Change formatters from 80 columns to 100 columns.

biome.json

@@ -1,6 +1,7 @@
 {
   "formatter": {
     "ignore": ["**/node_modules/**", "**/dist/**"],
+    "lineWidth": 100,
     "indentStyle": "space"
   },
   "linter": {

lynxkite-app/src/lynxkite_app/crdt.py

@@ -40,9 +40,7 @@ class WebsocketServer(pycrdt_websocket.WebsocketServer):
         ydoc["workspace"] = ws = pycrdt.Map()
         # Replay updates from the store.
         try:
-            for update, timestamp in [
-                (item[0], item[-1]) async for item in ystore.read()
-            ]:
+            for update, timestamp in [(item[0], item[-1]) async for item in ystore.read()]:
                 ydoc.apply_update(update)
         except pycrdt_websocket.ystore.YDocNotFound:
             pass
@@ -212,9 +210,7 @@ async def workspace_changed(name: str, changes: pycrdt.MapEvent, ws_crdt: pycrdt
         await execute(name, ws_crdt, ws_pyd)
 
 
-async def execute(
-    name: str, ws_crdt: pycrdt.Map, ws_pyd: workspace.Workspace, delay: int = 0
-):
+async def execute(name: str, ws_crdt: pycrdt.Map, ws_pyd: workspace.Workspace, delay: int = 0):
     """Execute the workspace and update the CRDT object with the results.
 
     Args:

lynxkite-app/src/lynxkite_app/main.py

@@ -34,10 +34,7 @@ app.add_middleware(GZipMiddleware)
 
 @app.get("/api/catalog")
 def get_catalog():
-    return {
-        k: {op.name: op.model_dump() for op in v.values()}
-        for k, v in ops.CATALOGS.items()
-    }
+    return {k: {op.name: op.model_dump() for op in v.values()} for k, v in ops.CATALOGS.items()}
 
 
 class SaveRequest(workspace.BaseConfig):

lynxkite-app/web/eslint.config.js

@@ -19,10 +19,7 @@ export default tseslint.config(
     },
     rules: {
       ...reactHooks.configs.recommended.rules,
-      "react-refresh/only-export-components": [
-        "warn",
-        { allowConstantExport: true },
-      ],
+      "react-refresh/only-export-components": ["warn", { allowConstantExport: true }],
     },
   },
 );

lynxkite-app/web/src/Directory.tsx

@@ -52,21 +52,13 @@ export default function () {
     }
   }
 
-  function newWorkspaceIn(
-    path: string,
-    list: DirectoryEntry[],
-    workspaceName?: string,
-  ) {
+  function newWorkspaceIn(path: string, list: DirectoryEntry[], workspaceName?: string) {
     const pathSlash = path ? `${path}/` : "";
     const name = workspaceName || newName(list);
     navigate(`/edit/${pathSlash}${name}`, { replace: true });
   }
 
-  async function newFolderIn(
-    path: string,
-    list: DirectoryEntry[],
-    folderName?: string,
-  ) {
+  async function newFolderIn(path: string, list: DirectoryEntry[], folderName?: string) {
     const name = folderName || newName(list, "New Folder");
     const pathSlash = path ? `${path}/` : "";
 
@@ -83,12 +75,10 @@ export default function () {
   }
 
   async function deleteItem(item: DirectoryEntry) {
-    if (!window.confirm(`Are you sure you want to delete "${item.name}"?`))
-      return;
+    if (!window.confirm(`Are you sure you want to delete "${item.name}"?`)) return;
     const pathSlash = path ? `${path}/` : "";
 
-    const apiPath =
-      item.type === "directory" ? "/api/dir/delete" : "/api/delete";
+    const apiPath = item.type === "directory" ? "/api/dir/delete" : "/api/delete";
     await fetch(apiPath, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
@@ -124,9 +114,7 @@ export default function () {
                       newWorkspaceIn(
                         path || "",
                         list.data,
-                        (
-                          e.target as HTMLFormElement
-                        ).workspaceName.value.trim(),
+                        (e.target as HTMLFormElement).workspaceName.value.trim(),
                       );
                     }}
                   >
@@ -138,10 +126,7 @@ export default function () {
                     />
                   </form>
                 )}
-                <button
-                  type="button"
-                  onClick={() => setIsCreatingWorkspace(true)}
-                >
+                <button type="button" onClick={() => setIsCreatingWorkspace(true)}>
                   <FolderPlus /> New workspace
                 </button>
               </div>

lynxkite-app/web/src/index.css

@@ -102,8 +102,7 @@ body {
     --status-color-1: oklch(75% 0.2 55);
     --status-color-2: oklch(75% 0.2 55);
     --status-color-3: oklch(75% 0.2 55);
-    transition: --status-color-1 0.3s, --status-color-2 0.3s, --status-color-3
-      0.3s;
+    transition: --status-color-1 0.3s, --status-color-2 0.3s, --status-color-3 0.3s;
   }
 
   .lynxkite-node .title.active {

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

@@ -30,9 +30,7 @@ export default function (props: {
     boxes.sort((a, b) => a.item.name.localeCompare(b.item.name));
     return boxes;
   }, [props.boxes]);
-  const hits: { item: OpsOp }[] = searchText
-    ? fuse.search<OpsOp>(searchText)
-    : allOps;
+  const hits: { item: OpsOp }[] = searchText ? fuse.search<OpsOp>(searchText) : allOps;
   const [selectedIndex, setSelectedIndex] = useState(0);
   useEffect(() => searchBox.current.focus());
   function typed(text: string) {
@@ -64,10 +62,7 @@ export default function (props: {
   }
 
   return (
-    <div
-      className="node-search"
-      style={{ top: props.pos.y, left: props.pos.x }}
-    >
+    <div className="node-search" style={{ top: props.pos.y, left: props.pos.x }}>
       <input
         ref={searchBox}
         value={searchText}

