Merge branch 'main' into feat-mantra

geometric-intelligence · Dec 17, 2024 · b8c03bc · b8c03bc
2 parents 2aa3de1 + 48f9fcf
commit b8c03bc
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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/codecov.yml b/codecov.yml
@@ -4,4 +4,5 @@ coverage:
   round: down
   precision: 2
 ignore:
-  - "test/"
+  - "test/"
+  - "topobenchmark/run.py"
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-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/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/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/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/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/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/model/cell/ccxn.yaml b/configs/model/cell/ccxn.yaml
@@ -1,10 +1,10 @@
-_target_: topobenchmarkx.model.TBXModel
+_target_: topobenchmark.model.TBModel
 
 model_name: ccxn
 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
@@ -22,14 +22,14 @@ backbone_additional_params:
   hidden_channels: ${model.feature_encoder.out_channels}
 
 backbone_wrapper:
-  _target_: topobenchmarkx.nn.wrappers.CCXNWrapper
+  _target_: topobenchmark.nn.wrappers.CCXNWrapper
   _partial_: true
   wrapper_name: CCXNWrapper
   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/graph/gat.yaml b/configs/model/graph/gat.yaml
@@ -1,10 +1,10 @@
-_target_: topobenchmarkx.model.TBXModel
+_target_: topobenchmark.model.TBModel
 
 model_name: gat
 model_domain: graph
 
 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
@@ -22,14 +22,14 @@ backbone:
   concat: true
 
 backbone_wrapper:
-  _target_: topobenchmarkx.nn.wrappers.GNNWrapper
+  _target_: topobenchmark.nn.wrappers.GNNWrapper
   _partial_: true
   wrapper_name: GNNWrapper
   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: NoReadOut #  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/graph/gin.yaml b/configs/model/graph/gin.yaml
@@ -1,10 +1,10 @@
-_target_: topobenchmarkx.model.TBXModel
+_target_: topobenchmark.model.TBModel
 
 model_name: gin
 model_domain: graph
 
 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
@@ -19,14 +19,14 @@ backbone:
   act: relu
 
 backbone_wrapper:
-  _target_: topobenchmarkx.nn.wrappers.GNNWrapper
+  _target_: topobenchmark.nn.wrappers.GNNWrapper
   _partial_: true
   wrapper_name: GNNWrapper
   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: NoReadOut #  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/hypergraph/alldeepset.yaml b/configs/model/hypergraph/alldeepset.yaml
@@ -1,10 +1,10 @@
-_target_: topobenchmarkx.model.TBXModel
+_target_: topobenchmark.model.TBModel
 
 model_name: alldeepset
 model_domain: hypergraph
 
 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
@@ -27,14 +27,14 @@ backbone:
     #num_features: ${model.backbone.hidden_channels}
 
 backbone_wrapper:
-  _target_: topobenchmarkx.nn.wrappers.HypergraphWrapper
+  _target_: topobenchmark.nn.wrappers.HypergraphWrapper
   _partial_: true
   wrapper_name: HypergraphWrapper
   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/hypergraph/unignn2.yaml b/configs/model/hypergraph/unignn2.yaml
@@ -1,10 +1,10 @@
-_target_: topobenchmarkx.model.TBXModel
+_target_: topobenchmark.model.TBModel
 
 model_name: unignn2
 model_domain: hypergraph
 
 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
@@ -21,14 +21,14 @@ backbone:
   layer_drop: 0.0
 
 backbone_wrapper:
-  _target_: topobenchmarkx.nn.wrappers.HypergraphWrapper
+  _target_: topobenchmark.nn.wrappers.HypergraphWrapper
   _partial_: true
   wrapper_name: HypergraphWrapper
   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/simplicial/sccn.yaml b/configs/model/simplicial/sccn.yaml
@@ -1,10 +1,10 @@
-_target_: topobenchmarkx.model.TBXModel
+_target_: topobenchmark.model.TBModel
 
 model_name: sccn
 model_domain: simplicial
 
 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
@@ -18,14 +18,14 @@ backbone:
   update_func: "sigmoid"
 
 backbone_wrapper:
-  _target_: topobenchmarkx.nn.wrappers.SCCNWrapper
+  _target_: topobenchmark.nn.wrappers.SCCNWrapper
   _partial_: true
   wrapper_name: SCCNWrapper
   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/simplicial/sccnn.yaml b/configs/model/simplicial/sccnn.yaml
@@ -1,10 +1,10 @@
-_target_: topobenchmarkx.model.TBXModel
+_target_: topobenchmark.model.TBModel
 
