Open code files from directory + related stuff.

biome.json

@@ -1,4 +1,7 @@
 {
+  "files": {
+    "ignore": ["**/*.lynxkite.json"]
+  },
   "formatter": {
     "ignore": ["**/node_modules/**", "**/dist/**"],
     "lineWidth": 100,
@@ -21,6 +24,7 @@
         "useKeyWithClickEvents": "off",
         "useValidAnchor": "off",
         "useButtonType": "off",
+        "noAutofocus": "off",
         "noNoninteractiveTabindex": "off"
       }
     }

examples/ODE-GNN experiment

@@ -1,466 +0,0 @@
-{
-  "edges": [
-    {
-      "id": "Import CSV 1 Train/test split 1",
-      "source": "Import CSV 1",
-      "sourceHandle": "output",
-      "target": "Train/test split 1",
-      "targetHandle": "bundle"
-    },
-    {
-      "id": "Train/test split 1 Create graph 1",
-      "source": "Train/test split 1",
-      "sourceHandle": "output",
-      "target": "Create graph 1",
-      "targetHandle": "bundle"
-    },
-    {
-      "id": "Biomedical foundation graph (PLACEHOLDER) 1 Create graph 1",
-      "source": "Biomedical foundation graph (PLACEHOLDER) 1",
-      "sourceHandle": "output",
-      "target": "Create graph 1",
-      "targetHandle": "bundle"
-    },
-    {
-      "id": "Define model 1 Create graph 1",
-      "source": "Define model 1",
-      "sourceHandle": "output",
-      "target": "Create graph 1",
-      "targetHandle": "bundle"
-    },
-    {
-      "id": "Create graph 1 Train model 1",
-      "source": "Create graph 1",
-      "sourceHandle": "output",
-      "target": "Train model 1",
-      "targetHandle": "bundle"
-    },
-    {
-      "id": "Train model 1 Model inference 1",
-      "source": "Train model 1",
-      "sourceHandle": "output",
-      "target": "Model inference 1",
-      "targetHandle": "bundle"
-    }
-  ],
-  "env": "LynxKite Graph Analytics",
-  "nodes": [
-    {
-      "data": {
-        "__execution_delay": 0.0,
-        "collapsed": null,
-        "display": null,
-        "error": null,
-        "meta": {
-          "inputs": {},
-          "name": "Biomedical foundation graph (PLACEHOLDER)",
-          "outputs": {
-            "output": {
-              "name": "output",
-              "position": "right",
-              "type": {
-                "type": "None"
-              }
-            }
-          },
-          "params": {
-            "filter_nodes": {
-              "default": null,
-              "name": "filter_nodes",
-              "type": {
-                "type": "<class 'str'>"
-              }
-            }
-          },
-          "type": "basic"
-        },
-        "params": {
-          "filter_nodes": "drug,gene,disease"
-        },
-        "status": "done",
-        "title": "Biomedical foundation graph (PLACEHOLDER)"
-      },
-      "dragHandle": ".bg-primary",
-      "height": 200.0,
-      "id": "Biomedical foundation graph (PLACEHOLDER) 1",
-      "position": {
-        "x": 230.1082040835347,
-        "y": 643.2454063689602
-      },
-      "type": "basic",
-      "width": 200.0
-    },
-    {
-      "data": {
-        "__execution_delay": null,
-        "collapsed": true,
-        "display": null,
-        "error": "Missing input: bundle",
-        "meta": {
-          "inputs": {
-            "bundle": {
-              "name": "bundle",
-              "position": "left",
-              "type": {
-                "type": "<class 'lynxkite_graph_analytics.core.Bundle'>"
-              }
-            }
-          },
-          "name": "Train/test split",
-          "outputs": {
-            "output": {
-              "name": "output",
-              "position": "right",
-              "type": {
-                "type": "None"
-              }
-            }
-          },
-          "params": {
-            "table_name": {
-              "default": null,
-              "name": "table_name",
-              "type": {
-                "type": "<class 'str'>"
-              }
-            },
-            "test_ratio": {
-              "default": 0.1,
-              "name": "test_ratio",
-              "type": {
-                "type": "<class 'float'>"
-              }
-            }
-          },
-          "type": "basic"
-        },
-        "params": {
-          "table_name": null,
