From 2656f8200c8346a3cc7cd47845095788e25ff52c Mon Sep 17 00:00:00 2001 From: Louisa Cornelis Date: Fri, 15 May 2026 01:11:18 +0000 Subject: [PATCH] changing bgbench to ogbench everywhere --- .cursorrrules | 2 +- README.md | 16 ++++++++-------- .../multi_dataset_grid_search.yaml | 2 +- configs/hparams_search/smoke_test.yaml | 2 +- env_setup.sh | 6 +++--- notebooks/datasets.ipynb | 2 +- pyproject.toml | 4 ++-- tutorials/benchmarking_stats.ipynb | 2 +- 8 files changed, 18 insertions(+), 18 deletions(-) diff --git a/.cursorrrules b/.cursorrrules index 81cafc3c..dc990877 100644 --- a/.cursorrrules +++ b/.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. diff --git a/README.md b/README.md index 3ec0ad85..8043287b 100644 --- a/README.md +++ b/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 diff --git a/configs/hparams_search/multi_dataset_grid_search.yaml b/configs/hparams_search/multi_dataset_grid_search.yaml index 3a40ae17..f2e2429e 100644 --- a/configs/hparams_search/multi_dataset_grid_search.yaml +++ b/configs/hparams_search/multi_dataset_grid_search.yaml @@ -22,7 +22,7 @@ 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 diff --git a/configs/hparams_search/smoke_test.yaml b/configs/hparams_search/smoke_test.yaml index f213f57d..a7e2766f 100644 --- a/configs/hparams_search/smoke_test.yaml +++ b/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: diff --git a/env_setup.sh b/env_setup.sh index 8a2d0b35..e570fa2c 100755 --- a/env_setup.sh +++ b/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]' diff --git a/notebooks/datasets.ipynb b/notebooks/datasets.ipynb index a40af1c5..cc55fde2 100644 --- a/notebooks/datasets.ipynb +++ b/notebooks/datasets.ipynb @@ -115,7 +115,7 @@ ], "metadata": { "kernelspec": { - "display_name": "bgbench", + "display_name": "ogbench", "language": "python", "name": "python3" }, diff --git a/pyproject.toml b/pyproject.toml index 72b9b693..26e465b7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -96,8 +96,8 @@ 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 diff --git a/tutorials/benchmarking_stats.ipynb b/tutorials/benchmarking_stats.ipynb index 3a3d0b56..af7e64da 100644 --- a/tutorials/benchmarking_stats.ipynb +++ b/tutorials/benchmarking_stats.ipynb @@ -281,7 +281,7 @@ ], "metadata": { "kernelspec": { - "display_name": "bgbench", + "display_name": "ogbench", "language": "python", "name": "python3" },