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Documentation audit: align remaining docs with the code - #5
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… study Add mneme.analysis.steady_state for the question the project is meant to answer: does a system have more than one stable state? - assess_steady_state decides whether a relaxing run has settled. A low rate of change is not accepted on its own: the remaining distance is estimated from the fitted relaxation time. - count_distinct_states groups end states against a stated threshold and reports how clean the grouping is. Tested on exponential relaxations with known time constants and on a double-well system with two known stable states. studies/convergence holds the configuration generator, runner and analysis for a BETSE experiment that starts one tissue from six ion concentrations, with and without gap-junction coupling. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Thirteen BETSE runs of one 42-cell tissue, from six starting ion concentrations, with and without gap-junction coupling, plus an exact repeat. Runs that started up to 48.8 mV apart ended within 0.32 mV of each other: one stable state, no multistability. The runs did not meet the settling criterion fixed beforehand (estimated remaining drift 0.20 to 0.32 mV against a limit of 0.1 mV). The results say so. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Audit of every document not touched by the correctness work: the 11-module course, the demo notebook, the setup, structure, pipeline, API-design and testing guides, CONTRIBUTING, the API reference pages, the default config and the setup script. - Removed or renamed APIs updated (reconstructor names, method names, removed Lyapunov functions, CLI behaviour). - Claims of validated results removed; experimental components marked as such with pointers to docs/SCOPE.md; Lyapunov material points to the operating-range document and states the 39-surrogate and 4,000-point requirements. - Stale numbers (test count, coverage, Python version, install commands) corrected. Every mkdocstrings directive verified to import. - Historical documents get a one-line note and are otherwise untouched. - New API page for mneme.analysis.steady_state. - studies/multistability: config generator for the two multistability candidates (gene network, voltage-gated channels). Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PPeuxmAc47j5SKMb65CMRT
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PPeuxmAc47j5SKMb65CMRT
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Summary
Audits every document that the correctness work did not touch and brings it in line with the code: the 11-module course, the demo notebook, the setup, structure, pipeline, API-design and testing guides, CONTRIBUTING, the API reference pages,
config/default.yamlandscripts/setup_dev_env.sh.Stacked on #4. Retarget to
mainonce #4 is merged.What changed
docs/SCOPE.md. Lyapunov material points todocs/LYAPUNOV_OPERATING_RANGE.mdand states the 39-surrogate and 4,000-point requirements.:::directive underdocs/api/was checked to import (68 targets). New page formneme.analysis.steady_state.REPO_AUDIT_2025-08-18, the v1 plan, the Tier 0 spec and plan) get a one-line "historical" note and are otherwise untouched.studies/multistability/make_configs.py, the config generator for the two multistability experiments now running.Not verified
The course's CLI walkthroughs were checked against
cli.pyflags, not run end to end. The docs site build runs in CI once this is retargeted tomain.🤖 Generated with Claude Code
https://claude.ai/code/session_01PPeuxmAc47j5SKMb65CMRT