Changes to ensemble-matrix

[MathiasMNilsen]

No description provided.

[Copilot]

Pull request overview

This PR refactors the ensemble-matrix data structure across the codebase, transitioning from dictionary-based state representations to numpy array-based ensemble matrices. The changes improve performance and code clarity while maintaining functionality.

Changes:

• Replaced dictionary-based state variables with numpy array ensemble matrices (enX)
• Updated the toggle_ml_state function to work with matrices instead of dictionaries
• Modified logging infrastructure to use a custom PetLogger class with formatted table output
• Refactored update schemes to accept ensemble matrices directly

Reviewed changes

Copilot reviewed 27 out of 27 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tests/test_toggle_ml_state.py	Added comprehensive test suite for the refactored toggle_ml_state function
popt/update_schemes/subroutines/subroutines.py	Enhanced line search logging with formatted output and condition tracking
popt/update_schemes/linesearch.py	Updated to use new logger format and corrected logical condition bug
popt/misc_tools/optim_tools.py	Refactored toggle_ml_state to work with matrices; fixed variable name typo
popt/loop/optimize.py	Integrated new PetLogger and updated state variable handling
popt/loop/ensemble_generalized.py	Updated to use matrix-based state representation
popt/loop/ensemble_gaussian.py	Major refactoring to use ensemble matrices instead of dictionaries
popt/loop/ensemble_base.py	Core refactoring to matrix-based ensemble representation
popt/cost_functions/npv.py	Removed extraneous blank line
pipt/update_schemes/update_methods_ns/subspace_update.py	Updated to accept ensemble matrices as function parameters
pipt/update_schemes/update_methods_ns/hybrid_update.py	Refactored to work with ensemble matrices
pipt/update_schemes/update_methods_ns/full_update.py	Updated update method signature and implementation
pipt/update_schemes/update_methods_ns/approx_update.py	Comprehensive refactoring for matrix-based updates
pipt/update_schemes/multilevel.py	Significant cleanup and refactoring for multilevel ensemble handling
pipt/update_schemes/esmda.py	Updated to use ensemble matrices and new logging
pipt/update_schemes/es.py	Updated state variable handling
pipt/update_schemes/enrml.py	Refactored for matrix-based ensembles
pipt/update_schemes/enkf.py	Updated to work with ensemble matrices
pipt/misc_tools/extract_tools.py	Fixed typo and added new extraction functions
pipt/misc_tools/ensemble_tools.py	New module with ensemble matrix manipulation utilities
pipt/misc_tools/analysis_tools.py	Added helper functions and updated existing ones
pipt/loop/ensemble.py	Major refactoring to use PetLogger and ensemble matrices
pipt/loop/assimilation.py	Updated to work with new ensemble matrix structure
misc/ecl.py	Commented out logging statements
input_output/read_config.py	Enhanced configuration reading with new formats
ensemble/logger.py	New custom logger class with table formatting
ensemble/ensemble.py	Core refactoring for matrix-based ensemble handling

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.