docs: modernize documentation with layered Arbor-inspired architecture#103
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Add Get Started, Concepts, File Formats & IO, Developer Guide, and Troubleshooting sections; rewrite the landing page with a feature grid and doc-organization map; add filter/io API reference pages. Correct example APIs (NeuroMorpho loading), fix a pre-existing orphan page and a broken notebook link, and update deprecated MyST-NB config keys.
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Summary
Rewrites and modernizes the
braincelldocumentation, using the Arbor docs as a structural/UX reference (structure adapted, not copied). The docs are now layered by user intent.New sections
getting_started/) —installation(CPU/GPU/TPU, extras, dev, WSL+NEURON),overview(library map + pipeline + "where to go next"),first_steps(a runnable HH neuron end-to-end).concepts/) — the previously-missing mental-model layer: architecture, units, cells, morphology, mechanisms, ions & channels, regions & locsets, discretization, integration.file_formats/) — SWC, ASC, NeuroML2, NeuroMorpho.Org, checkpointing (documentingbraincell.io, which had no narrative docs).developer/) — contributing, project layout, testing, extending.apis/filter.rstandapis/io.rstfor previously-undocumented public APIs.Landing page rewritten with a feature grid, capability table, verified quick-start, and a doc-organization map; top-level toctrees regrouped into clear captions.
Accuracy & cleanup
braincell.load_neuromorpho("cnic_001")→Morphology.from_neuromorpho(<id>)(verified against the real API).runpipeline as under active development.single_compartment/examples/index.rstand a broken../apis/...link inchannel.ipynb.conf.py.All cross-references in new content resolve to real symbols/pages.
Test plan
sphinx -b htmlbuilds cleanly (exit 0, 435 pages){class}refs resolve to generated API pages; inter-section doc links resolve