Set up formatting for VS Code and as a pre-commit.

.gitignore

@@ -1,5 +1,6 @@
 .vscode/*
 !.vscode/extensions.json
+!.vscode/settings.json
 .idea
 .DS_Store
 *.suo
@@ -14,4 +15,4 @@ build
 joblib-cache
 *.egg-info
 
-lynxkite-app/crdt_data
+lynxkite-app/crdt_data

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  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
+  hooks:
+    - id: ruff
+      args: [ --fix ]
+    - id: ruff-format
+- repo: https://github.com/biomejs/pre-commit
+  rev: v1.9.4
+  hooks:
+    - id: biome-check

.python-version

@@ -0,0 +1 @@
+3.11

.vscode/settings.json

@@ -0,0 +1,12 @@
+{
+	"editor.formatOnSave": true,
+	"ruff.enable": true,
+	"html.format.enable": true,
+	"css.format.enable": true,
+	"typescript.format.enable": true,
+	"files.insertFinalNewline": true,
+	"files.trimTrailingWhitespace": true,
+	"[python]": {
+		"editor.defaultFormatter": "charliermarsh.ruff"
+	}
+}

README.md

@@ -23,6 +23,7 @@ Install everything like this:
 ```bash
 uv venv
 source .venv/bin/activate
+uvx pre-commit install
 # The [dev] tag is only needed if you intend on running tests
 uv pip install -e lynxkite-core/[dev] -e lynxkite-app/[dev] -e lynxkite-graph-analytics/[dev] -e lynxkite-lynxscribe/ -e lynxkite-pillow-example/
 ```