-          "test_ratio": 0.1
-        },
-        "status": "planned",
-        "title": "Train/test split"
-      },
-      "dragHandle": ".bg-primary",
-      "height": 200.0,
-      "id": "Train/test split 1",
-      "position": {
-        "x": 313.3745540124723,
-        "y": 412.5466021460861
-      },
-      "type": "basic",
-      "width": 200.0
-    },
-    {
-      "data": {
-        "display": null,
-        "error": "[Errno 2] No such file or directory: ''",
-        "meta": {
-          "inputs": {},
-          "name": "Import CSV",
-          "outputs": {
-            "output": {
-              "name": "output",
-              "position": "right",
-              "type": {
-                "type": "None"
-              }
-            }
-          },
-          "params": {
-            "columns": {
-              "default": "<from file>",
-              "name": "columns",
-              "type": {
-                "type": "<class 'str'>"
-              }
-            },
-            "filename": {
-              "default": null,
-              "name": "filename",
-              "type": {
-                "type": "<class 'str'>"
-              }
-            },
-            "separator": {
-              "default": "<auto>",
-              "name": "separator",
-              "type": {
-                "type": "<class 'str'>"
-              }
-            }
-          },
-          "type": "basic"
-        },
-        "params": {
-          "columns": "<from file>",
-          "filename": null,
-          "separator": "<auto>"
-        },
-        "status": "done",
-        "title": "Import CSV"
-      },
-      "dragHandle": ".bg-primary",
-      "height": 200.0,
-      "id": "Import CSV 1",
-      "position": {
-        "x": -2.1743215714344757,
-        "y": 346.06014722935214
-      },
-      "type": "basic",
-      "width": 200.0
-    },
-    {
-      "data": {
-        "__execution_delay": 0.0,
-        "collapsed": null,
-        "display": null,
-        "error": "Missing input: bundle",
-        "meta": {
-          "inputs": {
-            "bundle": {
-              "name": "bundle",
-              "position": "left",
-              "type": {
-                "type": "<class 'lynxkite_graph_analytics.core.Bundle'>"
-              }
-            }
-          },
-          "name": "Model inference",
-          "outputs": {
-            "output": {
-              "name": "output",
-              "position": "right",
-              "type": {
-                "type": "None"
-              }
-            }
-          },
-          "params": {
-            "model_mapping": {
-              "default": null,
-              "name": "model_mapping",
-              "type": {
-                "type": "<class 'str'>"
-              }
-            },
-            "model_name": {
-              "default": null,
-              "name": "model_name",
-              "type": {
-                "type": "<class 'str'>"
-              }
-            },
-            "save_output_as": {
-              "default": "prediction",
-              "name": "save_output_as",
-              "type": {
-                "type": "<class 'str'>"
-              }
-            }
-          },
-          "type": "basic"
-        },
-        "params": {
-          "model_mapping": "input: data_test",
-          "model_name": "model",
-          "save_output_as": "prediction"
-        },
-        "status": "done",
-        "title": "Model inference"
-      },
-      "dragHandle": ".bg-primary",
-      "height": 339.0,
-      "id": "Model inference 1",
-      "position": {
-        "x": 1736.5697434242886,
-        "y": 357.0743204289906
-      },
-      "type": "basic",
-      "width": 281.0
-    },
-    {
-      "data": {
-        "__execution_delay": null,
-        "collapsed": true,
-        "display": null,
-        "error": "Missing input: bundle",
-        "meta": {
-          "inputs": {
-            "bundle": {
-              "name": "bundle",
-              "position": "left",
-              "type": {
-                "type": "list[lynxkite_graph_analytics.core.Bundle]"
-              }
-            }
-          },
-          "name": "Organize",
