chore: nightly skills sync by github-actions[bot] · Pull Request #26 · NVIDIA-BioNeMo/bionemo-agent-toolkit

github-actions · 2026-08-05T07:55:11Z

Automated skills sync

Components updated:

Proteina-Complexa
aggregate payload
compliance backfill
nvMolKit

Failed to sync:

KERMT (NVIDIA-BioNeMo/KERMT): agent/skills empty or missing

Cards backfilled from compliance.d (upstream still owes a skill-card.md):

open-models-skills/kermt/kermt-infer
open-models-skills/kermt/kermt-monitor
open-models-skills/kermt/kermt-pretrain-scratch
open-models-skills/kermt/kermt-continue-pretrain
open-models-skills/kermt/kermt-finetune
open-models-skills/kermt/kermt-setup
open-models-skills/kermt/kermt-add-cmim-pretrain
open-models-skills/kermt/kermt-embed
open-models-skills/proteina-complexa/complexa-target
open-models-skills/proteina-complexa/complexa-setup
open-models-skills/proteina-complexa/complexa-sweep
open-models-skills/proteina-complexa/complexa-evaluate-pdbs
open-models-skills/proteina-complexa/complexa-design

Upstream now ships its own card — delete these compliance.d entries:

compliance.d/library-skills/nvmolkit-usage/skill-card.md

Sourced content changes + any pruning are shown in the diff. Native
skills (NIM, workflows, parabricks, genomics, cuEquivariance) are untouched.
Review the diff and merge — nothing merges unattended.

greptile-apps · 2026-08-13T07:38:13Z

Confidence Score: 4/5

[Low impact] Nightly sync of skill documentation and evaluation metadata.

The PR needs the remaining signed-file mismatch fixed before merging.

Findings

Signature resources do not match ▶
Documentation map links are broken ▶
Published hardware link is broken ▶
Cards say included tests are missing ▶

Summary

Syncs upstream Complexa and nvMolKit skills and backfills KERMT and Complexa cards.

The nvMolKit guide covers more ways to work with molecule batches.
Complexa design guidance points agents to the full design pipeline.
Complexa evaluation guidance covers scoring existing PDB folders.
Complexa setup guidance uses clearer .env and download details.
Complexa sweep guides link directly to their references.
Complexa target cards explain how target setup fits the design workflow.
KERMT cards describe eight workflows across both skill catalogs.

_{Reviews (21) · Last reviewed commit: "chore: sync skills from source repos" · Reviewed by Greptile}

greptile-apps · 2026-08-13T07:38:16Z

+> - Running a design? See [Inference Guide](INFERENCE.md)
+> - Tuning YAML configs? See [Configuration Guide](CONFIGURATION_GUIDE.md)
+> - Understanding metrics? See [Evaluation Guide](EVALUATION_METRICS.md)
+> - Search metadata? See [Search Metadata](SEARCH_METADATA.md)


Documentation map links are broken

The new links to INFERENCE.md, CONFIGURATION_GUIDE.md, EVALUATION_METRICS.md, and SEARCH_METADATA.md resolve relative to this directory, but none of those files exists. Readers following the documentation map therefore receive file-not-found errors instead of the promised guidance; the mirrored plugin file contains the same broken links.

greptile-apps · 2026-09-05T07:13:31Z

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Signature resources do not match

The new signature bundle records SKILL.md with SHA-256 31375d..., but the current file hashes to 39ec45.... It also requires a BENCHMARK.md that is absent from this directory. Consumers verifying this skill against the bundle will reject it because the signed resources are missing or do not match.

greptile-apps · 2026-10-15T07:22:26Z

 Total GPU-time for a sweep = `N_configs × per_run_GPU_time`. A single `search_binder_local_pipeline` run on one A100 is roughly 30–90 min (binder length + nsteps dependent). A 4-axis × 4-value sweep = 256 configs × ~60 min = ~256 GPU-hours — at that scale, plan on a multi-GPU host with the Step-4 sharding pattern.

-Refer to the shared hardware reference for the per-run baseline + VRAM minima.
+Refer to [`.claude/skills/_shared/reference/hardware.md`](../_shared/reference/hardware.md) for the per-run baseline + VRAM minima.


Published hardware link is broken

The new ../_shared/reference/hardware.md link works in the source tree, but the marketplace aggregate has no _shared directory. Installed users cannot open the promised GPU requirements. Copy the reference into the published skill and update both links.

greptile-apps · 2026-10-15T07:22:26Z

+Target agents: `claude-code`, `codex`. NVSkills-Eval has not yet been run against this skill — see Evaluation Results. <br>
+
+## Evaluation Tasks: <br>
+Not yet present on this branch. A co-located `evals/evals.json` with 4 tasks — covering pipeline selection, pre-flight validation, design execution, and result collection with manifest emission — is introduced by [PR #57](https://github.com/NVIDIA-BioNeMo/Proteina-Complexa/pull/57) (branch `aggregator-compat`) and lands on `dev` when that merges. <br>


Cards say included tests are missing

The new Complexa cards say evals/evals.json is not yet present, but all five skills already ship that file with four tasks. Readers are incorrectly told to wait for another change. Update the cards and their aggregate copies to describe the included tests, while keeping the separate notice that they have not been run. This also appears in complexa-setup, complexa-evaluate-pdbs, and the other Complexa cards.

Note: If this suggestion doesn't match your team's coding style, reply to this and let me know. I'll remember it for next time!

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Comment thread library-skills/nvmolkit-usage/BENCHMARK.md Outdated

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chore: sync skills from source repos

a6eced5

github-actions Bot force-pushed the automated/sync-skills branch from a47e542 to a6eced5 Compare October 16, 2026 07:15

ohadmo merged commit b4be868 into main Oct 19, 2026
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chore: nightly skills sync - #26

chore: nightly skills sync#26
ohadmo merged 1 commit into
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		@@ -0,0 +1 @@
		{"mediaType":"application/vnd.dev.sigstore.bundle.v0.3+json","verificationMaterial":{"x509CertificateChain":{"certificates":[{"rawBytes":"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"},{"rawBytes":"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"},{"rawBytes":"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"}]},"tlogEntries":[]},"dsseEnvelope":{"payload":"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","payloadType":"application/vnd.in-toto+json","signatures":[{"sig":"MGUCMBn0BSJgFYvoQi2dx6Sv/L6x3ge9NWCxRlpFLvb4wPa/7cdIsDblPsOEBlokVaQ0awIxAPe/ulb0kunUu68m04Wz9Nsy4dxaXXaRpg3upzXc/uz0wIXQCn8hMcQd1S6hhA2t4A==","keyid":""}]}} No newline at end of file

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