Merge branch 'main' into feature/image-search-v0

.dockerignore

@@ -0,0 +1,25 @@
+.venv
+.vscode/*
+!.vscode/extensions.json
+!.vscode/settings.json
+.idea
+.DS_Store
+*.suo
+*.ntvs*
+*.njsproj
+*.sln
+*.sw?
+__pycache__
+node_modules
+dist
+build
+joblib-cache
+*.egg-info
+
+lynxkite_crdt_data
+
+# Playwright
+test-results
+playwright-report
+/blob-report/
+/playwright/.cache/

.gitignore

@@ -1,3 +1,4 @@
+.venv
 .vscode/*
 !.vscode/extensions.json
 !.vscode/settings.json
@@ -18,7 +19,7 @@ joblib-cache
 lynxkite_crdt_data
 
 # Playwright
-/test-results/
-/playwright-report/
+test-results
+playwright-report
 /blob-report/
 /playwright/.cache/

.pre-commit-config.yaml

@@ -1,12 +1,12 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v5.0.0
   hooks:
     - id: trailing-whitespace
     - id: end-of-file-fixer
     - id: check-yaml
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.9.6
+  rev: v0.9.10
   hooks:
     - id: ruff
       args: [ --fix ]

Dockerfile

@@ -0,0 +1,16 @@
+FROM node:22
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+RUN apt-get update && apt-get install -y git
+USER node
+ENV HOME=/home/node PATH=/home/node/.local/bin:$PATH
+WORKDIR $HOME/app
+COPY --chown=node . $HOME/app
+RUN uv venv && uv pip install \
+  -e lynxkite-core \
+  -e lynxkite-app \
+  -e lynxkite-graph-analytics \
+  -e lynxkite-bio \
+  -e lynxkite-pillow-example
+WORKDIR $HOME/app/examples
+ENV PORT=7860
+CMD ["uv", "run", "lynxkite"]

README.md

@@ -1,3 +1,12 @@
+---
+title: LynxKite 2000:MM
+emoji: 🪁
+colorFrom: purple
+colorTo: gray
+sdk: docker
+app_port: 7860
+---
+
 # LynxKite 2024
 
 This is an experimental rewrite of [LynxKite](https://github.com/lynxkite/lynxkite). It is not compatible with the
@@ -32,7 +41,7 @@ uv pip install -e lynxkite-core/[dev] -e lynxkite-app/[dev] -e lynxkite-graph-an
 This also builds the frontend, hopefully very quickly. To run it:
 
 ```bash
-LYNXKITE_DATA=examples LYNXKITE_RELOAD=1 lynxkite
+cd examples && LYNXKITE_RELOAD=1 lynxkite
 ```
 
 If you also want to make changes to the frontend with hot reloading:

examples/AIMO

@@ -786,7 +786,7 @@
       "data": {
         "title": "Input CSV",
         "params": {
-          "filename": "data/aimo-examples.csv",
+          "filename": "uploads/aimo-examples.csv",
           "key": "problem"
         },
         "display": null,

examples/Bio demo

@@ -7,7 +7,7 @@
       "data": {
         "title": "Import CSV",
         "params": {
-          "filename": "examples/drug_target_data_sample.csv",
+          "filename": "uploads/drug_target_data_sample.csv",
           "separator": "<auto>",
           "columns": "<from file>"
         },

examples/Graph RAG

@@ -7,7 +7,7 @@
       "data": {
         "title": "Input document",
         "params": {
-          "filename": "examples/example-pizza.md"
+          "filename": "uploads/example-pizza.md"
         },
         "display": null,
         "error": null,

examples/LynxScribe demo

@@ -138,7 +138,7 @@
       "data": {
         "title": "Scenario selector",
         "params": {
-          "scenario_file": "/home/darabos/nvme/lynxscribe/examples/chat_api/scenarios.yaml",
+          "scenario_file": "uploads/chat_api/scenarios.yaml",
           "node_types": "intent_cluster"
         },
         "display": null,
@@ -252,9 +252,9 @@
       "data": {
         "title": "Knowledge base",
         "params": {
-          "template_cluster_path": "/home/darabos/nvme/lynxscribe/examples/chat_api/data/lynx/tempclusters.pickle",
-          "edges_path": "/home/darabos/nvme/lynxscribe/examples/chat_api/data/lynx/edges.pickle",
-          "nodes_path": "/home/darabos/nvme/lynxscribe/examples/chat_api/data/lynx/nodes.pickle"
+          "template_cluster_path": "uploads/chat_api/data/lynx/tempclusters.pickle",
+          "edges_path": "uploads/chat_api/data/lynx/edges.pickle",
+          "nodes_path": "uploads/chat_api/data/lynx/nodes.pickle"
         },
         "display": null,
         "error": null,

lynxkite-app/README.md

@@ -13,7 +13,7 @@ To run the backend:
 
 ```bash
 uv pip install -e .
-LYNXKITE_DATA=../examples LYNXKITE_RELOAD=1 lynxkite
+cd ../examples && LYNXKITE_RELOAD=1 lynxkite
 ```
 
 To run the frontend:

lynxkite-app/src/lynxkite_app/__main__.py

@@ -12,6 +12,7 @@ def main():
         port=port,
         reload=reload,
         loop="asyncio",
+        proxy_headers=True,
     )
 
 

lynxkite-app/src/lynxkite_app/config.py

@@ -1,8 +0,0 @@
-"""Some common configuration."""
-
-import os
-import pathlib
-
-
-DATA_PATH = pathlib.Path(os.environ.get("LYNXKITE_DATA", "lynxkite_data"))
-CRDT_PATH = pathlib.Path(os.environ.get("LYNXKITE_CRDT_DATA", "lynxkite_crdt_data"))

lynxkite-app/src/lynxkite_app/crdt.py

@@ -3,6 +3,7 @@
 import asyncio
 import contextlib
 import enum
+import pathlib
 import fastapi
 import os.path
 import pycrdt
@@ -11,7 +12,6 @@ import pycrdt_websocket.ystore
 import uvicorn
 import builtins
 from lynxkite.core import workspace, ops
-from . import config
 
 router = fastapi.APIRouter()
 
@@ -32,8 +32,9 @@ class WebsocketServer(pycrdt_websocket.WebsocketServer):
 
         The workspace is loaded from "crdt_data" if it exists there, or from "data", or a new workspace is created.
         """
-        path = config.CRDT_PATH / f"{name}.crdt"
-        assert path.is_relative_to(config.CRDT_PATH)
+        crdt_path = pathlib.Path(".crdt")
+        path = crdt_path / f"{name}.crdt"
+        assert path.is_relative_to(crdt_path)
         ystore = pycrdt_websocket.ystore.FileYStore(path)
         ydoc = pycrdt.Doc()
         ydoc["workspace"] = ws = pycrdt.Map()
@@ -54,6 +55,10 @@ class WebsocketServer(pycrdt_websocket.WebsocketServer):
             # We have two possible sources of truth for the workspaces, the YStore and the JSON files.
             # In case we didn't find the workspace in the YStore, we try to load it from the JSON files.
             try_to_load_workspace(ws, name)
+        ws_simple = workspace.Workspace.model_validate(ws.to_py())
+        clean_input(ws_simple)
+        # Set the last known version to the current state, so we don't trigger a change event.
+        last_known_versions[name] = ws_simple
         room = pycrdt_websocket.YRoom(
             ystore=ystore, ydoc=ydoc, exception_handler=ws_exception_handler
         )
@@ -161,9 +166,8 @@ def try_to_load_workspace(ws: pycrdt.Map, name: str):
         ws: CRDT object to udpate with the workspace contents.
         name: Name of the workspace to load.
     """
-    json_path = f"{config.DATA_PATH}/{name}"
-    if os.path.exists(json_path):
-        ws_pyd = workspace.load(json_path)
+    if os.path.exists(name):
+        ws_pyd = workspace.load(name)
         # We treat the display field as a black box, since it is a large
         # dictionary that is meant to change as a whole.
         crdt_update(ws, ws_pyd.model_dump(), non_collaborative_fields={"display"})
@@ -197,7 +201,6 @@ async def workspace_changed(name: str, changes: pycrdt.MapEvent, ws_crdt: pycrdt
         getattr(change, "keys", {}).get("__execution_delay", {}).get("newValue", 0)
         for change in changes
     )
-    print(f"Running {name} in {ws_pyd.env}...")
     if delay:
         task = asyncio.create_task(execute(name, ws_crdt, ws_pyd, delay))
         delayed_executions[name] = task
@@ -221,10 +224,13 @@ async def execute(
             await asyncio.sleep(delay)
         except asyncio.CancelledError:
             return
-    path = config.DATA_PATH / name
-    assert path.is_relative_to(config.DATA_PATH), "Provided workspace path is invalid"
+    print(f"Running {name} in {ws_pyd.env}...")
+    cwd = pathlib.Path()
+    path = cwd / name
+    assert path.is_relative_to(cwd), "Provided workspace path is invalid"
     # Save user changes before executing, in case the execution fails.
     workspace.save(ws_pyd, path)
+    ws_pyd._crdt = ws_crdt
     with ws_crdt.doc.transaction():
         for nc, np in zip(ws_crdt["nodes"], ws_pyd.nodes):
             if "data" not in nc:
@@ -234,6 +240,7 @@ async def execute(
             np._crdt = nc
     await workspace.execute(ws_pyd)
     workspace.save(ws_pyd, path)
+    print(f"Finished running {name} in {ws_pyd.env}.")
 
