darabos commited on
Commit
d1bbedf
·
1 Parent(s): aa9d27d

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

Browse files
.github/workflows/test.yaml CHANGED
@@ -24,16 +24,12 @@ jobs:
24
 
25
  - name: Install dependencies
26
  run: |
27
- eval `ssh-agent -s`
28
- ssh-add - <<< '${{ secrets.LYNXSCRIBE_DEPLOY_KEY }}'
29
  uv venv
30
  . .venv/bin/activate
31
  uv pip install \
32
  -e lynxkite-core/[dev] \
33
  -e lynxkite-app/[dev] \
34
  -e lynxkite-graph-analytics/[dev] \
35
- -e lynxkite-bio \
36
- -e lynxkite-lynxscribe/ \
37
  -e lynxkite-pillow-example/
38
 
39
  - name: Run pre-commits
@@ -56,11 +52,6 @@ jobs:
56
  cd lynxkite-graph-analytics
57
  pytest
58
 
59
- - name: Run LynxScribe tests
60
- run: |
61
- cd lynxkite-lynxscribe
62
- pytest
63
-
64
  - name: Try building the documentation
65
  run: |
66
  uv pip install mkdocs-material mkdocstrings[python]
 
24
 
25
  - name: Install dependencies
26
  run: |
 
 
27
  uv venv
28
  . .venv/bin/activate
29
  uv pip install \
30
  -e lynxkite-core/[dev] \
31
  -e lynxkite-app/[dev] \
32
  -e lynxkite-graph-analytics/[dev] \
 
 
33
  -e lynxkite-pillow-example/
34
 
35
  - name: Run pre-commits
 
52
  cd lynxkite-graph-analytics
53
  pytest
54
 
 
 
 
 
 
55
  - name: Try building the documentation
56
  run: |
57
  uv pip install mkdocs-material mkdocstrings[python]
Dockerfile CHANGED
@@ -5,14 +5,11 @@ USER node
5
  ENV HOME=/home/node PATH=/home/node/.local/bin:$PATH
6
  WORKDIR $HOME/app
7
  COPY --chown=node . $HOME/app
8
- ENV GIT_SSH_COMMAND="ssh -i /run/secrets/LYNXSCRIBE_DEPLOY_KEY -o StrictHostKeyChecking=no"
9
- RUN --mount=type=secret,id=LYNXSCRIBE_DEPLOY_KEY,mode=0444,required=true \
10
  uv venv && uv pip install \
11
  -e lynxkite-core \
12
  -e lynxkite-app \
13
  -e lynxkite-graph-analytics \
14
- -e lynxkite-bio \
15
- -e lynxkite-lynxscribe \
16
  -e lynxkite-pillow-example \
17
  chromadb openai
18
  WORKDIR $HOME/app/examples
 
5
  ENV HOME=/home/node PATH=/home/node/.local/bin:$PATH
6
  WORKDIR $HOME/app
7
  COPY --chown=node . $HOME/app
8
+ RUN \
 
9
  uv venv && uv pip install \
10
  -e lynxkite-core \
11
  -e lynxkite-app \
12
  -e lynxkite-graph-analytics \
 
 
13
  -e lynxkite-pillow-example \
14
  chromadb openai
15
  WORKDIR $HOME/app/examples
README.md CHANGED
@@ -22,8 +22,6 @@ original LynxKite. The primary goals of this rewrite are:
22
  - `lynxkite-app`: The LynxKite web application. Install some plugins then run this to use LynxKite.
23
  - `lynxkite-graph-analytics`: Graph analytics plugin. The classical LynxKite experience!
24
  - `lynxkite-pillow`: A simple example plugin.
25
- - `lynxkite-lynxscribe`: A plugin for building and running LynxScribe applications.
26
- - `lynxkite-bio`: Bioinformatics additions for LynxKite Graph Analytics.
27
  - `docs`: User-facing documentation. It's shared between all packages.
28
 
29
  ## Development
@@ -35,7 +33,7 @@ uv venv
35
  source .venv/bin/activate
36
  uvx pre-commit install
37
  # The [dev] tag is only needed if you intend on running tests
38
- 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/
39
  ```
40
 
41
  This also builds the frontend, hopefully very quickly. To run it:
 
22
  - `lynxkite-app`: The LynxKite web application. Install some plugins then run this to use LynxKite.
23
  - `lynxkite-graph-analytics`: Graph analytics plugin. The classical LynxKite experience!
24
  - `lynxkite-pillow`: A simple example plugin.
 
 
25
  - `docs`: User-facing documentation. It's shared between all packages.
26
 
27
  ## Development
 
33
  source .venv/bin/activate
34
  uvx pre-commit install
35
  # The [dev] tag is only needed if you intend on running tests
36
+ uv pip install -e lynxkite-core/[dev] -e lynxkite-app/[dev] -e lynxkite-graph-analytics/[dev] -e lynxkite-pillow-example/
37
  ```
38
 
39
  This also builds the frontend, hopefully very quickly. To run it:
lynxkite-app/tests/test_main.py CHANGED
@@ -17,7 +17,6 @@ def test_detect_plugins_with_plugins():
17
  plugin in plugins.keys()
18
  for plugin in [
19
  "lynxkite_graph_analytics",
20
- "lynxkite_lynxscribe",
21
  "lynxkite_pillow_example",
22
  ]
23
  )
 
17
  plugin in plugins.keys()
18
  for plugin in [
19
  "lynxkite_graph_analytics",
 
