Finish bgbench->ogbench cleanup and unbreak CI

.cursorrrules

@@ -1,3 +1,3 @@
-Launch all commands in the conda environement "bgbench"
+Launch all commands in the conda environement "ogbench"
 
 It should be done via the conda shell activate.

README.md

@@ -1,6 +1,6 @@
-[![Code Quality](https://github.com/geometric-intelligence/bgbench/actions/workflows/code-quality-main.yaml/badge.svg)](https://github.com/geometric-intelligence/bgbench/actions/workflows/code-quality-main.yaml)
-[![Dependencies](https://github.com/geometric-intelligence/bgbench/actions/workflows/dependabot/dependabot-updates/badge.svg)](https://github.com/geometric-intelligence/bgbench/actions/workflows/dependabot/dependabot-updates)
-[![Tests](https://github.com/geometric-intelligence/bgbench/actions/workflows/test.yml/badge.svg)](https://github.com/geometric-intelligence/bgbench/actions/workflows/test.yml)
+[![Code Quality](https://github.com/geometric-intelligence/ogbench/actions/workflows/code-quality-main.yaml/badge.svg)](https://github.com/geometric-intelligence/ogbench/actions/workflows/code-quality-main.yaml)
+[![Dependencies](https://github.com/geometric-intelligence/ogbench/actions/workflows/dependabot/dependabot-updates/badge.svg)](https://github.com/geometric-intelligence/ogbench/actions/workflows/dependabot/dependabot-updates)
+[![Tests](https://github.com/geometric-intelligence/ogbench/actions/workflows/test.yml/badge.svg)](https://github.com/geometric-intelligence/ogbench/actions/workflows/test.yml)
 
 # OGBench — Omics Graph Benchmarking
 
@@ -19,12 +19,12 @@ A benchmarking framework for Graph Neural Networks on omics datasets. OGBench pr
 ## Installation
 
 ```bash
-git clone git@github.com:geometric-intelligence/bgbench.git
-cd bgbench
+git clone git@github.com:geometric-intelligence/ogbench.git
+cd ogbench
 
-conda create -n bgbench python=3.12
+conda create -n ogbench python=3.12
 curl -LsSf https://astral.sh/uv/install.sh | sh
-conda activate bgbench
+conda activate ogbench
 
 uv venv
 uv pip install -e '.[all]'
@@ -175,7 +175,7 @@ pytest tests/nn/ -v  # specific module
 ### Project Structure
 
 ```
-bgbench/
+ogbench/
 ├── ogbench/                    # Main Python package
 │   ├── run.py                  # Training entry point
 │   ├── baseline.py             # Sklearn baseline experiments

configs/hparams_search/multi_dataset_grid_search.yaml

@@ -22,9 +22,9 @@ seeds: [42, 123, 456]
 
 # Fixed parameters (not searched)
 fixed:
-  logger.wandb.project: bgbench_dataset_grid_search_final
+  logger.wandb.project: ogbench_dataset_grid_search_final
   logger.wandb.entity: bioshape-lab
-  paths.root_dir: /scratch/lcornelis/bgbench
+  paths.root_dir: /scratch/lcornelis/ogbench
 
 # Shared hyperparameter grid (applied to all models)
 shared_grid:

configs/hparams_search/smoke_test.yaml

@@ -10,7 +10,7 @@ models:
 seeds: [42]
 
 fixed:
-  logger.wandb.project: bgbench_smoke_test
+  logger.wandb.project: ogbench_smoke_test
 
 shared_grid:
   dataset.loader.parameters.node_sample_ratio:

env_setup.sh

@@ -26,11 +26,11 @@ if ! command -v conda &> /dev/null; then
     echo "Conda installation complete"
 fi
 
-if ! conda env list | grep -q "bgbench"; then
-    conda create -n bgbench python=3.12 -y
+if ! conda env list | grep -q "ogbench"; then
+    conda create -n ogbench python=3.12 -y
 fi
 