lynxkite-app/README.md

@@ -23,3 +23,9 @@ cd web
 npm i
 npm run dev
 ```
+
+To update the frontend types with the backend types:
+
+```bash
+$ uv run pydantic2ts --module lynxkite_app.main --output ./web/src/apiTypes.ts --json2ts-cmd "npx json-schema-to-typescript"
+```

lynxkite-app/pyproject.toml

@@ -9,12 +9,12 @@ dependencies = [
     "lynxkite-core",
     "orjson>=3.10.13",
     "pycrdt-websocket>=0.15.3",
-    "pydantic-to-typescript>=2.0.0",
     "sse-starlette>=2.2.1",
 ]
 
 [project.optional-dependencies]
 dev = [
+    "pydantic-to-typescript>=2.0.0",
     "pytest>=8.3.4",
 ]
 

lynxkite-app/src/lynxkite_app/main.py

@@ -2,12 +2,7 @@
 
 import os
 import shutil
-
-if os.environ.get("NX_CUGRAPH_AUTOCONFIG", "").strip().lower() == "true":
-    import cudf.pandas
-
-    cudf.pandas.install()
-import dataclasses
+import pydantic
 import fastapi
 import importlib
 import pathlib
@@ -18,6 +13,11 @@ from lynxkite.core import ops
 from lynxkite.core import workspace
 from . import crdt
 
+if os.environ.get("NX_CUGRAPH_AUTOCONFIG", "").strip().lower() == "true":
+    import cudf.pandas
+
+    cudf.pandas.install()
+
 
 def detect_plugins():
     plugins = {}
@@ -86,8 +86,7 @@ DATA_PATH = pathlib.Path(os.environ.get("LYNXKITE_DATA", "lynxkite_data"))
 CRDT_PATH = pathlib.Path(os.environ.get("LYNXKITE_CRDT_DATA", "lynxkite_crdt_data"))
 
 
-@dataclasses.dataclass(order=True)
-class DirectoryEntry:
+class DirectoryEntry(pydantic.BaseModel):
     name: str
     type: str
 

lynxkite-app/uv.lock

@@ -194,6 +194,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/76/c6/c88e154df9c4e1a2a66ccf0005a88dfb2650c1dffb6f5ce603dfbd452ce3/idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3", size = 70442 },
 ]
 
+[[package]]
+name = "iniconfig"
+version = "2.0.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/d7/4b/cbd8e699e64a6f16ca3a8220661b5f83792b3017d0f79807cb8708d33913/iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3", size = 4646 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/ef/a6/62565a6e1cf69e10f5727360368e451d4b7f58beeac6173dc9db836a5b46/iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374", size = 5892 },
+]
+
 [[package]]
 name = "jinja2"
 version = "3.1.5"
@@ -215,17 +224,23 @@ dependencies = [
     { name = "lynxkite-core" },
     { name = "orjson" },
     { name = "pycrdt-websocket" },
-    { name = "pydantic-to-typescript" },
     { name = "sse-starlette" },
 ]
 
+[package.optional-dependencies]
+dev = [
+    { name = "pydantic-to-typescript" },
+    { name = "pytest" },
+]
+
 [package.metadata]
 requires-dist = [
     { name = "fastapi", extras = ["standard"], specifier = ">=0.115.6" },
     { name = "lynxkite-core", virtual = "../lynxkite-core" },
     { name = "orjson", specifier = ">=3.10.13" },
     { name = "pycrdt-websocket", specifier = ">=0.15.3" },
-    { name = "pydantic-to-typescript", specifier = ">=2.0.0" },
+    { name = "pydantic-to-typescript", marker = "extra == 'dev'", specifier = ">=2.0.0" },
+    { name = "pytest", marker = "extra == 'dev'", specifier = ">=8.3.4" },
     { name = "sse-starlette", specifier = ">=2.2.1" },
 ]
 
@@ -234,6 +249,9 @@ name = "lynxkite-core"
 version = "0.1.0"
 source = { virtual = "../lynxkite-core" }
 
+[package.metadata]
+requires-dist = [{ name = "pytest", marker = "extra == 'dev'" }]
+
 [[package]]
 name = "markdown-it-py"
 version = "3.0.0"
@@ -346,6 +364,24 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/59/ac/5e96cad01083015f7bfdb02ccafa489da8e6caa7f4c519e215f04d2bd856/orjson-3.10.14-cp313-cp313-win_amd64.whl", hash = "sha256:eca04dfd792cedad53dc9a917da1a522486255360cb4e77619343a20d9f35364", size = 133388 },
 ]
 
+[[package]]
+name = "packaging"
+version = "24.2"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/d0/63/68dbb6eb2de9cb10ee4c9c14a0148804425e13c4fb20d61cce69f53106da/packaging-24.2.tar.gz", hash = "sha256:c228a6dc5e932d346bc5739379109d49e8853dd8223571c7c5b55260edc0b97f", size = 163950 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/88/ef/eb23f262cca3c0c4eb7ab1933c3b1f03d021f2c48f54763065b6f0e321be/packaging-24.2-py3-none-any.whl", hash = "sha256:09abb1bccd265c01f4a3aa3f7a7db064b36514d2cba19a2f694fe6150451a759", size = 65451 },