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

@@ -15,13 +15,7 @@ import {
   useUpdateNodeInternals,
 } from "@xyflow/react";
 import axios from "axios";
-import {
-  type MouseEvent,
-  useCallback,
-  useEffect,
-  useMemo,
-  useState,
-} from "react";
+import { type MouseEvent, useCallback, useEffect, useMemo, useState } from "react";
 // The LynxKite workspace editor.
 import { useParams } from "react-router";
 import useSWR, { type Fetcher } from "swr";
@@ -37,11 +31,7 @@ import favicon from "../assets/favicon.ico";
 // import NodeWithTableView from './NodeWithTableView';
 import EnvironmentSelector from "./EnvironmentSelector";
 import { LynxKiteState } from "./LynxKiteState";
-import NodeSearch, {
-  type OpsOp,
-  type Catalog,
-  type Catalogs,
-} from "./NodeSearch.tsx";
+import NodeSearch, { type OpsOp, type Catalog, type Catalogs } from "./NodeSearch.tsx";
 import NodeWithGraphCreationView from "./nodes/GraphCreationNode.tsx";
 import NodeWithImage from "./nodes/NodeWithImage.tsx";
 import NodeWithParams from "./nodes/NodeWithParams";
@@ -69,11 +59,7 @@ function LynxKiteFlow() {
     setState(state);
     const doc = getYjsDoc(state);
     const proto = location.protocol === "https:" ? "wss:" : "ws:";
-    const wsProvider = new WebsocketProvider(
-      `${proto}//${location.host}/ws/crdt`,
-      path!,
-      doc,
-    );
+    const wsProvider = new WebsocketProvider(`${proto}//${location.host}/ws/crdt`, path!, doc);
     const onChange = (_update: any, origin: any, _doc: any, _tr: any) => {
       if (origin === wsProvider) {
         // An update from the CRDT. Apply it to the local state.
@@ -190,11 +176,7 @@ function LynxKiteFlow() {
   useEffect(() => {
     const handleKeyDown = (event: KeyboardEvent) => {
       // Show the node search dialog on "/".
-      if (
-        event.key === "/" &&
-        !nodeSearchSettings &&
-        !isTypingInFormElement()
-      ) {
+      if (event.key === "/" && !nodeSearchSettings && !isTypingInFormElement()) {
         event.preventDefault();
         setNodeSearchSettings({
           pos: { x: 100, y: 100 },
@@ -238,11 +220,7 @@ function LynxKiteFlow() {
     },
     [catalog, state, nodeSearchSettings, suppressSearchUntil, closeNodeSearch],
   );
-  function addNode(
-    node: Partial<WorkspaceNode>,
-    state: { workspace: Workspace },
-    nodes: Node[],
-  ) {
+  function addNode(node: Partial<WorkspaceNode>, state: { workspace: Workspace }, nodes: Node[]) {
     const title = node.data?.title;
     let i = 1;
     node.id = `${title} ${i}`;
@@ -260,9 +238,7 @@ function LynxKiteFlow() {
       data: {
         meta: meta,
         title: meta.name,
-        params: Object.fromEntries(
-          Object.values(meta.params).map((p) => [p.name, p.default]),
-        ),
+        params: Object.fromEntries(Object.values(meta.params).map((p) => [p.name, p.default])),
       },
     };
     return node;
@@ -310,9 +286,7 @@ function LynxKiteFlow() {
     try {
       await axios.post("/api/upload", formData, {
         onUploadProgress: (progressEvent) => {
-          const percentCompleted = Math.round(
-            (100 * progressEvent.loaded) / progressEvent.total!,
-          );
+          const percentCompleted = Math.round((100 * progressEvent.loaded) / progressEvent.total!);
           if (percentCompleted === 100) setMessage("Processing file...");
           else setMessage(`Uploading ${percentCompleted}%`);
         },
@@ -365,11 +339,7 @@ function LynxKiteFlow() {
           </a>
         </div>
       </div>
-      <div
-        style={{ height: "100%", width: "100vw" }}
-        onDragOver={onDragOver}
-        onDrop={onDrop}
-      >
+      <div style={{ height: "100%", width: "100vw" }} onDragOver={onDragOver} onDrop={onDrop}>
         <LynxKiteState.Provider value={state}>
           <ReactFlow
             nodes={nodes}

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

@@ -20,12 +20,7 @@ function toMD(v: any): string {
 function displayTable(name: string, df: any) {
   if (df.data.length > 1) {
     return (
-      <Table
-        key={`${name}-table`}
-        name={`${name}-table`}
-        columns={df.columns}
-        data={df.data}
-      />
+      <Table key={`${name}-table`} name={`${name}-table`} columns={df.columns} data={df.data} />
     );
   }
   if (df.data.length) {
@@ -60,9 +55,7 @@ export default function NodeWithGraphCreationView(props: any) {
   const display = props.data.display?.value;
   const tables = display?.dataframes || {};
   const singleTable = tables && Object.keys(tables).length === 1;
-  const [relations, setRelations] = useState(
-    relationsToDict(display?.relations) || {},
-  );
+  const [relations, setRelations] = useState(relationsToDict(display?.relations) || {});
   const singleRelation = relations && Object.keys(relations).length === 1;
   function setParam(name: string, newValue: any, opts: UpdateOptions) {
     reactFlow.updateNodeData(props.id, {
@@ -211,9 +204,7 @@ export default function NodeWithGraphCreationView(props: any) {
 
         <datalist id="edges-column-options">
           {tables[relation.source_table] &&
-            tables[relation.df].columns.map((name: string) => (
-              <option key={name} value={name} />
-            ))}
+            tables[relation.df].columns.map((name: string) => <option key={name} value={name} />)}
         </datalist>
 
