Mega Notebook PR by aritraghsh09 · Pull Request #848 · lincc-frameworks/hyrax

aritraghsh09 · 2026-03-28T02:27:33Z

This turned into too big of a PR. Here's what it does

Redoes the Getting Started Section:-
- Splits it into four subsections covering installation, Hyrax Hello World, Astronomy Supervised, and Astronomy Unsupervised. The Astronomy Unsupervised is what used to exist in our old science examples notebook.
Redoes the Science Section.
- Adds a detailed unsupervised discovery notebook and time-domain classification example using light curve data.
Also does some aesthetic changes on these pages to make them pleasing overall.

Provides text in the initial landing page to guide users. Set's up the four empty pages. Assisted by: Codex GPT 5.4

Sets up a dedicated installation page with instructions for pip, conda, and github Assisted by: Codex GPT 5.4

…n Hyrax.

…istent with each other. Assisted by: Codex GPT 5.4

Science Example.

…on accuracy) Code Assist by Claude Opus 4.6 and Codex GPT 5.4

… pipeline example

review-notebook-app · 2026-03-28T02:27:38Z

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codecov · 2026-03-28T02:34:09Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 64.86%. Comparing base (bf5725a) to head (5a0f399).
⚠️ Report is 16 commits behind head on main.

Additional details and impacted files

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##             main     #848   +/-   ##
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  Coverage   64.86%   64.86%           
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  Files          61       61           
  Lines        5906     5906           
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  Hits         3831     3831           
  Misses       2075     2075

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github-actions · 2026-03-28T03:25:29Z

Before [`bf5725a`]	After [`cbcbbd0`]	Ratio	Benchmark (Parameter)
39.7±0.7ms	42.0±0.7ms	1.06	benchmarks.time_nb_obj_dir
6.95±0.06s	7.31±0.1s	1.05	benchmarks.time_save_to_database_help
15.34397523333843	16.00526809454944	1.04	data_cache_benchmarks.DataCacheBenchmarks.track_cache_hsc1k_hyrax_size_undercount
38.3±0.1ms	39.5±0.7ms	1.03	benchmarks.time_nb_obj_construct
7.02±0.07s	7.20±0.1s	1.03	benchmarks.time_rebuild_manifest_help
6.99±0.01s	7.20±0.01s	1.03	benchmarks.time_umap_help
10.2±0.1ms	10.4±0.07ms	1.03	vector_db_benchmarks.VectorDBSearchBenchmarks.time_search_by_vector_many_shards(128, 'chromadb')
7.01±0.03s	7.16±0.01s	1.02	benchmarks.time_help
6.96±0.07s	7.07±0.03s	1.02	benchmarks.time_lookup_help
7.00±0.04s	7.17±0.04s	1.02	benchmarks.time_prepare_help

Click here to view all benchmarks.

Assisted by Claude Opus 4.6

…yrax into getting_started_take2

mtauraso · 2026-03-30T19:48:41Z

@aritraghsh09 This file has some issue rendering on ReviewNB. Not sure what's going on, was this supposed to be deleted?

@mtauraso This file, in reality, is a symlink because that's the only way I found to have it appear to two different places on the toctree. I can explain more during our sync today.

mtauraso · 2026-03-30T19:50:13Z

This looks pretty reasonable to me, other than the one comment which I think is easy cleanup.

mtauraso · 2026-03-30T19:51:56Z

+stage of the workflow should use.
+
+Hyrax also includes built-in datasets for several astronomy workflows, and
+users can :doc:`define custom dataset classes <external_libraries>` when needed.


Might be better as direct link to custom dataset doc (but I think that is new as-of the writing of this)

mtauraso · 2026-03-30T19:52:09Z

+In Hyrax terms, specifying the model is one of the :doc:`required inputs <required_input>` for a run.
+
+You do not need to use a built-in model. Hyrax also supports
+:doc:`defining custom models <external_libraries>`.


Same as below, direct link to custom dataset doc.

drewoldag · 2026-03-30T20:11:15Z

Just FYI - I reviewed the readthedocs rendered version

These are more stylistic:

Swap the first two paragraphs on the landing page. Let the “what is Hyrax” section be the intro paragraph, and then embed what is currently in the first paragraph in a “Why Hyrax?” box.
On the installation page:
- Move the warning about bleeding edge to the “Install from source” section.
- It’s probably just me, but I’m not a fan of “bleeding edge”, we could use the term “pre-release”?
I think we could combine the Install with Pip and Install in a conda environment sections. “Install in a virtual environment”, Then the “tip” (most astronomers use conda), then the block creating the env and installing with pip. Then the note about Hyrax officially supports 3.11,…

These seem more important so that we provide consistent guidance:

Astronomy Supervised page:
- The note admonition at the top renders oddly (ok, maybe this one isn't super important 😄)
- In the dataset class, discourage the use of .get() from the config to avoid multiple default values
- If guard in collate for sequence. It complicates things, but it's what we're advising for now.