 
 @contextlib.asynccontextmanager

lynxkite-app/src/lynxkite_app/main.py

@@ -7,10 +7,11 @@ import importlib
 import pathlib
 import pkgutil
 from fastapi.staticfiles import StaticFiles
+from fastapi.middleware.gzip import GZipMiddleware
 import starlette
 from lynxkite.core import ops
 from lynxkite.core import workspace
-from . import crdt, config
+from . import crdt
 
 
 def detect_plugins():
@@ -28,6 +29,7 @@ lynxkite_plugins = detect_plugins()
 
 app = fastapi.FastAPI(lifespan=crdt.lifespan)
 app.include_router(crdt.router)
+app.add_middleware(GZipMiddleware)
 
 
 @app.get("/api/catalog")
@@ -43,9 +45,12 @@ class SaveRequest(workspace.BaseConfig):
     ws: workspace.Workspace
 
 
+data_path = pathlib.Path()
+
+
 def save(req: SaveRequest):
-    path = config.DATA_PATH / req.path
-    assert path.is_relative_to(config.DATA_PATH)
+    path = data_path / req.path
+    assert path.is_relative_to(data_path)
     workspace.save(req.ws, path)
 
 
@@ -59,18 +64,17 @@ async def save_and_execute(req: SaveRequest):
 
 @app.post("/api/delete")
 async def delete_workspace(req: dict):
-    json_path: pathlib.Path = config.DATA_PATH / req["path"]
-    crdt_path: pathlib.Path = config.CRDT_PATH / f"{req['path']}.crdt"
-    assert json_path.is_relative_to(config.DATA_PATH)
-    assert crdt_path.is_relative_to(config.CRDT_PATH)
+    json_path: pathlib.Path = data_path / req["path"]
+    crdt_path: pathlib.Path = data_path / ".crdt" / f"{req['path']}.crdt"
+    assert json_path.is_relative_to(data_path)
     json_path.unlink()
     crdt_path.unlink()
 
 
 @app.get("/api/load")
 def load(path: str):
-    path = config.DATA_PATH / path
-    assert path.is_relative_to(config.DATA_PATH)
+    path = data_path / path
+    assert path.is_relative_to(data_path)
     if not path.exists():
         return workspace.Workspace()
     return workspace.load(path)
@@ -83,15 +87,16 @@ class DirectoryEntry(pydantic.BaseModel):
 
 @app.get("/api/dir/list")
 def list_dir(path: str):
-    path = config.DATA_PATH / path
-    assert path.is_relative_to(config.DATA_PATH)
+    path = data_path / path
+    assert path.is_relative_to(data_path)
     return sorted(
         [
             DirectoryEntry(
-                name=str(p.relative_to(config.DATA_PATH)),
+                name=str(p.relative_to(data_path)),
                 type="directory" if p.is_dir() else "workspace",
             )
             for p in path.iterdir()
+            if not p.name.startswith(".")
         ],
         key=lambda x: x.name,
     )
@@ -99,16 +104,16 @@ def list_dir(path: str):
 
 @app.post("/api/dir/mkdir")
 def make_dir(req: dict):
-    path = config.DATA_PATH / req["path"]
-    assert path.is_relative_to(config.DATA_PATH)
+    path = data_path / req["path"]
+    assert path.is_relative_to(data_path)
     assert not path.exists(), f"{path} already exists"
     path.mkdir()
 
 
 @app.post("/api/dir/delete")
 def delete_dir(req: dict):
-    path: pathlib.Path = config.DATA_PATH / req["path"]
-    assert all([path.is_relative_to(config.DATA_PATH), path.exists(), path.is_dir()])
+    path: pathlib.Path = data_path / req["path"]
+    assert all([path.is_relative_to(data_path), path.exists(), path.is_dir()])
     shutil.rmtree(path)
 
 
@@ -126,6 +131,18 @@ async def service_post(req: fastapi.Request, module_path: str):
     return await module.api_service_post(req)
 
 
+@app.post("/api/upload")
+async def upload(req: fastapi.Request):
+    """Receives file uploads and stores them in DATA_PATH."""
+    form = await req.form()
+    for file in form.values():
+        file_path = data_path / "uploads" / file.filename
+        assert file_path.is_relative_to(data_path), "Invalid file path"
+        with file_path.open("wb") as buffer:
+            shutil.copyfileobj(file.file, buffer)
+    return {"status": "ok"}
+
+
 class SPAStaticFiles(StaticFiles):
     """Route everything to index.html. https://stackoverflow.com/a/73552966/3318517"""
 

lynxkite-app/tests/test_main.py

@@ -1,7 +1,7 @@
+import pathlib
 import uuid
 from fastapi.testclient import TestClient
 from lynxkite_app.main import app, detect_plugins
-from lynxkite_app.config import DATA_PATH
 import os
 
 
@@ -56,10 +56,9 @@ def test_save_and_load():
 
 
 def test_list_dir():
-    test_dir = str(uuid.uuid4())
-    test_dir_full_path = DATA_PATH / test_dir
-    test_dir_full_path.mkdir(parents=True, exist_ok=True)
-    test_file = test_dir_full_path / "test_file.txt"
+    test_dir = pathlib.Path() / str(uuid.uuid4())
+    test_dir.mkdir(parents=True, exist_ok=True)
+    test_file = test_dir / "test_file.txt"
     test_file.touch()
     response = client.get(f"/api/dir/list?path={str(test_dir)}")
     assert response.status_code == 200
@@ -67,12 +66,12 @@ def test_list_dir():
     assert response.json()[0]["name"] == f"{test_dir}/test_file.txt"
     assert response.json()[0]["type"] == "workspace"
     test_file.unlink()
-    test_dir_full_path.rmdir()
+    test_dir.rmdir()
 
 
 def test_make_dir():
     dir_name = str(uuid.uuid4())
     response = client.post("/api/dir/mkdir", json={"path": dir_name})
     assert response.status_code == 200
-    assert os.path.exists(DATA_PATH / dir_name)
-    os.rmdir(DATA_PATH / dir_name)
+    assert os.path.exists(dir_name)
+    os.rmdir(dir_name)