+]
+
+[[package]]
+name = "pluggy"
+version = "1.5.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/96/2d/02d4312c973c6050a18b314a5ad0b3210edb65a906f868e31c111dede4a6/pluggy-1.5.0.tar.gz", hash = "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1", size = 67955 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/88/5f/e351af9a41f866ac3f1fac4ca0613908d9a41741cfcf2228f4ad853b697d/pluggy-1.5.0-py3-none-any.whl", hash = "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669", size = 20556 },
+]
+
 [[package]]
 name = "pycrdt"
 version = "0.10.9"
@@ -486,6 +522,21 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/8a/0b/9fcc47d19c48b59121088dd6da2488a49d5f72dacf8262e2790a1d2c7d15/pygments-2.19.1-py3-none-any.whl", hash = "sha256:9ea1544ad55cecf4b8242fab6dd35a93bbce657034b0611ee383099054ab6d8c", size = 1225293 },
 ]
 
+[[package]]
+name = "pytest"
+version = "8.3.4"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "colorama", marker = "sys_platform == 'win32'" },
+    { name = "iniconfig" },
+    { name = "packaging" },
+    { name = "pluggy" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/05/35/30e0d83068951d90a01852cb1cef56e5d8a09d20c7f511634cc2f7e0372a/pytest-8.3.4.tar.gz", hash = "sha256:965370d062bce11e73868e0335abac31b4d3de0e82f4007408d242b4f8610761", size = 1445919 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/11/92/76a1c94d3afee238333bc0a42b82935dd8f9cf8ce9e336ff87ee14d9e1cf/pytest-8.3.4-py3-none-any.whl", hash = "sha256:50e16d954148559c9a74109af1eaf0c945ba2d8f30f0a3d3335edde19788b6f6", size = 343083 },
+]
+
 [[package]]
 name = "python-dotenv"
 version = "1.0.1"

lynxkite-app/web/src/Directory.tsx

@@ -1,172 +1,202 @@
-// The directory browser.
-import { useParams, useNavigate } from "react-router";
 import { useState } from "react";
-import useSWR from 'swr'
-
+// The directory browser.
+import { useNavigate, useParams } from "react-router";
+import useSWR from "swr";
+import type { DirectoryEntry } from "./apiTypes.ts";
 
-import logo from './assets/logo.png';
 // @ts-ignore
-import Home from '~icons/tabler/home'
+import File from "~icons/tabler/file";
 // @ts-ignore
-import Folder from '~icons/tabler/folder'
+import FilePlus from "~icons/tabler/file-plus";
 // @ts-ignore
-import FolderPlus from '~icons/tabler/folder-plus'
+import Folder from "~icons/tabler/folder";
 // @ts-ignore
-import File from '~icons/tabler/file'
+import FolderPlus from "~icons/tabler/folder-plus";
 // @ts-ignore
-import FilePlus from '~icons/tabler/file-plus'
+import Home from "~icons/tabler/home";
 // @ts-ignore
-import Trash from '~icons/tabler/trash';
-
-
+import Trash from "~icons/tabler/trash";
+import logo from "./assets/logo.png";
 
 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=${encodedPath}`, fetcher);
-  const navigate = useNavigate();
-  const [isCreatingDir, setIsCreatingDir] = useState(false);
-  const [isCreatingWorkspace, setIsCreatingWorkspace] = useState(false);
-
-
-  function link(item: any) {
-    if (item.type === 'directory') {
-      return `/dir/${item.name}`;
-    } else {
-      return `/edit/${item.name}`;
-    }
-  }
-
-  function shortName(item: any) {
-    return item.name.split('/').pop();
-  }
-
-  function newName(list: any[], baseName: string = "Untitled") {
-    let i = 0;
-    while (true) {
-      const name = `${baseName}${i ? ` ${i}` : ''}`;
-      if (!list.find(item => item.name === name)) {
-        return name;
-      }
-      i++;
-    }
-  }
-
-  function newWorkspaceIn(path: string, list: any[], workspaceName?: string) {
-    const pathSlash = path ? `${path}/` : "";
-    const name = workspaceName || newName(list);
-    navigate(`/edit/${pathSlash}${name}`, { replace: true });
-  }
-
-
-  async function newFolderIn(path: string, list: any[], folderName?: string) {
-    const name = folderName || newName(list, "New Folder");
-    const pathSlash = path ? `${path}/` : "";
