Fix Space stuck on APP_STARTING: migrate gradio 5.49 -> 6.18

The dev Space hung forever on APP_STARTING (app bound 7860, served, 49 tools
loaded) but HF never flipped it to Running. The earlier "disable SSR" change
(d38496a) was a red herring: the known-good orchestrator Space runs gradio 6.x
WITH SSR enabled and reaches Running, while this Space on 5.49.0 hangs
regardless of ssr_mode. Root cause is that gradio 5.49.0 no longer completes
HF's current Spaces readiness handshake; 6.x does.

Changes:
- README sdk_version 5.49.0 -> 6.18.0 (matches the running orchestrator Space).
- requirements.in: gradio[oauth,mcp] 5.49.0 -> 6.18.0. This lifts the old
mcp==1.10.1 hard-pin, so langchain-mcp-adapters floats 0.2.2 -> 0.3.0 and
mcp -> 1.28.0. fastmcp pinned ==3.2.3: 2.11.2 is incompatible with mcp>=1.28
(@mcp.tool returns a non-callable FunctionTool, breaking every direct tool
call + the whole suite) and 3.4.x breaks `from fastmcp import FastMCP`.
- gradio_ui.py: port to the 6.0 API — move theme+css off Blocks() onto
launch(); drop removed Chatbot(type=, show_copy_button=) and Textbox(
show_copy_button=) args; remove the obsolete ssr_mode=False override.

Verified locally on the pinned set (gradio 6.18.0 / mcp 1.28.0 /
langchain-mcp-adapters 0.3.0 / fastmcp 3.2.3): UI builds, 49 MCP tools
discover with no errors, full suite 851 passed / 55 skipped.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

README.md

@@ -4,7 +4,7 @@ colorFrom: blue
 python_version: 3.11
 colorTo: gray
 sdk: gradio
-sdk_version: 5.49.0
+sdk_version: 6.18.0
 app_file: app.py
 pinned: false
 ---

gradio_ui.py

@@ -756,14 +756,9 @@ class GradioAgentUI(_UIFormattingMixin):
             gr.DownloadButton(value=log, interactive=log is not None),
         )
 
-    def create_app(self):
-        """Create the Gradio app with sidebar layout."""
-        modern_theme = gr.themes.Monochrome(
-            font=fonts.GoogleFont("Inter"),
-            font_mono=fonts.GoogleFont("JetBrains Mono")
-        )
-
-        with gr.Blocks(theme=modern_theme, fill_height=True, title=self.name, css="""
+    # theme + css moved out of the gr.Blocks() constructor: Gradio 6.0 removed
+    # those args from Blocks and only accepts them on launch().
+    _GRADIO_CSS = """
             .footer {display: none !important;}
             footer {display: none !important;}
             .gradio-footer {display: none !important;}
@@ -773,7 +768,17 @@ class GradioAgentUI(_UIFormattingMixin):
             .block.svelte-1scc9gv {display: none !important;}
             .built-with-gradio {display: none !important;}
             .gradio-container footer {display: none !important;}
-            """) as demo:
+            """
+
+    def _gradio_theme(self):
+        return gr.themes.Monochrome(
+            font=fonts.GoogleFont("Inter"),
+            font_mono=fonts.GoogleFont("JetBrains Mono")
+        )
+
+    def create_app(self):
+        """Create the Gradio app with sidebar layout."""
+        with gr.Blocks(fill_height=True, title=self.name) as demo:
             demo.load(js="""
             () => {
                 document.body.classList.remove('dark');
@@ -869,9 +874,7 @@ class GradioAgentUI(_UIFormattingMixin):
                 with gr.Column(scale=3):
                     chatbot = gr.Chatbot(
                         label="Agent Conversation",
-                        type="messages",
                         height=700,
-                        show_copy_button=True,
                         avatar_images=(None, "images.png"),
                         latex_delimiters=[
                             {"left": r"$$", "right": r"$$", "display": True},
@@ -898,7 +901,6 @@ class GradioAgentUI(_UIFormattingMixin):
                         lines=10,
                         visible=False,
                         interactive=False,
-                        show_copy_button=True,
                     )
 