-          "outputs": {
-            "output": {
-              "name": "output",
-              "position": "right",
-              "type": {
-                "type": "None"
-              }
-            }
-          },
-          "params": {
-            "relations": {
-              "default": null,
-              "name": "relations",
-              "type": {
-                "type": "<class 'str'>"
-              }
-            }
-          },
-          "type": "graph_creation_view"
-        },
-        "params": {
-          "relations": null
-        },
-        "status": "planned",
-        "title": "Organize"
-      },
-      "dragHandle": ".bg-primary",
-      "height": 322.0,
-      "id": "Create graph 1",
-      "position": {
-        "x": 846.6882598271658,
-        "y": 480.6258932907771
-      },
-      "type": "graph_creation_view",
-      "width": 313.0
-    },
-    {
-      "data": {
-        "__execution_delay": 0.0,
-        "collapsed": null,
-        "display": null,
-        "error": null,
-        "meta": {
-          "inputs": {},
-          "name": "Define model",
-          "outputs": {
-            "output": {
-              "name": "output",
-              "position": "right",
-              "type": {
-                "type": "None"
-              }
-            }
-          },
-          "params": {
-            "model_workspace": {
-              "default": null,
-              "name": "model_workspace",
-              "type": {
-                "type": "<class 'str'>"
-              }
-            },
-            "save_as": {
-              "default": "model",
-              "name": "save_as",
-              "type": {
-                "type": "<class 'str'>"
-              }
-            }
-          },
-          "position": {
-            "x": 286.0,
-            "y": 208.0
-          },
-          "type": "basic"
-        },
-        "params": {
-          "model_workspace": "ODE-GNN",
-          "save_as": "model"
-        },
-        "status": "done",
-        "title": "Define model"
-      },
-      "dragHandle": ".bg-primary",
-      "height": 200.0,
-      "id": "Define model 1",
-      "position": {
-        "x": 311.976524267066,
-        "y": 146.99006795914332
-      },
-      "type": "basic",
-      "width": 200.0
-    },
-    {
-      "data": {
-        "__execution_delay": 0.0,
-        "collapsed": null,
-        "display": null,
-        "error": "Missing input: bundle",
-        "meta": {
-          "inputs": {
-            "bundle": {
-              "name": "bundle",
-              "position": "left",
-              "type": {
-                "type": "<class 'lynxkite_graph_analytics.core.Bundle'>"
-              }
-            }
-          },
-          "name": "Train model",
-          "outputs": {
-            "output": {
-              "name": "output",
-              "position": "right",
-              "type": {
-                "type": "None"
-              }
-            }
-          },
-          "params": {
-            "epochs": {
-              "default": 1.0,
-              "name": "epochs",
-              "type": {
-                "type": "<class 'int'>"
-              }
-            },
-            "model_mapping": {
-              "default": null,
-              "name": "model_mapping",
-              "type": {
-                "type": "<class 'str'>"
-              }
-            },
-            "model_name": {
-              "default": null,
-              "name": "model_name",
-              "type": {
-                "type": "<class 'str'>"
-              }
-            }
-          },
-          "position": {
-            "x": 995.0,
-            "y": 350.0
-          },
-          "type": "basic"
-        },
-        "params": {
-          "epochs": 1.0,
-          "model_mapping": "input: data_train",
-          "model_name": "model"
-        },
-        "status": "planned",
-        "title": "Train model"
-      },
-      "dragHandle": ".bg-primary",
-      "height": 342.0,
-      "id": "Train model 1",
-      "position": {
-        "x": 1358.7213662492159,
-        "y": 352.03096133771896
-      },
-      "type": "basic",
-      "width": 296.0
-    }
-  ]
-}