-
-    const res = await fetch(`/api/dir/mkdir`, {
-      method: 'POST',
-      headers: { 'Content-Type': 'application/json' },
-      body: JSON.stringify({ path: pathSlash + name }),
-    });
-    if (res.ok) {
-      navigate(`/dir/${pathSlash}${name}`);
-    } else {
-      alert("Failed to create folder.");
-    }
-  }
-
-  async function deleteItem(item: any) {
-    if (!window.confirm(`Are you sure you want to delete "${item.name}"?`)) return;
-    const pathSlash = path ? `${path}/` : "";
-
-    const apiPath = item.type === "directory" ? `/api/dir/delete` : `/api/delete`;
-    await fetch(apiPath, {
-      method: "POST",
-      headers: { "Content-Type": "application/json" },
-      body: JSON.stringify({ path: pathSlash + item.name }),
-    });
-  }
-
-  return (
-    <div className="directory">
-      <div className="logo">
-        <a href="https://lynxkite.com/">
-          <img src={logo} className="logo-image" alt="LynxKite logo" />
-        </a>
-        <div className="tagline">The Complete Graph Data Science Platform</div>
-      </div>
-
-      <div className="entry-list">
-        {list.error && <p className="error">{list.error.message}</p>}
-        {list.isLoading && (
-          <div className="loading spinner-border" role="status">
-            <span className="visually-hidden">Loading...</span>
-          </div>
-        )}
-
-        {list.data && (
-          <>
-            <div className="actions">
-              <div className="new-workspace">
-                {isCreatingWorkspace &&
-                  // @ts-ignore
-                  <form onSubmit={(e) => { e.preventDefault(); newWorkspaceIn(path || "", list.data, e.target.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.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>
-            </div>
-
-            {path && (
-              <div className="breadcrumbs">
-                <a href="/dir/">
-                  <Home />
-                </a>{" "}
-                <span className="current-folder">{path}</span>
-              </div>
-            )}
-
-            {list.data.map((item: any) => (
-              <div key={item.name} className="entry">
-                <a key={link(item)} href={link(item)}>
-                  {item.type === 'directory' ? <Folder /> : <File />}
-                  {shortName(item)}
-                </a>
-                <button onClick={() => { deleteItem(item) }}>
-                  <Trash />
-                </button>
-              </div>
-            ))}
-          </>
-        )}
-      </div>
-    </div>
-  );
+	const { path } = useParams();
+	const encodedPath = encodeURIComponent(path || "");
+	const list = useSWR(`/api/dir/list?path=${encodedPath}`, fetcher);
+	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}`;
+	}
+
+	function shortName(item: DirectoryEntry) {
+		return item.name.split("/").pop();
+	}
+
+	function newName(list: DirectoryEntry[], baseName = "Untitled") {
+		let i = 0;
+		while (true) {
+			const name = `${baseName}${i ? ` ${i}` : ""}`;
+			if (!list.find((item) => item.name === name)) {
+				return name;
+			}
+			i++;
+		}
+	}
+
+	function newWorkspaceIn(
+		path: string,
+		list: DirectoryEntry[],
+		workspaceName?: string,
+	) {
+		const pathSlash = path ? `${path}/` : "";
+		const name = workspaceName || newName(list);
+		navigate(`/edit/${pathSlash}${name}`, { replace: true });
+	}
+
+	async function newFolderIn(
+		path: string,
+		list: DirectoryEntry[],
+		folderName?: string,
+	) {
+		const name = folderName || newName(list, "New Folder");
+		const pathSlash = path ? `${path}/` : "";
+
+		const res = await fetch("/api/dir/mkdir", {
+			method: "POST",
+			headers: { "Content-Type": "application/json" },
+			body: JSON.stringify({ path: pathSlash + name }),
+		});
+		if (res.ok) {
+			navigate(`/dir/${pathSlash}${name}`);
+		} else {
+			alert("Failed to create folder.");
+		}
+	}
+
+	async function deleteItem(item: DirectoryEntry) {
+		if (!window.confirm(`Are you sure you want to delete "${item.name}"?`))
+			return;