             def _inputs_dir():
@@ -1081,8 +1083,7 @@ class GradioAgentUI(_UIFormattingMixin):
         kwargs.setdefault('server_name', '0.0.0.0')
         kwargs.setdefault('server_port', 7860)
         kwargs.setdefault('show_error', True)
-        # Disable Gradio 5.x experimental SSR: on HF Spaces it auto-enables (Node
-        # present) and the readiness check hangs the Space on "Starting" forever
-        # even though the app binds 7860. Overridable via kwargs / GRADIO_SSR_MODE.
-        kwargs.setdefault('ssr_mode', False)
+        # Gradio 6.0 moved theme + css off the Blocks() constructor onto launch().
+        kwargs.setdefault('theme', self._gradio_theme())
+        kwargs.setdefault('css', self._GRADIO_CSS)
         app.queue(max_size=10).launch(share=share, show_api=False, favicon_path=None, **kwargs)

requirements.in

@@ -21,10 +21,14 @@ biodata-registry @ https://huggingface.co/anne-voigt/biodata-registry/resolve/56
 GEOparse==2.0.4
 
 # --- Agent / UI ---
-# Pinned to match the Space's sdk_version (README frontmatter) exactly; the
-# [oauth,mcp] extras hard-pin mcp==1.10.1 (see langchain-mcp-adapters note).
-# Do not float to gradio 6.x — it diverges from the Space runtime.
-gradio[oauth,mcp]==5.49.0
+# Pinned to match the Space's sdk_version (README frontmatter) exactly.
+# gradio 5.49.0 stopped completing HF's Spaces readiness handshake on the
+# current runtime (Space hangs forever on APP_STARTING even though the app
+# binds 7860). 6.x is what the current HF runtime expects; 6.18.0 matches the
+# known-good orchestrator Space on this account. The [oauth,mcp] extras no
+# longer hard-pin the old mcp==1.10.1, so langchain-mcp-adapters can float up
+# (see its note below).
+gradio[oauth,mcp]==6.18.0
 huggingface_hub
 python-dotenv
 jinja2
@@ -40,15 +44,25 @@ langchain-core
 # Pinned: 1.x requires a thread_id in graph config when a checkpointer is
 # attached (see workflow_engine.run_workflow). Verified working on 1.1.6.
 langgraph>=1.1.6,<2
-# Pinned <=0.2.2: 0.3.0 imports the renamed `streamable_http_client` from
-# mcp.client.streamable_http, absent in mcp==1.10.1 (hard-pinned by
-# gradio[oauth,mcp]==5.49.0 on this Space). Fails at import time in
-# MCPManager.add_mcp(), silently yielding 0 MCP tools. 0.2.2 uses the old name.
-langchain-mcp-adapters<=0.2.2
+# Floats up now that gradio 6.x no longer hard-pins mcp==1.10.1. 0.3.0+ imports
+# `streamable_http_client` from mcp.client.streamable_http, which exists in the
+# newer mcp that gradio 6.x pulls. (The old <=0.2.2 cap was required only by the
+# mcp==1.10.1 pin that gradio 5.49.0 forced.) Verify 49 MCP tools still load
+# after any bump — a mismatch silently yields 0 tools.
+langchain-mcp-adapters>=0.3.0
 
 # --- MCP ---
-fastmcp
-mcp
+# fastmcp pinned to 3.2.3 exactly:
+#  - 2.11.2 (what gradio 5.49 forced) is incompatible with the newer mcp (>=1.28)
+#    that gradio 6.x + langchain-mcp-adapters 0.3.0 pull in: under that combo
+#    `@mcp.tool` returns a non-callable FunctionTool and every direct tool call
+#    (and the whole test suite) breaks.
+#  - 3.4.x breaks the top-level `from fastmcp import FastMCP` import ("unknown
+#    location"), so don't float up.
+# 3.2.3 keeps tools callable, imports cleanly, discovers all 49, and the full
+# test suite passes (851).
+fastmcp==3.2.3
+mcp>=1.28
 starlette
 nest_asyncio
 

