Clean up notebook outputs and improve documentation#847
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Clean up notebook outputs and improve documentation#847
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Adds :doc: and :ref: links throughout the 15 RST documentation files so readers can navigate between related concepts. Key connections include: verbs ↔ configuration, data flow ↔ dataset/model class references, required inputs ↔ class reference pages, configuration system ↔ external package setup, and concept pages ↔ hands-on workflow notebooks. https://claude.ai/code/session_018Ni98cUN4gA2ymfJvxptR9
Adopts 9 of 11 unique cross-references identified by the other agent: - architecture_overview: link to getting_started and science_examples - configuration: immutable config → model_comparison - configuration_system: back-link to configuration; validation → dataset_class_reference - dataset_class_reference: fields list → data_flow pipeline overview - dataset_splits: config editing primer → configuration - external_libraries: → required_input for minimum requirements - getting_started: data_request → dataset_class_reference contract - model_class_reference: train_batch metrics → model_comparison Skipped: dataset_class_reference metadata→verbs (weak connection to a legacy path) and model_class_reference checklist→external_library_package (already linked a few lines later in __init__ section). https://claude.ai/code/session_018Ni98cUN4gA2ymfJvxptR9
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Red-light fixes: - CLAUDE.md / HYRAX_GUIDE.md: train_step → train_batch (matches model_registry.py) - dev_guide.rst: Python 3.10 → 3.11 (matches pyproject.toml requires-python) - notebooks.rst: Remove dead link to nonexistent export_model notebook - using_umap.ipynb: n_epochs → epochs (correct config key) Yellow-light fixes: - index.rst: Replace incorrect h.search_by_vector() with actual verb chain, add h.umap() - model_comparison.rst: f.config → h.config - required_input.rst: Clarify prepare_inputs is a model @staticmethod, not a free function - reference_and_faq.rst: Comment out empty FAQ "TBD" section - science_examples.rst: Add note that more science workflows are in development - HYRAX_GUIDE.md: Add missing dataset classes to built-in list - using_tensorboard_and_mlflow.ipynb: Fix "TenosrBoard" and "reactiviating" typos - custom_dataset.ipynb: Remove unnecessary torch Dataset dual-inheritance - train_model.ipynb: Standardize on h.set_config() instead of direct dict mutation - hyraxql_demo.ipynb: Rename title from misleading "GraphQL alternative" - mpr_demo.ipynb: Replace stale "FIBAD" project name with "Hyrax" - hyrax_hats_cutouts.ipynb: Add intro noting LSSTDataset-specific config pattern, fix typo https://claude.ai/code/session_01XXeVghMRKhSmMQ5XVxdSC4
verbs.rst: - Document all 15 verbs (was 6, with a nonexistent "index" verb) - Add: test, save_to_database, database_connection, lookup, model, to_onnx, engine, download, rebuild_manifest, search - Remove nonexistent "index" verb - Mark notebook-only verbs (visualize, prepare, model, database_connection) - Show return types for notebook context data_flow.rst: - Remove incorrect claim that inference uses ONNX (it uses PyTorch) - Clarify that ONNX is an optional export path via the engine verb - Document that prepare_inputs returns numpy (not tensors) - Add data format summary table showing types at each pipeline stage - Clarify the numpy→tensor conversion is automatic https://claude.ai/code/session_01XXeVghMRKhSmMQ5XVxdSC4
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@mtauraso I think that we have finished reorganizing the docs for the time being. If you wnat to reengage claude on this, now is a good time. |
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Change Description
This PR cleans up pre-executed Jupyter notebooks by removing cell outputs and execution counts, and improves documentation across multiple files.
Solution Description
Notebook Cleanup
null. Updated code to useh.set_config()API instead of direct dictionary assignment (e.g.,h.set_config("model.name", ...)instead ofh.config["model"]["name"] = ...). Fixed widget value formatting (float to int).Datasetinheritance andtorch.utils.dataimports. Fixed widget value formatting.Documentation Improvements
test,model,download,rebuild_manifest,lookup,save_to_database,database_connection,to_onnx,engine). Improved existing verb descriptions with return types and usage context.Code Quality
https://claude.ai/code/session_01XXeVghMRKhSmMQ5XVxdSC4