         <datalist id="source-node-column-options">
@@ -274,10 +265,7 @@ export default function NodeWithGraphCreationView(props: any) {
         <div className="graph-relations">
           <div className="graph-table-header">
             Relationships
-            <button
-              className="add-relationship-button"
-              onClick={(_) => addRelation()}
-            >
+            <button className="add-relationship-button" onClick={(_) => addRelation()}>
               +
             </button>
           </div>

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

@@ -1,9 +1,4 @@
-import {
-  Handle,
-  NodeResizeControl,
-  type Position,
-  useReactFlow,
-} from "@xyflow/react";
+import { Handle, NodeResizeControl, type Position, useReactFlow } from "@xyflow/react";
 // @ts-ignore
 import ChevronDownRight from "~icons/tabler/chevron-down-right.jsx";
 
@@ -38,10 +33,8 @@ function getHandles(inputs: object, outputs: object) {
   }
   for (const e of handles) {
     e.offsetPercentage = (100 * (e.index + 1)) / (counts[e.position] + 1);
-    const simpleHorizontal =
-      counts.top === 0 && counts.bottom === 0 && handles.length <= 2;
-    const simpleVertical =
-      counts.left === 0 && counts.right === 0 && handles.length <= 2;
+    const simpleHorizontal = counts.top === 0 && counts.bottom === 0 && handles.length <= 2;
+    const simpleVertical = counts.left === 0 && counts.right === 0 && handles.length <= 2;
     e.showLabel = !simpleHorizontal && !simpleVertical;
   }
   return handles;
@@ -71,10 +64,7 @@ export default function LynxKiteNode(props: LynxKiteNodeProps) {
       }}
     >
       <div className="lynxkite-node" style={props.nodeStyle}>
-        <div
-          className={`title bg-primary ${data.status}`}
-          onClick={titleClicked}
-        >
+        <div className={`title bg-primary ${data.status}`} onClick={titleClicked}>
           {data.title}
           {data.error && <span className="title-icon">⚠️</span>}
           {expanded || <span className="title-icon">⋯</span>}
@@ -99,14 +89,11 @@ export default function LynxKiteNode(props: LynxKiteNodeProps) {
             type={handle.type}
             position={handle.position as Position}
             style={{
-              [handleOffsetDirection[handle.position]]:
-                `${handle.offsetPercentage}% `,
+              [handleOffsetDirection[handle.position]]: `${handle.offsetPercentage}% `,
             }}
           >
             {handle.showLabel && (
-              <span className="handle-name">
-                {handle.name.replace(/_/g, " ")}
-              </span>
+              <span className="handle-name">{handle.name.replace(/_/g, " ")}</span>
             )}
           </Handle>
         ))}

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

@@ -38,9 +38,7 @@ export default function NodeGroupParameter({
 }: NodeGroupParameterProps) {
   const selector = meta.selector;
   const groups = meta.groups;
-  const [selectedValue, setSelectedValue] = useState<string>(
-    value || selector.default,
-  );
+  const [selectedValue, setSelectedValue] = useState<string>(value || selector.default);
 
   const handleSelectorChange = (value: any, opts?: { delay: number }) => {
     setSelectedValue(value);
@@ -49,9 +47,7 @@ export default function NodeGroupParameter({
 
   useEffect(() => {
     // Clean possible previous parameters first
-    Object.values(groups).flatMap((group) =>
-      group.map((entry) => deleteParam(entry.name)),
-    );
+    Object.values(groups).flatMap((group) => group.map((entry) => deleteParam(entry.name)));
     for (const param of groups[selectedValue]) {
       setParam(param.name, param.default);
     }

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

@@ -6,12 +6,9 @@ const MODEL_TRAINING_INPUT_MAPPING =
   "<class 'lynxkite_graph_analytics.lynxkite_ops.ModelTrainingInputMapping'>";
 const MODEL_INFERENCE_INPUT_MAPPING =
   "<class 'lynxkite_graph_analytics.lynxkite_ops.ModelInferenceInputMapping'>";
-const MODEL_OUTPUT_MAPPING =
-  "<class 'lynxkite_graph_analytics.lynxkite_ops.ModelOutputMapping'>";
+const MODEL_OUTPUT_MAPPING = "<class 'lynxkite_graph_analytics.lynxkite_ops.ModelOutputMapping'>";
 function ParamName({ name }: { name: string }) {
-  return (
-    <span className="param-name bg-base-200">{name.replace(/_/g, " ")}</span>
-  );
+  return <span className="param-name bg-base-200">{name.replace(/_/g, " ")}</span>;
 }
 
 function Input({
@@ -27,9 +24,7 @@ function Input({
       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 })
-      }
+      onKeyDown={(evt) => evt.code === "Enter" && onChange(evt.currentTarget.value, { delay: 0 })}
     />
   );
 }
@@ -41,10 +36,7 @@ function getModelBindings(
   function bindingsOfModel(m: any): string[] {
     switch (variant) {
       case "training input":
-        return [
-          ...m.inputs,
-          ...m.loss_inputs.filter((i: string) => !m.outputs.includes(i)),
-        ];
+        return [...m.inputs, ...m.loss_inputs.filter((i: string) => !m.outputs.includes(i))];
       case "inference input":
         return m.inputs;
       case "output":
@@ -185,13 +177,7 @@ interface NodeParameterProps {
   onChange: (value: any, options?: { delay: number }) => void;
 }
 