+		const pathSlash = path ? `${path}/` : "";
+
+		const apiPath =
+			item.type === "directory" ? "/api/dir/delete" : "/api/delete";
+		await fetch(apiPath, {
+			method: "POST",
+			headers: { "Content-Type": "application/json" },
+			body: JSON.stringify({ path: pathSlash + item.name }),
+		});
+	}
+
+	return (
+		<div className="directory">
+			<div className="logo">
+				<a href="https://lynxkite.com/">
+					<img src={logo} className="logo-image" alt="LynxKite logo" />
+				</a>
+				<div className="tagline">The Complete Graph Data Science Platform</div>
+			</div>
+			<div className="entry-list">
+				{list.error && <p className="error">{list.error.message}</p>}
+				{list.isLoading && (
+					<output className="loading spinner-border">
+						<span className="visually-hidden">Loading...</span>
+					</output>
+				)}
+
+				{list.data && (
+					<>
+						<div className="actions">
+							<div className="new-workspace">
+								{isCreatingWorkspace && (
+									// @ts-ignore
+									<form
+										onSubmit={(e) => {
+											e.preventDefault();
+											newWorkspaceIn(
+												path || "",
+												list.data,
+												e.target.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.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>
+						</div>
+
+						{path && (
+							<div className="breadcrumbs">
+								<a href="/dir/">
+									<Home />
+								</a>{" "}
+								<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)}>
+									{item.type === "directory" ? <Folder /> : <File />}
+									{shortName(item)}
+								</a>
+								<button
+									type="button"
+									onClick={() => {
+										deleteItem(item);
+									}}
+								>
+									<Trash />
+								</button>
+							</div>
+						))}
+					</>
+				)}
+			</div>{" "}
+		</div>
+	);
 }

lynxkite-app/web/src/apiTypes.ts

@@ -5,48 +5,54 @@
 /* Do not modify it by hand - just update the pydantic models and then re-run the script
 */
 
-/* eslint-disable */
-/**
- * This file was automatically generated by json-schema-to-typescript.
- * DO NOT MODIFY IT BY HAND. Instead, modify the source JSONSchema file,
- * and run json-schema-to-typescript to regenerate this file.
- */
-
-export interface BaseConfig {
-  [k: string]: unknown;
+export interface DirectoryEntry {
+	name: string;
+	type: string;
 }
-export interface Position {
-  x: number;
-  y: number;
-  [k: string]: unknown;
+export interface SaveRequest {
+	path: string;
+	ws: Workspace;
+	[k: string]: unknown;
 }
+/**
+ * A workspace is a representation of a computational graph that consists of nodes and edges.
+ *
+ * Each node represents an operation or task, and the edges represent the flow of data between
+ * the nodes. Each workspace is associated with an environment, which determines the operations
+ * that can be performed in the workspace and the execution method for the operations.
+ */
 export interface Workspace {
-  env?: string;
-  nodes?: WorkspaceNode[];
-  edges?: WorkspaceEdge[];
-  [k: string]: unknown;
+	env?: string;
+	nodes?: WorkspaceNode[];
+	edges?: WorkspaceEdge[];
+	[k: string]: unknown;
 }
 export interface WorkspaceNode {
-  id: string;
-  type: string;
-  data: WorkspaceNodeData;
-  position: Position;
-  [k: string]: unknown;
+	id: string;
+	type: string;
+	data: WorkspaceNodeData;
+	position: Position;
+	[k: string]: unknown;
 }
 export interface WorkspaceNodeData {
-  title: string;
-  params: {
-    [k: string]: unknown;
-  };
-  display?: unknown;
-  error?: string | null;
-  [k: string]: unknown;
+	title: string;
+	params: {
+		[k: string]: unknown;
+	};
+	display?: unknown;
+	error?: string | null;
+	[k: string]: unknown;
+}
+export interface Position {
+	x: number;
+	y: number;
+	[k: string]: unknown;
 }
 export interface WorkspaceEdge {
-  id: string;
-  source: string;
-  target: string;
-  sourceHandle: string;
-  targetHandle: string;
-  [k: string]: unknown;
+	id: string;
+	source: string;
+	target: string;
+	sourceHandle: string;
+	targetHandle: string;
+	[k: string]: unknown;
 }