Delete AGENTS.md

AGENTS.md

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-# ZSP — Agent Guide
-
-**What it is.** Gradio web app that scores protein sequence variants using ESM2, E1, and ESMC language models. Implements ESM-Scan methodology ([doi:10.1002/pro.5221](https://doi.org/10.1002/pro.5221)).
-
-## Structure
-
-```
-app.py        — Gradio UI, entry point
-model.py      — ModelFactory + wrappers for ESM/E1/ESMC models
-data.py       — Input parsing, scoring modes, output rendering (heatmap/table)
-requirements.txt — deps (gradio, torch, esm[Biohub], pandas, seaborn, E1)
-header.md     — UI header text
-instructions.md — user instructions tab content
-out.*         — generated outputs (gitignored)
-```
-
-## Run
-
-```bash
-source .venv/bin/activate   # or however you activate
-python app.py
-```
-
-Deploys as a HuggingFace Space (`sdk: gradio`, `app_file: app.py`). Python 3.12.
-
-## Scoring Modes
-
-Parsed from the substitutions input in `data.py`:
-
-| Mode | Trigger | What it does |
-|------|---------|-------------|
-| **TMS** (triple mutational scan) | No match to other patterns | All-positions × all-amino-acids sweep → heatmap image |
-| **DMS** (deep mutational scan) | All tokens are integers | Specified positions × all alternatives → sorted table |
-| **MUT** (single mutations) | Tokens match `[A-Z]\d+[A-Z]` | Explicit substitution list → scored table |
-| **MUT-seq-vs-seq** | Single token same length as sequence | Align two sequences, score differences → scored table |
-
-Scoring strategy flag: `"masked-marginals"` (higher accuracy, slower) vs `"wt-marginals"`.
-
-## Key Design Notes
-
-- Models loaded lazily via `ModelFactory`; ESM and ESMC use shared `ESMModel` wrapper, E1 uses its own package (`E1@git+...`)
-- ESMC requires `esm@git+Biohub/esm` — registers custom `esmc` architecture with transformers fork
-- GPU auto-detected; falls back to CPU
-- E1 model chunks batches at 60 to avoid OOM
-- TMS mode produces a seaborn heatmap PNG; other modes produce styled HTML tables
-- Output files always written to `out.csv` / `out.png` in CWD
-- Progress tracking wired into Gradio's `Progress` object
-
-## Edit Rules
-
-- Match existing style: one-line docstrings on classes/methods, minimal comments
-- No new dependencies unless absolutely necessary — stdlib or already-installed first
-- Torch/transformers signatures: grep before guessing versions
-- Output format changes affect both CSV and image/table paths — update both
-- ModelFactory registry is class-level `_models` dict; adding a model type means registering there