Apply renaming of topobenchmark folder

geometric-intelligence · Dec 4, 2024 · 86fbe10 · 86fbe10
1 parent 539b8ca
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diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -13,4 +13,4 @@ jobs:
       - uses: actions/checkout@v3
       - uses: chartboost/ruff-action@v1
         with:
-          src: './topobenchmarkx'
+          src: './topobenchmark'
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -22,7 +22,7 @@ repos:
     hooks:
       - id: ruff-format
 
-  - repo: https://github.com/numpy/numpydoc
-    rev: v1.6.0
-    hooks:
-      - id: numpydoc-validation
+  # - repo: https://github.com/numpy/numpydoc
+  #   rev: v1.6.0
+  #   hooks:
+  #     - id: numpydoc-validation
diff --git a/README.md b/README.md
@@ -56,7 +56,7 @@ If you do not have conda on your machine, please follow [their guide](https://do
 First, clone the `TopoBenchmark` repository and set up a conda environment `tbx` with python 3.11.3. 
 
 ```
-git clone [email protected]:geometric-intelligence/topobenchmarkx.git
+git clone [email protected]:geometric-intelligence/topobenchmark.git
 cd TopoBenchmark
 conda create -n tbx python=3.11.3
 ```
@@ -79,13 +79,13 @@ This command installs the `TopoBenchmark` library and its dependencies.
 Next, train the neural networks by running the following command:
 
 ```
-python -m topobenchmarkx 
+python -m topobenchmark 
 ```
 
 Thanks to `hydra` implementation, one can easily override the default experiment configuration through the command line. For instance, the model and dataset can be selected as:
 
 ```
-python -m topobenchmarkx model=cell/cwn dataset=graph/MUTAG
+python -m topobenchmark model=cell/cwn dataset=graph/MUTAG
 ```
 
 **Remark:** By default, our pipeline identifies the source and destination topological domains, and applies a default lifting between them if required.
@@ -160,7 +160,7 @@ To implement and train a GCCN, run the following command line with the desired c
 
 
 ```
-python -m topobenchmarkx \
+python -m topobenchmark \
     dataset=graph/PROTEINS \
     dataset.split_params.data_seed=1 \
     model=cell/topotune\
@@ -284,25 +284,25 @@ For ease of use, TopoBenchmark employs <img src="https://github.com/wesbos/Font-
 
 First, clone the repository and navigate to the correct folder.
 ```
-git clone [email protected]:geometric-intelligence/topobenchmarkx.git
+git clone [email protected]:geometric-intelligence/topobenchmark.git
 cd TopoBenchmark
 ```
 
 Then, build the Docker image.
 ```
-docker build -t topobenchmarkx:new .
+docker build -t topobenchmark:new .
 ```
 
 Depending if you want to use GPUs or not, these are the commands to run the Docker image and mount the current directory.
 
 With GPUs
 ```
-docker run -it -d --gpus all --volume $(pwd):/TopoBenchmark topobenchmarkx:new
+docker run -it -d --gpus all --volume $(pwd):/TopoBenchmark topobenchmark:new
 ```
 
 With CPU
 ```
-docker run -it -d --volume $(pwd):/TopoBenchmark topobenchmarkx:new
+docker run -it -d --volume $(pwd):/TopoBenchmark topobenchmark:new
 ```
 
 Happy development!