lynxkite-app/web/package-lock.json

@@ -17,6 +17,7 @@
         "@syncedstore/react": "^0.6.0",
         "@types/node": "^22.10.1",
         "@xyflow/react": "^12.3.5",
+        "axios": "^1.8.2",
         "daisyui": "^4.12.20",
         "echarts": "^5.5.1",
         "fuse.js": "^7.0.0",
@@ -278,25 +279,25 @@
       }
     },
     "node_modules/@babel/helpers": {
-      "version": "7.26.0",
-      "resolved": "https://registry.npmjs.org/@babel/helpers/-/helpers-7.26.0.tgz",
-      "integrity": "sha512-tbhNuIxNcVb21pInl3ZSjksLCvgdZy9KwJ8brv993QtIVKJBBkYXz4q4ZbAv31GdnC+R90np23L5FbEBlthAEw==",
+      "version": "7.26.10",
+      "resolved": "https://registry.npmjs.org/@babel/helpers/-/helpers-7.26.10.tgz",
+      "integrity": "sha512-UPYc3SauzZ3JGgj87GgZ89JVdC5dj0AoetR5Bw6wj4niittNyFh6+eOGonYvJ1ao6B8lEa3Q3klS7ADZ53bc5g==",
       "license": "MIT",
       "dependencies": {
-        "@babel/template": "^7.25.9",
-        "@babel/types": "^7.26.0"
+        "@babel/template": "^7.26.9",
+        "@babel/types": "^7.26.10"
       },
       "engines": {
         "node": ">=6.9.0"
       }
     },
     "node_modules/@babel/parser": {
-      "version": "7.26.3",
-      "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.26.3.tgz",
-      "integrity": "sha512-WJ/CvmY8Mea8iDXo6a7RK2wbmJITT5fN3BEkRuFlxVyNx8jOKIIhmC4fSkTcPcf8JyavbBwIe6OpiCOBXt/IcA==",
+      "version": "7.26.10",
+      "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.26.10.tgz",
+      "integrity": "sha512-6aQR2zGE/QFi8JpDLjUZEPYOs7+mhKXm86VaKFiLP35JQwQb6bwUE+XbvkH0EptsYhbNBSUGaUBLKqxH1xSgsA==",
       "license": "MIT",
       "dependencies": {
-        "@babel/types": "^7.26.3"
+        "@babel/types": "^7.26.10"
       },
       "bin": {
         "parser": "bin/babel-parser.js"
@@ -306,14 +307,14 @@
       }
     },
     "node_modules/@babel/template": {
-      "version": "7.25.9",
-      "resolved": "https://registry.npmjs.org/@babel/template/-/template-7.25.9.tgz",
-      "integrity": "sha512-9DGttpmPvIxBb/2uwpVo3dqJ+O6RooAFOS+lB+xDqoE2PVCE8nfoHMdZLpfCQRLwvohzXISPZcgxt80xLfsuwg==",
+      "version": "7.26.9",
+      "resolved": "https://registry.npmjs.org/@babel/template/-/template-7.26.9.tgz",
+      "integrity": "sha512-qyRplbeIpNZhmzOysF/wFMuP9sctmh2cFzRAZOn1YapxBsE1i9bJIY586R/WBLfLcmcBlM8ROBiQURnnNy+zfA==",
       "license": "MIT",
       "dependencies": {
-        "@babel/code-frame": "^7.25.9",
-        "@babel/parser": "^7.25.9",
-        "@babel/types": "^7.25.9"
+        "@babel/code-frame": "^7.26.2",
+        "@babel/parser": "^7.26.9",
+        "@babel/types": "^7.26.9"
       },
       "engines": {
         "node": ">=6.9.0"
@@ -347,9 +348,9 @@
       }
     },
     "node_modules/@babel/types": {
-      "version": "7.26.3",
-      "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.26.3.tgz",
-      "integrity": "sha512-vN5p+1kl59GVKMvTHt55NzzmYVxprfJD+ql7U9NFIfKCBkYE55LYtS+WtPlaYOyzydrKI8Nezd+aZextrd+FMA==",
+      "version": "7.26.10",
+      "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.26.10.tgz",
+      "integrity": "sha512-emqcG3vHrpxUKTrxcblR36dcrcoRDvKmnL/dCL6ZsHaShW80qxCAcNhzQZrpeM765VzEos+xOi4s+r4IXzTwdQ==",
       "license": "MIT",
       "dependencies": {
         "@babel/helper-string-parser": "^7.25.9",
@@ -2467,6 +2468,12 @@
       "license": "MIT",
       "optional": true
     },
+    "node_modules/asynckit": {
+      "version": "0.4.0",
+      "resolved": "https://registry.npmjs.org/asynckit/-/asynckit-0.4.0.tgz",
+      "integrity": "sha512-Oei9OH4tRh0YqU3GxhX79dM/mwVgvbZJaSNaRk+bshkj0S5cfHcgYakreBjrHwatXKbz+IoIdYLxrKim2MjW0Q==",
+      "license": "MIT"
+    },
     "node_modules/autoprefixer": {
       "version": "10.4.20",
       "resolved": "https://registry.npmjs.org/autoprefixer/-/autoprefixer-10.4.20.tgz",
@@ -2505,6 +2512,17 @@
         "postcss": "^8.1.0"
       }
     },
+    "node_modules/axios": {
+      "version": "1.8.2",
+      "resolved": "https://registry.npmjs.org/axios/-/axios-1.8.2.tgz",
+      "integrity": "sha512-ls4GYBm5aig9vWx8AWDSGLpnpDQRtWAfrjU+EuytuODrFBkqesN2RkOQCBzrA1RQNHw1SmRMSDDDSwzNAYQ6Rg==",
+      "license": "MIT",
+      "dependencies": {
+        "follow-redirects": "^1.15.6",
+        "form-data": "^4.0.0",
+        "proxy-from-env": "^1.1.0"
+      }
+    },
     "node_modules/bail": {
       "version": "2.0.2",
       "resolved": "https://registry.npmjs.org/bail/-/bail-2.0.2.tgz",
@@ -2637,6 +2655,19 @@
         "ieee754": "^1.1.13"
       }
     },
+    "node_modules/call-bind-apply-helpers": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/call-bind-apply-helpers/-/call-bind-apply-helpers-1.0.2.tgz",
+      "integrity": "sha512-Sp1ablJ0ivDkSzjcaJdxEunN5/XvksFJ2sMBFfq6x0ryhQV/2b/KwFe21cMpmHtPOSij8K99/wSfoEuTObmuMQ==",
+      "license": "MIT",
+      "dependencies": {
+        "es-errors": "^1.3.0",
+        "function-bind": "^1.1.2"
+      },
+      "engines": {
+        "node": ">= 0.4"
+      }
+    },
     "node_modules/callsites": {
       "version": "3.1.0",
       "resolved": "https://registry.npmjs.org/callsites/-/callsites-3.1.0.tgz",
@@ -2824,6 +2855,18 @@
       "dev": true,
       "license": "MIT"
     },
+    "node_modules/combined-stream": {
+      "version": "1.0.8",
+      "resolved": "https://registry.npmjs.org/combined-stream/-/combined-stream-1.0.8.tgz",
+      "integrity": "sha512-FQN4MRfuJeHf7cBbBMJFXhKSDq+2kAArBlmRBvcvFE5BB1HZKXtSFASDhdlz9zOYwxh8lDdnvmMOe/+5cdoEdg==",
+      "license": "MIT",
+      "dependencies": {
+        "delayed-stream": "~1.0.0"
+      },
+      "engines": {
+        "node": ">= 0.8"
+      }
+    },
     "node_modules/comma-separated-tokens": {
       "version": "2.0.3",
       "resolved": "https://registry.npmjs.org/comma-separated-tokens/-/comma-separated-tokens-2.0.3.tgz",
@@ -3126,6 +3169,15 @@
         "node": ">=6"
       }
     },
+    "node_modules/delayed-stream": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/delayed-stream/-/delayed-stream-1.0.0.tgz",
+      "integrity": "sha512-ZySD7Nf91aLB0RxL4KGrKHBXl7Eds1DAmEdcoVawXnLD7SDhpNgtuII2aAkg7a7QS41jxPSZ17p4VdGnMHk3MQ==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=0.4.0"
+      }
+    },
     "node_modules/dequal": {
       "version": "2.0.3",
       "resolved": "https://registry.npmjs.org/dequal/-/dequal-2.0.3.tgz",
@@ -3172,6 +3224,20 @@
         "tslib": "^2.0.3"
       }
     },
+    "node_modules/dunder-proto": {
+      "version": "1.0.1",
+      "resolved": "https://registry.npmjs.org/dunder-proto/-/dunder-proto-1.0.1.tgz",
+      "integrity": "sha512-KIN/nDJBQRcXw0MLVhZE9iQHmG68qAVIBg9CqmUYjmQIhgij9U5MFvrqkUL5FbtyyzZuOeOt0zdeRe4UY7ct+A==",
+      "license": "MIT",
+      "dependencies": {
+        "call-bind-apply-helpers": "^1.0.1",
+        "es-errors": "^1.3.0",
+        "gopd": "^1.2.0"
+      },
+      "engines": {
+        "node": ">= 0.4"
+      }
+    },
     "node_modules/eastasianwidth": {
       "version": "0.2.0",
       "resolved": "https://registry.npmjs.org/eastasianwidth/-/eastasianwidth-0.2.0.tgz",
@@ -3252,6 +3318,51 @@
         "is-arrayish": "^0.2.1"
       }
     },
+    "node_modules/es-define-property": {
+      "version": "1.0.1",
+      "resolved": "https://registry.npmjs.org/es-define-property/-/es-define-property-1.0.1.tgz",
+      "integrity": "sha512-e3nRfgfUZ4rNGL232gUgX06QNyyez04KdjFrF+LTRoOXmrOgFKDg4BCdsjW8EnT69eqdYGmRpJwiPVYNrCaW3g==",
+      "license": "MIT",
+      "engines": {
+        "node": ">= 0.4"
+      }
+    },
+    "node_modules/es-errors": {
+      "version": "1.3.0",
+      "resolved": "https://registry.npmjs.org/es-errors/-/es-errors-1.3.0.tgz",
+      "integrity": "sha512-Zf5H2Kxt2xjTvbJvP2ZWLEICxA6j+hAmMzIlypy4xcBg1vKVnx89Wy0GbS+kf5cwCVFFzdCFh2XSCFNULS6csw==",
+      "license": "MIT",
+      "engines": {
+        "node": ">= 0.4"
+      }
+    },
+    "node_modules/es-object-atoms": {
+      "version": "1.1.1",
+      "resolved": "https://registry.npmjs.org/es-object-atoms/-/es-object-atoms-1.1.1.tgz",
+      "integrity": "sha512-FGgH2h8zKNim9ljj7dankFPcICIK9Cp5bm+c2gQSYePhpaG5+esrLODihIorn+Pe6FGJzWhXQotPv73jTaldXA==",
+      "license": "MIT",
+      "dependencies": {
+        "es-errors": "^1.3.0"
+      },
+      "engines": {
+        "node": ">= 0.4"
+      }
+    },
+    "node_modules/es-set-tostringtag": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/es-set-tostringtag/-/es-set-tostringtag-2.1.0.tgz",
+      "integrity": "sha512-j6vWzfrGVfyXxge+O0x5sh6cvxAog0a/4Rdd2K36zCMV5eJ+/+tOAngRO8cODMNWbVRdVlmGZQL2YS3yR8bIUA==",
+      "license": "MIT",
+      "dependencies": {
+        "es-errors": "^1.3.0",
+        "get-intrinsic": "^1.2.6",
+        "has-tostringtag": "^1.0.2",
+        "hasown": "^2.0.2"
+      },
+      "engines": {
+        "node": ">= 0.4"
+      }
+    },
     "node_modules/esbuild": {
       "version": "0.25.0",
       "resolved": "https://registry.npmjs.org/esbuild/-/esbuild-0.25.0.tgz",
@@ -3639,6 +3750,26 @@
       "dev": true,
       "license": "ISC"
     },
+    "node_modules/follow-redirects": {
+      "version": "1.15.9",
+      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.15.9.tgz",
+      "integrity": "sha512-gew4GsXizNgdoRyqmyfMHyAmXsZDk6mHkSxZFCzW9gwlbtOW44CDtYavM+y+72qD/Vq2l550kMF52DT8fOLJqQ==",
+      "funding": [
+        {
+          "type": "individual",
+          "url": "https://github.com/sponsors/RubenVerborgh"
+        }
+      ],
+      "license": "MIT",
+      "engines": {
+        "node": ">=4.0"
+      },
+      "peerDependenciesMeta": {
+        "debug": {
+          "optional": true
+        }
+      }
+    },
     "node_modules/foreground-child": {
       "version": "3.3.0",
       "resolved": "https://registry.npmjs.org/foreground-child/-/foreground-child-3.3.0.tgz",
@@ -3656,6 +3787,21 @@
         "url": "https://github.com/sponsors/isaacs"
       }
     },
+    "node_modules/form-data": {
+      "version": "4.0.2",
+      "resolved": "https://registry.npmjs.org/form-data/-/form-data-4.0.2.tgz",
+      "integrity": "sha512-hGfm/slu0ZabnNt4oaRZ6uREyfCj6P4fT/n6A1rGV+Z0VdGXjfOhVUpkn6qVQONHGIFwmveGXyDs75+nr6FM8w==",
+      "license": "MIT",
+      "dependencies": {
+        "asynckit": "^0.4.0",
+        "combined-stream": "^1.0.8",
+        "es-set-tostringtag": "^2.1.0",
+        "mime-types": "^2.1.12"
+      },
+      "engines": {
+        "node": ">= 6"
+      }
+    },
     "node_modules/fraction.js": {
       "version": "4.3.7",
       "resolved": "https://registry.npmjs.org/fraction.js/-/fraction.js-4.3.7.tgz",
@@ -3689,7 +3835,6 @@
       "version": "1.1.2",
       "resolved": "https://registry.npmjs.org/function-bind/-/function-bind-1.1.2.tgz",
       "integrity": "sha512-7XHNxH7qX9xG5mIwxkhumTox/MIRNcOgDrxWsMt2pAr23WHp6MrRlN7FBSFpCpr+oVO0F744iUgR82nJMfG2SA==",
-      "dev": true,
       "license": "MIT",
       "funding": {
         "url": "https://github.com/sponsors/ljharb"
@@ -3713,6 +3858,43 @@
         "node": ">=6.9.0"
       }
     },
+    "node_modules/get-intrinsic": {
+      "version": "1.3.0",
+      "resolved": "https://registry.npmjs.org/get-intrinsic/-/get-intrinsic-1.3.0.tgz",
+      "integrity": "sha512-9fSjSaos/fRIVIp+xSJlE6lfwhES7LNtKaCBIamHsjr2na1BiABJPo0mOjjz8GJDURarmCPGqaiVg5mfjb98CQ==",
+      "license": "MIT",
+      "dependencies": {
+        "call-bind-apply-helpers": "^1.0.2",
+        "es-define-property": "^1.0.1",
+        "es-errors": "^1.3.0",
+        "es-object-atoms": "^1.1.1",
+        "function-bind": "^1.1.2",
+        "get-proto": "^1.0.1",
+        "gopd": "^1.2.0",
+        "has-symbols": "^1.1.0",
+        "hasown": "^2.0.2",
+        "math-intrinsics": "^1.1.0"
+      },
+      "engines": {
+        "node": ">= 0.4"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/ljharb"
+      }
+    },
+    "node_modules/get-proto": {
+      "version": "1.0.1",
+      "resolved": "https://registry.npmjs.org/get-proto/-/get-proto-1.0.1.tgz",
+      "integrity": "sha512-sTSfBjoXBp89JvIKIefqw7U2CCebsc74kiY6awiGogKtoSGbgjYE/G/+l9sF3MWFPNc9IcoOC4ODfKHfxFmp0g==",
+      "license": "MIT",
+      "dependencies": {
+        "dunder-proto": "^1.0.1",
+        "es-object-atoms": "^1.0.0"
+      },
+      "engines": {
+        "node": ">= 0.4"
+      }
+    },
     "node_modules/glob": {
       "version": "10.4.5",
       "resolved": "https://registry.npmjs.org/glob/-/glob-10.4.5.tgz",
@@ -3785,6 +3967,18 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
+    "node_modules/gopd": {
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/gopd/-/gopd-1.2.0.tgz",
+      "integrity": "sha512-ZUKRh6/kUFoAiTAtTYPZJ3hw9wNxx+BIBOijnlG9PnrJsCcSjs1wyyD6vJpaYtgnzDrKYRSqf3OO6Rfa93xsRg==",
+      "license": "MIT",
+      "engines": {
+        "node": ">= 0.4"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/ljharb"
+      }
+    },
     "node_modules/graphemer": {
       "version": "1.4.0",
       "resolved": "https://registry.npmjs.org/graphemer/-/graphemer-1.4.0.tgz",
@@ -3802,11 +3996,37 @@
         "node": ">=8"
       }
     },
+    "node_modules/has-symbols": {
+      "version": "1.1.0",
+      "resolved": "https://registry.npmjs.org/has-symbols/-/has-symbols-1.1.0.tgz",
+      "integrity": "sha512-1cDNdwJ2Jaohmb3sg4OmKaMBwuC48sYni5HUw2DvsC8LjGTLK9h+eb1X6RyuOHe4hT0ULCW68iomhjUoKUqlPQ==",
+      "license": "MIT",
+      "engines": {
+        "node": ">= 0.4"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/ljharb"
+      }
+    },
+    "node_modules/has-tostringtag": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/has-tostringtag/-/has-tostringtag-1.0.2.tgz",
+      "integrity": "sha512-NqADB8VjPFLM2V0VvHUewwwsw0ZWBaIdgo+ieHtK3hasLz4qeCRjYcqfB6AQrBggRKppKF8L52/VqdVsO47Dlw==",
+      "license": "MIT",
+      "dependencies": {
+        "has-symbols": "^1.0.3"
+      },
+      "engines": {
+        "node": ">= 0.4"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/ljharb"
+      }
+    },
     "node_modules/hasown": {
       "version": "2.0.2",
       "resolved": "https://registry.npmjs.org/hasown/-/hasown-2.0.2.tgz",
       "integrity": "sha512-0hJU9SCPvmMzIBdZFqNPXWa6dqh7WdH0cII9y+CyS8rG3nL48Bclra9HmKhVVUHyPWNH5Y7xDwAB7bfgSjkUMQ==",
-      "dev": true,
       "license": "MIT",
       "dependencies": {
         "function-bind": "^1.1.2"
@@ -4523,6 +4743,15 @@
       "license": "MIT",
       "optional": true
     },
+    "node_modules/math-intrinsics": {
+      "version": "1.1.0",
+      "resolved": "https://registry.npmjs.org/math-intrinsics/-/math-intrinsics-1.1.0.tgz",
+      "integrity": "sha512-/IXtbwEk5HTPyEwyKX6hGkYXxM9nbj64B+ilVJnC/R6B0pH5G4V3b0pVbL7DBj4tkhBAppbQUlf6F6Xl9LHu1g==",
+      "license": "MIT",
+      "engines": {
+        "node": ">= 0.4"
+      }
+    },
     "node_modules/mdast-util-from-markdown": {
       "version": "2.0.2",
       "resolved": "https://registry.npmjs.org/mdast-util-from-markdown/-/mdast-util-from-markdown-2.0.2.tgz",
@@ -5142,6 +5371,27 @@
         "node": ">=8.6"
       }
     },
+    "node_modules/mime-db": {
+      "version": "1.52.0",
+      "resolved": "https://registry.npmjs.org/mime-db/-/mime-db-1.52.0.tgz",
+      "integrity": "sha512-sPU4uV7dYlvtWJxwwxHD0PuihVNiE7TyAbQ5SWxDCB9mUYvOgroQOwYQQOKPJ8CIbE+1ETVlOoK1UC2nU3gYvg==",
+      "license": "MIT",
+      "engines": {
+        "node": ">= 0.6"
+      }
+    },
+    "node_modules/mime-types": {
+      "version": "2.1.35",
+      "resolved": "https://registry.npmjs.org/mime-types/-/mime-types-2.1.35.tgz",
+      "integrity": "sha512-ZDY+bPm5zTTF+YpCrAU9nK0UgICYPT0QtT1NZWFv4s++TNkcgVaT0g6+4R2uI4MjQjzysHB1zxuWL50hzaeXiw==",
+      "license": "MIT",
+      "dependencies": {
+        "mime-db": "1.52.0"
+      },
+      "engines": {
+        "node": ">= 0.6"
+      }
+    },
     "node_modules/minimatch": {
       "version": "3.1.2",
       "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.1.2.tgz",
@@ -5766,6 +6016,12 @@
         "url": "https://github.com/sponsors/wooorm"
       }
     },
+    "node_modules/proxy-from-env": {
+      "version": "1.1.0",
+      "resolved": "https://registry.npmjs.org/proxy-from-env/-/proxy-from-env-1.1.0.tgz",
+      "integrity": "sha512-D+zkORCbA9f1tdWRK0RaCR3GPv50cMxcrz4X8k5LTSUD1Dkw47mKJEZQNunItRTkWwgtaUSo1RVFRIG9ZXiFYg==",
+      "license": "MIT"
+    },
     "node_modules/prr": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/prr/-/prr-1.0.1.tgz",

