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review.md

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1# Review evidence and boundaries
2
3Reviewed 2026-10-01. The catalog fetcher is standard-library only. Resource examples
4were checked with Python 3.13, Transformers 5.18.0, Torch 2.14.1, Datasets 5.0.1,
5Hub 1.33.0 and Gradio Client 2.7.1. Datasets 5.0.1 rejects Hub 2.0 through its
6`<2.0` dependency bound; the combined workflow therefore uses Hub 1.33.0.
7

Review evidence and boundaries

Reviewed 2026-10-01. The catalog fetcher is standard-library only. Resource examples were checked with Python 3.13, Transformers 5.18.0, Torch 2.14.1, Datasets 5.0.1, Hub 1.33.0 and Gradio Client 2.7.1. Datasets 5.0.1 rejects Hub 2.0 through its <2.0 dependency bound; the combined workflow therefore uses Hub 1.33.0.

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8## Catalog contract
9
10Public unauthenticated GET requests retrieved and parsed
11[the index](https://huggingscience.co/llms.txt),
12[the full catalog](https://huggingscience.co/llms-full.txt),
13all 17 [topic routes](https://huggingscience.co/topics/biology.md), and
14[the RSS feed](https://huggingscience.co/feed.xml).
15The full document had 1,329 H3 occurrences representing 544 unique section/URL
16pairs because topics overlap; the feed contained 50 items. These are snapshots,
17not stable counts or evidence of resource quality. The helper has no auth,
18request body, server-side search, or pagination; filtering/search are local.

Catalog contract

Public unauthenticated GET requests retrieved and parsed the index, the full catalog, all 17 topic routes, and the RSS feed. The full document had 1,329 H3 occurrences representing 544 unique section/URL pairs because topics overlap; the feed contained 50 items. These are snapshots, not stable counts or evidence of resource quality. The helper has no auth, request body, server-side search, or pagination; filtering/search are local.

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20## Hub and dataset contracts
22[Hub API](https://huggingface.co/docs/hub/api) and
23[HfApi reference](https://huggingface.co/docs/huggingface_hub/package_reference/hf_api)
24were checked against actual public responses. Read-only routes used were
25`GET /api/models/{repo}`, `/api/datasets/{repo}`, `/api/spaces/{repo}` and
26`/api/spaces?author=hugging-science&limit=100` at `huggingface.co`.
27Individual metadata returns an object; lists paginate with Link headers, which
28the SDK iterator follows. Public tests explicitly suppressed token use. Gated
29repositories may expose metadata while returning 401 for card/artifact access;
30401 does not establish that a repository was deleted.
32The provider check uses `GET /api/models/{repo}?expand=inferenceProviderMapping`.
33Its raw JSON object becomes a **list** of `InferenceProviderMapping` records in
34the tested SDK. ESM2-650M had a live `hf-inference` mapping for `fill-mask`;
35Evo2-40B had no mappings. The fill-mask request/typed-result contract was exercised
36with a mocked transport, not an authenticated provider call.
38[Datasets loading](https://huggingface.co/docs/datasets/loading),
39[streaming](https://huggingface.co/docs/datasets/stream), and
40[5.0.1 loader source](https://github.com/huggingface/datasets/blob/5.0.1/src/datasets/load.py)
41confirm iterable behavior and removal of dataset-script execution.
42The live OAS metadata helpers returned configs `default`, `paired` and paired
43split `train`. Synthetic CSV tests ran the documented lazy filter and bounded
44materialization, including failure on absent `meta_Species`.

Hub and dataset contracts

Hub API and HfApi reference were checked against actual public responses. Read-only routes used were GET /api/models/{repo}, /api/datasets/{repo}, /api/spaces/{repo} and /api/spaces?author=hugging-science&limit=100 at huggingface.co. Individual metadata returns an object; lists paginate with Link headers, which the SDK iterator follows. Public tests explicitly suppressed token use. Gated repositories may expose metadata while returning 401 for card/artifact access; 401 does not establish that a repository was deleted.

The provider check uses GET /api/models/{repo}?expand=inferenceProviderMapping. Its raw JSON object becomes a list of InferenceProviderMapping records in the tested SDK. ESM2-650M had a live hf-inference mapping for fill-mask; Evo2-40B had no mappings. The fill-mask request/typed-result contract was exercised with a mocked transport, not an authenticated provider call.

Datasets loading, streaming, and 5.0.1 loader source confirm iterable behavior and removal of dataset-script execution. The live OAS metadata helpers returned configs default, paired and paired split train. Synthetic CSV tests ran the documented lazy filter and bounded materialization, including failure on absent meta_Species.

