Ensmeble-matrix changes

[MathiasMNilsen]

No description provided.

[Copilot]

Pull request overview

This pull request implements changes to handle ensemble-matrix state representations and improve logging functionality across the codebase. The changes involve transitioning from dictionary-based state storage to matrix-based ensemble handling, introducing a new logger class, and adding comprehensive test coverage for the toggle_ml_state function.

Changes:

• Introduced new test file for toggle_ml_state function with comprehensive test coverage
• Refactored state handling from dictionary-based to matrix-based ensemble representation
• Added new PetLogger class for improved logging with formatted table output
• Updated multiple update schemes to use new ensemble matrix interface

Reviewed changes

Copilot reviewed 27 out of 27 changed files in this pull request and generated 12 comments.

Show a summary per file

File	Description
tests/test_toggle_ml_state.py	New test suite for toggle_ml_state function
popt/update_schemes/subroutines/subroutines.py	Added logging decorators for line search procedures
popt/update_schemes/linesearch.py	Updated to use new logger and state handling
popt/misc_tools/optim_tools.py	Simplified toggle_ml_state to work with matrices instead of dictionaries
popt/loop/optimize.py	Replaced standard logging with PetLogger
popt/loop/ensemble_generalized.py	Updated to use matrix-based state representation
popt/loop/ensemble_gaussian.py	Refactored gradient/hessian methods for matrix ensemble
popt/loop/ensemble_base.py	Core changes to support matrix-based ensemble handling
popt/cost_functions/npv.py	Removed blank line
pipt/update_schemes/update_methods_ns/*	Updated update methods to use new ensemble matrix interface
pipt/update_schemes/multilevel.py	Simplified multilevel handling with new structure
pipt/update_schemes/esmda.py	Updated to use matrix ensemble and new logger
pipt/update_schemes/es.py	Updated state handling
pipt/update_schemes/enrml.py	Updated to use matrix ensemble
pipt/update_schemes/enkf.py	Updated to use matrix ensemble
pipt/misc_tools/extract_tools.py	Added extract_initial_controls function and corrected spelling
pipt/misc_tools/ensemble_tools.py	New module with ensemble manipulation utilities
pipt/misc_tools/analysis_tools.py	Added truncSVD function and removed deprecated code
pipt/loop/ensemble.py	Major refactoring to use matrix-based ensemble
pipt/loop/assimilation.py	Updated to use new ensemble matrix interface
misc/ecl.py	Commented out logging statements
input_output/read_config.py	Added read function and improved error handling
ensemble/logger.py	New PetLogger class implementation
ensemble/ensemble.py	Updated to use matrix-based ensemble and new logger

Comments suppressed due to low confidence (1)

popt/loop/ensemble_base.py:1

• Duplicate condition check: isinstance(limits, dict) is checked twice. This appears to be a copy-paste error.

# External imports

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[Copilot]

The logger is being called with keyword arguments but fun_xk_symbol and jac_inf_symbol are undefined variables. These should be string literals or defined elsewhere in the code.

[Copilot]

Inconsistent attribute naming: uses self.jk, self.Hk, self.xk but also self._jac. Either all should have underscore prefix or none should.

Suggested change

	pk = newton_cg(self.jk, Hk=self.Hk, xk=self.xk, jac=self._jac, logger=self.logger)
	pk = newton_cg(self.jk, Hk=self.Hk, xk=self.xk, jac=self.jac, logger=self.logger)

[Copilot]

Line 543 uses self.jk but line 545 uses self._jk. This inconsistency suggests one might be incorrect.

Suggested change

	if (self.step_size_adapt == 1) and (np.dot(pk, self.jk) != 0):
	alpha = 2*(self.fk - self.f_old)/np.dot(pk, self.jk)
	elif (self.step_size_adapt == 2) and (np.dot(pk, self.jk) != 0):
	if (self.step_size_adapt == 1) and (np.dot(pk, self._jk) != 0):
	alpha = 2*(self.fk - self.f_old)/np.dot(pk, self._jk)
	elif (self.step_size_adapt == 2) and (np.dot(pk, self._jk) != 0):

[Copilot]

Corrected spelling of 'indecies' to 'indices' (used consistently throughout the file).

[Copilot]

Potential AttributeError: self.enX may not exist at this point since it was set to None earlier (line 216). Should use the local enX variable instead.

Suggested change

	enX[:, list_crash[index]] = deepcopy(self.enX[:, element])
	enX[:, list_crash[index]] = deepcopy(enX[:, element])

[rolfjl]

Oppdater PR