-export default function NodeParameter({
-  name,
-  value,
-  meta,
-  data,
-  onChange,
-}: NodeParameterProps) {
+export default function NodeParameter({ name, value, meta, data, onChange }: NodeParameterProps) {
   return (
     // biome-ignore lint/a11y/noLabelWithoutControl: Most of the time there is a control.
     <label className="param">
@@ -241,32 +227,17 @@ export default function NodeParameter({
       ) : meta?.type?.type === MODEL_TRAINING_INPUT_MAPPING ? (
         <>
           <ParamName name={name} />
-          <ModelMapping
-            value={value}
-            data={data}
-            variant="training input"
-            onChange={onChange}
-          />
+          <ModelMapping value={value} data={data} variant="training input" onChange={onChange} />
         </>
       ) : meta?.type?.type === MODEL_INFERENCE_INPUT_MAPPING ? (
         <>
           <ParamName name={name} />
-          <ModelMapping
-            value={value}
-            data={data}
-            variant="inference input"
-            onChange={onChange}
-          />
+          <ModelMapping value={value} data={data} variant="inference input" onChange={onChange} />
         </>
       ) : meta?.type?.type === MODEL_OUTPUT_MAPPING ? (
         <>
           <ParamName name={name} />
-          <ModelMapping
-            value={value}
-            data={data}
-            variant="output"
-            onChange={onChange}
-          />
+          <ModelMapping value={value} data={data} variant="output" onChange={onChange} />
         </>
       ) : (
         <>

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

@@ -3,9 +3,7 @@ import NodeWithParams from "./NodeWithParams";
 const NodeWithImage = (props: any) => {
   return (
     <NodeWithParams {...props}>
-      {props.data.display && (
-        <img src={props.data.display} alt="Node Display" />
-      )}
+      {props.data.display && <img src={props.data.display} alt="Node Display" />}
     </NodeWithParams>
   );
 };

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

@@ -36,10 +36,7 @@ function NodeWithParams(props: any) {
   return (
     <LynxKiteNode {...props}>
       {props.collapsed && (
-        <div
-          className="params-expander"
-          onClick={() => setCollapsed(!collapsed)}
-        >
+        <div className="params-expander" onClick={() => setCollapsed(!collapsed)}>
           <Triangle className={`flippy ${collapsed ? "flippy-90" : ""}`} />
         </div>
       )}
@@ -54,9 +51,7 @@ function NodeWithParams(props: any) {
               setParam={(name: string, value: any, opts?: UpdateOptions) =>
                 setParam(name, value, opts || {})
               }
-              deleteParam={(name: string, opts?: UpdateOptions) =>
-                deleteParam(name, opts || {})
-              }
+              deleteParam={(name: string, opts?: UpdateOptions) => deleteParam(name, opts || {})}
             />
           ) : (
             <NodeParameter
@@ -65,9 +60,7 @@ function NodeWithParams(props: any) {
               value={value}
               data={props.data}
               meta={metaParams?.[name]}
-              onChange={(value: any, opts?: UpdateOptions) =>
-                setParam(name, value, opts || {})
-              }
+              onChange={(value: any, opts?: UpdateOptions) => setParam(name, value, opts || {})}
             />
           ),
         )}

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

@@ -17,8 +17,7 @@ function toMD(v: any): string {
 export default function NodeWithTableView(props: any) {
   const [open, setOpen] = useState({} as { [name: string]: boolean });
   const display = props.data.display?.value;
-  const single =
-    display?.dataframes && Object.keys(display?.dataframes).length === 1;
+  const single = display?.dataframes && Object.keys(display?.dataframes).length === 1;
   const dfs = Object.entries(display?.dataframes || {});
   dfs.sort();
   return (
@@ -37,11 +36,7 @@ export default function NodeWithTableView(props: any) {
             )}
             {(single || open[name]) &&
               (df.data.length > 1 ? (
-                <Table
-                  key={`${name}-table`}
-                  columns={df.columns}
-                  data={df.data}
-                />
+                <Table key={`${name}-table`} columns={df.columns} data={df.data} />
               ) : df.data.length ? (
                 <dl key={`${name}-dl`}>
                   {df.columns.map((c: string, i: number) => (

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

@@ -35,9 +35,7 @@ test("unknown operation", async () => {
   await graphBox.getByLabel("n", { exact: true }).fill("10");
   await workspace.setEnv("LynxScribe");
   const csvBox = workspace.getBox("NX › Scale-Free Graph 1");
-  await expect(csvBox.locator(".error")).toHaveText(
-    'Operation "NX › Scale-Free Graph" not found.',
-  );
+  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/graph_creation.spec.ts

@@ -5,15 +5,9 @@ import { Splash, Workspace } from "./lynxkite";
 let workspace: Workspace;
 
 test.beforeEach(async ({ browser }) => {
-  workspace = await Workspace.empty(
-    await browser.newPage(),
-    "graph_creation_spec_test",
-  );
+  workspace = await Workspace.empty(await browser.newPage(), "graph_creation_spec_test");
   await workspace.addBox("NX › Scale-Free Graph");
-  await workspace
-    .getBox("NX › Scale-Free Graph 1")
-    .getByLabel("n", { exact: true })
-    .fill("10");
+  await workspace.getBox("NX › Scale-Free Graph 1").getByLabel("n", { exact: true }).fill("10");
   await workspace.addBox("Create graph");
   await workspace.connectBoxes("NX › Scale-Free Graph 1", "Create graph 1");
 });
@@ -45,9 +39,7 @@ test("Tables are displayed in the Graph creation box", async () => {
 
 test("Adding and removing relationships", async () => {
   const graphBox = await workspace.getBox("Create graph 1");
-  const addRelationshipButton = await graphBox.locator(
-    ".add-relationship-button",
-  );
+  const addRelationshipButton = await graphBox.locator(".add-relationship-button");
   await addRelationshipButton.click();
   const formData: Record<string, string> = {
     name: "relation_1",
@@ -69,10 +61,9 @@ test("Adding and removing relationships", async () => {
   // check that the relationship has been saved in the backend
   await workspace.page.reload();
   const graphBoxAfterReload = await workspace.getBox("Create graph 1");
-  const relationHeader = await graphBoxAfterReload.locator(
-    ".graph-relations .df-head",
-    { hasText: "relation_1" },
-  );
+  const relationHeader = await graphBoxAfterReload.locator(".graph-relations .df-head", {
+    hasText: "relation_1",
+  });
   await expect(relationHeader).toBeVisible();
   await relationHeader.locator("button").click(); // Delete the relationship
   await expect(relationHeader).not.toBeVisible();