…yrax into getting_started_take2

Cherry-pick relevant doc improvements from the review-stale-docs branch, excluding changes that conflict with the getting_started rewrite (#848), science_examples rewrite (#851), and archived_notebooks structure. Key changes: - Rewrite verbs.rst with accurate descriptions and newly documented verbs (test, model, download, rebuild_manifest, lookup, save_to_database, database_connection, to_onnx, engine) - Rewrite data_flow.rst with accurate collate/prepare_inputs descriptions and a data format summary table - Fix train_step -> train_batch in CLAUDE.md and HYRAX_GUIDE.md - Fix index.rst code snippet: replace invalid h.search_by_vector() with correct umap -> save_to_database -> database_connection flow - Fix f.config -> h.config typo in model_comparison.rst - Fix n_epochs -> epochs config key in using_umap.ipynb - Fix TensorBoard typos in using_tensorboard_and_mlflow.ipynb - Update dev_guide.rst Python version 3.10 -> 3.11 - Clarify prepare_inputs as static method in required_input.rst - Remove broken export_model link and rename HyraxQL in notebooks.rst - Add reference toctree entries and comment out empty FAQ - Update HYRAX_GUIDE.md dataset registry list https://claude.ai/code/session_017pvWpwH69HPfdJaziEZyCf

aritraghsh09 added 7 commits March 27, 2026 11:57

Setting up Getting Started Landing page with four sub-pages

aab4271

Provides text in the initial landing page to guide users. Set's up the four empty pages. Assisted by: Codex GPT 5.4

Adding a dedicated installation page.

7bdf696

Sets up a dedicated installation page with instructions for pip, conda, and github Assisted by: Codex GPT 5.4

Brings back our old getting started page as the hello world example i…

14520e5

…n Hyrax.

Making the Getting Started Notebook and Landing Pages completely cons…

6366cc1

…istent with each other. Assisted by: Codex GPT 5.4

Making the Astronomy Unsupervised Getting Started Identical to the

1e30839

Science Example.

Adding an supervised lightcurve example (toy-doesn't work super well …

f04e0da

…on accuracy) Code Assist by Claude Opus 4.6 and Codex GPT 5.4

Redoing the science exampels and adding a full unsupervised discovery…

37b6b5a

… pipeline example

aritraghsh09 marked this pull request as draft March 28, 2026 02:28

aritraghsh09 self-assigned this Mar 28, 2026

aritraghsh09 changed the title ~~Getting started take2~~ Mega Notebook PR Mar 28, 2026

Merge branch 'main' into getting_started_take2

4e50421

aritraghsh09 added 4 commits March 28, 2026 00:24

Updating the supervised Example to a better model

d7fbb72

Assisted by Claude Opus 4.6

Formatting modifications

3bef7e3

Merge branch 'getting_started_take2' of github.com:lincc-frameworks/h…

660d5a5

…yrax into getting_started_take2

Ruff formatting fixes

d58fec3

aritraghsh09 marked this pull request as ready for review March 28, 2026 07:56

aritraghsh09 requested review from SamSandwich07, drewoldag and mtauraso March 28, 2026 07:56

mtauraso reviewed Mar 30, 2026

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mtauraso approved these changes Mar 30, 2026

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mtauraso reviewed Mar 30, 2026

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aritraghsh09 added 2 commits March 30, 2026 16:32

Merge branch 'main' into getting_started_take2

b63320c

Addressing PR comments.

6235d32

Merge branch 'getting_started_take2' of github.com:lincc-frameworks/h…

5a0f399

…yrax into getting_started_take2

aritraghsh09 merged commit 8028f95 into main Mar 31, 2026
9 checks passed

aritraghsh09 deleted the getting_started_take2 branch March 31, 2026 00:15

mtauraso mentioned this pull request Mar 31, 2026

Fix stale documentation: verbs, data flow, config keys, and typos #853

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Mega Notebook PR#848

Mega Notebook PR#848
aritraghsh09 merged 15 commits intomainfrom
getting_started_take2

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