lynxkite-app/web/package.json

@@ -20,6 +20,7 @@
     "@syncedstore/react": "^0.6.0",
     "@types/node": "^22.10.1",
     "@xyflow/react": "^12.3.5",
+    "axios": "^1.8.2",
     "daisyui": "^4.12.20",
     "echarts": "^5.5.1",
     "fuse.js": "^7.0.0",
@@ -35,6 +36,8 @@
   },
   "devDependencies": {
     "@eslint/js": "^9.15.0",
+    "@playwright/test": "^1.50.1",
+    "@types/node": "^22.13.1",
     "@types/react": "^18.3.14",
     "@types/react-dom": "^18.3.2",
     "@vitejs/plugin-react-swc": "^3.5.0",
@@ -47,9 +50,7 @@
     "tailwindcss": "^3.4.16",
     "typescript": "~5.6.2",
     "typescript-eslint": "^8.15.0",
-    "vite": "^6.2.0",
-    "@playwright/test": "^1.50.1",
-    "@types/node": "^22.13.1"
+    "vite": "^6.2.0"
   },
   "optionalDependencies": {
     "@rollup/rollup-linux-x64-gnu": "^4.28.1"

lynxkite-app/web/playwright.config.ts

@@ -23,7 +23,7 @@ export default defineConfig({
     },
   ],
   webServer: {
-    command: "cd ../.. && LYNXKITE_DATA=examples lynxkite",
+    command: "cd ../../examples && lynxkite",
     url: "http://127.0.0.1:8000",
     reuseExistingServer: false,
   },

lynxkite-app/web/src/Directory.tsx

@@ -1,6 +1,6 @@
 import { useState } from "react";
 // The directory browser.
-import { useNavigate, useParams } from "react-router";
+import { Link, useNavigate, useParams } from "react-router";
 import useSWR from "swr";
 import type { DirectoryEntry } from "./apiTypes.ts";
 
@@ -23,7 +23,9 @@ const fetcher = (url: string) => fetch(url).then((res) => res.json());
 export default function () {
   const { path } = useParams();
   const encodedPath = encodeURIComponent(path || "");
-  const list = useSWR(`/api/dir/list?path=${encodedPath}`, fetcher);
+  const list = useSWR(`/api/dir/list?path=${encodedPath}`, fetcher, {
+    dedupingInterval: 0,
+  });
   const navigate = useNavigate();
   const [isCreatingDir, setIsCreatingDir] = useState(false);
   const [isCreatingWorkspace, setIsCreatingWorkspace] = useState(false);
@@ -173,19 +175,19 @@ export default function () {
 
             {path && (
               <div className="breadcrumbs">
-                <a href="/dir/">
+                <Link to="/dir/">
                   <Home />
-                </a>{" "}
+                </Link>{" "}
                 <span className="current-folder">{path}</span>
               </div>
             )}
 
             {list.data.map((item: DirectoryEntry) => (
               <div key={item.name} className="entry">
-                <a key={link(item)} href={link(item)}>
+                <Link key={link(item)} to={link(item)}>
                   {item.type === "directory" ? <Folder /> : <File />}
                   {shortName(item)}
-                </a>
+                </Link>
                 <button
                   type="button"
                   onClick={() => {

lynxkite-app/web/src/index.css

@@ -235,6 +235,41 @@ body {
       margin: 10px;
     }
   }
+
+  .env-select {
+    background: transparent;
+    color: #39bcf3;
+  }
+
+  .workspace-message {
+    position: absolute;
+    left: 50%;
+    bottom: 20px;
+    transform: translateX(-50%);
+    box-shadow: 0 5px 50px 0px #8008;
+    padding: 10px 40px 10px 20px;
+    border-radius: 5px;
+
+    .close {
+      position: absolute;
+      right: 10px;
+      cursor: pointer;
+    }
+  }
+}
+
+.params-expander {
+  font-size: 15px;
+  padding: 4px;
+  color: #000a;
+}
+
+.flippy {
+  transition: transform 0.5s;
+}
+
+.flippy.flippy-90 {
+  transform: rotate(-90deg);
 }
 
 .directory {

lynxkite-app/web/src/workspace/EnvironmentSelector.tsx

@@ -6,7 +6,7 @@ export default function EnvironmentSelector(props: {
   return (
     <>
       <select
-        className="select w-full max-w-xs"
+        className="env-select select w-full max-w-xs"
         name="workspace-env"
         value={props.value}
         onChange={(evt) => props.onChange(evt.currentTarget.value)}

lynxkite-app/web/src/workspace/NodeSearch.tsx

@@ -25,9 +25,14 @@ export default function (props: {
       }),
     [props.boxes],
   );
+  const allOps = useMemo(() => {
+    const boxes = Object.values(props.boxes).map((box) => ({ item: box }));
+    boxes.sort((a, b) => a.item.name.localeCompare(b.item.name));
+    return boxes;
+  }, [props.boxes]);
   const hits: { item: OpsOp }[] = searchText
     ? fuse.search<OpsOp>(searchText)
-    : Object.values(props.boxes).map((box) => ({ item: box }));
+    : allOps;
   const [selectedIndex, setSelectedIndex] = useState(0);
   useEffect(() => searchBox.current.focus());
   function typed(text: string) {