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

@@ -7,10 +7,7 @@ import { Splash, Workspace } from "./lynxkite";
 let workspace: Workspace;
 
 test.beforeEach(async ({ browser }) => {
-  workspace = await Workspace.empty(
-    await browser.newPage(),
-    "import_spec_test",
-  );
+  workspace = await Workspace.empty(await browser.newPage(), "import_spec_test");
 });
 
 test.afterEach(async () => {
@@ -22,11 +19,7 @@ test.afterEach(async () => {
   await splash.deleteEntry("import_spec_test");
 });
 
-async function validateImport(
-  workspace: Workspace,
-  fileName: string,
-  fileFormat: string,
-) {
+async function validateImport(workspace: Workspace, fileName: string, fileFormat: string) {
   const __filename = fileURLToPath(import.meta.url);
   const __dirname = dirname(__filename);
   const filePath = join(__dirname, "data", fileName);

lynxkite-app/web/tests/lynxkite.ts

@@ -63,10 +63,7 @@ export class Workspace {
 
     await this.page.locator(".ws-name").click();
     await this.page.keyboard.press("/");
-    await this.page
-      .locator(".node-search")
-      .getByText(boxName, { exact: true })
-      .click();
+    await this.page.locator(".node-search").getByText(boxName, { exact: true }).click();
     await expect(this.getBoxes()).toHaveCount(allBoxes.length + 1);
   }
 
@@ -107,9 +104,7 @@ export class Workspace {
 
   getBoxHandle(boxId: string, pos?: string) {
     if (pos) {
-      return this.page.locator(
-        `[data-id="${boxId}"] [data-handlepos="${pos}"]`,
-      );
+      return this.page.locator(`[data-id="${boxId}"] [data-handlepos="${pos}"]`);
     }
     return this.page.getByTestId(boxId);
   }
@@ -133,11 +128,9 @@ export class Workspace {
     } else if (offset) {
       // Without steps the movement is too fast and the box is not dragged. The more steps,
       // the better the movement is captured
-      await this.page.mouse.move(
-        boxCenterX + offset.offsetX,
-        boxCenterY + offset.offsetY,
-        { steps: 5 },
-      );
+      await this.page.mouse.move(boxCenterX + offset.offsetX, boxCenterY + offset.offsetY, {
+        steps: 5,
+      });
     }
     await this.page.mouse.up();
   }
@@ -197,9 +190,7 @@ export class Splash {
       workspaceName = name;
       await this.page.locator('input[name="workspaceName"]').fill(name);
     } else {
-      workspaceName = await this.page
-        .locator('input[name="workspaceName"]')
-        .inputValue();
+      workspaceName = await this.page.locator('input[name="workspaceName"]').inputValue();
     }
     await this.page.locator('input[name="workspaceName"]').press("Enter");
     const ws = new Workspace(this.page, workspaceName);

lynxkite-app/web/tsconfig.json

@@ -1,7 +1,4 @@
 {
   "files": [],
-  "references": [
-    { "path": "./tsconfig.app.json" },
-    { "path": "./tsconfig.node.json" }
-  ]
+  "references": [{ "path": "./tsconfig.app.json" }, { "path": "./tsconfig.node.json" }]
 }

lynxkite-bio/src/lynxkite_bio/rdkit.py

@@ -36,9 +36,7 @@ def _get_similarity_matrix(mols):
 
 
 @op("Graph from molecule similarity")
-def graph_from_similarity(
-    bundle: Bundle, *, table="df", mols_column="mols", average_degree=10
-):
+def graph_from_similarity(bundle: Bundle, *, table="df", mols_column="mols", average_degree=10):
     """Creates edges for pairs of molecules that are the most similar."""
     df = bundle.dfs[table]
     mols = df[mols_column]

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

@@ -167,9 +167,9 @@ async def execute(ws: workspace.Workspace, catalog, cache=None):
                     op = catalog[t.data.title]
                     i = op.inputs[edge.targetHandle]
                     if i.position in "top or bottom":
-                        batch_inputs.setdefault(
-                            (edge.target, edge.targetHandle), []
-                        ).extend(results)
+                        batch_inputs.setdefault((edge.target, edge.targetHandle), []).extend(
+                            results
+                        )
                     else:
                         tasks.setdefault(edge.target, []).extend(results)
                 node.publish_result(result)

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

@@ -208,9 +208,7 @@ def op(env: str, name: str, *, view="basic", outputs=None, params=None):
         if outputs:
             _outputs = {name: Output(name=name, type=None) for name in outputs}
         else:
-            _outputs = (
-                {"output": Output(name="output", type=None)} if view == "basic" else {}
-            )
+            _outputs = {"output": Output(name="output", type=None)} if view == "basic" else {}
         op = Op(
             func=func,
             name=name,
@@ -264,12 +262,10 @@ def register_passive_op(env: str, name: str, inputs=[], outputs=["output"], para
         name=name,
         params={p.name: p for p in params},
         inputs=dict(
-            (i, Input(name=i, type=None)) if isinstance(i, str) else (i.name, i)
-            for i in inputs
+            (i, Input(name=i, type=None)) if isinstance(i, str) else (i.name, i) for i in inputs
         ),
         outputs=dict(
-            (o, Output(name=o, type=None)) if isinstance(o, str) else (o.name, o)
-            for o in outputs
+            (o, Output(name=o, type=None)) if isinstance(o, str) else (o.name, o) for o in outputs
         ),
     )
     CATALOGS.setdefault(env, {})