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46## Model and resource cards
48Cards/manifests were inspected for all named flagship repository IDs. Key fixes:
50- [Evo2 official runtime](https://github.com/ArcInstitute/evo2): native Evo2/Vortex,
51 BF16/FP8 and hardware distinctions; 7B is not an instruction-tuned variant.
52 [40B card](https://huggingface.co/arcinstitute/evo2_40b) and
53 [7B card](https://huggingface.co/arcinstitute/evo2_7b) point to that runtime.
54- [ESM2-650M](https://huggingface.co/facebook/esm2_t33_650M_UR50D),
55 [ESM2-35M](https://huggingface.co/facebook/esm2_t12_35M_UR50D), and
56 [ESM API](https://huggingface.co/docs/transformers/model_doc/esm): native
57 Transformers support; tiny random CPU model tested special/padding exclusion
58 and equivalence of a short sequence alone versus in a padded batch.
59- [TEDDY](https://huggingface.co/Merck/TEDDY): model/code repository, 116 million
60 training cells; [STACK](https://huggingface.co/arcinstitute/Stack-Large): its own
61 package/checkpoints, not a generic AutoModel guarantee.
62- [OAS](https://huggingface.co/datasets/opig/OAS): `meta_Species` and paired CSVs;
63 [OpenGenome2](https://huggingface.co/datasets/arcinstitute/opengenome2): raw
64 multipart FASTA plus complete JSONL shards, with pretraining-specific content.
65- [NatureLM-audio](https://huggingface.co/EarthSpeciesProject/NatureLM-audio) and
66 [AVEX checkpoint](https://huggingface.co/EarthSpeciesProject/esp-aves2-sl-beats-all):
67 dedicated loaders/preprocessing, not generic provider availability.
68- [AQAffinity](https://huggingface.co/SandboxAQ/AQAffinity) metadata is public and
69 gated; its raw card and [SAIR card](https://huggingface.co/datasets/SandboxAQ/SAIR)
70 returned 401 anonymously. Access and execution remain unverified.
71- [LeMat-Bulk](https://huggingface.co/datasets/LeMaterial/LeMat-Bulk),
72 [breast ultrasound checkpoint](https://huggingface.co/hugging-science/breast-cancer-detector-2),
73 [Kimina-Prover](https://huggingface.co/AI-MO/Kimina-Prover-72B), and
74 [Legacy Survey release](https://huggingface.co/datasets/hugging-science/mmu_legacysurvey_dr10_south_21)
75 were checked as discovery pointers; the astronomy release uses HATS/Parquet.
76 No claim of clinical, proof, affinity or structural accuracy was tested.

Model and resource cards

Cards/manifests were inspected for all named flagship repository IDs. Key fixes:

  • Evo2 official runtime: native Evo2/Vortex, BF16/FP8 and hardware distinctions; 7B is not an instruction-tuned variant. 40B card and 7B card point to that runtime.
  • ESM2-650M, ESM2-35M, and ESM API: native Transformers support; tiny random CPU model tested special/padding exclusion and equivalence of a short sequence alone versus in a padded batch.
  • TEDDY: model/code repository, 116 million training cells; STACK: its own package/checkpoints, not a generic AutoModel guarantee.
  • OAS: meta_Species and paired CSVs; OpenGenome2: raw multipart FASTA plus complete JSONL shards, with pretraining-specific content.
  • NatureLM-audio and AVEX checkpoint: dedicated loaders/preprocessing, not generic provider availability.
  • AQAffinity metadata is public and gated; its raw card and SAIR card returned 401 anonymously. Access and execution remain unverified.
  • LeMat-Bulk, breast ultrasound checkpoint, Kimina-Prover, and Legacy Survey release were checked as discovery pointers; the astronomy release uses HATS/Parquet. No claim of clinical, proof, affinity or structural accuracy was tested.
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78## Spaces and verification limits
80[Gradio Client 2.7.1 source](https://github.com/gradio-app/gradio/blob/gradio_client%402.7.1/client/python/gradio_client/client.py)
81verifies `token`, separate endpoint-scoped `oauth_token`, `view_api`, prediction,
82queue and download behavior. Local `handle_file` tests confirm file marking only.
83The current [BoltzGen demo source](https://huggingface.co/spaces/hugging-science/BoltzGen_Demo/blob/main/app.py)
84at commit `829bdf3baf7ac85f252fea917028a813f4d0aebd` must be rechecked if the app changes.
85Its runtime was `PAUSED`; public `/config` and `/gradio_api/info` returned 503.
86The five-input design contract and status-string return are source verified only;
87no endpoint name or downloadable artifact has been validated against a live job.
88The old lower-case demo ID and old heatmap ID returned 401; live organization
89metadata identified `BoltzGen_Demo` and Docker `science-release-map` instead.
91No large dataset shard, pretrained model weight, native Evo2/CUDA runtime,
92authenticated inference, upload, moderation action or design job was executed.
93Use the live application schema before any of those operations.

Spaces and verification limits

Gradio Client 2.7.1 source verifies token, separate endpoint-scoped oauth_token, view_api, prediction, queue and download behavior. Local handle_file tests confirm file marking only. The current BoltzGen demo source at commit 829bdf3baf7ac85f252fea917028a813f4d0aebd must be rechecked if the app changes. Its runtime was PAUSED; public /config and /gradio_api/info returned 503. The five-input design contract and status-string return are source verified only; no endpoint name or downloadable artifact has been validated against a live job. The old lower-case demo ID and old heatmap ID returned 401; live organization metadata identified BoltzGen_Demo and Docker science-release-map instead.

No large dataset shard, pretrained model weight, native Evo2/CUDA runtime, authenticated inference, upload, moderation action or design job was executed. Use the live application schema before any of those operations.

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