lynxkite-app/web/src/workspace/Workspace.tsx

@@ -14,6 +14,7 @@ import {
   useReactFlow,
   useUpdateNodeInternals,
 } from "@xyflow/react";
+import axios from "axios";
 import {
   type MouseEvent,
   useCallback,
@@ -26,11 +27,11 @@ import { useParams } from "react-router";
 import useSWR, { type Fetcher } from "swr";
 import { WebsocketProvider } from "y-websocket";
 // @ts-ignore
-import ArrowBack from "~icons/tabler/arrow-back.jsx";
-// @ts-ignore
 import Atom from "~icons/tabler/atom.jsx";
 // @ts-ignore
 import Backspace from "~icons/tabler/backspace.jsx";
+// @ts-ignore
+import Close from "~icons/tabler/x.jsx";
 import type { Workspace, WorkspaceNode } from "../apiTypes.ts";
 import favicon from "../assets/favicon.ico";
 // import NodeWithTableView from './NodeWithTableView';
@@ -62,12 +63,14 @@ function LynxKiteFlow() {
   const [edges, setEdges] = useState([] as Edge[]);
   const { path } = useParams();
   const [state, setState] = useState({ workspace: {} as Workspace });
+  const [message, setMessage] = useState(null as string | null);
   useEffect(() => {
     const state = syncedStore({ workspace: {} as Workspace });
     setState(state);
     const doc = getYjsDoc(state);
+    const proto = location.protocol === "https:" ? "wss:" : "ws:";
     const wsProvider = new WebsocketProvider(
-      `ws://${location.host}/ws/crdt`,
+      `${proto}//${location.host}/ws/crdt`,
       path!,
       doc,
     );
@@ -79,7 +82,9 @@ function LynxKiteFlow() {
         if (!state.workspace.nodes) return;
         if (!state.workspace.edges) return;
         for (const n of state.workspace.nodes) {
-          n.dragHandle = ".bg-primary";
+          if (n.dragHandle !== ".bg-primary") {
+            n.dragHandle = ".bg-primary";
+          }
         }
         setNodes([...state.workspace.nodes] as Node[]);
         setEdges([...state.workspace.edges] as Edge[]);
@@ -233,33 +238,44 @@ function LynxKiteFlow() {
     },
     [catalog, state, nodeSearchSettings, suppressSearchUntil, closeNodeSearch],
   );
-  const addNode = useCallback(
+  function addNode(
+    node: Partial<WorkspaceNode>,
+    state: { workspace: Workspace },
+    nodes: Node[],
+  ) {
+    const title = node.data?.title;
+    let i = 1;
+    node.id = `${title} ${i}`;
+    const wnodes = state.workspace.nodes!;
+    while (wnodes.find((x) => x.id === node.id)) {
+      i += 1;
+      node.id = `${title} ${i}`;
+    }
+    wnodes.push(node as WorkspaceNode);
+    setNodes([...nodes, node as WorkspaceNode]);
+  }
+  function nodeFromMeta(meta: OpsOp): Partial<WorkspaceNode> {
+    const node: Partial<WorkspaceNode> = {
+      type: meta.type,
+      data: {
+        meta: meta,
+        title: meta.name,
+        params: Object.fromEntries(
+          Object.values(meta.params).map((p) => [p.name, p.default]),
+        ),
+      },
+    };
+    return node;
+  }
+  const addNodeFromSearch = useCallback(
     (meta: OpsOp) => {
-      const node: Partial<WorkspaceNode> = {
-        type: meta.type,
-        data: {
-          meta: meta,
-          title: meta.name,
-          params: Object.fromEntries(
-            Object.values(meta.params).map((p) => [p.name, p.default]),
-          ),
-        },
-      };
+      const node = nodeFromMeta(meta);
       const nss = nodeSearchSettings!;
       node.position = reactFlow.screenToFlowPosition({
         x: nss.pos.x,
         y: nss.pos.y,
       });
-      const title = meta.name;
-      let i = 1;
-      node.id = `${title} ${i}`;
-      const wnodes = state.workspace.nodes!;
-      while (wnodes.find((x) => x.id === node.id)) {
-        i += 1;
-        node.id = `${title} ${i}`;
-      }
-      wnodes.push(node as WorkspaceNode);
-      setNodes([...nodes, node as WorkspaceNode]);
+      addNode(node, state, nodes);
       closeNodeSearch();
     },
     [nodeSearchSettings, state, reactFlow, nodes, closeNodeSearch],
@@ -281,6 +297,48 @@ function LynxKiteFlow() {
     [state],
   );
   const parentDir = path!.split("/").slice(0, -1).join("/");
+  function onDragOver(e: React.DragEvent<HTMLDivElement>) {
+    e.stopPropagation();
+    e.preventDefault();
+  }
+  async function onDrop(e: React.DragEvent<HTMLDivElement>) {
+    e.stopPropagation();
+    e.preventDefault();
+    const file = e.dataTransfer.files[0];
+    const formData = new FormData();
+    formData.append("file", file);
+    try {
+      await axios.post("/api/upload", formData, {
+        onUploadProgress: (progressEvent) => {
+          const percentCompleted = Math.round(
+            (100 * progressEvent.loaded) / progressEvent.total!,
+          );
+          if (percentCompleted === 100) setMessage("Processing file...");
+          else setMessage(`Uploading ${percentCompleted}%`);
+        },
+      });
+      setMessage(null);
+      const cat = catalog.data![state.workspace.env!];
+      const node = nodeFromMeta(cat["Import file"]);
+      node.position = reactFlow.screenToFlowPosition({
+        x: e.clientX,
+        y: e.clientY,
+      });
+      node.data!.params.file_path = `uploads/${file.name}`;
+      if (file.name.includes(".csv")) {
+        node.data!.params.file_format = "csv";
+      } else if (file.name.includes(".parquet")) {
+        node.data!.params.file_format = "parquet";
+      } else if (file.name.includes(".json")) {
+        node.data!.params.file_format = "json";
+      } else if (file.name.includes(".xls")) {
+        node.data!.params.file_format = "excel";
+      }
+      addNode(node, state, nodes);
+    } catch (error) {
+      setMessage("File upload failed.");
+    }
+  }
   return (
     <div className="workspace">
       <div className="top-bar bg-neutral">
@@ -303,11 +361,15 @@ function LynxKiteFlow() {
             <Backspace />
           </a>
           <a href={`/dir/${parentDir}`}>
-            <ArrowBack />
+            <Close />
           </a>
         </div>
       </div>
-      <div style={{ height: "100%", width: "100vw" }}>
+      <div
+        style={{ height: "100%", width: "100vw" }}
+        onDragOver={onDragOver}
+        onDrop={onDrop}
+      >
         <LynxKiteState.Provider value={state}>
           <ReactFlow
             nodes={nodes}
@@ -319,7 +381,7 @@ function LynxKiteFlow() {
             onPaneClick={toggleNodeSearch}
             onConnect={onConnect}
             proOptions={{ hideAttribution: true }}
-            maxZoom={3}
+            maxZoom={1}
             minZoom={0.3}
             defaultEdgeOptions={{
               markerEnd: {
@@ -341,11 +403,19 @@ function LynxKiteFlow() {
                 pos={nodeSearchSettings.pos}
                 boxes={nodeSearchSettings.boxes}
                 onCancel={closeNodeSearch}
-                onAdd={addNode}
+                onAdd={addNodeFromSearch}
               />
             )}
           </ReactFlow>
         </LynxKiteState.Provider>
+        {message && (
+          <div className="workspace-message">
+            <span className="close" onClick={() => setMessage(null)}>
+              <Close />
+            </span>
+            {message}
+          </div>
+        )}
       </div>
     </div>
   );

lynxkite-app/web/src/workspace/nodes/NodeParameter.tsx

@@ -73,6 +73,10 @@ export default function NodeParameter({
             value={value || ""}
             onChange={(evt) => onChange(evt.currentTarget.value, { delay: 2 })}
             onBlur={(evt) => onChange(evt.currentTarget.value, { delay: 0 })}
+            onKeyDown={(evt) =>
+              evt.code === "Enter" &&
+              onChange(evt.currentTarget.value, { delay: 0 })
+            }
           />
         </>
       )}

lynxkite-app/web/src/workspace/nodes/NodeWithParams.tsx

@@ -1,4 +1,7 @@
 import { useReactFlow } from "@xyflow/react";
+import React from "react";
+// @ts-ignore
+import Triangle from "~icons/tabler/triangle-inverted-filled.jsx";
 import LynxKiteNode from "./LynxKiteNode";
 import NodeGroupParameter from "./NodeGroupParameter";
 import NodeParameter from "./NodeParameter";
@@ -8,6 +11,7 @@ export type UpdateOptions = { delay?: number };
 function NodeWithParams(props: any) {
   const reactFlow = useReactFlow();
   const metaParams = props.data.meta?.params;
+  const [collapsed, setCollapsed] = React.useState(props.collapsed);
 
   function setParam(name: string, newValue: any, opts: UpdateOptions) {
     reactFlow.updateNodeData(props.id, (prevData: any) => ({
@@ -31,31 +35,40 @@ function NodeWithParams(props: any) {
 
   return (
     <LynxKiteNode {...props}>
-      {params.map(([name, value]) =>
-        metaParams?.[name]?.type === "group" ? (
-          <NodeGroupParameter
-            key={name}
-            value={value}
-            meta={metaParams?.[name]}
-            setParam={(name: string, value: any, opts?: UpdateOptions) =>
-              setParam(name, value, opts || {})
-            }
-            deleteParam={(name: string, opts?: UpdateOptions) =>
-              deleteParam(name, opts || {})
-            }
-          />
-        ) : (
-          <NodeParameter
-            name={name}
-            key={name}
-            value={value}
-            meta={metaParams?.[name]}
-            onChange={(value: any, opts?: UpdateOptions) =>
-              setParam(name, value, opts || {})
-            }
-          />
-        ),
+      {props.collapsed && (
+        <div
+          className="params-expander"
+          onClick={() => setCollapsed(!collapsed)}
+        >
+          <Triangle className={`flippy ${collapsed ? "flippy-90" : ""}`} />
+        </div>
       )}
+      {!collapsed &&
+        params.map(([name, value]) =>
+          metaParams?.[name]?.type === "group" ? (
+            <NodeGroupParameter
+              key={name}
+              value={value}
+              meta={metaParams?.[name]}
+              setParam={(name: string, value: any, opts?: UpdateOptions) =>
+                setParam(name, value, opts || {})
+              }
+              deleteParam={(name: string, opts?: UpdateOptions) =>
+                deleteParam(name, opts || {})
+              }
+            />
+          ) : (
+            <NodeParameter
+              name={name}
+              key={name}
+              value={value}
+              meta={metaParams?.[name]}
+              onChange={(value: any, opts?: UpdateOptions) =>
+                setParam(name, value, opts || {})
+              }
+            />
+          ),
+        )}
       {props.children}
     </LynxKiteNode>
   );

lynxkite-app/web/src/workspace/nodes/NodeWithVisualization.tsx

@@ -10,20 +10,28 @@ const NodeWithVisualization = (props: any) => {
     if (!opts || !chartsRef.current) return;
     chartsInstanceRef.current = echarts.init(chartsRef.current, null, {
       renderer: "canvas",
-      width: 800,
-      height: 800,
+      width: "auto",
+      height: "auto",
     });
     chartsInstanceRef.current.setOption(opts);
-    const onResize = () => chartsInstanceRef.current?.resize();
-    window.addEventListener("resize", onResize);
+    const resizeObserver = new ResizeObserver(() => {
+      const e = chartsRef.current!;
+      e.style.padding = "1px";
+      chartsInstanceRef.current?.resize();
+      e.style.padding = "0";
+    });
+    const observed = chartsRef.current;
+    resizeObserver.observe(observed);
     return () => {
-      window.removeEventListener("resize", onResize);
+      resizeObserver.unobserve(observed);
       chartsInstanceRef.current?.dispose();
     };
   }, [props.data?.display?.value]);
+  const nodeStyle = { display: "flex", flexDirection: "column" };
+  const vizStyle = { flex: 1 };
   return (
-    <NodeWithParams {...props}>
-      <div className="box" draggable={false} ref={chartsRef} />
+    <NodeWithParams nodeStyle={nodeStyle} collapsed {...props}>
+      <div style={vizStyle} ref={chartsRef} />
     </NodeWithParams>
   );
 };

