Remove references to lynxkite-lynxscribe and lynxkite-bio. These live in a separate repo now.

.github/workflows/test.yaml

@@ -24,16 +24,12 @@ jobs:
 
       - name: Install dependencies
         run: |
-          eval `ssh-agent -s`
-          ssh-add - <<< '${{ secrets.LYNXSCRIBE_DEPLOY_KEY }}'
           uv venv
           . .venv/bin/activate
           uv pip install \
             -e lynxkite-core/[dev] \
             -e lynxkite-app/[dev] \
             -e lynxkite-graph-analytics/[dev] \
-            -e lynxkite-bio \
-            -e lynxkite-lynxscribe/ \
             -e lynxkite-pillow-example/
 
       - name: Run pre-commits
@@ -56,11 +52,6 @@ jobs:
           cd lynxkite-graph-analytics
           pytest
 
-      - name: Run LynxScribe tests
-        run: |
-          cd lynxkite-lynxscribe
-          pytest
-
       - name: Try building the documentation
         run: |
           uv pip install mkdocs-material mkdocstrings[python]

Dockerfile

@@ -5,14 +5,11 @@ USER node
 ENV HOME=/home/node PATH=/home/node/.local/bin:$PATH
 WORKDIR $HOME/app
 COPY --chown=node . $HOME/app
-ENV GIT_SSH_COMMAND="ssh -i /run/secrets/LYNXSCRIBE_DEPLOY_KEY -o StrictHostKeyChecking=no"
-RUN --mount=type=secret,id=LYNXSCRIBE_DEPLOY_KEY,mode=0444,required=true \
+RUN \
   uv venv && uv pip install \
   -e lynxkite-core \
   -e lynxkite-app \
   -e lynxkite-graph-analytics \
-  -e lynxkite-bio \
-  -e lynxkite-lynxscribe \
   -e lynxkite-pillow-example \
   chromadb openai
 WORKDIR $HOME/app/examples

README.md

@@ -22,8 +22,6 @@ original LynxKite. The primary goals of this rewrite are:
 - `lynxkite-app`: The LynxKite web application. Install some plugins then run this to use LynxKite.
 - `lynxkite-graph-analytics`: Graph analytics plugin. The classical LynxKite experience!
 - `lynxkite-pillow`: A simple example plugin.
-- `lynxkite-lynxscribe`: A plugin for building and running LynxScribe applications.
-- `lynxkite-bio`: Bioinformatics additions for LynxKite Graph Analytics.
 - `docs`: User-facing documentation. It's shared between all packages.
 
 ## Development
@@ -35,7 +33,7 @@ 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-bio -e lynxkite-lynxscribe/ -e lynxkite-pillow-example/
+uv pip install -e lynxkite-core/[dev] -e lynxkite-app/[dev] -e lynxkite-graph-analytics/[dev] -e lynxkite-pillow-example/
 ```
 
 This also builds the frontend, hopefully very quickly. To run it:

lynxkite-app/tests/test_main.py

@@ -17,7 +17,6 @@ def test_detect_plugins_with_plugins():
         plugin in plugins.keys()
         for plugin in [
             "lynxkite_graph_analytics",
-            "lynxkite_lynxscribe",
             "lynxkite_pillow_example",
         ]
     )

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

@@ -33,7 +33,7 @@ test("unknown operation", async () => {
   await workspace.addBox("NX › Scale-Free Graph");
   const graphBox = workspace.getBox("NX › Scale-Free Graph 1");
   await graphBox.getByLabel("n", { exact: true }).fill("10");
-  await workspace.setEnv("LynxScribe");
+  await workspace.setEnv("Pillow");
   const csvBox = workspace.getBox("NX › Scale-Free Graph 1");
   await expect(csvBox.locator(".error")).toHaveText('Operation "NX › Scale-Free Graph" not found.');
   await workspace.setEnv("LynxKite Graph Analytics");

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

@@ -3,12 +3,9 @@ import { expect, test } from "@playwright/test";
 import { Workspace } from "./lynxkite";
 
 const WORKSPACES = [
-  // "AIMO",
   "Airlines demo",
-  "Bio Cypher demo",
   // "Graph RAG",
   "Image processing",
-  // "LynxScribe demo",
   "NetworkX demo",
   "Model use",
 ];

lynxkite-graph-analytics/README.md

@@ -11,43 +11,3 @@ pip install lynxkite lynxkite-graph-analytics
 ```
 
 Run LynxKite with `NX_CUGRAPH_AUTOCONFIG=True` to enable GPU-accelerated graph data science operations.
-
-
-## BioNemo
-
-If you want to use BioNemo operations, then you will have to use the provided Docker image, or
-install BioNemo manually in your environment.
-Take into account that BioNemo needs a GPU to work, you can find the specific requirements
-[here](https://docs.nvidia.com/bionemo-framework/latest/user-guide/getting-started/pre-reqs/).
-
-The import of BioNemo operations is gate keeped behing the `LYNXKITE_BIONEMO_INSTALLED` variable.
-BioNemo operations will only be imported if this environment variable is set to true.
-
-To build the image:
-
-```bash
-# in lynxkite-graph-analytics folder
-$ docker build -f Dockerfile.bionemo -t lynxkite-bionemo ..
-$ docker run --name bionemo -d -p8000:8000 --gpus=all lynxkite-bionemo
-```
-
-Take into account that this Dockerfile does not include the lynxkite-lynxscribe package. If you want to include it you will
-need to set up git credentials inside the container.
-
-If you want to do some development, then it is recommend to use the [devcontainers](https://code.visualstudio.com/docs/devcontainers/containers)
-vscode extension. The following is a basic configuration to get started:
-
-```json
-// .devcontainer/devcontainer.json
-{
-	"name": "Existing Dockerfile",
-	"runArgs": [
-		"--gpus=all",
-		"--shm-size=4g"
-	],
-	"build": {
-		"context": "..",
-		"dockerfile": "../lynxkite-graph-analytics/Dockerfile.bionemo"
-	}
-}
-```

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

@@ -15,6 +15,3 @@ from . import lynxkite_ops  # noqa (imported to trigger registration)
 from . import networkx_ops  # noqa (imported to trigger registration)
 from . import pytorch  # noqa (imported to trigger registration)
 from . import ml_ops  # noqa (imported to trigger registration)
-
-if os.environ.get("LYNXKITE_BIONEMO_INSTALLED", "").strip().lower() == "true":
-    from . import bionemo_ops  # noqa (imported to trigger registration)

mkdocs.yml

@@ -22,4 +22,4 @@ plugins:
 - mkdocstrings:
     handlers:
       python:
-        paths: ["./lynxkite-app/src", "./lynxkite-core/src", "./lynxkite-graph-analytics/src", "./lynxkite-lynxscribe/src"]
+        paths: ["./lynxkite-app/src", "./lynxkite-core/src", "./lynxkite-graph-analytics/src"]