chore: update Gradio dependency to include MCP extras and version bump

- Modified `pyproject.toml` to specify Gradio with MCP extras and updated the version to 6.0.1.
- Updated `uv.lock` to reflect the new Gradio dependency structure and version.
- Made minor formatting adjustments in the MCP server documentation for clarity.

Files modified:
- pyproject.toml
- uv.lock
- docs/implementation/12_phase_mcp_server.md

docs/implementation/12_phase_mcp_server.md

@@ -808,12 +808,12 @@ Phase 12 is **COMPLETE** when:
 
 ```
 ┌────────────────────────────────────────────────────────────────┐
-│                      Claude Desktop / Cursor                    │
-│                           (MCP Client)                          │
+│                      Claude Desktop / Cursor                   │
+│                           (MCP Client)                         │
 └─────────────────────────────┬──────────────────────────────────┘
                               │ MCP Protocol
                               ▼
-┌────────────────────────────────────────────────────────────────┐
+┌─────────────────────────────────────────────────────────────────┐
 │                        Gradio MCP Server                        │
 │                  /gradio_api/mcp/                               │
 │  ┌──────────────┐ ┌──────────────┐ ┌──────────────┐ ┌─────────┐ │

pyproject.toml

@@ -17,7 +17,7 @@ dependencies = [
     "beautifulsoup4>=4.12", # HTML parsing
     "xmltodict>=0.13", # PubMed XML -> dict
     # UI
-    "gradio>=5.0", # Chat interface
+    "gradio[mcp]>=5.0.0", # Chat interface
     # Utils
     "python-dotenv>=1.0", # .env loading
     "tenacity>=8.2", # Retry logic

tests/unit/test_mcp_tools.py

@@ -0,0 +1,200 @@
+"""Unit tests for MCP tool wrappers."""
+
+from unittest.mock import AsyncMock, patch
+
+import pytest
+
+from src.mcp_tools import (
+    search_all_sources,
+    search_biorxiv,
+    search_clinical_trials,
+    search_pubmed,
+)
+from src.utils.models import Citation, Evidence
+
+
+@pytest.fixture
+def mock_evidence() -> Evidence:
+    """Sample evidence for testing."""
+    return Evidence(
+        content="Metformin shows neuroprotective effects in preclinical models.",
+        citation=Citation(
+            source="pubmed",
+            title="Metformin and Alzheimer's Disease",
+            url="https://pubmed.ncbi.nlm.nih.gov/12345678/",
+            date="2024-01-15",
+            authors=["Smith J", "Jones M", "Brown K"],
+        ),
+        relevance=0.85,
+    )
+
+
+class TestSearchPubMed:
+    """Tests for search_pubmed MCP tool."""
+
+    @pytest.mark.asyncio
+    async def test_returns_formatted_string(self, mock_evidence: Evidence) -> None:
+        """Should return formatted markdown string."""
+        with patch("src.mcp_tools._pubmed") as mock_tool:
+            mock_tool.search = AsyncMock(return_value=[mock_evidence])
+
+            result = await search_pubmed("metformin alzheimer", 10)
+
+            assert isinstance(result, str)
+            assert "PubMed Results" in result
+            assert "Metformin and Alzheimer's Disease" in result
+            assert "Smith J" in result
+
+    @pytest.mark.asyncio
+    async def test_clamps_max_results(self) -> None:
+        """Should clamp max_results to valid range (1-50)."""
+        with patch("src.mcp_tools._pubmed") as mock_tool:
+            mock_tool.search = AsyncMock(return_value=[])
+
+            # Test lower bound
+            await search_pubmed("test", 0)
+            mock_tool.search.assert_called_with("test", 1)
+
+            # Test upper bound
+            await search_pubmed("test", 100)
+            mock_tool.search.assert_called_with("test", 50)
+
+    @pytest.mark.asyncio
+    async def test_handles_no_results(self) -> None:
+        """Should return appropriate message when no results."""
+        with patch("src.mcp_tools._pubmed") as mock_tool:
+            mock_tool.search = AsyncMock(return_value=[])
+
+            result = await search_pubmed("xyznonexistent", 10)
+
+            assert "No PubMed results found" in result
+
+
+class TestSearchClinicalTrials:
+    """Tests for search_clinical_trials MCP tool."""
+
+    @pytest.mark.asyncio
+    async def test_returns_formatted_string(self, mock_evidence: Evidence) -> None:
+        """Should return formatted markdown string."""
