references/source-pins.md

# Source pins and primary references

Verified 2026-07-14. These pins fix first-party source and model selection; re-resolve and test before deliberately upgrading them. They do not constitute a complete environment lock because the pinned ESM package retains broad transitive dependency ranges and execution still depends on the Python, accelerator, driver, and hardware runtime.

## Code and model revisions

| Artifact | Revision |
| --- | --- |
| `Biohub/esm` | `ba4d7124864eed323a93bf3cfefcd958f573b75a` |
| `Biohub/transformers` | `ef32577f55da19a4989cd7b22e004dc43a4998cb` |
| `biohub/ESMC-300M` | `a59b831785f907e96e6a246b1d142bfb76df31ee` |
| `biohub/ESMC-600M` | `a7e82012c83126b9eedb055fea9fa84b6c02f094` |
| `biohub/ESMC-6B` | `45b0fa5d7fb06faefbd5e3b89bdcef35d564e79a` |
| `biohub/ESMFold2` | `1ebf0e3481a5184eb6171d40615c79e384b48796` |
| `biohub/ESMFold2-Fast` | `b28d8ace5e05e61e5bec1e6820cfd3e221819d12` |
| Modal Python SDK | `1.5.2` |

## Official tutorial snapshots

The plugin's expanded use cases are derived from these notebooks at the exact `Biohub/esm` revision above. SHA-256 values cover the raw notebook bytes retrieved from that revision on 2026-07-14; the machine-readable mapping lives in [`examples/tutorial-use-cases.json`](../examples/tutorial-use-cases.json).

| Notebook | Repository path | SHA-256 |
| --- | --- | --- |
| ESMC mutation scoring | `cookbook/tutorials/esmc_mutation_scoring.ipynb` | `40b49cecb80c18a1076013999a06b90f9f77bb6c06f81789d071335d09ae1482` |
| ESMC SAE feature interpretation | `cookbook/tutorials/esmc_sae_feature_interpretation.ipynb` | `4ac0dd7b39d694787f3ce858221f1d045fd225c16c580762e3c2af5919ed59d2` |
| ESMFold2 | `cookbook/tutorials/esmfold2.ipynb` | `efc47094be02ea99c409e09830a1275fc1fe46c46accda2e942bbef876c357b3` |

The bounded binder smoke separately verifies Modal examples commit `84939b0e7441198d16d3b37c937d18c0637b9729` and its two reviewed source-file checksums before copying it to a temporary directory. The smoke pins:

| Binder artifact | Revision |
| --- | --- |
| `Biohub/esm` used by the official binder example | `f652b471d29da828b31e9b7a9cf7d0a7803240f5` |
| `biohub/ESMFold2-Experimental-Fast` | `04dec820ede9283c9893e318e5ca5a9ac2ab93bc` |
| `biohub/ESMFold2-Experimental-Fast-Cutoff2025` | `74b88548bf19688b8727432db0d698cb2e1d8783` |
| `biohub/ESMFold2-Experimental` | `0515a1177d6e6aab93750cbadf7b54da77bac592` |
| `biohub/ESMFold2-Experimental-Cutoff2025` | `56f94f5c1069ecde17512c96928850518340d287` |

The ESMC-6B and Transformers revisions remain the pins listed above. The temporary copy injects every checkpoint revision because the reviewed upstream example otherwise resolves model weights from mutable Hub defaults. It uses the direct `main` entry point with scaling critics disabled.

Use the full revisions, not `main`, in installs and `from_pretrained(..., revision=...)`. The pinned `Biohub/esm` package currently declares the Biohub Transformers fork from mutable `main`. Install ESM first, then force-reinstall exact Transformers with `--no-deps`; a combined resolver invocation can retain `requested_revision = main` even when its resolved commit happens to match. Verify both PEP 610 fields before execution. Record both code revisions and the Hugging Face model revision in every self-hosted or Modal provenance sidecar. Atlas and raw-HTTP paths record these code revisions as `null` because those dependencies did not execute. Live SDK/local smokes verify PEP 610 install metadata before asserting a local code commit.

The generic Modal job controller requires the exact SDK version above because its resumability decisions depend on the documented `FunctionCall` methods and exception classes. It also requires a positive deployed Function version and uses Modal's version-pinned `Function.from_name` lookup. Both values are recorded in durable job state; update the SDK pin only after revalidating spawn, reattachment, polling, cancellation, and exception classification against the new release. Modal's official changelog and PyPI release metadata both identify `1.5.2` as the current stable release on 2026-07-13; the version-pinned Function lookup used here was introduced in 1.5.0.

## Primary sources

- [Biohub protein world model](https://biohub.ai/esm/protein)
- [Biohub ESM get-started guide](https://biohub.ai/esm/protein/get-started)
- [ESMC model page](https://biohub.ai/models/esmc)
- [ESMFold2 model page](https://biohub.ai/models/esmfold2)
- [Biohub managed API reference](https://biohub.ai/api-reference)
- [ESM Atlas API overview](https://biohub.ai/esm/protein/atlas/api-docs/overview.html)
- [ESM Atlas API reference](https://biohub.ai/esm/protein/atlas/api-docs/api_reference.html)
- [ESM Atlas OpenAPI document](https://biohub.ai/esm/protein/atlas/api-docs/_static/openapi.json)
- [Biohub/esm source](https://github.com/Biohub/esm)
- [Official ESMC mutation-scoring tutorial](https://github.com/Biohub/esm/blob/ba4d7124864eed323a93bf3cfefcd958f573b75a/cookbook/tutorials/esmc_mutation_scoring.ipynb)
- [Official ESMC SAE-interpretation tutorial](https://github.com/Biohub/esm/blob/ba4d7124864eed323a93bf3cfefcd958f573b75a/cookbook/tutorials/esmc_sae_feature_interpretation.ipynb)
- [Official ESMFold2 tutorial](https://github.com/Biohub/esm/blob/ba4d7124864eed323a93bf3cfefcd958f573b75a/cookbook/tutorials/esmfold2.ipynb)
- [ESMC-6B model card](https://huggingface.co/biohub/ESMC-6B)
- [ESMFold2 model card](https://huggingface.co/biohub/ESMFold2)
- [Modal ESMFold2 example](https://modal.com/docs/examples/esmfold2)
- [Modal ESMFold2 binder-design example](https://modal.com/docs/examples/esmfold2_binder_design)
- [Modal authentication configuration](https://modal.com/docs/sdk/py/latest/modal.config)
- [Modal Python SDK changelog](https://modal.com/docs/sdk/py/changelog)
- [Modal Function and version-pinned lookup](https://modal.com/docs/sdk/py/latest/modal.Function)
- [Modal FunctionCall lifecycle](https://modal.com/docs/sdk/py/latest/modal.FunctionCall)
- [Modal scale-out guide and limits](https://modal.com/docs/guide/scale)
- [Language Modeling Materializes a World Model of Protein Biology, bioRxiv v1](https://www.biorxiv.org/content/10.64898/2026.06.03.729735v1)

The Atlas reference explicitly labels the API alpha, unauthenticated, mutable, and unsuitable for production assumptions. Preserve raw responses alongside normalized artifacts so schema drift can be diagnosed.