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

@@ -111,9 +111,7 @@ def save(ws: Workspace, path: str):
     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
-    ) as f:
+    with tempfile.NamedTemporaryFile("w", prefix=f".{basename}.", dir=dirname, delete=False) as f:
         temp_name = f.name
         f.write(j)
     os.replace(temp_name, path)

lynxkite-core/tests/test_ops.py

@@ -14,9 +14,7 @@ def test_op_decorator_no_params_no_types_default_positions():
         "a": ops.Input(name="a", type=inspect._empty, position="left"),
         "b": ops.Input(name="b", type=inspect._empty, position="left"),
     }
-    assert add.__op__.outputs == {
-        "result": ops.Output(name="result", type=None, position="right")
-    }
+    assert add.__op__.outputs == {"result": ops.Output(name="result", type=None, position="right")}
     assert add.__op__.type == "basic"
     assert ops.CATALOGS["test"]["add"] == add.__op__
 
@@ -34,9 +32,7 @@ def test_op_decorator_custom_positions():
         "a": ops.Input(name="a", type=inspect._empty, position="right"),
         "b": ops.Input(name="b", type=inspect._empty, position="top"),
     }
-    assert add.__op__.outputs == {
-        "result": ops.Output(name="result", type=None, position="bottom")
-    }
+    assert add.__op__.outputs == {"result": ops.Output(name="result", type=None, position="bottom")}
     assert add.__op__.type == "basic"
     assert ops.CATALOGS["test"]["add"] == add.__op__
 
@@ -76,9 +72,7 @@ def test_op_decorator_with_complex_types():
     assert complex_op.__op__.inputs == {
         "color": ops.Input(name="color", type=Color, position="left"),
         "color_list": ops.Input(name="color_list", type=list[Color], position="left"),
-        "color_dict": ops.Input(
-            name="color_dict", type=dict[str, Color], position="left"
-        ),
+        "color_dict": ops.Input(name="color_dict", type=dict[str, Color], position="left"),
     }
     assert complex_op.__op__.type == "basic"
     assert complex_op.__op__.outputs == {

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

@@ -89,9 +89,7 @@ def download_cellxgene_dataset(
     adata.write_h5ad(h5ad_outfile)
     with tempfile.TemporaryDirectory() as temp_dir:
         coll = SingleCellCollection(temp_dir)
-        coll.load_h5ad_multi(
-            h5ad_outfile.parent, max_workers=max_workers, use_processes=use_mp
-        )
+        coll.load_h5ad_multi(h5ad_outfile.parent, max_workers=max_workers, use_processes=use_mp)
         coll.flatten(DATA_PATH / save_path, destroy_on_copy=True)
     return DATA_PATH / save_path
 
@@ -148,9 +146,7 @@ def download_model(*, model_name: str) -> str:
 
 @op("BioNeMo > Infer")
 @mem.cache(verbose=1)
-def infer(
-    dataset_path: str, model_path: str | None = None, *, results_path: str
-) -> str:
+def infer(dataset_path: str, model_path: str | None = None, *, results_path: str) -> str:
     """Infer on a dataset."""
     # This import is slow, so we only import it when we need it.
     from bionemo.geneformer.scripts.infer_geneformer import infer_model
@@ -175,10 +171,7 @@ def infer(
 @op("BioNeMo > Load results")
 def load_results(results_path: str):
     embeddings = (
-        torch.load(f"{results_path}/predictions__rank_0.pt")["embeddings"]
-        .float()
-        .cpu()
-        .numpy()
+        torch.load(f"{results_path}/predictions__rank_0.pt")["embeddings"].float().cpu().numpy()
     )
     return embeddings
 
@@ -248,9 +241,7 @@ def run_benchmark(data, labels, *, use_pca: bool = False):
             ]
         )
     else:
-        pipeline = Pipeline(
-            [("classifier", RandomForestClassifier(class_weight="balanced"))]
-        )
+        pipeline = Pipeline([("classifier", RandomForestClassifier(class_weight="balanced"))])
 
     # Set up StratifiedKFold to ensure each fold reflects the overall distribution of labels
     cv = StratifiedKFold(n_splits=5)
@@ -258,9 +249,7 @@ def run_benchmark(data, labels, *, use_pca: bool = False):
     # Define the scoring functions
     scoring = {
         "accuracy": make_scorer(accuracy_score),
-        "precision": make_scorer(
-            precision_score, average="macro"
-        ),  # 'macro' averages over classes
+        "precision": make_scorer(precision_score, average="macro"),  # 'macro' averages over classes
         "recall": make_scorer(recall_score, average="macro"),
         "f1_score": make_scorer(f1_score, average="macro"),
         # 'roc_auc' requires probability or decision function; hence use multi_class if applicable
@@ -298,9 +287,7 @@ def plot_confusion_matrix(benchmark_output, labels):
     # heatmap has the 0,0 at the bottom left corner
     num_rows = len(str_labels)
     heatmap_data = [
-        [j, num_rows - i - 1, norm_cm[i][j]]
-        for i in range(len(labels))
-        for j in range(len(labels))
+        [j, num_rows - i - 1, norm_cm[i][j]] for i in range(len(labels)) for j in range(len(labels))
     ]
 
     options = {
@@ -332,9 +319,7 @@ def plot_confusion_matrix(benchmark_output, labels):
             "orient": "vertical",
             "right": 10,
             "top": "center",
-            "inRange": {
-                "color": ["#E0F7FA", "#81D4FA", "#29B6F6", "#0288D1", "#01579B"]
-            },
+            "inRange": {"color": ["#E0F7FA", "#81D4FA", "#29B6F6", "#0288D1", "#01579B"]},
         },
         "series": [
             {
@@ -424,9 +409,7 @@ def accuracy_comparison(benchmark_output10m, benchmark_output100m):
             {
                 "name": "Error Bars",
                 "type": "errorbar",
-                "data": [
-                    [val - err, val + err] for val, err in zip(values, error_bars)
-                ],
+                "data": [[val - err, val + err] for val, err in zip(values, error_bars)],
                 "itemStyle": {"color": "#1f77b4"},
             },
         ],
@@ -509,9 +492,7 @@ def f1_comparison(benchmark_output10m, benchmark_output100m):
             {
                 "name": "Error Bars",
                 "type": "errorbar",
-                "data": [
-                    [val - err, val + err] for val, err in zip(values, error_bars)
-                ],
+                "data": [[val - err, val + err] for val, err in zip(values, error_bars)],
                 "itemStyle": {"color": "#1f77b4"},
             },
         ],