lynxkite-app/web/tests/basic.spec.ts

@@ -21,9 +21,6 @@ test("Box creation & deletion per env", async () => {
   const envs = await workspace.getEnvs();
   for (const env of envs) {
     await workspace.setEnv(env);
-    // TODO: Opening the catalog immediately after setting the env can fail.
-    // Let's fix this!
-    await new Promise((resolve) => setTimeout(resolve, 500));
     const catalog = await workspace.getCatalog();
     expect(catalog).not.toHaveLength(0);
     const op = catalog[0];
@@ -35,9 +32,9 @@ test("Box creation & deletion per env", async () => {
 });
 
 test("Delete multi-handle boxes", async () => {
-  await workspace.addBox("Compute PageRank");
-  await workspace.deleteBoxes(["Compute PageRank 1"]);
-  await expect(workspace.getBox("Compute PageRank 1")).not.toBeVisible();
+  await workspace.addBox("NX › PageRank");
+  await workspace.deleteBoxes(["NX › PageRank 1"]);
+  await expect(workspace.getBox("NX › PageRank 1")).not.toBeVisible();
 });
 
 test("Drag box", async () => {

lynxkite-app/web/tests/errors.spec.ts

@@ -20,24 +20,24 @@ test.afterEach(async () => {
 test("missing parameter", async () => {
   // Test the correct error message is displayed when a required parameter is missing,
   // and that the error message is removed when the parameter is filled.
-  await workspace.addBox("Create scale-free graph");
-  const graphBox = workspace.getBox("Create scale-free graph 1");
-  await graphBox.locator("input").fill("");
-  expect(await graphBox.locator(".error").innerText()).toBe(
-    "invalid literal for int() with base 10: ''",
-  );
-  await graphBox.locator("input").fill("10");
+  await workspace.addBox("NX › Scale-Free Graph");
+  const graphBox = workspace.getBox("NX › Scale-Free Graph 1");
+  await expect(graphBox.locator(".error")).toHaveText("n is unset.");
+  await graphBox.getByLabel("n", { exact: true }).fill("10");
   await expect(graphBox.locator(".error")).not.toBeVisible();
 });
 
 test("unknown operation", async () => {
   // Test that the correct error is displayed when the operation does not belong to
   // the current environment.
-  await workspace.addBox("Create scale-free graph");
+  await workspace.addBox("NX › Scale-Free Graph");
+  const graphBox = workspace.getBox("NX › Scale-Free Graph 1");
+  await graphBox.getByLabel("n", { exact: true }).fill("10");
   await workspace.setEnv("LynxScribe");
-  const csvBox = workspace.getBox("Create scale-free graph 1");
-  const errorText = await csvBox.locator(".error").innerText();
-  expect(errorText).toBe('Operation "Create scale-free graph" not found.');
+  const csvBox = workspace.getBox("NX › Scale-Free Graph 1");
+  await expect(csvBox.locator(".error")).toHaveText(
+    'Operation "NX › Scale-Free Graph" not found.',
+  );
   await workspace.setEnv("LynxKite Graph Analytics");
   await expect(csvBox.locator(".error")).not.toBeVisible();
 });

lynxkite-app/web/tests/examples.spec.ts

@@ -17,30 +17,23 @@ test("Pytorch example", async ({ page }) => {
   await ws.expectErrorFree();
 });
 
-test.fail("AIMO example", async ({ page }) => {
-  // Fails because of missing OPENAI_API_KEY
+test("AIMO example", async ({ page }) => {
   const ws = await Workspace.open(page, "AIMO");
   await ws.expectErrorFree();
 });
 
-test.fail("LynxScribe example", async ({ page }) => {
+test("LynxScribe example", async ({ page }) => {
   // Fails because of missing OPENAI_API_KEY
   const ws = await Workspace.open(page, "LynxScribe demo");
   await ws.expectErrorFree();
 });
 
-test.fail("Graph RAG", async ({ page }) => {
+test("Graph RAG", async ({ page }) => {
   // Fails due to some issue with ChromaDB
   const ws = await Workspace.open(page, "Graph RAG");
   await ws.expectErrorFree(process.env.CI ? 2000 : 500);
 });
 
-test.fail("RAG chatbot app", async ({ page }) => {
-  // Fail due to all operation being unknown
-  const ws = await Workspace.open(page, "RAG chatbot app");
-  await ws.expectErrorFree();
-});
-
 test("Airlines demo", async ({ page }) => {
   const ws = await Workspace.open(page, "Airlines demo");
   await ws.expectErrorFree(process.env.CI ? 10000 : 500);

lynxkite-app/web/tests/graph_creation.spec.ts

@@ -9,9 +9,13 @@ test.beforeEach(async ({ browser }) => {
     await browser.newPage(),
     "graph_creation_spec_test",
   );
-  await workspace.addBox("Create scale-free graph");
+  await workspace.addBox("NX › Scale-Free Graph");
+  await workspace
+    .getBox("NX › Scale-Free Graph 1")
+    .getByLabel("n", { exact: true })
+    .fill("10");
   await workspace.addBox("Create graph");
-  await workspace.connectBoxes("Create scale-free graph 1", "Create graph 1");
+  await workspace.connectBoxes("NX › Scale-Free Graph 1", "Create graph 1");
 });
 
 test.afterEach(async () => {

lynxkite-app/web/tests/lynxkite.ts

@@ -59,21 +59,23 @@ export class Workspace {
       // Avoid overlapping with existing nodes
       const numNodes = allBoxes.length || 1;
       await this.page.mouse.wheel(0, numNodes * 400);
-      await new Promise((resolve) => setTimeout(resolve, 200));
     }
 
-    // Some x,y offset, otherwise the box handle may fall outside the viewport.
     await this.page.locator(".ws-name").click();
     await this.page.keyboard.press("/");
-    await this.page.locator(".node-search").getByText(boxName).click();
+    await this.page
+      .locator(".node-search")
+      .getByText(boxName, { exact: true })
+      .click();
     await expect(this.getBoxes()).toHaveCount(allBoxes.length + 1);
   }
 
   async getCatalog() {
-    await this.page.locator(".react-flow__pane").click();
-    const catalog = await this.page
-      .locator(".node-search .matches .search-result")
-      .allInnerTexts();
+    await this.page.locator(".ws-name").click();
+    await this.page.keyboard.press("/");
+    const results = this.page.locator(".node-search .matches .search-result");
+    await expect(results.first()).toBeVisible();
+    const catalog = await results.allInnerTexts();
     // Dismiss the catalog menu
     await this.page.keyboard.press("Escape");
     await expect(this.page.locator(".node-search")).not.toBeVisible();
@@ -150,11 +152,6 @@ export class Workspace {
   }
 
   async expectErrorFree(executionWaitTime?) {
-    // TODO: Workaround, to account for workspace execution. Once
-    // we have a load indicator we can use that instead.
-    await new Promise((resolve) =>
-      setTimeout(resolve, executionWaitTime ? executionWaitTime : 500),
-    );
     await expect(this.getBoxes().locator(".error").first()).not.toBeVisible();
   }
 
@@ -185,7 +182,7 @@ export class Splash {
   }
 
   workspace(name: string) {
-    return this.page.getByRole("link", { name: name });
+    return this.page.getByRole("link", { name: name, exact: true });
   }
 
   getEntry(name: string) {

lynxkite-bio/src/lynxkite_bio/__init__.py

@@ -10,7 +10,7 @@ import rdkit.Chem.rdFingerprintGenerator
 import rdkit.Chem.Fingerprints.ClusterMols
 import scipy
 
-mem = joblib.Memory("../joblib-cache")
+mem = joblib.Memory("joblib-cache")
 ENV = "LynxKite Graph Analytics"
 op = ops.op_registration(ENV)
 

lynxkite-core/src/lynxkite/core/executors/one_by_one.py

@@ -142,12 +142,12 @@ async def execute(ws: workspace.Workspace, catalog, cache=None):
                         key = make_cache_key((inputs, params))
                         if key not in cache:
                             result: ops.Result = op(*inputs, **params)
-                            output = await await_if_needed(result.output)
-                            cache[key] = output
-                        output = cache[key]
+                            result.output = await await_if_needed(result.output)
+                            cache[key] = result
+                        result = cache[key]
                     else:
                         result = op(*inputs, **params)
-                        output = await await_if_needed(result.output)
+                    output = await await_if_needed(result.output)
                 except Exception as e:
                     traceback.print_exc()
                     node.publish_error(e)

lynxkite-core/src/lynxkite/core/ops.py

@@ -4,6 +4,7 @@ from __future__ import annotations
 import enum
 import functools
 import inspect
+import types
 import pydantic
 import typing
 from dataclasses import dataclass
@@ -123,6 +124,25 @@ def basic_outputs(*names):
     return {name: Output(name=name, type=None) for name in names}
 
 
+def _param_to_type(name, value, type):
+    value = value or ""
+    if type is int:
+        assert value != "", f"{name} is unset."
+        return int(value)
+    if type is float:
+        assert value != "", f"{name} is unset."
+        return float(value)
+    if isinstance(type, enum.EnumMeta):
+        return type[value]
+    if isinstance(type, types.UnionType):
+        match type.__args__:
+            case (types.NoneType, type):
+                return None if value == "" else _param_to_type(name, value, type)
+            case (type, types.NoneType):
+                return None if value == "" else _param_to_type(name, value, type)
+    return value
+
+
 class Op(BaseConfig):
     func: typing.Callable = pydantic.Field(exclude=True)
     name: str
@@ -136,12 +156,7 @@ class Op(BaseConfig):
         # Convert parameters.
         for p in params:
             if p in self.params:
-                if self.params[p].type is int:
-                    params[p] = int(params[p])
-                elif self.params[p].type is float:
-                    params[p] = float(params[p])
-                elif isinstance(self.params[p].type, enum.EnumMeta):
-                    params[p] = self.params[p].type[params[p]]
+                params[p] = _param_to_type(p, params[p], self.params[p].type)
         res = self.func(*inputs, **params)
         if not isinstance(res, Result):
             # Automatically wrap the result in a Result object, if it isn't already.

lynxkite-core/src/lynxkite/core/workspace.py

@@ -92,6 +92,7 @@ class Workspace(BaseConfig):
     env: str = ""
     nodes: list[WorkspaceNode] = dataclasses.field(default_factory=list)
     edges: list[WorkspaceEdge] = dataclasses.field(default_factory=list)
+    _crdt: pycrdt.Map
 
 
 async def execute(ws: Workspace):
@@ -104,7 +105,8 @@ def save(ws: Workspace, path: str):
     j = ws.model_dump()
     j = json.dumps(j, indent=2, sort_keys=True) + "\n"
     dirname, basename = os.path.split(path)
-    os.makedirs(dirname, exist_ok=True)
+    if dirname:
+        os.makedirs(dirname, exist_ok=True)
     # Create temp file in the same directory to make sure it's on the same filesystem.
     with tempfile.NamedTemporaryFile(
         "w", prefix=f".{basename}.", dir=dirname, delete=False

lynxkite-graph-analytics/Dockerfile.bionemo

@@ -15,3 +15,7 @@ RUN uv pip install -e lynxkite-core/[dev] -e lynxkite-app/[dev] -e lynxkite-grap
 
 # bionemo cellxgene_census needs this version of numpy
 RUN uv pip install numpy==1.26.4
+
+ENV LYNXKITE_DATA=examples
+
+CMD ["lynxkite"]

lynxkite-graph-analytics/README.md

@@ -28,13 +28,12 @@ To build the image:
 ```bash
 # in lynxkite-graph-analytics folder
 $ docker build -f Dockerfile.bionemo -t lynxkite-bionemo ..
+$ docker run --name bionemo -d -p8000:8000 --gpus=all lynxkite-bionemo
 ```
 
 Take into account that this Dockerfile does not include the lynxkite-lynxscribe package. If you want to include it you will
 need to set up git credentials inside the container.
 
