BioNemo demo (#84)

* Add BioNeMo integration, single demo for now
---------

Co-authored-by: JMLizano <[email protected]>
Co-authored-by: Daniel Darabos <[email protected]>

examples/BioNemo demo

@@ -0,0 +1,985 @@
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+          "type": "visualization"
+        },
+        "params": {},
+        "status": "done",
+        "title": "BioNeMo > Plot f1 comparison"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 863.0,
+      "id": "BioNeMo > Plot f1 comparison 1",
+      "position": {
+        "x": 2091.687426186124,
+        "y": -368.096892874947
+      },
+      "type": "visualization",
+      "width": 1034.0
+    },
+    {
+      "data": {
+        "display": {
+          "grid": {
+            "bottom": "10%",
+            "height": "70%",
+            "left": "20%",
+            "right": "10%",
+            "top": "10%",
+            "width": "70%"
+          },
+          "series": [
+            {
+              "data": [
+                0.8385031821273431,
+                0.9053958718388249
+              ],
+              "itemStyle": {
+                "color": "#440154"
+              },
+              "name": "Accuracy",
+              "type": "bar"
+            },
+            {
+              "data": [
+                [
+                  0.8221974395834195,
+                  0.8548089246712667
+                ],
+                [
+                  0.8901141406971089,
+                  0.9206776029805408
+                ]
+              ],
+              "itemStyle": {
+                "color": "#1f77b4"
+              },
+              "name": "Error Bars",
+              "type": "errorbar"
+            }
+          ],
+          "title": {
+            "left": "center",
+            "text": "Accuracy Comparison",
+            "textStyle": {
+              "fontSize": 20,
+              "fontWeight": "bold"
+            }
+          },
+          "tooltip": {
+            "axisPointer": {
+              "type": "shadow"
+            },
+            "trigger": "axis"
+          },
+          "xAxis": {
+            "axisLabel": {
+              "align": "right",
+              "rotate": 45,
+              "textStyle": {
+                "fontSize": 14,
+                "fontWeight": "bold"
+              }
+            },
+            "data": [
+              "10M parameters",
+              "106M parameters"
+            ],
+            "type": "category"
+          },
+          "yAxis": {
+            "axisLabel": {
+              "textStyle": {
+                "fontSize": 14,
+                "fontWeight": "bold"
+              }
+            },
+            "interval": 0.1,
+            "max": 1,
+            "min": 0,
+            "name": "Accuracy",
+            "type": "value"
+          }
+        },
+        "error": null,
+        "meta": {
+          "inputs": {
+            "benchmark_output100m": {
+              "name": "benchmark_output100m",
+              "position": "left",
+              "type": {
+                "type": "<class 'inspect._empty'>"
+              }
+            },
+            "benchmark_output10m": {
+              "name": "benchmark_output10m",
+              "position": "left",
+              "type": {
+                "type": "<class 'inspect._empty'>"
+              }
+            }
+          },
+          "name": "BioNeMo > Plot accuracy comparison",
+          "outputs": {},
+          "params": {},
+          "position": {
+            "x": 1574.0,
+            "y": 720.0
+          },
+          "type": "visualization"
+        },
+        "params": {},
+        "status": "done",
+        "title": "BioNeMo > Plot accuracy comparison"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 200.0,
+      "id": "BioNeMo > Plot accuracy comparison 1",
+      "position": {
+        "x": 2160.0,
+        "y": 915.0
+      },
+      "type": "visualization",
+      "width": 200.0
+    }
+  ]
+}

lynxkite-app/src/lynxkite_app/__main__.py

@@ -6,7 +6,13 @@ import os
 def main():
     port = int(os.environ.get("PORT", "8000"))
     reload = bool(os.environ.get("LYNXKITE_RELOAD", ""))
-    uvicorn.run("lynxkite_app.main:app", host="0.0.0.0", port=port, reload=reload)
+    uvicorn.run(
+        "lynxkite_app.main:app",
+        host="0.0.0.0",
+        port=port,
+        reload=reload,
+        loop="asyncio",
+    )
 
 
 if __name__ == "__main__":

lynxkite-app/web/src/workspace/nodes/NodeWithVisualization.tsx

@@ -10,8 +10,8 @@ const NodeWithVisualization = (props: any) => {
     if (!opts || !chartsRef.current) return;
     chartsInstanceRef.current = echarts.init(chartsRef.current, null, {
       renderer: "canvas",
-      width: 250,
-      height: 250,
+      width: 800,
+      height: 800,
     });
     chartsInstanceRef.current.setOption(opts);
     const onResize = () => chartsInstanceRef.current?.resize();

lynxkite-graph-analytics/README.md

@@ -11,3 +11,44 @@ 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 ..
+```
+
+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.
+
+Then, inside the image you can start LynxKite as usual.
+
+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

@@ -14,3 +14,6 @@ from .core import *  # noqa (easier access for core classes)
 from . import lynxkite_ops  # noqa (imported to trigger registration)
 from . import networkx_ops  # noqa (imported to trigger registration)
 from . import pytorch_model_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)