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

@@ -19,12 +19,8 @@ class RelationDefinition:
     """Defines a set of edges."""
 
     df: str  # The DataFrame that contains the edges.
-    source_column: (
-        str  # The column in the edge DataFrame that contains the source node ID.
-    )
-    target_column: (
-        str  # The column in the edge DataFrame that contains the target node ID.
-    )
+    source_column: str  # The column in the edge DataFrame that contains the source node ID.
+    target_column: str  # The column in the edge DataFrame that contains the target node ID.
     source_table: str  # The DataFrame that contains the source nodes.
     target_table: str  # The DataFrame that contains the target nodes.
     source_key: str  # The column in the source table that contains the node ID.
@@ -86,11 +82,7 @@ class Bundle:
                     (
                         e["source"],
                         e["target"],
-                        {
-                            k: e[k]
-                            for k in edges.columns
-                            if k not in ["source", "target"]
-                        },
+                        {k: e[k] for k in edges.columns if k not in ["source", "target"]},
                     )
                     for e in edges.to_records()
                 ]
@@ -129,9 +121,7 @@ class Bundle:
                 for name, df in self.dfs.items()
             },
             "relations": [dataclasses.asdict(relation) for relation in self.relations],
-            "other": {
-                k: getattr(v, "metadata", lambda: {})() for k, v in self.other.items()
-            },
+            "other": {k: getattr(v, "metadata", lambda: {})() for k, v in self.other.items()},
         }
 
 
@@ -199,9 +189,7 @@ def _execute_node(node, ws, catalog, outputs):
     node.publish_started()
     # TODO: Handle multi-inputs.
     input_map = {
-        edge.targetHandle: outputs[edge.source]
-        for edge in ws.edges
-        if edge.target == node.id
+        edge.targetHandle: outputs[edge.source] for edge in ws.edges if edge.target == node.id
     }
     # Convert inputs types to match operation signature.
     try:

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

@@ -35,9 +35,7 @@ class FileFormat(enum.StrEnum):
     params={
         "file_format": ops.ParameterGroup(
             name="file_format",
-            selector=ops.Parameter(
-                name="file_format", type=FileFormat, default=FileFormat.csv
-            ),
+            selector=ops.Parameter(name="file_format", type=FileFormat, default=FileFormat.csv),
             groups={
                 "csv": [
                     ops.Parameter.basic("columns", type=str, default="<from file>"),
@@ -45,9 +43,7 @@ class FileFormat(enum.StrEnum):
                 ],
                 "parquet": [],
                 "json": [],
-                "excel": [
-                    ops.Parameter.basic("sheet_name", type=str, default="Sheet1")
-                ],
+                "excel": [ops.Parameter.basic("sheet_name", type=str, default="Sheet1")],
             },
             default=FileFormat.csv,
         ),
@@ -68,9 +64,7 @@ def import_file(
     """
     if file_format == "csv":
         names = kwargs.pop("columns", "<from file>")
-        names = (
-            pd.api.extensions.no_default if names == "<from file>" else names.split(",")
-        )
+        names = pd.api.extensions.no_default if names == "<from file>" else names.split(",")
         sep = kwargs.pop("separator", "<auto>")
         sep = pd.api.extensions.no_default if sep == "<auto>" else sep
         df = pd.read_csv(file_path, names=names, sep=sep, **kwargs)
@@ -93,15 +87,11 @@ def import_parquet(*, filename: str):
 
 @op("Import CSV")
 @mem.cache
-def import_csv(
-    *, filename: str, columns: str = "<from file>", separator: str = "<auto>"
-):
+def import_csv(*, filename: str, columns: str = "<from file>", separator: str = "<auto>"):
     """Imports a CSV file."""
     return pd.read_csv(
         filename,
-        names=pd.api.extensions.no_default
-        if columns == "<from file>"
-        else columns.split(","),
+        names=pd.api.extensions.no_default if columns == "<from file>" else columns.split(","),
         sep=pd.api.extensions.no_default if separator == "<auto>" else separator,
     )
 
@@ -145,12 +135,7 @@ def sql(bundle: core.Bundle, *, query: ops.LongStr, save_as: str = "result"):
     if os.environ.get("NX_CUGRAPH_AUTOCONFIG", "").strip().lower() == "true":
         with pl.Config() as cfg:
             cfg.set_verbose(True)
-            res = (
-                pl.SQLContext(bundle.dfs)
-                .execute(query)
-                .collect(engine="gpu")
-                .to_pandas()
-            )
+            res = pl.SQLContext(bundle.dfs).execute(query).collect(engine="gpu").to_pandas()
             # TODO: Currently `collect()` moves the data from cuDF to Polars. Then we convert it to Pandas,
             # which (hopefully) puts it back into cuDF. Hopefully we will be able to keep it in cuDF.
     else:
@@ -211,9 +196,7 @@ def _map_color(value):
         colors = cmap.colors[: len(categories)]
         return [
             "#{:02x}{:02x}{:02x}".format(int(r * 255), int(g * 255), int(b * 255))
-            for r, g, b in [
-                colors[min(len(colors) - 1, categories.get_loc(v))] for v in value
-            ]
+            for r, g, b in [colors[min(len(colors) - 1, categories.get_loc(v))] for v in value]
         ]
 