20
  "lynxkite_pillow_example",
21
  ]
22
  )
lynxkite-app/web/tests/errors.spec.ts CHANGED
@@ -33,7 +33,7 @@ test("unknown operation", async () => {
33
  await workspace.addBox("NX › Scale-Free Graph");
34
  const graphBox = workspace.getBox("NX › Scale-Free Graph 1");
35
  await graphBox.getByLabel("n", { exact: true }).fill("10");
36
- await workspace.setEnv("LynxScribe");
37
  const csvBox = workspace.getBox("NX › Scale-Free Graph 1");
38
  await expect(csvBox.locator(".error")).toHaveText('Operation "NX › Scale-Free Graph" not found.');
39
  await workspace.setEnv("LynxKite Graph Analytics");
 
33
  await workspace.addBox("NX › Scale-Free Graph");
34
  const graphBox = workspace.getBox("NX › Scale-Free Graph 1");
35
  await graphBox.getByLabel("n", { exact: true }).fill("10");
36
+ await workspace.setEnv("Pillow");
37
  const csvBox = workspace.getBox("NX › Scale-Free Graph 1");
38
  await expect(csvBox.locator(".error")).toHaveText('Operation "NX › Scale-Free Graph" not found.');
39
  await workspace.setEnv("LynxKite Graph Analytics");
lynxkite-app/web/tests/examples.spec.ts CHANGED
@@ -3,12 +3,9 @@ import { expect, test } from "@playwright/test";
3
  import { Workspace } from "./lynxkite";
4
 
5
  const WORKSPACES = [
6
- // "AIMO",
7
  "Airlines demo",
8
- "Bio Cypher demo",
9
  // "Graph RAG",
10
  "Image processing",
11
- // "LynxScribe demo",
12
  "NetworkX demo",
13
  "Model use",
14
  ];
 
3
  import { Workspace } from "./lynxkite";
4
 
5
  const WORKSPACES = [
 
6
  "Airlines demo",
 
7
  // "Graph RAG",
8
  "Image processing",
 
9
  "NetworkX demo",
10
  "Model use",
11
  ];
lynxkite-graph-analytics/README.md CHANGED
@@ -11,43 +11,3 @@ pip install lynxkite lynxkite-graph-analytics
11
  ```
12
 
13
  Run LynxKite with `NX_CUGRAPH_AUTOCONFIG=True` to enable GPU-accelerated graph data science operations.
14
-
15
-
16
- ## BioNemo
17
-
18
- If you want to use BioNemo operations, then you will have to use the provided Docker image, or
19
- install BioNemo manually in your environment.
20
- Take into account that BioNemo needs a GPU to work, you can find the specific requirements
21
- [here](https://docs.nvidia.com/bionemo-framework/latest/user-guide/getting-started/pre-reqs/).
22
-
23
- The import of BioNemo operations is gate keeped behing the `LYNXKITE_BIONEMO_INSTALLED` variable.
24
- BioNemo operations will only be imported if this environment variable is set to true.
25
-
26
- To build the image:
27
-
28
- ```bash
29
- # in lynxkite-graph-analytics folder
30
- $ docker build -f Dockerfile.bionemo -t lynxkite-bionemo ..
31
- $ docker run --name bionemo -d -p8000:8000 --gpus=all lynxkite-bionemo
32
- ```
33
-
34
- Take into account that this Dockerfile does not include the lynxkite-lynxscribe package. If you want to include it you will
35
- need to set up git credentials inside the container.
36
-
37
- If you want to do some development, then it is recommend to use the [devcontainers](https://code.visualstudio.com/docs/devcontainers/containers)
38
- vscode extension. The following is a basic configuration to get started:
39
-
40
- ```json
41
- // .devcontainer/devcontainer.json
42
- {
43
- "name": "Existing Dockerfile",
44
- "runArgs": [
45
- "--gpus=all",
46
- "--shm-size=4g"
47
- ],
48
- "build": {
49
- "context": "..",
50
- "dockerfile": "../lynxkite-graph-analytics/Dockerfile.bionemo"
51
- }
52
- }
53
- ```
 
11
  ```
12
 
13
  Run LynxKite with `NX_CUGRAPH_AUTOCONFIG=True` to enable GPU-accelerated graph data science operations.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
lynxkite-graph-analytics/src/lynxkite_graph_analytics/__init__.py CHANGED
@@ -15,6 +15,3 @@ from . import lynxkite_ops # noqa (imported to trigger registration)
15
  from . import networkx_ops # noqa (imported to trigger registration)
16
  from . import pytorch # noqa (imported to trigger registration)
17
  from . import ml_ops # noqa (imported to trigger registration)
18
-
19
- if os.environ.get("LYNXKITE_BIONEMO_INSTALLED", "").strip().lower() == "true":
20
- from . import bionemo_ops # noqa (imported to trigger registration)
 
15
  from . import networkx_ops # noqa (imported to trigger registration)
16
  from . import pytorch # noqa (imported to trigger registration)
17
  from . import ml_ops # noqa (imported to trigger registration)
 
 
 
mkdocs.yml CHANGED
@@ -22,4 +22,4 @@ plugins:
22
  - mkdocstrings:
23
  handlers:
24
  python:
25
- paths: ["./lynxkite-app/src", "./lynxkite-core/src", "./lynxkite-graph-analytics/src", "./lynxkite-lynxscribe/src"]
 
22
  - mkdocstrings:
23
  handlers:
24
  python:
25
+ paths: ["./lynxkite-app/src", "./lynxkite-core/src", "./lynxkite-graph-analytics/src"]