-Then, inside the image you can start LynxKite as usual.
-
 If you want to do some development, then it is recommend to use the [devcontainers](https://code.visualstudio.com/docs/devcontainers/containers)
 vscode extension. The following is a basic configuration to get started:
 

lynxkite-graph-analytics/src/lynxkite_graph_analytics/bionemo_ops.py

@@ -40,7 +40,7 @@ from bionemo.scdl.io.single_cell_collection import SingleCellCollection
 import scanpy
 
 
-mem = joblib.Memory("../joblib-cache")
+mem = joblib.Memory("joblib-cache")
 op = ops.op_registration(core.ENV)
 DATA_PATH = Path("/workspace")
 

lynxkite-graph-analytics/src/lynxkite_graph_analytics/core.py

@@ -1,6 +1,7 @@
 """Graph analytics executor and data types."""
 
-from lynxkite.core import ops
+import os
+from lynxkite.core import ops, workspace
 import dataclasses
 import functools
 import networkx as nx
@@ -134,54 +135,73 @@ def nx_node_attribute_func(name):
     return decorator
 
 
-def disambiguate_edges(ws):
+def disambiguate_edges(ws: workspace.Workspace):
     """If an input plug is connected to multiple edges, keep only the last edge."""
     seen = set()
     for edge in reversed(ws.edges):
         if (edge.target, edge.targetHandle) in seen:
-            ws.edges.remove(edge)
+            i = ws.edges.index(edge)
+            del ws.edges[i]
+            if hasattr(ws, "_crdt"):
+                del ws._crdt["edges"][i]
         seen.add((edge.target, edge.targetHandle))
 
 
 @ops.register_executor(ENV)
-async def execute(ws):
+async def execute(ws: workspace.Workspace):
     catalog: dict[str, ops.Op] = ops.CATALOGS[ws.env]
     disambiguate_edges(ws)
     outputs = {}
-    failed = 0
-    while len(outputs) + failed < len(ws.nodes):
-        for node in ws.nodes:
-            if node.id in outputs:
-                continue
-            # TODO: Take the input/output handles into account.
-            inputs = [edge.source for edge in ws.edges if edge.target == node.id]
-            if all(input in outputs for input in inputs):
+    nodes = {node.id: node for node in ws.nodes}
+    todo = set(nodes.keys())
+    progress = True
+    while progress:
+        progress = False
+        for id in list(todo):
+            node = nodes[id]
+            input_nodes = [edge.source for edge in ws.edges if edge.target == id]
+            if all(input in outputs for input in input_nodes):
                 # All inputs for this node are ready, we can compute the output.
-                inputs = [outputs[input] for input in inputs]
-                params = {**node.data.params}
-                op = catalog.get(node.data.title)
-                if not op:
-                    node.publish_error("Operation not found in catalog")
-                    failed += 1
-                    continue
-                node.publish_started()
-                try:
-                    # Convert inputs types  to match operation signature.
-                    for i, (x, p) in enumerate(zip(inputs, op.inputs.values())):
-                        if p.type == nx.Graph and isinstance(x, Bundle):
-                            inputs[i] = x.to_nx()
-                        elif p.type == Bundle and isinstance(x, nx.Graph):
-                            inputs[i] = Bundle.from_nx(x)
-                        elif p.type == Bundle and isinstance(x, pd.DataFrame):
-                            inputs[i] = Bundle.from_df(x)
-                    result = op(*inputs, **params)
-                except Exception as e:
-                    traceback.print_exc()
-                    node.publish_error(e)
-                    failed += 1
-                    continue
-                outputs[node.id] = result.output
-                node.publish_result(result)
+                todo.remove(id)
+                progress = True
+                _execute_node(node, ws, catalog, outputs)
+
+
+def _execute_node(node, ws, catalog, outputs):
+    params = {**node.data.params}
+    op = catalog.get(node.data.title)
+    if not op:
+        node.publish_error("Operation not found in catalog")
+        return
+    node.publish_started()
+    input_map = {
+        edge.targetHandle: outputs[edge.source]
+        for edge in ws.edges
+        if edge.target == node.id
+    }
+    try:
+        # Convert inputs types to match operation signature.
+        inputs = []
+        for p in op.inputs.values():
+            if p.name not in input_map:
+                node.publish_error(f"Missing input: {p.name}")
+                return
+            x = input_map[p.name]
+            if p.type == nx.Graph and isinstance(x, Bundle):
+                x = x.to_nx()
+            elif p.type == Bundle and isinstance(x, nx.Graph):
+                x = Bundle.from_nx(x)
+            elif p.type == Bundle and isinstance(x, pd.DataFrame):
+                x = Bundle.from_df(x)
+            inputs.append(x)
+        result = op(*inputs, **params)
+    except Exception as e:
+        if os.environ.get("LYNXKITE_LOG_OP_ERRORS"):
+            traceback.print_exc()
+        node.publish_error(e)
+        return
+    outputs[node.id] = result.output
+    node.publish_result(result)
 
 
 def df_for_frontend(df: pd.DataFrame, limit: int) -> pd.DataFrame:

lynxkite-graph-analytics/src/lynxkite_graph_analytics/lynxkite_ops.py

@@ -15,7 +15,7 @@ import polars as pl
 import json
 
 
-mem = joblib.Memory("../joblib-cache")
+mem = joblib.Memory("joblib-cache")
 op = ops.op_registration(core.ENV)
 
 
@@ -122,25 +122,6 @@ def import_osm(*, location: str):
     return ox.graph.graph_from_place(location, network_type="drive")
 
 
-@op("Create scale-free graph")
-def create_scale_free_graph(*, nodes: int = 10):
-    """Creates a scale-free graph with the given number of nodes."""
-    return nx.scale_free_graph(nodes)
-
-
-@op("Compute PageRank")
-@core.nx_node_attribute_func("pagerank")
-def compute_pagerank(graph: nx.Graph, *, damping=0.85, iterations=100):
-    # TODO: This requires scipy to be installed.
-    return nx.pagerank(graph, alpha=damping, max_iter=iterations)
-
-
-@op("Compute betweenness centrality")
-@core.nx_node_attribute_func("betweenness_centrality")
-def compute_betweenness_centrality(graph: nx.Graph, *, k=10):
-    return nx.betweenness_centrality(graph, k=k)
-
-
 @op("Discard loop edges")
 def discard_loop_edges(graph: nx.Graph):
     graph = graph.copy()

lynxkite-graph-analytics/src/lynxkite_graph_analytics/networkx_ops.py

@@ -1,13 +1,155 @@
 """Automatically wraps all NetworkX functions as LynxKite operations."""
 
+import collections
+import types
 from lynxkite.core import ops
 import functools
 import inspect
 import networkx as nx
+import re
+
+import pandas as pd
 
 ENV = "LynxKite Graph Analytics"
 
 
+class UnsupportedParameterType(Exception):
+    pass
+
+
+_UNSUPPORTED = object()
+_SKIP = object()
+
+
+def doc_to_type(name: str, type_hint: str) -> type:
+    type_hint = type_hint.lower()
+    type_hint = re.sub("[(][^)]+[)]", "", type_hint).strip().strip(".")
+    if " " in name or "http" in name:
+        return _UNSUPPORTED  # Not a parameter type.
+    if type_hint.endswith(", optional"):
+        w = doc_to_type(name, type_hint.removesuffix(", optional").strip())
+        if w is _UNSUPPORTED:
+            return _SKIP
+        return w if w is _SKIP else w | None
+    if type_hint in [
+        "a digraph or multidigraph",
+        "a graph g",
+        "graph",
+        "graphs",
+        "networkx graph instance",
+        "networkx graph",
+        "networkx undirected graph",
+        "nx.graph",
+        "undirected graph",
+        "undirected networkx graph",
+    ] or type_hint.startswith("networkx graph"):
+        return nx.Graph
+    elif type_hint in [
+        "digraph-like",
+        "digraph",
+        "directed graph",
+        "networkx digraph",
+        "networkx directed graph",
+        "nx.digraph",
+    ]:
+        return nx.DiGraph
+    elif type_hint == "node":
+        return _UNSUPPORTED
+    elif type_hint == '"node (optional)"':
+        return _SKIP
+    elif type_hint == '"edge"':
+        return _UNSUPPORTED
+    elif type_hint == '"edge (optional)"':
+        return _SKIP
+    elif type_hint in ["class", "data type"]:
+        return _UNSUPPORTED
+    elif type_hint in ["string", "str", "node label"]:
+        return str
+    elif type_hint in ["string or none", "none or string", "string, or none"]:
+        return str | None
+    elif type_hint in ["int", "integer"]:
+        return int
+    elif type_hint in ["bool", "boolean"]:
+        return bool
+    elif type_hint == "tuple":
+        return _UNSUPPORTED
+    elif type_hint == "set":
+        return _UNSUPPORTED
+    elif type_hint == "list of floats":
+        return _UNSUPPORTED
+    elif type_hint == "list of floats or float":
+        return float
+    elif type_hint in ["dict", "dictionary"]:
+        return _UNSUPPORTED
+    elif type_hint == "scalar or dictionary":
+        return float
+    elif type_hint == "none or dict":
+        return _SKIP
+    elif type_hint in ["function", "callable"]:
+        return _UNSUPPORTED
+    elif type_hint in [
+        "collection",
+        "container of nodes",
+        "list of nodes",
+    ]:
+        return _UNSUPPORTED
+    elif type_hint in [
+        "container",
+        "generator",
+        "iterable",
+        "iterator",
+        "list or iterable container",
+        "list or iterable",
+        "list or set",
+        "list or tuple",
+        "list",
+    ]:
+        return _UNSUPPORTED
+    elif type_hint == "generator of sets":
+        return _UNSUPPORTED
+    elif type_hint == "dict or a set of 2 or 3 tuples":
+        return _UNSUPPORTED
+    elif type_hint == "set of 2 or 3 tuples":
+        return _UNSUPPORTED
+    elif type_hint == "none, string or function":
+        return str | None
+    elif type_hint == "string or function" and name == "weight":
+        return str
+    elif type_hint == "integer, float, or none":
+        return float | None
+    elif type_hint in [
+        "float",
+        "int or float",
+        "integer or float",
+        "integer, float",
+        "number",
+        "numeric",
+        "real",
+        "scalar",
+    ]:
+        return float
+    elif type_hint in ["integer or none", "int or none"]:
+        return int | None
+    elif name == "seed":
+        return int | None
+    elif name == "weight":
+        return str
+    elif type_hint == "object":
+        return _UNSUPPORTED
+    return _SKIP
+
+
+def types_from_doc(doc: str) -> dict[str, type]:
+    types = {}
+    for line in doc.splitlines():
+        if ":" in line:
+            a, b = line.split(":", 1)
+            for a in a.split(","):
+                a = a.strip()
+                types[a] = doc_to_type(a, b)
+    return types
+
+
 def wrapped(name: str, func):
     @functools.wraps(func)
     def wrapper(*args, **kwargs):
@@ -15,48 +157,118 @@ def wrapped(name: str, func):
             if v == "None":
                 kwargs[k] = None
         res = func(*args, **kwargs)
+        # Figure out what the returned value is.
         if isinstance(res, nx.Graph):
             return res
-        # Otherwise it's a node attribute.
-        graph = args[0].copy()
-        nx.set_node_attributes(graph, values=res, name=name)
-        return graph
+        if isinstance(res, types.GeneratorType):
+            res = list(res)
+        if name in ["articulation_points"]:
+            graph = args[0].copy()
+            nx.set_node_attributes(graph, 0, name=name)
+            nx.set_node_attributes(graph, {r: 1 for r in res}, name=name)
+            return graph
+        if isinstance(res, collections.abc.Sized):
+            if len(res) == 0:
+                return pd.DataFrame()
+            for a in args:
+                if isinstance(a, nx.Graph):
+                    if a.number_of_nodes() == len(res):
+                        graph = a.copy()
+                        nx.set_node_attributes(graph, values=res, name=name)
+                        return graph
+                    if a.number_of_edges() == len(res):
+                        graph = a.copy()
+                        nx.set_edge_attributes(graph, values=res, name=name)
+                        return graph
+            return pd.DataFrame({name: res})
+        return pd.DataFrame({name: [res]})
 
