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chore: nightly skills sync - #26

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@github-actions github-actions Bot commented Aug 5, 2026 •

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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.

@github-actions
github-actions Bot force-pushed the automated/sync-skills branch 4 times, most recently from 1bb02b0 to bda76c4 Compare August 13, 2026 07:33
@greptile-apps

greptile-apps Bot commented Aug 13, 2026 •

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RetriggerConfidence Score: 4/5

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

The PR does not yet appear safe to merge because the previously reported aggregate nvMolKit publication artifacts remain stale.

Findings

  1. P1 Signature resources do not match ▶
  2. P1 Aggregate publication artifacts remain stale ▶
  3. P2 Documentation map links are broken ▶

Summary

This PR syncs nvMolKit and Proteina-Complexa skills, adds KERMT and Complexa cards, and updates the aggregate payload. Since the previous review, it also adds NIM evaluation and signing artifacts, changes license declarations, and improves scanner diagnostics.

  • The new repository-level license declaration conflicts with existing per-file SPDX declarations.

Reviews (14) · Last reviewed commit: "chore: sync skills from source repos"

Comment on lines +6 to +9
> - 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)

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P2 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.

@github-actions
github-actions Bot force-pushed the automated/sync-skills branch 3 times, most recently from 3a5f680 to 43368d0 Compare August 21, 2026 07:19
@github-actions
github-actions Bot force-pushed the automated/sync-skills branch 2 times, most recently from 89aa260 to 8af329a Compare August 27, 2026 10:21
@github-actions
github-actions Bot force-pushed the automated/sync-skills branch from 8af329a to 957ca54 Compare September 5, 2026 07:11
@@ -0,0 +1 @@
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P1 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.

@github-actions
github-actions Bot force-pushed the automated/sync-skills branch 3 times, most recently from 11a4317 to deea36a Compare September 16, 2026 07:15
@github-actions
github-actions Bot force-pushed the automated/sync-skills branch from deea36a to 61841dc Compare September 20, 2026 07:12
Comment on lines +12 to +18
- Evaluation date: 2026-09-18
- Evaluator version: `1.5.6`
- Agents: Claude Code (`aws/anthropic/bedrock-claude-opus-4-8`), Codex (`openai/openai/gpt-5.5`)
- Tasks: 12 evaluation tasks (12 positive)
- Dataset digest: `sha256:ce8098e0dd2fc0698933b7d4d303fe13bdd1d9be7e87d142bdfc44baae7a9f90` (skill-evaluator-dataset-snapshot/1)
- Attempts per task: 3
- Environment: `k8s-sandbox`

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P1 Aggregate publication artifacts remain stale

The refreshed 12-task benchmark, skill card, and matching signature were added under library-skills/nvmolkit-usage, but the marketplace aggregate still contains its older 11-task benchmark, version 0.1.0 card, and signature. These files are treated as aggregate-only artifacts and excluded from normal sync freshness checks, so consumers will continue receiving stale publication metadata and a signature that does not cover the aggregate's updated SKILL.md and eval files. Please refresh the generated artifacts in skills/bionemo-agent-toolkit/skills/nvmolkit-usage.

@github-actions
github-actions Bot force-pushed the automated/sync-skills branch 2 times, most recently from 6015714 to 73a9620 Compare September 29, 2026 07:20
@github-actions
github-actions Bot force-pushed the automated/sync-skills branch from 73a9620 to 6cef36b Compare September 30, 2026 07:20
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