update ui extra

Author: forrestzhang

README.md

@@ -140,12 +140,13 @@ uv pip install -e '.[all,cuda128]'
 
 | Group | Purpose | Includes |
 |-------|---------|----------|
-| `all` | Install everything | `base` + `docs` |
+| `all` | Install everything | `base` + `docs` + `ui` |
 | `base` | Full dev environment | `dev` + `test` + `notebook` + `mcp` + extra tools |
 | `dev` | Development | `test` + `notebook` + linting/typing tools |
 | `test` | Testing only | pytest and plugins |
 | `notebook` | Interactive notebooks | Jupyter, Marimo |
 | `docs` | Build documentation | mkdocs and plugins |
+| `ui` | Gradio web interface | Gradio |
 | `mcp` | MCP server | (included in core) |
 
 **Hardware groups (mutually exclusive, NOT included in `all`):**

docs/getting_started/installation.md

@@ -115,12 +115,13 @@ DNALLM provides multiple dependency groups for different use cases:
 
 | Group | Purpose | Includes |
 |-------|---------|----------|
-| **all** | Install all optional dependencies | `base` + `docs` |
+| **all** | Install all optional dependencies | `base` + `docs` + `ui` |
 | **base** | Full development environment | `dev` + `test` + `notebook` + `mcp` + extra tools (isort, types-transformers) |
 | **dev** | Complete development environment | `test` + `notebook` + linting/typing (ruff, flake8, pre-commit, mypy, pandas-stubs) |
 | **test** | Testing environment only | pytest and plugins |
 | **notebook** | Jupyter and Marimo support | Jupyter Lab, Marimo |
 | **docs** | Documentation building | mkdocs-material, mkdocstrings, mkdocs-jupyter |
+| **ui** | Gradio web interface | Gradio |
 | **mcp** | MCP server support | Included in core dependencies (no extra install needed) |
 
 > **Note:** `mcp` is an empty extra because MCP dependencies (`mcp`, `starlette`, `uvicorn`, `websockets`) are already part of the core dependencies. You can still use `.[mcp]` for clarity but it won't install additional packages.

pyproject.toml

@@ -100,14 +100,17 @@ docs = [
     "mkdocstrings-python>=1.16.10",
     "click<8.2.2",
 ]
+ui = [
+    "gradio>=4.0.0",
+]
 mcp = []
 base = [
     "dnallm[dev,test,notebook,mcp]",
     "isort>=6.0.1",
     "types-transformers>=0.1.0",
 ]
 all = [
-    "dnallm[base,docs]",
+    "dnallm[base,docs,ui]",
 ]
 cpu = [
     "torch>=2.4.0,<2.7",