line with the contract
  
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  5c06046
- Make the tutorial scheme log its iterations
  
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  5f67d0d
- Trim the loop's commentary back to what a reader can get wrong
  
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  16b5676
- Tidy the execution counts in the auto-adaptive localization tutorial
  
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Commits on Aug 25, 2026
- Move the extending tutorials under pipt
  
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- Add comments
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Commits on Aug 28, 2026
- Move the inner damping loop into update_step, and scoring into score()
  
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Commits on Sep 7, 2026
- Keep at least the requested energy fraction in truncSVD
  
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  a371527
- Fix the idX offset for the second and later prior variables
  
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- Move a replaced member's adjoint together with its state
  
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  45badac
- Stop the analyses allocating what they never use
  
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- Import QA/QC, wavelets and geostat only where they are used
  
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  03fc1bd
- Drop mako, psutil and six; pin geostat to a commit
  
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- Drop two full-ensemble copies that nothing reads
  
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- Remove code with no callers
  
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  cdff13d
- Make co_lm_enrml and gn_enrml thin names for the algorithms they were
  
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  2e2c8f6
- Run every test in a temporary directory; seed the pipeline tests
  
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  af394aa
- Root the API reference at src and rewrite the developer guide for this repository
  
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- Give every module a docstring so the API reference lists it
  
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  e55ce9a
- Pin the five untested scheme/analysis pairs in the golden suite
  
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  d4006de
- Remove the twelve analysis_tools functions nothing calls
  
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  fb89d9c
- Clip through PETStateArray in EnKF; drop the duplicate clipper and three dead ensemble_tools functions
  
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  e2d96e1
- Let esmda_hybrid inherit update_step and check_convergence
  
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  f73b275
- Write down the simulator contract as ensemble.protocols.ForwardSimulator
  
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  3039b08
- Record the unwhitened subspace anomalies as a known issue, with a strict xfail
  
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- Include pet_cli in the standalone-import check
  
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Commits on Sep 8, 2026
- Whiten the predicted anomalies in the subspace analysis
  
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- Score EnKF and ES against the data covariance, not its square root
  
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  24f1b80
- Apply the state scaling in the approx and full analyses
  
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  committed
  9efdf2f
- Replace a crashed member's state along with its prediction; make the null localization picklable
  
  MathiasMNilsen
  and
  claude
  committed
  34961d6
- Place localization kernels with their own axes
  
  MathiasMNilsen
  and
  claude
  committed
  0d8796a
- Refuse the unsupported screendata option with an explanation
  
  MathiasMNilsen
  and
  claude
  committed
  7b1688b
- Fix five verified bugs in popt's numerical subroutines
  
  MathiasMNilsen
  and
  claude
  committed
  9b2254e
- Fix six small crash and correctness bugs across misc, simulator and pipt
  
  MathiasMNilsen
  and
  claude
  committed
  acb5637
- Port QA/QC to the ensemble's frames
  
  MathiasMNilsen
  and
  claude
  committed
  1318945
- Return analysis results instead of writing them onto the scheme
  
  MathiasMNilsen
  and
  claude
  committed
  dfd9c70
- Collapse LM-EnRML and GN-EnRML onto one IterativeEnRML base
  
  MathiasMNilsen
  and
  claude
  committed
  f6b4324
- Let schemes take a ready-made ensemble; select localization from a registry
  
  MathiasMNilsen
  and
  claude
  committed
  236bf41
- Give each log file its own logger; raise instead of exiting; create folders only when writing
  
  MathiasMNilsen
  and
  claude
  committed
  2a1b976
- Draw every random number from the ensemble's stream; add a `seed` option
  
  MathiasMNilsen
  and
  claude
  committed
  7a199fd
- Honour restart_sim_results.pkl only on a restart; fix popt's save_prediction
  
  MathiasMNilsen
  and
  claude
  committed
  ce1ce58
- Let OptimizerBase own the choreography around a step
  
  MathiasMNilsen
  and
  claude
  committed
  6c9c9bc
- Unify restart on RestartMixin: one checkpoint the scheme writes and reads
  
  MathiasMNilsen
  and
  claude
  committed
  fff9583
- Split calc_prediction into orchestration and four named steps
  
  MathiasMNilsen
  and
  claude
  committed
  8d59232
Commits on Sep 9, 2026
- Remove the uncalled module-level readers from read_input_csv
  
  MathiasMNilsen
  and
  claude
  committed
  0895fbd
- Add DataLayout; build the observation vector from it
  
  MathiasMNilsen
  and
  claude
  committed
  c44529f
- Fill the prediction matrix directly from the member outputs
  
  MathiasMNilsen
  and
  claude
  committed
  d4767ea
- Keep the forecast as the members returned it; adjoints as an array
  
  MathiasMNilsen
  and
  claude
  committed
  2469fae
- Build the observation variance from the layout; retire construct_data_cov
  
  MathiasMNilsen
  and
  claude
  committed
  4cbed9f
- Replace PETStateArray with a plain state array and a StateLayout
  
  MathiasMNilsen
  and
  claude
  committed
  b4f273e
- Tutorials: describe the layout-ordered matrices, not the frame flatten
  
  MathiasMNilsen
  and
  claude
  committed
  fb590f1
Commits on Sep 17, 2026
- Move StateLayout into layout.py
  
  MathiasMNilsen
  and
  claude
  committed
  5c1e370
- Compress seismic vintages as the prediction matrix is filled
  
  MathiasMNilsen
  and
  claude
  committed
  c1f9619
- Drop the schemes' max_iter attribute; keep maxiter
  
  MathiasMNilsen
  and
  claude
  committed
  4e85819
- max_iter counts update iterations, not the prior forecast
  
  MathiasMNilsen
  and
  claude
  committed
  6a0d4ac
- One configuration boundary: normalise once, validate by key
  
  MathiasMNilsen
  and
  claude
  committed
  54cbb06
- Document the configuration and the architecture; a public popt API
  
  MathiasMNilsen
  and
  claude
  committed
  4285094
- Merge upstream/main: reconcile the restructuring with upstream's 15 commits
  
  MathiasMNilsen
  and
  claude
  committed
  d49a323
- Write the PET log file as UTF-8
  
  MathiasMNilsen
  and
  claude
  committed
  3ecbb0c
- Record an HPC extraction failure against its own member, not the batch
  
  MathiasMNilsen
  and
  claude
  committed
  5019717
- Converge the outer EPF loop on the constraint violation, not the step size
  
  MathiasMNilsen
  and
  claude
  committed
  0f336b3
- Understand a LOCALIZATION block that names no mode
  
  MathiasMNilsen
  and
  claude
  committed
  c894f3e
- Build the distance localization operator over the active cells
  
  MathiasMNilsen
  and
  claude
  committed
  9fc7010
- Read a pickled localization file into localization entries
  
  MathiasMNilsen
  and
  claude
  committed
  7306525
- Add the subspace2 analysis: Gauss-Newton on the ensemble transform
  
  MathiasMNilsen
  and
  claude
  committed
  d77d72b
- Restore GenOpt and CMA on the current optimizer base
  
  MathiasMNilsen
  and
  claude
  committed
  1ccd840
- Let the optimizer reject a crashed evaluation instead of ending the run
  
  MathiasMNilsen
  and
  claude
  committed
  f45657b

Commits

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Commits on Jul 7, 2026