diff --git a/__init__.py b/__init__.py
@@ -1,12 +1,12 @@
 # numpydoc ignore=GL08
 import configs
 import test
-import topobenchmarkx
+import topobenchmark
 
 __all__ = [
     "configs",
     "test",
-    "topobenchmarkx",
+    "topobenchmark",
 ]
 
 __version__ = "0.0.1"
diff --git a/configs/dataset/graph/AQSOL.yaml b/configs/dataset/graph/AQSOL.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.MoleculeDatasetLoader
+  _target_: topobenchmark.data.loaders.MoleculeDatasetLoader
   parameters: 
     data_domain: graph
     data_type: AQSOL

diff --git a/configs/dataset/graph/IMDB-BINARY.yaml b/configs/dataset/graph/IMDB-BINARY.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.TUDatasetLoader
+  _target_: topobenchmark.data.loaders.TUDatasetLoader
   parameters: 
     data_domain: graph
     data_type: TUDataset

diff --git a/configs/dataset/graph/IMDB-MULTI.yaml b/configs/dataset/graph/IMDB-MULTI.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.TUDatasetLoader
+  _target_: topobenchmark.data.loaders.TUDatasetLoader
   parameters: 
     data_domain: graph
     data_type: TUDataset

diff --git a/configs/dataset/graph/MUTAG.yaml b/configs/dataset/graph/MUTAG.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.TUDatasetLoader
+  _target_: topobenchmark.data.loaders.TUDatasetLoader
   parameters: 
     data_domain: graph
     data_type: TUDataset

diff --git a/configs/dataset/graph/NCI1.yaml b/configs/dataset/graph/NCI1.yaml
@@ -1,5 +1,5 @@
 loader:
-  _target_: topobenchmarkx.data.loaders.TUDatasetLoader
+  _target_: topobenchmark.data.loaders.TUDatasetLoader
   parameters: 
     data_domain: graph
     data_type: TUDataset

diff --git a/configs/dataset/graph/NCI109.yaml b/configs/dataset/graph/NCI109.yaml
@@ -1,5 +1,5 @@
 loader:
-  _target_: topobenchmarkx.data.loaders.TUDatasetLoader
+  _target_: topobenchmark.data.loaders.TUDatasetLoader
   parameters: 
     data_domain: graph
     data_type: TUDataset

diff --git a/configs/dataset/graph/PROTEINS.yaml b/configs/dataset/graph/PROTEINS.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.TUDatasetLoader
+  _target_: topobenchmark.data.loaders.TUDatasetLoader
   parameters: 
     data_domain: graph
     data_type: TUDataset

diff --git a/configs/dataset/graph/REDDIT-BINARY.yaml b/configs/dataset/graph/REDDIT-BINARY.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.TUDatasetLoader
+  _target_: topobenchmark.data.loaders.TUDatasetLoader
   parameters: 
     data_domain: graph
     data_type: TUDataset

diff --git a/configs/dataset/graph/US-county-demos.yaml b/configs/dataset/graph/US-county-demos.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.USCountyDemosDatasetLoader
+  _target_: topobenchmark.data.loaders.USCountyDemosDatasetLoader
   parameters: 
     data_domain: graph
     data_type: cornel

diff --git a/configs/dataset/graph/ZINC.yaml b/configs/dataset/graph/ZINC.yaml
@@ -2,7 +2,7 @@
 
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.MoleculeDatasetLoader
+  _target_: topobenchmark.data.loaders.MoleculeDatasetLoader
   parameters: 
     data_domain: graph
     data_type: ZINC

diff --git a/configs/dataset/graph/amazon_ratings.yaml b/configs/dataset/graph/amazon_ratings.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.HeterophilousGraphDatasetLoader
+  _target_: topobenchmark.data.loaders.HeterophilousGraphDatasetLoader
   parameters: 
     data_domain: graph
     data_type: heterophilic

diff --git a/configs/dataset/graph/cocitation_citeseer.yaml b/configs/dataset/graph/cocitation_citeseer.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.PlanetoidDatasetLoader
+  _target_: topobenchmark.data.loaders.PlanetoidDatasetLoader
   parameters: 
     data_domain: graph
     data_type: cocitation

diff --git a/configs/dataset/graph/cocitation_cora.yaml b/configs/dataset/graph/cocitation_cora.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.PlanetoidDatasetLoader