 
@@ -250,14 +233,10 @@ def visualize_graph(
             curveness = 0  # Street maps are better with straight streets.
             break
     else:
-        pos = nx.spring_layout(
-            graph.to_nx(), iterations=max(1, int(10000 / len(nodes)))
-        )
+        pos = nx.spring_layout(graph.to_nx(), iterations=max(1, int(10000 / len(nodes))))
         curveness = 0.3
     nodes = nodes.to_records()
-    edges = core.df_for_frontend(
-        graph.dfs["edges"].drop_duplicates(["source", "target"]), 10_000
-    )
+    edges = core.df_for_frontend(graph.dfs["edges"].drop_duplicates(["source", "target"]), 10_000)
     if color_edges_by:
         edges["color"] = _map_color(edges[color_edges_by])
     edges = edges.to_records()
@@ -291,9 +270,7 @@ def visualize_graph(
                         "itemStyle": {"color": n.color} if color_nodes_by else {},
                         "label": {"show": label_by is not None},
                         "name": str(getattr(n, label_by, "")) if label_by else None,
-                        "value": str(getattr(n, color_nodes_by, ""))
-                        if color_nodes_by
-                        else None,
+                        "value": str(getattr(n, color_nodes_by, "")) if color_nodes_by else None,
                     }
                     for n in nodes
                 ],
@@ -302,9 +279,7 @@ def visualize_graph(
                         "source": str(r.source),
                         "target": str(r.target),
                         "lineStyle": {"color": r.color} if color_edges_by else {},
-                        "value": str(getattr(r, color_edges_by, ""))
-                        if color_edges_by
-                        else None,
+                        "value": str(getattr(r, color_edges_by, "")) if color_edges_by else None,
                     }
                     for r in edges
                 ],
@@ -342,9 +317,7 @@ def create_graph(bundle: core.Bundle, *, relations: str = None) -> core.Bundle:
     """
     bundle = bundle.copy()
     if not (relations is None or relations.strip() == ""):
-        bundle.relations = [
-            core.RelationDefinition(**r) for r in json.loads(relations).values()
-        ]
+        bundle.relations = [core.RelationDefinition(**r) for r in json.loads(relations).values()]
     return ops.Result(output=bundle, display=bundle.to_dict(limit=100))
 
 

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

@@ -210,9 +210,7 @@ def _get_params(func) -> dict | None:
             continue
         params[name] = ops.Parameter.basic(
             name=name,
-            default=str(param.default)
-            if type(param.default) in [str, int, float]
-            else None,
+            default=str(param.default) if type(param.default) in [str, int, float] else None,
             type=_type,
         )
     return params

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

@@ -21,12 +21,8 @@ def reg(name, inputs=[], outputs=None, params=[]):
     return ops.register_passive_op(
         ENV,
         name,
-        inputs=[
-            ops.Input(name=name, position="bottom", type="tensor") for name in inputs
-        ],
-        outputs=[
-            ops.Output(name=name, position="top", type="tensor") for name in outputs
-        ],
+        inputs=[ops.Input(name=name, position="bottom", type="tensor") for name in inputs],
+        outputs=[ops.Output(name=name, position="top", type="tensor") for name in outputs],
         params=params,
     )
 
@@ -196,9 +192,7 @@ class ModelConfig:
         }
 
 
-def build_model(
-    ws: workspace.Workspace, inputs: dict[str, torch.Tensor]
-) -> ModelConfig:
+def build_model(ws: workspace.Workspace, inputs: dict[str, torch.Tensor]) -> ModelConfig:
     """Builds the model described in the workspace."""
     catalog = ops.CATALOGS[ENV]
     optimizers = []
@@ -272,9 +266,7 @@ def build_model(
                 ls.append((torch.nn.Linear(isize, osize), f"{inputs.x} -> {outputs.x}"))
                 sizes[outputs.x] = osize
             case "Activation":
-                f = getattr(
-                    torch.nn.functional, p["type"].name.lower().replace(" ", "_")
-                )
+                f = getattr(torch.nn.functional, p["type"].name.lower().replace(" ", "_"))
                 ls.append((f, f"{inputs.x} -> {outputs.x}"))
                 sizes[outputs.x] = sizes.get(inputs.x, 1)
             case "MSE loss":
@@ -316,7 +308,5 @@ def to_tensors(b: core.Bundle, m: ModelMapping | None) -> dict[str, torch.Tensor
     tensors = {}
     for k, v in m.map.items():
         if v.df in b.dfs and v.column in b.dfs[v.df]:
-            tensors[k] = torch.tensor(
-                b.dfs[v.df][v.column].to_list(), dtype=torch.float32
-            )
+            tensors[k] = torch.tensor(b.dfs[v.df][v.column].to_list(), dtype=torch.float32)
     return tensors

lynxkite-lynxscribe/src/lynxkite_lynxscribe/llm_ops.py

@@ -32,9 +32,7 @@ def chat(*args, **kwargs):
 
     chat_client = openai.OpenAI(base_url=LLM_BASE_URL)
     kwargs.setdefault("model", LLM_MODEL)
-    key = json.dumps(
-        {"method": "chat", "base_url": LLM_BASE_URL, "args": args, "kwargs": kwargs}
-    )
+    key = json.dumps({"method": "chat", "base_url": LLM_BASE_URL, "args": args, "kwargs": kwargs})
     if key not in LLM_CACHE:
         completion = chat_client.chat.completions.create(*args, **kwargs)
         LLM_CACHE[key] = [c.message.content for c in completion.choices]
@@ -121,9 +119,7 @@ def add_neighbors(nodes, edges, item):
 
 @op("Create prompt")
 def create_prompt(input, *, save_as="prompt", template: ops.LongStr):
-    assert template, (
-        "Please specify the template. Refer to columns using the Jinja2 syntax."
-    )
+    assert template, "Please specify the template. Refer to columns using the Jinja2 syntax."
     t = jinja.from_string(template)
     prompt = t.render(**input)
     return {**input, save_as: prompt}