 model_name: sccnn 
 model_domain: simplicial
 
 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
@@ -31,14 +31,14 @@ backbone:
   n_layers: 1
 
 backbone_wrapper:
-  _target_: topobenchmarkx.nn.wrappers.SCCNNWrapper
+  _target_: topobenchmark.nn.wrappers.SCCNNWrapper
   _partial_: true
   wrapper_name: SCCNNWrapper
   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/simplicial/topotune.yaml b/configs/model/simplicial/topotune.yaml
@@ -1,11 +1,11 @@
-_target_: topobenchmarkx.model.TBXModel
+_target_: topobenchmark.model.TBModel
 
 model_name: topotune
 model_domain: simplicial
 tune_gnn: GIN
 
 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
@@ -16,9 +16,9 @@ feature_encoder:
     - 2
 
 backbone:
-  _target_: topobenchmarkx.nn.backbones.combinatorial.gccn.TopoTune
+  _target_: topobenchmark.nn.backbones.combinatorial.gccn.TopoTune
   GNN:
-    _target_: topobenchmarkx.nn.backbones.graph.${model.tune_gnn}
+    _target_: topobenchmark.nn.backbones.graph.${model.tune_gnn}
     in_channels: ${model.feature_encoder.out_channels}
     out_channels: ${model.feature_encoder.out_channels}
     hidden_channels: ${model.feature_encoder.out_channels}
@@ -35,14 +35,14 @@ backbone:
   activation: relu
 
 backbone_wrapper:
-  _target_: topobenchmarkx.nn.wrappers.combinatorial.TuneWrapper
+  _target_: topobenchmark.nn.wrappers.combinatorial.TuneWrapper
   _partial_: true
   wrapper_name: TuneWrapper
   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/simplicial/topotune_onehasse.yaml b/configs/model/simplicial/topotune_onehasse.yaml
@@ -1,11 +1,11 @@
-_target_: topobenchmarkx.model.TBXModel
+_target_: topobenchmark.model.TBModel
 
 model_name: topotune_onehasse
 model_domain: simplicial
 tune_gnn: GCN
 
 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
@@ -16,9 +16,9 @@ feature_encoder:
     - 2
 
 backbone:
-  _target_: topobenchmarkx.nn.backbones.combinatorial.gccn_onehasse.TopoTune_OneHasse
+  _target_: topobenchmark.nn.backbones.combinatorial.gccn_onehasse.TopoTune_OneHasse
   GNN:
-    _target_: topobenchmarkx.nn.backbones.graph.${model.tune_gnn}
+    _target_: topobenchmark.nn.backbones.graph.${model.tune_gnn}
     in_channels: ${model.feature_encoder.out_channels}
     out_channels: ${model.feature_encoder.out_channels}
     hidden_channels: ${model.feature_encoder.out_channels}
@@ -34,14 +34,14 @@ backbone:
   activation: relu
 
 backbone_wrapper:
-  _target_: topobenchmarkx.nn.wrappers.combinatorial.TuneWrapper
+  _target_: topobenchmark.nn.wrappers.combinatorial.TuneWrapper
   _partial_: true
   wrapper_name: TuneWrapper
   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/transforms/data_manipulations/identity.yaml b/configs/transforms/data_manipulations/identity.yaml
@@ -1,3 +1,3 @@
-_target_: topobenchmarkx.transforms.data_transform.DataTransform
+_target_: topobenchmark.transforms.data_transform.DataTransform
 transform_name: "Identity"
 transform_type: null
diff --git a/configs/transforms/data_manipulations/mp_homophily.yaml b/configs/transforms/data_manipulations/mp_homophily.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.transforms.data_transform.DataTransform
+_target_: topobenchmark.transforms.data_transform.DataTransform
 transform_name: "MessagePassingHomophily"
 transform_type: "data manipulation"
 num_steps: 10

diff --git a/configs/transforms/liftings/graph2hypergraph/khop.yaml b/configs/transforms/liftings/graph2hypergraph/khop.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.transforms.data_transform.DataTransform
+_target_: topobenchmark.transforms.data_transform.DataTransform
 transform_type: 'lifting'
 transform_name: "HypergraphKHopLifting"
 k_value: 1