     return wrapper
 
 
+def _get_params(func) -> dict | None:
+    sig = inspect.signature(func)
+    # Get types from docstring.
+    types = types_from_doc(func.__doc__)
+    # Always hide these.
+    for k in ["backend", "backend_kwargs", "create_using"]:
+        types[k] = _SKIP
+    # Add in types based on signature.
+    for k, param in sig.parameters.items():
+        if k in types:
+            continue
+        if param.annotation is not param.empty:
+            types[k] = param.annotation
+        if k in ["i", "j", "n"]:
+            types[k] = int
+    params = {}
+    for name, param in sig.parameters.items():
+        _type = types.get(name, _UNSUPPORTED)
+        if _type is _UNSUPPORTED:
+            raise UnsupportedParameterType(name)
+        if _type is _SKIP or _type in [nx.Graph, nx.DiGraph]:
+            continue
+        params[name] = ops.Parameter.basic(
+            name=name,
+            default=str(param.default)
+            if type(param.default) in [str, int, float]
+            else None,
+            type=_type,
+        )
+    return params
+
+
+_REPLACEMENTS = [
+    ("Barabasi Albert", "Barabasi–Albert"),
+    ("Bellman Ford", "Bellman–Ford"),
+    ("Bethe Hessian", "Bethe–Hessian"),
+    ("Bfs", "BFS"),
+    ("Dag ", "DAG "),
+    ("Dfs", "DFS"),
+    ("Dorogovtsev Goltsev Mendes", "Dorogovtsev–Goltsev–Mendes"),
+    ("Erdos Renyi", "Erdos–Renyi"),
+    ("Floyd Warshall", "Floyd–Warshall"),
+    ("Gnc", "G(n,c)"),
+    ("Gnm", "G(n,m)"),
+    ("Gnp", "G(n,p)"),
+    ("Gnr", "G(n,r)"),
+    ("Havel Hakimi", "Havel–Hakimi"),
+    ("Hkn", "H(k,n)"),
+    ("Hnm", "H(n,m)"),
+    ("Kl ", "KL "),
+    ("Moebius Kantor", "Moebius–Kantor"),
+    ("Pagerank", "PageRank"),
+    ("Scale Free", "Scale-Free"),
+    ("Vf2Pp", "VF2++"),
+    ("Watts Strogatz", "Watts–Strogatz"),
+    ("Weisfeiler Lehman", "Weisfeiler–Lehman"),
+]
+
+
 def register_networkx(env: str):
     cat = ops.CATALOGS.setdefault(env, {})
+    counter = 0
     for name, func in nx.__dict__.items():
         if hasattr(func, "graphs"):
-            sig = inspect.signature(func)
+            try:
+                params = _get_params(func)
+            except UnsupportedParameterType:
+                continue
             inputs = {k: ops.Input(name=k, type=nx.Graph) for k in func.graphs}
-            params = {
-                name: ops.Parameter.basic(
-                    name,
-                    str(param.default)
-                    if type(param.default) in [str, int, float]
-                    else None,
-                    param.annotation,
-                )
-                for name, param in sig.parameters.items()
-                if name not in ["G", "backend", "backend_kwargs", "create_using"]
-            }
-            for p in params.values():
-                if not p.type:
-                    # Guess the type based on the name.
-                    if len(p.name) == 1:
-                        p.type = int
-            name = "NX › " + name.replace("_", " ").title()
+            nicename = "NX › " + name.replace("_", " ").title()
+            for a, b in _REPLACEMENTS:
+                nicename = nicename.replace(a, b)
             op = ops.Op(
                 func=wrapped(name, func),
-                name=name,
+                name=nicename,
                 params=params,
                 inputs=inputs,
                 outputs={"output": ops.Output(name="output", type=nx.Graph)},
                 type="basic",
             )
-            cat[name] = op
+            cat[nicename] = op
+            counter += 1
+    print(f"Registered {counter} NetworkX operations.")
 
 
 register_networkx(ENV)

lynxkite-graph-analytics/tests/test_lynxkite_ops.py

@@ -77,13 +77,13 @@ async def test_execute_operation_inputs_correct_cast():
     )
     ws.edges = [
         workspace.WorkspaceEdge(
-            id="1", source="1", target="2", sourceHandle="1", targetHandle="2"
+            id="1", source="1", target="2", sourceHandle="output", targetHandle="graph"
         ),
         workspace.WorkspaceEdge(
-            id="2", source="2", target="3", sourceHandle="2", targetHandle="3"
+            id="2", source="2", target="3", sourceHandle="output", targetHandle="bundle"
         ),
         workspace.WorkspaceEdge(
-            id="3", source="3", target="4", sourceHandle="3", targetHandle="4"
+            id="3", source="3", target="4", sourceHandle="output", targetHandle="bundle"
         ),
     ]
 
@@ -92,5 +92,73 @@ async def test_execute_operation_inputs_correct_cast():
     assert all([node.data.error is None for node in ws.nodes])
 
 
+async def test_multiple_inputs():
+    """Make sure each input goes to the right argument."""
+    op = ops.op_registration("test")
+
+    @op("One")
+    def one():
+        return 1
+
+    @op("Two")
+    def two():
+        return 2
+
+    @op("Smaller?", view="visualization")
+    def is_smaller(a, b):
+        return a < b
+
+    ws = workspace.Workspace(env="test")
+    ws.nodes.append(
+        workspace.WorkspaceNode(
+            id="one",
+            type="cool",
+            data=workspace.WorkspaceNodeData(title="One", params={}),
+            position=workspace.Position(x=0, y=0),
+        )
+    )
+    ws.nodes.append(
+        workspace.WorkspaceNode(
+            id="two",
+            type="cool",
+            data=workspace.WorkspaceNodeData(title="Two", params={}),
+            position=workspace.Position(x=100, y=0),
+        )
+    )
+    ws.nodes.append(
+        workspace.WorkspaceNode(
+            id="smaller",
+            type="cool",
+            data=workspace.WorkspaceNodeData(title="Smaller?", params={}),
+            position=workspace.Position(x=200, y=0),
+        )
+    )
+    ws.edges = [
+        workspace.WorkspaceEdge(
+            id="one",
+            source="one",
+            target="smaller",
+            sourceHandle="output",
+            targetHandle="a",
+        ),
+        workspace.WorkspaceEdge(
+            id="two",
+            source="two",
+            target="smaller",
+            sourceHandle="output",
+            targetHandle="b",
+        ),
+    ]
+
+    await execute(ws)
+
+    assert ws.nodes[-1].data.display is True
+    # Flip the inputs.
+    ws.edges[0].targetHandle = "b"
+    ws.edges[1].targetHandle = "a"
+    await execute(ws)
+    assert ws.nodes[-1].data.display is False
+
+
 if __name__ == "__main__":
     pytest.main()

lynxkite-lynxscribe/README.md

@@ -5,7 +5,7 @@ LynxKite UI for building LynxScribe chat applications. Also runs the chat applic
 To run a chat UI for LynxScribe workspaces:
 
 ```bash
-WEBUI_AUTH=false OPENAI_API_BASE_URL=http://localhost:8000/api/service/lynxscribe/lynxscribe_ops uvx open-webui serve
+WEBUI_AUTH=false OPENAI_API_BASE_URL=http://localhost:8000/api/service/lynxkite_lynxscribe uvx open-webui serve
 ```
 
 Or use [Lynx WebUI](https://github.com/biggraph/lynx-webui/) instead of Open WebUI.

lynxkite-lynxscribe/src/lynxkite_lynxscribe/lynxscribe_ops.py

@@ -9,6 +9,7 @@ import pandas as pd
 import os
 import joblib
 
+import pathlib
 from lynxscribe.core.llm.base import get_llm_engine
 from lynxscribe.core.vector_store.base import get_vector_store
 from lynxscribe.common.config import load_config
@@ -483,13 +484,12 @@ def view(input):
     return v
 
 
-async def get_chat_api(ws):
-    import pathlib
+async def get_chat_api(ws: str):
     from lynxkite.core import workspace
 
-    DATA_PATH = pathlib.Path.cwd() / "data"
-    path = DATA_PATH / ws
-    assert path.is_relative_to(DATA_PATH)
+    cwd = pathlib.Path()
+    path = cwd / ws
+    assert path.is_relative_to(cwd)
     assert path.exists(), f"Workspace {path} does not exist"
     ws = workspace.load(path)
     contexts = await ops.EXECUTORS[ENV](ws)
@@ -549,17 +549,15 @@ async def api_service_get(request):
 
 
 def get_lynxscribe_workspaces():
-    import pathlib
     from lynxkite.core import workspace
 
-    DATA_DIR = pathlib.Path.cwd() / "data"
     workspaces = []
-    for p in DATA_DIR.glob("**/*"):
+    for p in pathlib.Path().glob("**/*"):
         if p.is_file():
             try:
                 ws = workspace.load(p)
                 if ws.env == ENV:
-                    workspaces.append(p.relative_to(DATA_DIR))
+                    workspaces.append(p)
             except Exception:
                 pass  # Ignore files that are not valid workspaces.
     workspaces.sort()