+        mock_evidence.citation.source = "clinicaltrials"  # type: ignore
+
+        with patch("src.mcp_tools._trials") as mock_tool:
+            mock_tool.search = AsyncMock(return_value=[mock_evidence])
+
+            result = await search_clinical_trials("diabetes", 10)
+
+            assert isinstance(result, str)
+            assert "Clinical Trials" in result
+
+
+class TestSearchBiorxiv:
+    """Tests for search_biorxiv MCP tool."""
+
+    @pytest.mark.asyncio
+    async def test_returns_formatted_string(self, mock_evidence: Evidence) -> None:
+        """Should return formatted markdown string."""
+        mock_evidence.citation.source = "biorxiv"  # type: ignore
+
+        with patch("src.mcp_tools._biorxiv") as mock_tool:
+            mock_tool.search = AsyncMock(return_value=[mock_evidence])
+
+            result = await search_biorxiv("preprint search", 10)
+
+            assert isinstance(result, str)
+            assert "Preprint Results" in result
+
+
+class TestSearchAllSources:
+    """Tests for search_all_sources MCP tool."""
+
+    @pytest.mark.asyncio
+    async def test_combines_all_sources(self, mock_evidence: Evidence) -> None:
+        """Should combine results from all sources."""
+        with (
+            patch("src.mcp_tools.search_pubmed", new_callable=AsyncMock) as mock_pubmed,
+            patch("src.mcp_tools.search_clinical_trials", new_callable=AsyncMock) as mock_trials,
+            patch("src.mcp_tools.search_biorxiv", new_callable=AsyncMock) as mock_biorxiv,
+        ):
+            mock_pubmed.return_value = "## PubMed Results"
+            mock_trials.return_value = "## Clinical Trials"
+            mock_biorxiv.return_value = "## Preprints"
+
+            result = await search_all_sources("metformin", 5)
+
+            assert "Comprehensive Search" in result
+            assert "PubMed" in result
+            assert "Clinical Trials" in result
+            assert "Preprints" in result
+
+    @pytest.mark.asyncio
+    async def test_handles_partial_failures(self) -> None:
+        """Should handle partial failures gracefully."""
+        with (
+            patch("src.mcp_tools.search_pubmed", new_callable=AsyncMock) as mock_pubmed,
+            patch("src.mcp_tools.search_clinical_trials", new_callable=AsyncMock) as mock_trials,
+            patch("src.mcp_tools.search_biorxiv", new_callable=AsyncMock) as mock_biorxiv,
+        ):
+            mock_pubmed.return_value = "## PubMed Results"
+            mock_trials.side_effect = Exception("API Error")
+            mock_biorxiv.return_value = "## Preprints"
+
+            result = await search_all_sources("metformin", 5)
+
+            # Should still contain working sources
+            assert "PubMed" in result
+            assert "Preprints" in result
+            # Should show error for failed source
+            assert "Error" in result
+
+
+class TestMCPDocstrings:
+    """Tests that docstrings follow MCP format."""
+
+    def test_search_pubmed_has_args_section(self) -> None:
+        """Docstring must have Args section for MCP schema generation."""
+        assert search_pubmed.__doc__ is not None
+        assert "Args:" in search_pubmed.__doc__
+        assert "query:" in search_pubmed.__doc__
+        assert "max_results:" in search_pubmed.__doc__
+        assert "Returns:" in search_pubmed.__doc__
+
+    def test_search_clinical_trials_has_args_section(self) -> None:
+        """Docstring must have Args section for MCP schema generation."""
+        assert search_clinical_trials.__doc__ is not None
+        assert "Args:" in search_clinical_trials.__doc__
+
+    def test_search_biorxiv_has_args_section(self) -> None:
+        """Docstring must have Args section for MCP schema generation."""
+        assert search_biorxiv.__doc__ is not None
+        assert "Args:" in search_biorxiv.__doc__
+
+    def test_search_all_sources_has_args_section(self) -> None:
+        """Docstring must have Args section for MCP schema generation."""
+        assert search_all_sources.__doc__ is not None
+        assert "Args:" in search_all_sources.__doc__
+
+
+class TestMCPTypeHints:
+    """Tests that type hints are complete for MCP."""
+
+    def test_search_pubmed_type_hints(self) -> None:
+        """All parameters and return must have type hints."""
+        import inspect
+
+        sig = inspect.signature(search_pubmed)
+
+        # Check parameter hints
+        assert sig.parameters["query"].annotation == str
+        assert sig.parameters["max_results"].annotation == int
+
+        # Check return hint
+        assert sig.return_annotation == str
+
+    def test_search_clinical_trials_type_hints(self) -> None:
+        """All parameters and return must have type hints."""