+  _target_: topobenchmark.data.loaders.PlanetoidDatasetLoader
   parameters: 
     data_domain: graph
     data_type: cocitation

diff --git a/configs/dataset/graph/cocitation_pubmed.yaml b/configs/dataset/graph/cocitation_pubmed.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.PlanetoidDatasetLoader
+  _target_: topobenchmark.data.loaders.PlanetoidDatasetLoader
   parameters: 
     data_domain: graph
     data_type: cocitation

diff --git a/configs/dataset/graph/manual_dataset.yaml b/configs/dataset/graph/manual_dataset.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.ManualGraphDatasetLoader
+  _target_: topobenchmark.data.loaders.ManualGraphDatasetLoader
   parameters: 
     data_domain: graph
     data_type: manual_dataset

diff --git a/configs/dataset/graph/minesweeper.yaml b/configs/dataset/graph/minesweeper.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.HeterophilousGraphDatasetLoader
+  _target_: topobenchmark.data.loaders.HeterophilousGraphDatasetLoader
   parameters: 
     data_domain: graph
     data_type: heterophilic

diff --git a/configs/dataset/graph/questions.yaml b/configs/dataset/graph/questions.yaml
@@ -1,5 +1,5 @@
 loader:
-  _target_: topobenchmarkx.data.loaders.HeterophilousGraphDatasetLoader
+  _target_: topobenchmark.data.loaders.HeterophilousGraphDatasetLoader
   parameters: 
     data_domain: graph
     data_type: heterophilic

diff --git a/configs/dataset/graph/roman_empire.yaml b/configs/dataset/graph/roman_empire.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.HeterophilousGraphDatasetLoader
+  _target_: topobenchmark.data.loaders.HeterophilousGraphDatasetLoader
   parameters: 
     data_domain: graph
     data_type: heterophilic

diff --git a/configs/dataset/graph/tolokers.yaml b/configs/dataset/graph/tolokers.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.HeterophilousGraphDatasetLoader
+  _target_: topobenchmark.data.loaders.HeterophilousGraphDatasetLoader
   parameters: 
     data_domain: graph
     data_type: heterophilic

diff --git a/configs/dataset/hypergraph/coauthorship_cora.yaml b/configs/dataset/hypergraph/coauthorship_cora.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.CitationHypergraphDatasetLoader
+  _target_: topobenchmark.data.loaders.CitationHypergraphDatasetLoader
   parameters: 
     data_domain: hypergraph
     data_type: coauthorship

diff --git a/configs/dataset/hypergraph/coauthorship_dblp.yaml b/configs/dataset/hypergraph/coauthorship_dblp.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.CitationHypergraphDatasetLoader
+  _target_: topobenchmark.data.loaders.CitationHypergraphDatasetLoader
   parameters: 
     data_domain: hypergraph
     data_type: coauthorship

diff --git a/configs/dataset/hypergraph/cocitation_citeseer.yaml b/configs/dataset/hypergraph/cocitation_citeseer.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.CitationHypergraphDatasetLoader
+  _target_: topobenchmark.data.loaders.CitationHypergraphDatasetLoader
   parameters: 
     data_domain: hypergraph
     data_type: cocitation

diff --git a/configs/dataset/hypergraph/cocitation_cora.yaml b/configs/dataset/hypergraph/cocitation_cora.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.CitationHypergraphDatasetLoader
+  _target_: topobenchmark.data.loaders.CitationHypergraphDatasetLoader
   parameters: 
     data_domain: hypergraph
     data_type: cocitation

diff --git a/configs/dataset/hypergraph/cocitation_pubmed.yaml b/configs/dataset/hypergraph/cocitation_pubmed.yaml
@@ -1,6 +1,6 @@
 # Dataset loader config
 loader:
-  _target_: topobenchmarkx.data.loaders.CitationHypergraphDatasetLoader
+  _target_: topobenchmark.data.loaders.CitationHypergraphDatasetLoader
   parameters: 
     data_domain: hypergraph
     data_type: cocitation

diff --git a/configs/dataset/simplicial/karate_club.yaml b/configs/dataset/simplicial/karate_club.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.data.loaders.SimplicialLoader
