Spaces:
Running
Running
Remove references to lynxkite-lynxscribe and lynxkite-bio. These live in a separate repo now.
Browse files- .github/workflows/test.yaml +0 -9
- Dockerfile +1 -4
- README.md +1 -3
- lynxkite-app/tests/test_main.py +0 -1
- lynxkite-app/web/tests/errors.spec.ts +1 -1
- lynxkite-app/web/tests/examples.spec.ts +0 -3
- lynxkite-graph-analytics/README.md +0 -40
- lynxkite-graph-analytics/src/lynxkite_graph_analytics/__init__.py +0 -3
- mkdocs.yml +1 -1
.github/workflows/test.yaml
CHANGED
@@ -24,16 +24,12 @@ jobs:
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- name: Install dependencies
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run: |
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-
eval `ssh-agent -s`
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-
ssh-add - <<< '${{ secrets.LYNXSCRIBE_DEPLOY_KEY }}'
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uv venv
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. .venv/bin/activate
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uv pip install \
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-e lynxkite-core/[dev] \
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-e lynxkite-app/[dev] \
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-e lynxkite-graph-analytics/[dev] \
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-
-e lynxkite-bio \
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-
-e lynxkite-lynxscribe/ \
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-e lynxkite-pillow-example/
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- name: Run pre-commits
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@@ -56,11 +52,6 @@ jobs:
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cd lynxkite-graph-analytics
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pytest
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-
- name: Run LynxScribe tests
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-
run: |
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cd lynxkite-lynxscribe
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-
pytest
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-
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- name: Try building the documentation
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run: |
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uv pip install mkdocs-material mkdocstrings[python]
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- name: Install dependencies
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run: |
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uv venv
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. .venv/bin/activate
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uv pip install \
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-e lynxkite-core/[dev] \
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-e lynxkite-app/[dev] \
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-e lynxkite-graph-analytics/[dev] \
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-e lynxkite-pillow-example/
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- name: Run pre-commits
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cd lynxkite-graph-analytics
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pytest
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- name: Try building the documentation
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run: |
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uv pip install mkdocs-material mkdocstrings[python]
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Dockerfile
CHANGED
@@ -5,14 +5,11 @@ USER node
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ENV HOME=/home/node PATH=/home/node/.local/bin:$PATH
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WORKDIR $HOME/app
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COPY --chown=node . $HOME/app
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-
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-
RUN --mount=type=secret,id=LYNXSCRIBE_DEPLOY_KEY,mode=0444,required=true \
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uv venv && uv pip install \
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-e lynxkite-core \
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-e lynxkite-app \
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-e lynxkite-graph-analytics \
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-
-e lynxkite-bio \
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-
-e lynxkite-lynxscribe \
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-e lynxkite-pillow-example \
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chromadb openai
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WORKDIR $HOME/app/examples
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ENV HOME=/home/node PATH=/home/node/.local/bin:$PATH
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WORKDIR $HOME/app
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COPY --chown=node . $HOME/app
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+
RUN \
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uv venv && uv pip install \
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-e lynxkite-core \
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-e lynxkite-app \
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-e lynxkite-graph-analytics \
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-e lynxkite-pillow-example \
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chromadb openai
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WORKDIR $HOME/app/examples
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README.md
CHANGED
@@ -22,8 +22,6 @@ original LynxKite. The primary goals of this rewrite are:
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- `lynxkite-app`: The LynxKite web application. Install some plugins then run this to use LynxKite.
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- `lynxkite-graph-analytics`: Graph analytics plugin. The classical LynxKite experience!
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- `lynxkite-pillow`: A simple example plugin.
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-
- `lynxkite-lynxscribe`: A plugin for building and running LynxScribe applications.
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-
- `lynxkite-bio`: Bioinformatics additions for LynxKite Graph Analytics.
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- `docs`: User-facing documentation. It's shared between all packages.
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## Development
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@@ -35,7 +33,7 @@ uv venv
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source .venv/bin/activate
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uvx pre-commit install
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# The [dev] tag is only needed if you intend on running tests
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-
uv pip install -e lynxkite-core/[dev] -e lynxkite-app/[dev] -e lynxkite-graph-analytics/[dev] -e lynxkite-
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```
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This also builds the frontend, hopefully very quickly. To run it:
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- `lynxkite-app`: The LynxKite web application. Install some plugins then run this to use LynxKite.
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- `lynxkite-graph-analytics`: Graph analytics plugin. The classical LynxKite experience!
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- `lynxkite-pillow`: A simple example plugin.
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- `docs`: User-facing documentation. It's shared between all packages.