+        import inspect
+
+        sig = inspect.signature(search_clinical_trials)
+        assert sig.parameters["query"].annotation == str
+        assert sig.parameters["max_results"].annotation == int
+        assert sig.return_annotation == str

uv.lock

@@ -1063,7 +1063,7 @@ source = { editable = "." }
 dependencies = [
     { name = "anthropic" },
     { name = "beautifulsoup4" },
-    { name = "gradio" },
+    { name = "gradio", extra = ["mcp"] },
     { name = "httpx" },
     { name = "openai" },
     { name = "pydantic" },
@@ -1111,7 +1111,7 @@ requires-dist = [
     { name = "beautifulsoup4", specifier = ">=4.12" },
     { name = "chromadb", marker = "extra == 'embeddings'", specifier = ">=0.4.0" },
     { name = "chromadb", marker = "extra == 'modal'", specifier = ">=0.4.0" },
-    { name = "gradio", specifier = ">=5.0" },
+    { name = "gradio", extras = ["mcp"], specifier = ">=5.0.0" },
     { name = "httpx", specifier = ">=0.27" },
     { name = "llama-index", marker = "extra == 'modal'", specifier = ">=0.11.0" },
     { name = "llama-index-embeddings-openai", marker = "extra == 'modal'" },
@@ -1568,7 +1568,7 @@ wheels = [
 
 [[package]]
 name = "gradio"
-version = "5.50.0"
+version = "6.0.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiofiles" },
@@ -1592,7 +1592,6 @@ dependencies = [
     { name = "pydub" },
     { name = "python-multipart" },
     { name = "pyyaml" },
-    { name = "ruff" },
     { name = "safehttpx" },
     { name = "semantic-version" },
     { name = "starlette" },
@@ -1601,13 +1600,20 @@ dependencies = [
     { name = "typing-extensions" },
     { name = "uvicorn" },
 ]
+sdist = { url = "https://files.pythonhosted.org/packages/65/13/f2bfe1237b8700f63e21c5e39f2843ac8346f7ba4525b582f30f40249863/gradio-6.0.1.tar.gz", hash = "sha256:5d02e6ac34c67aea26b938b8628c8f9f504871392e71f2db559ab8d6799bdf69", size = 36440914 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/22/04/8daf96bd6d2470f03e2a15a9fc900c7ecf6549619173f16c5944c7ec15a7/gradio-5.50.0-py3-none-any.whl", hash = "sha256:d06770d57cdda9b703ef9cf767ac93a890a0e12d82679a310eef74203a3673f4", size = 63530991 },
+    { url = "https://files.pythonhosted.org/packages/09/21/27ae5f4b2191a5d58707fc610e67453781a2b948a675a7cf06c99497ffa1/gradio-6.0.1-py3-none-any.whl", hash = "sha256:0f98dc8b414a3f3773cbf3caf5a354507c8ae309ed8266e2f30ca9fa53f379b8", size = 21559963 },
+]
+
+[package.optional-dependencies]
+mcp = [
+    { name = "mcp" },
+    { name = "pydantic" },
 ]
 
 [[package]]
 name = "gradio-client"
-version = "1.14.0"
+version = "2.0.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "fsspec" },
@@ -1615,10 +1621,10 @@ dependencies = [
     { name = "huggingface-hub" },
     { name = "packaging" },
     { name = "typing-extensions" },
-    { name = "websockets" },
 ]
+sdist = { url = "https://files.pythonhosted.org/packages/cf/0a/906062fe0577c62ea6e14044ba74268ff9266fdc75d0e69257bddb7400b3/gradio_client-2.0.0.tar.gz", hash = "sha256:56b462183cb8741bd3e69b21db7d3b62c5abb03c2c2bb925223f1eb18f950e89", size = 315906 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/be/8a/f2a47134c5b5a7f3bad27eae749589a80d81efaaad8f59af47c136712bf6/gradio_client-1.14.0-py3-none-any.whl", hash = "sha256:9a2f5151978411e0f8b55a2d38cddd0a94491851149d14db4af96f5a09774825", size = 325555 },
+    { url = "https://files.pythonhosted.org/packages/07/5b/789403564754f1eba0273400c1cea2c155f984d82458279154977a088509/gradio_client-2.0.0-py3-none-any.whl", hash = "sha256:77bedf20edcc232d8e7986c1a22165b2bbca1c7c7df10ba808a093d5180dae18", size = 315180 },
 ]
 
 [[package]]