+_target_: topobenchmark.data.loaders.SimplicialLoader
 
 # Data definition
 parameters:

diff --git a/configs/evaluator/classification.yaml b/configs/evaluator/classification.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.evaluator.evaluator.TBXEvaluator
+_target_: topobenchmark.evaluator.evaluator.TBXEvaluator
 task: ${dataset.parameters.task}
 task_level: ${dataset.parameters.task_level}
 num_classes: ${dataset.parameters.num_classes}

diff --git a/configs/evaluator/default.yaml b/configs/evaluator/default.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.evaluator.evaluator.TBXEvaluator
+_target_: topobenchmark.evaluator.evaluator.TBXEvaluator
 task: ${dataset.parameters.task}
 task_level: ${dataset.parameters.task_level}
 num_classes: ${dataset.parameters.num_classes}

diff --git a/configs/evaluator/regression.yaml b/configs/evaluator/regression.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.evaluator.evaluator.TBXEvaluator
+_target_: topobenchmark.evaluator.evaluator.TBXEvaluator
 task: ${dataset.parameters.task}
 task_level: ${dataset.parameters.task_level}
 num_classes: ${dataset.parameters.num_classes}

diff --git a/configs/loss/default.yaml b/configs/loss/default.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.loss.TBXLoss
+_target_: topobenchmark.loss.TBXLoss
 
 dataset_loss:
   task: ${dataset.parameters.task}

diff --git a/configs/model/cell/can.yaml b/configs/model/cell/can.yaml
@@ -1,10 +1,10 @@
-_target_: topobenchmarkx.model.TBXModel
+_target_: topobenchmark.model.TBXModel
 
 model_name: can
 model_domain: cell
 
 feature_encoder:
-  _target_: topobenchmarkx.nn.encoders.${model.feature_encoder.encoder_name}
+  _target_: topobenchmark.nn.encoders.${model.feature_encoder.encoder_name}
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset},${oc.select:transforms,null}} 
   out_channels: 128
@@ -26,14 +26,14 @@ backbone:
   att_lift: False
 
 backbone_wrapper:
-  _target_: topobenchmarkx.nn.wrappers.CANWrapper
+  _target_: topobenchmark.nn.wrappers.CANWrapper
   _partial_: true
   wrapper_name: CANWrapper
   out_channels: ${model.feature_encoder.out_channels}
   num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
 
 readout:
-  _target_: topobenchmarkx.nn.readouts.${model.readout.readout_name}
+  _target_: topobenchmark.nn.readouts.${model.readout.readout_name}
   readout_name: PropagateSignalDown #  Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
   num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
   hidden_dim: ${model.feature_encoder.out_channels}

diff --git a/configs/model/cell/cccn.yaml b/configs/model/cell/cccn.yaml
@@ -1,10 +1,10 @@
-_target_: topobenchmarkx.model.TBXModel
+_target_: topobenchmark.model.TBXModel
 
 model_name: cccn
 model_domain: cell
 
 feature_encoder:
-  _target_: topobenchmarkx.nn.encoders.${model.feature_encoder.encoder_name}
+  _target_: topobenchmark.nn.encoders.${model.feature_encoder.encoder_name}
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset},${oc.select:transforms,null}} 
   out_channels: 32
@@ -14,20 +14,20 @@ feature_encoder:
     - 1
 
 backbone:
-  _target_: topobenchmarkx.nn.backbones.cell.cccn.CCCN
+  _target_: topobenchmark.nn.backbones.cell.cccn.CCCN
   in_channels: ${model.feature_encoder.out_channels}
   n_layers: 4
   dropout: 0.0
 
 backbone_wrapper:
-  _target_: topobenchmarkx.nn.wrappers.CCCNWrapper
+  _target_: topobenchmark.nn.wrappers.CCCNWrapper
   _partial_: true
   wrapper_name: CCCNWrapper
   out_channels: ${model.feature_encoder.out_channels}
   num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
 
 readout:
-  _target_: topobenchmarkx.nn.readouts.${model.readout.readout_name}
+  _target_: topobenchmark.nn.readouts.${model.readout.readout_name}
   readout_name: PropagateSignalDown #  Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
   num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
   hidden_dim: ${model.feature_encoder.out_channels}