requirements.txt

@@ -1,15 +1,9 @@
-# GENERATED — do not hand-edit. Source of truth: requirements.in
-# Regenerate after editing requirements.in:
-#   uv pip compile requirements.in -o requirements.txt \
-#       --python-version 3.11 --python-platform linux
-# Fully version-pinned for reproducible HF builds. biodata-registry installs
-# from an immutable HF resolve URL (a wheel), so full --generate-hashes is now
-# possible (no git dep) but not yet applied. See requirements.in.
-#
+# This file was autogenerated by uv via the following command:
+#    uv pip compile requirements.in -o requirements.txt --python-version 3.11 --python-platform linux
 adjusttext==1.4.0
     # via decoupler
-aiofiles==24.1.0
-    # via gradio
+aiofile==3.11.1
+    # via py-key-value-aio
 anndata==0.12.17
     # via
     #   -r requirements.in
@@ -31,8 +25,10 @@ anyio==4.14.0
     #   httpx
     #   mcp
     #   openai
+    #   py-key-value-aio
     #   sse-starlette
     #   starlette
+    #   watchfiles
 array-api-compat==1.15.0
     # via anndata
 attrs==26.1.0
@@ -44,10 +40,18 @@ authlib==1.7.2
     # via
     #   fastmcp
     #   gradio
+backports-tarfile==1.2.0
+    # via jaraco-context
+beartype==0.22.9
+    # via py-key-value-aio
 biodata-registry @ https://huggingface.co/anne-voigt/biodata-registry/resolve/5654e86a8f3f5b369bf6ee2f71f51fc68ef912a8/biodata_registry-0.1.3-py3-none-any.whl
     # via -r requirements.in
 brotli==1.2.0
     # via gradio
+cachetools==7.1.4
+    # via py-key-value-aio
+caio==0.9.25
+    # via aiofile
 certifi==2026.5.20
     # via
     #   httpcore
@@ -70,6 +74,8 @@ cryptography==49.0.0
     # via
     #   authlib
     #   joserfc
+    #   pyjwt
+    #   secretstorage
 cycler==0.12.1
     # via matplotlib
 cyclopts==4.18.0
@@ -98,10 +104,8 @@ exceptiongroup==1.3.1
     # via fastmcp
 fastapi==0.137.1
     # via gradio
-fastmcp==2.11.2
+fastmcp==3.2.3
     # via -r requirements.in
-ffmpy==1.0.0
-    # via gradio
 filelock==3.29.4
     # via huggingface-hub
 fonttools==4.63.0
@@ -124,10 +128,12 @@ geoparse==2.0.4
     # via -r requirements.in
 google-crc32c==1.8.0
     # via zarr
-gradio==5.49.0
+gradio==6.18.0
     # via -r requirements.in
-gradio-client==1.13.3
-    # via gradio
+gradio-client==2.5.0
+    # via
+    #   gradio
+    #   hf-gradio
 groovy==0.1.2
     # via gradio
 h11==0.16.0
@@ -138,6 +144,8 @@ h5py==3.16.0
     # via
     #   anndata
     #   scanpy
+hf-gradio==0.4.1
+    # via gradio
 hf-xet==1.5.1
     # via huggingface-hub
 httpcore==1.0.9
@@ -167,12 +175,22 @@ idna==3.18
     #   email-validator
     #   httpx
     #   requests
+importlib-metadata==9.0.0
+    # via keyring
 interface-meta==2.0.1
     # via formulaic
-isodate==0.7.2
-    # via openapi-core
 itsdangerous==2.2.0
     # via gradio
+jaraco-classes==3.4.0
+    # via keyring
+jaraco-context==6.1.2
+    # via keyring
+jaraco-functools==4.5.0
+    # via keyring
+jeepney==0.9.0
+    # via
+    #   keyring
+    #   secretstorage
 jinja2==3.1.6
     # via
