Merge pull request #88 from biggraph/darabos-hf-spaces

.dockerignore

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

.gitignore

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

.pre-commit-config.yaml

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

Dockerfile

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

README.md

@@ -1,3 +1,12 @@
+---
+title: LynxKite 2000:MM
+emoji: 🪁
+colorFrom: purple
+colorTo: gray
+sdk: docker
+app_port: 7860
+---
+
 # LynxKite 2024
 
 This is an experimental rewrite of [LynxKite](https://github.com/lynxkite/lynxkite). It is not compatible with the

lynxkite-app/src/lynxkite_app/__main__.py

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

lynxkite-app/src/lynxkite_app/main.py

@@ -7,6 +7,7 @@ import importlib
 import pathlib
 import pkgutil
 from fastapi.staticfiles import StaticFiles
+from fastapi.middleware.gzip import GZipMiddleware
 import starlette
 from lynxkite.core import ops
 from lynxkite.core import workspace
@@ -28,6 +29,7 @@ lynxkite_plugins = detect_plugins()
 
 app = fastapi.FastAPI(lifespan=crdt.lifespan)
 app.include_router(crdt.router)
+app.add_middleware(GZipMiddleware)
 
 
 @app.get("/api/catalog")

lynxkite-app/web/src/Directory.tsx

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

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

@@ -66,8 +66,9 @@ function LynxKiteFlow() {
     const state = syncedStore({ workspace: {} as Workspace });
     setState(state);
     const doc = getYjsDoc(state);
+    const proto = location.protocol === "https:" ? "wss:" : "ws:";
     const wsProvider = new WebsocketProvider(
-      `ws://${location.host}/ws/crdt`,
+      `${proto}//${location.host}/ws/crdt`,
       path!,
       doc,
     );

lynxkite-bio/src/lynxkite_bio/__init__.py

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

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

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

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

@@ -15,7 +15,7 @@ import polars as pl
 import json
 
 
-mem = joblib.Memory("../joblib-cache")
+mem = joblib.Memory("joblib-cache")
 op = ops.op_registration(core.ENV)