examples/word2vec.py

@@ -5,17 +5,14 @@ import pandas as pd
 ENV = "LynxKite Graph Analytics"
 
 
-@op(ENV, "Word2vec for the top 1000 words", cache=True)
+@op(ENV, "Word2vec for the top 1000 words", slow=True)
 def word2vec_1000():
     model = staticvectors.StaticVectors("neuml/word2vec-quantized")
-    with open("wordlist.txt") as f:
-        words = [w.strip() for w in f.read().strip().split("\n")]
-    df = pd.DataFrame(
-        {
-            "word": words,
-            "embedding": model.embeddings(words).tolist(),
-        }
+    df = pd.read_csv(
+        "https://gist.githubusercontent.com/deekayen/4148741/raw/98d35708fa344717d8eee15d11987de6c8e26d7d/1-1000.txt",
+        names=["word"],
     )
+    df["embedding"] = model.embeddings(df.word.tolist()).tolist()
     return df
 
 

lynxkite-app/src/lynxkite_app/main.py

@@ -84,6 +84,15 @@ class DirectoryEntry(pydantic.BaseModel):
     type: str
 
 
+def _get_path_type(path: pathlib.Path) -> str:
+    if path.is_dir():
+        return "directory"
+    elif path.suffixes[-2:] == [".lynxkite", ".json"]:
+        return "workspace"
+    else:
+        return "file"
+
+
 @app.get("/api/dir/list")
 def list_dir(path: str):
     path = data_path / path
@@ -92,7 +101,7 @@ def list_dir(path: str):
         [
             DirectoryEntry(
                 name=str(p.relative_to(data_path)),
-                type="directory" if p.is_dir() else "workspace",
+                type=_get_path_type(p),
             )
             for p in path.iterdir()
             if not p.name.startswith(".")

lynxkite-app/web/index.html

@@ -4,7 +4,6 @@
     <meta charset="UTF-8" />
     <link rel="icon" type="image/svg+xml" href="/src/assets/favicon.ico" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>LynxKite 2025</title>
   </head>
   <body>
     <div id="root"></div>

lynxkite-app/web/src/Directory.tsx

@@ -15,9 +15,46 @@ import FolderPlus from "~icons/tabler/folder-plus";
 // @ts-ignore
 import Home from "~icons/tabler/home";
 // @ts-ignore
+import LayoutGrid from "~icons/tabler/layout-grid";
+// @ts-ignore
+import LayoutGridAdd from "~icons/tabler/layout-grid-add";
+// @ts-ignore
 import Trash from "~icons/tabler/trash";
 import logo from "./assets/logo.png";
 
+function EntryCreator(props: {
+  label: string;
+  icon: JSX.Element;
+  onCreate: (name: string) => void;
+}) {
+  const [isCreating, setIsCreating] = useState(false);
+  return (
+    <>
+      {isCreating ? (
+        <form
+          onSubmit={(e) => {
+            e.preventDefault();
+            props.onCreate((e.target as HTMLFormElement).entryName.value.trim());
+          }}
+        >
+          <input
+            className="input input-ghost w-full"
+            autoFocus
+            type="text"
+            name="entryName"
+            onBlur={() => setIsCreating(false)}
+            placeholder={`${props.label} name`}
+          />
+        </form>
+      ) : (
+        <button type="button" onClick={() => setIsCreating(true)}>
+          {props.icon} {props.label}
+        </button>
+      )}
+    </>
+  );
+}
+
 const fetcher = (url: string) => fetch(url).then((res) => res.json());
 
 export default function () {
@@ -27,48 +64,41 @@ export default function () {
     dedupingInterval: 0,
   });
   const navigate = useNavigate();
-  const [isCreatingDir, setIsCreatingDir] = useState(false);
-  const [isCreatingWorkspace, setIsCreatingWorkspace] = useState(false);
 
   function link(item: DirectoryEntry) {
     if (item.type === "directory") {
       return `/dir/${item.name}`;
     }
-    return `/edit/${item.name}`;
+    if (item.type === "workspace") {
+      return `/edit/${item.name}`;
+    }
+    return `/code/${item.name}`;
   }
 
   function shortName(item: DirectoryEntry) {
-    return item.name.split("/").pop();
+    return item.name
+      .split("/")
+      .pop()
+      ?.replace(/[.]lynxkite[.]json$/, "");
   }
 