     #   -r requirements.in
@@ -193,20 +211,16 @@ jsonpatch==1.33
     # via langchain-core
 jsonpointer==3.1.1
     # via jsonpatch
+jsonref==1.1.0
+    # via fastmcp
 jsonschema==4.26.0
-    # via
-    #   mcp
-    #   openapi-core
-    #   openapi-schema-validator
-    #   openapi-spec-validator
+    # via mcp
 jsonschema-path==0.4.6
-    # via
-    #   openapi-core
-    #   openapi-spec-validator
+    # via fastmcp
 jsonschema-specifications==2025.9.1
-    # via
-    #   jsonschema
-    #   openapi-schema-validator
+    # via jsonschema
+keyring==25.7.0
+    # via py-key-value-aio
 kiwisolver==1.5.0
     # via matplotlib
 langchain-anthropic==1.4.6
@@ -221,7 +235,7 @@ langchain-core==1.4.7
     #   langgraph-checkpoint
     #   langgraph-prebuilt
     #   langgraph-sdk
-langchain-mcp-adapters==0.2.2
+langchain-mcp-adapters==0.3.0
     # via -r requirements.in
 langchain-openai==1.3.2
     # via -r requirements.in
@@ -241,8 +255,6 @@ langgraph-sdk==0.4.2
     # via langgraph
 langsmith==0.8.16
     # via langchain-core
-lazy-object-proxy==1.12.0
-    # via openapi-spec-validator
 legacy-api-wrap==1.5
     # via
     #   anndata
@@ -261,7 +273,6 @@ markupsafe==3.0.3
     # via
     #   gradio
     #   jinja2
-    #   werkzeug
 marsilea==0.6.2
     # via decoupler
 matplotlib==3.11.0
@@ -274,7 +285,7 @@ matplotlib==3.11.0
     #   pydeseq2
     #   scanpy
     #   seaborn
-mcp==1.10.1
+mcp==1.28.0
     # via
     #   -r requirements.in
     #   fastmcp
@@ -285,7 +296,9 @@ mdurl==0.1.2
 mizani==0.14.4
     # via plotnine
 more-itertools==11.1.0
-    # via openapi-core
+    # via
+    #   jaraco-classes
+    #   jaraco-functools
 narwhals==2.22.1
     # via
     #   formulaic
@@ -334,16 +347,10 @@ numpy==2.4.6
     #   zarr
 openai==2.41.1
     # via langchain-openai
-openapi-core==0.23.1
-    # via fastmcp
 openapi-pydantic==0.5.1
     # via fastmcp
-openapi-schema-validator==0.8.1
-    # via
-    #   openapi-core
-    #   openapi-spec-validator
-openapi-spec-validator==0.8.5
-    # via openapi-core
+opentelemetry-api==1.42.1
+    # via fastmcp
 orjson==3.11.9
     # via
     #   gradio
@@ -354,6 +361,7 @@ ormsgpack==1.12.2
 packaging==26.2
     # via
     #   anndata
+    #   fastmcp
     #   gradio
     #   gradio-client
     #   huggingface-hub
@@ -390,9 +398,13 @@ pillow==11.3.0
     #   gradio
     #   matplotlib
 platformdirs==4.10.0
-    # via marsilea
+    # via
+    #   fastmcp
+    #   marsilea
 plotnine==0.15.7
     # via -r requirements.in
+py-key-value-aio==0.4.5
+    # via fastmcp
 pyarrow==24.0.0
     # via pandas
 pycparser==3.0
@@ -411,16 +423,11 @@ pydantic==2.11.10
     #   mcp
     #   openai
     #   openapi-pydantic
-    #   openapi-schema-validator
-    #   openapi-spec-validator
     #   pydantic-settings
 pydantic-core==2.33.2
     # via pydantic
 pydantic-settings==2.14.1
-    # via
-    #   mcp
-    #   openapi-schema-validator
-    #   openapi-spec-validator
+    # via mcp
 pydeseq2==0.5.4
     # via -r requirements.in
