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Analysis clean up... again#85

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BrendanKKrueger wants to merge 12 commits into
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bkk_analysis_cleanup2
Draft

Analysis clean up... again#85
BrendanKKrueger wants to merge 12 commits into
mainfrom
bkk_analysis_cleanup2

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bkkrueger added 12 commits July 23, 2026 17:09
…ch deeper than I thought. That suggested that changes may need to be much more incremental than I thought, working towards a goal.
…nvalues, but this does remove the need for the old calculations. Eventually (once I figure out the math error that's gotta be lurking somewhere), I can get rid of eigendecomposition_analysis because it's been replaced by the new 'flexible API' method.
The error_analysis function signature changed to accept OperatorRepresentation
objects (exact_op, approx_op) instead of raw matrices (exact_matrix, unitary_matrix,
exact_eigendecomp, approx_eigendecomp).

Changes:
- Updated all test_error_analysis.py tests to create OperatorRepresentation objects
- Added helper functions to create test OperatorRepresentation objects
- Marked matrix-free operator tests as skipped (Phase 3 functionality not yet implemented)
- All 16 error_analysis tests now pass (2 skipped)

Test results after this commit:
- common tests: 190/190 passed (100%)
- analysis tests: 266/285 passed (93.3%), 17 failed, 2 skipped

Remaining 17 failures require fixes to implementation code (not test code):
- test_analysis_integration.py: 7 failures due to debugging code in analysis.py
- test_operators.py: 6 failures in OperatorRepresentation energy shift logic
- test_time_evolution_algorithms.py: 4 resource estimation test failures

These remaining failures will be resolved by fixing analysis.py and operators.py
implementation code, which is still under development.
…ut later down to the bottom of the analysis routine.
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