-conda activate bgbench
+conda activate ogbench
 
 pip install --upgrade pip
 pip install -e '.[all]'

notebooks/datasets.ipynb

@@ -17,7 +17,7 @@
     "import pandas as pd\n",
     "import seaborn as sns\n",
     "\n",
-    "sys.path.append(\"/home/johmathe/bgbench\")\n",
+    "sys.path.append(\"/home/johmathe/ogbench\")\n",
     "os.environ[\"PYTHONPATH\"] = os.pathsep.join(sys.path)\n",
     "from src.data import hf_datamodule\n"
    ]
@@ -115,7 +115,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "bgbench",
+   "display_name": "ogbench",
    "language": "python",
    "name": "python3"
   },

ogbench/transforms/liftings/graph2hypergraph/knn_lifting.py

@@ -57,6 +57,14 @@ def lift_topology(self, data: torch_geometric.data.Data) -> dict:
             The lifted topology.
         """
         num_nodes = data.x.shape[0]
+        # pyg-lib's knn_graph segfaults on empty inputs, so short-circuit.
+        if num_nodes == 0:
+            empty_incidence = torch.zeros(0, 0).to_sparse_coo()
+            return {
+                'incidence_hyperedges': empty_incidence,
+                'num_hyperedges': 0,
+                'x_0': data.x,
+            }
         data.pos = data.x
         num_hyperedges = num_nodes
         incidence_1 = torch.zeros(num_nodes, num_nodes)

pyproject.toml

@@ -58,6 +58,7 @@ dependencies=[
     "torch-scatter",
     "torch==2.8.0",
     "torch-cluster",
+    "pyg-lib>=0.6.0",
     "combat>=0.3.3",
     "topomodelx @ git+https://github.com/pyt-team/TopoModelX.git",
     "toponetx @ git+https://github.com/pyt-team/TopoNetX.git",
@@ -96,8 +97,8 @@ all = ["ogbench[dev, doc]"]
 ogbench-train = "ogbench.run:main"
 
 [project.urls]
-homepage="https://geometric-intelligence.github.io/bgbench/index.html"
-repository="https://github.com/geometric-intelligence/bgbench"
+homepage="https://geometric-intelligence.github.io/ogbench/index.html"
+repository="https://github.com/geometric-intelligence/ogbench"
 
 [tool.ruff]
 line-length = 99

tutorials/benchmarking_stats.ipynb

@@ -281,7 +281,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "bgbench",
+   "display_name": "ogbench",
    "language": "python",
    "name": "python3"
   },

tutorials/dataset_stats.ipynb

@@ -83,7 +83,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "root = \"/home/lcornelis/code/bgbench/run_data/omics/\"\n",
+    "root = \"/home/lcornelis/code/ogbench/run_data/omics/\"\n",
     "name = osp.join(\n",
     "    root,\n",
     "    f\"{dataset.data_name}\",\n",
@@ -119,7 +119,7 @@
     "    Get statistics of the graph.\n",
     "    \"\"\"\n",
     "    # Load the adjacency matrix\n",
-    "    root = \"/home/lcornelis/code/bgbench/run_data/omics/\"\n",
+    "    root = \"/home/lcornelis/code/ogbench/run_data/omics/\"\n",
     "    name = osp.join(\n",
     "        root,\n",
     "        f\"{dataset.data_name}\",\n",

tutorials/dataset_stats_analysis.py

@@ -43,7 +43,7 @@ def load_dataset(
     # Pass 'full' as string, not None, because HFOmicsDataset checks for 'full' string
     ratio_value = 'full' if node_sample_ratio == 'full' else float(node_sample_ratio)
     dataset = HFOmicsDataset(
-        root='/scratch/lcornelis/bgbench-1/run_data/omics',
+        root='/scratch/lcornelis/ogbench-1/run_data/omics',
         data_name=dataset_name,
         method=method,
         adjacency_threshold=adj_thresh,
@@ -79,7 +79,7 @@ def get_graph_stats(dataset: Any) -> dict[str, float]:
             graph.add_nodes_from(range(num_nodes))
             graph.add_edges_from(edge_list)
         else:
-            root = '/home/lcornelis/code/bgbench-1/run_data/omics/'
+            root = '/home/lcornelis/code/ogbench-1/run_data/omics/'
             name = osp.join(
                 root,
                 f'{dataset.data_name}',
@@ -460,7 +460,7 @@ def main():
 if __name__ == '__main__':
     try:
         print('Testing dataset loading...')
-        dataset = load_dataset('addneuromed', 0.5, '0.3', 'variance', adjacency_method='string', string_data_dir='/home/johmathe/bgbench/data')
+        dataset = load_dataset('addneuromed', 0.5, '0.3', 'variance', adjacency_method='string', string_data_dir='/home/johmathe/ogbench/data')
         print(f'Dataset loaded successfully: {dataset}')
         print(f'Dataset length: {len(dataset)}')
         if len(dataset) > 0:

webapp/public/data/stats.json

@@ -12479,4 +12479,4 @@
     "dataset": "brca",
     "adjacency_method": "string"
   }
-}
+}