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## Development
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source .venv/bin/activate
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uvx pre-commit install
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# The [dev] tag is only needed if you intend on running tests
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+
uv pip install -e lynxkite-core/[dev] -e lynxkite-app/[dev] -e lynxkite-graph-analytics/[dev] -e lynxkite-pillow-example/
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```
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This also builds the frontend, hopefully very quickly. To run it:
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lynxkite-app/tests/test_main.py
CHANGED
@@ -17,7 +17,6 @@ def test_detect_plugins_with_plugins():
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plugin in plugins.keys()
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for plugin in [
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"lynxkite_graph_analytics",
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-
"lynxkite_lynxscribe",
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"lynxkite_pillow_example",
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]
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)
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plugin in plugins.keys()
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for plugin in [
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"lynxkite_graph_analytics",
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"lynxkite_pillow_example",
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]
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)
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lynxkite-app/web/tests/errors.spec.ts
CHANGED
@@ -33,7 +33,7 @@ test("unknown operation", async () => {
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await workspace.addBox("NX › Scale-Free Graph");
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const graphBox = workspace.getBox("NX › Scale-Free Graph 1");
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await graphBox.getByLabel("n", { exact: true }).fill("10");
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-
await workspace.setEnv("
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const csvBox = workspace.getBox("NX › Scale-Free Graph 1");
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await expect(csvBox.locator(".error")).toHaveText('Operation "NX › Scale-Free Graph" not found.');
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await workspace.setEnv("LynxKite Graph Analytics");
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await workspace.addBox("NX › Scale-Free Graph");
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const graphBox = workspace.getBox("NX › Scale-Free Graph 1");
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await graphBox.getByLabel("n", { exact: true }).fill("10");
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+
await workspace.setEnv("Pillow");
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const csvBox = workspace.getBox("NX › Scale-Free Graph 1");
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await expect(csvBox.locator(".error")).toHaveText('Operation "NX › Scale-Free Graph" not found.');
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await workspace.setEnv("LynxKite Graph Analytics");
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lynxkite-app/web/tests/examples.spec.ts
CHANGED
@@ -3,12 +3,9 @@ import { expect, test } from "@playwright/test";
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import { Workspace } from "./lynxkite";
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const WORKSPACES = [
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-
// "AIMO",
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"Airlines demo",
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-
"Bio Cypher demo",
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// "Graph RAG",
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"Image processing",
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// "LynxScribe demo",
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"NetworkX demo",
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"Model use",
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];
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import { Workspace } from "./lynxkite";
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const WORKSPACES = [
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"Airlines demo",
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// "Graph RAG",
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"Image processing",
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"NetworkX demo",
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"Model use",
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];
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lynxkite-graph-analytics/README.md
CHANGED
@@ -11,43 +11,3 @@ pip install lynxkite lynxkite-graph-analytics
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```
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Run LynxKite with `NX_CUGRAPH_AUTOCONFIG=True` to enable GPU-accelerated graph data science operations.
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-
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-
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## BioNemo
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-
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If you want to use BioNemo operations, then you will have to use the provided Docker image, or
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install BioNemo manually in your environment.
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Take into account that BioNemo needs a GPU to work, you can find the specific requirements
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[here](https://docs.nvidia.com/bionemo-framework/latest/user-guide/getting-started/pre-reqs/).
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-
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The import of BioNemo operations is gate keeped behing the `LYNXKITE_BIONEMO_INSTALLED` variable.
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BioNemo operations will only be imported if this environment variable is set to true.
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-
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To build the image:
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-
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```bash
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# in lynxkite-graph-analytics folder
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$ docker build -f Dockerfile.bionemo -t lynxkite-bionemo ..
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$ docker run --name bionemo -d -p8000:8000 --gpus=all lynxkite-bionemo
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```
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-
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Take into account that this Dockerfile does not include the lynxkite-lynxscribe package. If you want to include it you will
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need to set up git credentials inside the container.
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-
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If you want to do some development, then it is recommend to use the [devcontainers](https://code.visualstudio.com/docs/devcontainers/containers)
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vscode extension. The following is a basic configuration to get started:
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-
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```json
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// .devcontainer/devcontainer.json
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{
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"name": "Existing Dockerfile",
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"runArgs": [
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"--gpus=all",
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"--shm-size=4g"
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],
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"build": {
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"context": "..",
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"dockerfile": "../lynxkite-graph-analytics/Dockerfile.bionemo"
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}
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}
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```
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```
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Run LynxKite with `NX_CUGRAPH_AUTOCONFIG=True` to enable GPU-accelerated graph data science operations.
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lynxkite-graph-analytics/src/lynxkite_graph_analytics/__init__.py
CHANGED
@@ -15,6 +15,3 @@ from . import lynxkite_ops # noqa (imported to trigger registration)
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from . import networkx_ops # noqa (imported to trigger registration)
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from . import pytorch # noqa (imported to trigger registration)
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from . import ml_ops # noqa (imported to trigger registration)
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-
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if os.environ.get("LYNXKITE_BIONEMO_INSTALLED", "").strip().lower() == "true":
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-
from . import bionemo_ops # noqa (imported to trigger registration)
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from . import networkx_ops # noqa (imported to trigger registration)
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from . import pytorch # noqa (imported to trigger registration)
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from . import ml_ops # noqa (imported to trigger registration)
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mkdocs.yml
CHANGED
@@ -22,4 +22,4 @@ plugins:
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- mkdocstrings:
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handlers:
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python:
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paths: ["./lynxkite-app/src", "./lynxkite-core/src", "./lynxkite-graph-analytics/src"
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- mkdocstrings:
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handlers:
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python:
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+
paths: ["./lynxkite-app/src", "./lynxkite-core/src", "./lynxkite-graph-analytics/src"]
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