-  function newName(list: DirectoryEntry[], baseName = "Untitled") {
-    let i = 0;
-    while (true) {
-      const name = `${baseName}${i ? ` ${i}` : ""}`;
-      if (!list.find((item) => item.name === name)) {
-        return name;
-      }
-      i++;
-    }
+  function newWorkspaceIn(path: string, workspaceName: string) {
+    const pathSlash = path ? `${path}/` : "";
+    navigate(`/edit/${pathSlash}${workspaceName}.lynxkite.json`, { replace: true });
   }
-
-  function newWorkspaceIn(path: string, list: DirectoryEntry[], workspaceName?: string) {
+  function newCodeFile(path: string, name: string) {
     const pathSlash = path ? `${path}/` : "";
-    const name = workspaceName || newName(list);
-    navigate(`/edit/${pathSlash}${name}`, { replace: true });
+    navigate(`/code/${pathSlash}${name}`, { replace: true });
   }
-
-  async function newFolderIn(path: string, list: DirectoryEntry[], folderName?: string) {
-    const name = folderName || newName(list, "New Folder");
+  async function newFolderIn(path: string, folderName: string) {
     const pathSlash = path ? `${path}/` : "";
-
     const res = await fetch("/api/dir/mkdir", {
       method: "POST",
       headers: { "Content-Type": "application/json" },
-      body: JSON.stringify({ path: pathSlash + name }),
+      body: JSON.stringify({ path: pathSlash + folderName }),
     });
     if (res.ok) {
-      navigate(`/dir/${pathSlash}${name}`);
+      navigate(`/dir/${pathSlash}${folderName}`);
     } else {
       alert("Failed to create folder.");
     }
@@ -105,84 +135,66 @@ export default function () {
         {list.data && (
           <>
             <div className="actions">
-              <div className="new-workspace">
-                {isCreatingWorkspace && (
-                  // @ts-ignore
-                  <form
-                    onSubmit={(e) => {
-                      e.preventDefault();
-                      newWorkspaceIn(
-                        path || "",
-                        list.data,
-                        (e.target as HTMLFormElement).workspaceName.value.trim(),
-                      );
-                    }}
-                  >
-                    <input
-                      type="text"
-                      name="workspaceName"
-                      defaultValue={newName(list.data)}
-                      placeholder={newName(list.data)}
-                    />
-                  </form>
-                )}
-                <button type="button" onClick={() => setIsCreatingWorkspace(true)}>
-                  <FolderPlus /> New workspace
-                </button>
-              </div>
-
-              <div className="new-folder">
-                {isCreatingDir && (
-                  // @ts-ignore
-                  <form
-                    onSubmit={(e) => {
-                      e.preventDefault();
-                      newFolderIn(
-                        path || "",
-                        list.data,
-                        (e.target as HTMLFormElement).folderName.value.trim(),
-                      );
-                    }}
-                  >
-                    <input
-                      type="text"
-                      name="folderName"
-                      defaultValue={newName(list.data)}
-                      placeholder={newName(list.data)}
-                    />
-                  </form>
-                )}
-                <button type="button" onClick={() => setIsCreatingDir(true)}>
-                  <FolderPlus /> New folder
-                </button>
-              </div>
+              <EntryCreator
+                onCreate={(name) => {
+                  newWorkspaceIn(path || "", name);
+                }}
+                icon={<LayoutGridAdd />}
+                label="New workspace"
+              />
+              <EntryCreator
+                onCreate={(name) => {
+                  newCodeFile(path || "", name);
+                }}
+                icon={<FilePlus />}
+                label="New code file"
+              />
+              <EntryCreator
+                onCreate={(name: string) => {
+                  newFolderIn(path || "", name);
+                }}
+                icon={<FolderPlus />}
+                label="New folder"
+              />
             </div>
 