 pydub==0.25.1
@@ -429,6 +436,8 @@ pygments==2.20.0
     # via
     #   rich
     #   rich-rst
+pyjwt==2.13.0
+    # via mcp
 pynndescent==0.6.0
     # via
     #   scanpy
@@ -453,12 +462,15 @@ python-multipart==0.0.32
     #   gradio
     #   mcp
 pytz==2026.2
-    # via pandas
+    # via
+    #   gradio
+    #   pandas
 pyyaml==6.0.3
     # via
     #   -r requirements.in
     #   biodata-registry
     #   donfig
+    #   fastmcp
     #   gradio
     #   huggingface-hub
     #   jsonschema-path
@@ -468,7 +480,6 @@ referencing==0.37.0
     #   jsonschema
     #   jsonschema-path
     #   jsonschema-specifications
-    #   openapi-schema-validator
 regex==2026.5.9
     # via tiktoken
 requests==2.34.2
@@ -480,8 +491,6 @@ requests==2.34.2
     #   tiktoken
 requests-toolbelt==1.0.0
     # via langsmith
-rfc3339-validator==0.1.4
-    # via openapi-schema-validator
 rich==15.0.0
     # via
     #   -r requirements.in
@@ -503,8 +512,6 @@ rpy2-rinterface==3.6.6
     #   rpy2-robjects
 rpy2-robjects==3.6.5
     # via rpy2
-ruff==0.15.17
-    # via gradio
 safehttpx==0.1.7
     # via gradio
 scanpy==1.11.5
@@ -536,6 +543,8 @@ seaborn==0.13.2
     # via
     #   marsilea
     #   scanpy
+secretstorage==3.5.0
+    # via keyring
 semantic-version==2.10.0
     # via gradio
 session-info==1.0.1
@@ -551,14 +560,13 @@ six==1.17.0
     # via
     #   docrep
     #   python-dateutil
-    #   rfc3339-validator
 sniffio==1.3.1
     # via
     #   anthropic
     #   openai
 sse-starlette==3.4.4
     # via mcp
-starlette==0.52.1
+starlette==1.3.1
     # via
     #   -r requirements.in
     #   fastapi
@@ -590,6 +598,7 @@ tqdm==4.68.2
 typer==0.25.1
     # via
     #   gradio
+    #   hf-gradio
     #   huggingface-hub
 typing-extensions==4.15.0
     # via
@@ -604,9 +613,11 @@ typing-extensions==4.15.0
     #   langchain-core
     #   langchain-mcp-adapters
     #   langchain-protocol
+    #   mcp
     #   numcodecs
     #   openai
-    #   openapi-core
+    #   opentelemetry-api
+    #   py-key-value-aio
     #   pydantic
     #   pydantic-core
     #   python-docx
@@ -619,6 +630,7 @@ typing-extensions==4.15.0
 typing-inspection==0.4.2
     # via
     #   fastapi
+    #   mcp
     #   pydantic
     #   pydantic-settings
 tzdata==2026.2
@@ -627,6 +639,8 @@ tzlocal==5.4.2
     # via rpy2-robjects
 umap-learn==0.5.12
     # via scanpy
+uncalled-for==0.3.2
+    # via fastmcp
 urllib3==2.7.0
     # via requests
 uuid-utils==0.16.1
@@ -635,15 +649,16 @@ uuid-utils==0.16.1
     #   langsmith
 uvicorn==0.49.0
     # via
+    #   fastmcp
     #   gradio
     #   mcp
+watchfiles==1.2.0
+    # via fastmcp
 websockets==15.0.1
     # via
-    #   gradio-client
+    #   fastmcp
     #   langgraph-sdk
     #   langsmith
-werkzeug==3.1.8
-    # via openapi-core
 wrapt==2.2.1
     # via formulaic
 xxhash==3.7.0
@@ -652,5 +667,7 @@ xxhash==3.7.0
     #   langsmith
 zarr==3.1.6
     # via anndata
+zipp==4.1.0
+    # via importlib-metadata
 zstandard==0.25.0
     # via langsmith