proto-tools

Implements a new bioinformatics tool wrapper in proto-tools using a parallelized agent pipeline. Orchestrates phases: Research, Contract (core tool file), Fan-out (5 parallel subagents), Verify, then the decisive gates — Config Field Audit, Temp Integration & Stress, Docs Verification, Self-Audit & Full PR Review — and Ship. Use when creating tools from GitHub issues, wrapping models, or implementing new tool wrappers end-to-end.

Fixes tool environment setup failures in proto-tools, either just for the current machine (eject the tool's standalone dir, patch it, and point PROTO_<TOOLKIT>_STANDALONE_DIR at it; works for any install, including a non-editable pip install) or as a cross-platform fix contributed back to the repo. Same diagnosis for both: infrastructure failures (compute detection, env variable isolation, sitecustomize.py injection, micromamba install), PyTorch/CUDA issues (ABI mismatch, broken symlinks, triton coordination), JAX setup/downgrades, compilation failures (GCC/nvcc mismatch, source builds), network/binary download failures, platform issues (aarch64, Python version), and device management setup failures (standalone helpers, CUDA visibility). Use when a tool's setup.sh fails, an env breaks after a system update, or a standalone venv needs a fix — for your own use or to upstream.