AGENTS.md ยท diff
git:20260621.3a1e3de to git:20260830.9257ef9
21 added, 18 removed. Audit A to A.
# BioSymphony Small Molecules Agent Guide
- Guide for agents and operators working in this public-safe skill repo.
+ Use this guide when you update the public skill repository.
## Mission
Maintain an agent-readable map of open small-molecule design tools: synthesis
planning, synthesizable generation, docking, co-folding, free energy, QSAR,
ADMET, selectivity, and structure-based generation.
- The repo is a routing and diligence layer. It helps an agent choose a tool,
- understand the license stack, and avoid treating confidence scores or README
- badges as stronger support than they are.
+ The repository helps an agent choose a tool, review each license layer, and
+ distinguish model confidence from experimental evidence.
## Public Safety Rules
Do not add:
- - API keys, provider credentials, signed URLs, SSH keys, or registry auth
+ - API keys, provider credentials, signed URLs, SSH keys, or registry authentication
- local workstation paths or copied repository history
- pod IDs, network volume IDs, account IDs, raw provider logs, or cost ledgers
- non-public issue text, non-release planning notes, unpublished structures,
- non-public sequences, non-public assays, non-public datasets, raw reads, database mirrors, or
- model weights
- - generated media or large demo artifacts unless they are explicitly curated for
- public release
+ non-public sequences, non-public assays, non-public datasets, raw reads,
+ database mirrors, or model weights
+ - generated media or large demo artifacts unless they are reviewed for public
+ release
Use only public structures, public tool metadata, synthetic examples, or compact
- public demo artifacts. Keep claims tied to the support in the docs.
+ public demo artifacts. Cite the public repository, paper, model card, or license
+ file that supports each claim.
## Required Checks
Run before committing public-release changes:
```bash
make release-check
```
- That gate compiles the public Python scripts, scans for local paths and secret
- patterns, and checks the markdown links that can be checked locally.
+ This command compiles the public Python scripts, scans for local paths and secret
+ patterns, and checks the Markdown links that can be checked locally.
## Skill Loop
- Use `SKILL.md`. Summary: identify the task category, open the matching
- reference file, check code/weights/data/base-model licenses separately, then
- recommend the smallest tool path that fits the user request.
+ Use `SKILL.md`:
+ 1. Identify the task category.
+ 2. Open the matching reference file.
+ 3. Check the code, model weights, data, and base-model terms separately.
+ 4. Recommend the smallest tool path that fits the request.
+
## Claim Boundaries
- Treat this repo as tool-selection guidance, not legal advice, medical advice, or
- validated drug-discovery output. Before commercial use, re-check live upstream
- licenses and data terms.
+ Treat this repository as tool-selection guidance, not legal advice, medical
+ advice, or validated drug-discovery output. Before product use, re-check the
+ upstream licenses and data terms.