setuplisted

# Setup Guide Help users get their environment ready to run protein design tools. ## Quick checklist Run through this checklist when a user encounters setup issues: | Step | Check | Fix | |------|-------|-----| | 1. Modal CLI | `modal --version` | `pip install modal` | | 2. Modal auth | `modal token show` | `modal setup` | | 3. biomodals | `ls biomodals/modal_*.py` | `git clone https://github.com/hgbrian/biomodals` | | 4. Test | `cd biomodals && modal run modal_boltzgen.py --help` | See troubleshooting | ## Diagnosing issues ### Error: "modal: command not found" **Cause**: Modal CLI not installed. **Fix**: ```bash pip install modal ``` Then restart the terminal or run `hash -r`. ### Error: "Permission denied" or "Unauthorized" **Cause**: Modal not authenticated. **Fix**: ```bash modal setup ``` This opens a browser. Click "Authorize" to complete authentication. ### Error: "No such file or directory: modal_boltzgen.py" **Cause**: biomodals repository not cloned or not in correct directory. **Fix**: ```bash git clone https://github.com/hgbrian/biomodals cd biomodals ``` ### Error: "uvx: command not found" **Cause**: `uvx` is an optional wrapper from the `uv` package. It's not required. **Fix**: Run modal directly (recommended): ```bash modal run modal_boltzgen.py --help ``` Or install uv if you prefer using uvx: ```bash pip install uv ``` ## Full setup steps ### Step 1: Install Modal CLI ```bash pip install modal ``` Verify: `modal --version` ### Step 2