-            {path && (
+            {path ? (
               <div className="breadcrumbs">
                 <Link to="/dir/">
                   <Home />
                 </Link>{" "}
                 <span className="current-folder">{path}</span>
+                <title>{path}</title>
               </div>
+            ) : (
+              <title>LynxKite 2000:MM</title>
             )}
 
-            {list.data.map((item: DirectoryEntry) => (
-              <div key={item.name} className="entry">
-                <Link key={link(item)} to={link(item)}>
-                  {item.type === "directory" ? <Folder /> : <File />}
-                  {shortName(item)}
-                </Link>
-                <button
-                  type="button"
-                  onClick={() => {
-                    deleteItem(item);
-                  }}
-                >
-                  <Trash />
-                </button>
-              </div>
-            ))}
+            {list.data.map(
+              (item: DirectoryEntry) =>
+                !shortName(item)?.startsWith("__") && (
+                  <div key={item.name} className="entry">
+                    <Link key={link(item)} to={link(item)}>
+                      {item.type === "directory" ? (
+                        <Folder />
+                      ) : item.type === "workspace" ? (
+                        <LayoutGrid />
+                      ) : (
+                        <File />
+                      )}
+                      {shortName(item)}
+                    </Link>
+                    <button
+                      type="button"
+                      onClick={() => {
+                        deleteItem(item);
+                      }}
+                    >
+                      <Trash />
+                    </button>
+                  </div>
+                ),
+            )}
           </>
         )}
       </div>{" "}

lynxkite-app/web/src/index.css

@@ -326,7 +326,14 @@ body {
   .actions {
     display: flex;
     justify-content: space-evenly;
+    align-items: center;
+    height: 50px;
     padding: 5px;
+
+    form,
+    button {
+      flex: 1;
+    }
   }
 
   .actions a {

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

@@ -53,6 +53,10 @@ function LynxKiteFlow() {
   const [nodes, setNodes] = useState([] as Node[]);
   const [edges, setEdges] = useState([] as Edge[]);
   const { path } = useParams();
+  const shortPath = path!
+    .split("/")
+    .pop()!
+    .replace(/[.]lynxkite[.]json$/, "");
   const [state, setState] = useState({ workspace: {} as Workspace });
   const [message, setMessage] = useState(null as string | null);
   useEffect(() => {
@@ -320,7 +324,8 @@ function LynxKiteFlow() {
         <a className="logo" href="">
           <img alt="" src={favicon} />
         </a>
-        <div className="ws-name">{path}</div>
+        <div className="ws-name">{shortPath}</div>
+        <title>{shortPath}</title>
         <EnvironmentSelector
           options={Object.keys(catalog.data || {})}
           value={state.workspace.env!}

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

@@ -196,13 +196,14 @@ class Op(BaseConfig):
         return res
 
 
-def op(env: str, name: str, *, view="basic", outputs=None, params=None, cache=False):
+def op(env: str, name: str, *, view="basic", outputs=None, params=None, slow=False):
     """Decorator for defining an operation."""
 
     def decorator(func):
-        if cache:
-            func = mem.cache(func)
         sig = inspect.signature(func)
+        if slow:
+            func = mem.cache(func)
+            func = _global_slow(func)
         # Positional arguments are inputs.
         inputs = {
             name: Input(name=name, type=param.annotation)
@@ -319,6 +320,7 @@ def slow(func):
     return wrapper
 
 
+_global_slow = slow  # For access inside op().
 CATALOGS_SNAPSHOTS: dict[str, Catalogs] = {}