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geometric-intelligence · Jun 2, 2024 · 6c1a0c1 · 6c1a0c1
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Showing 9 changed files with 75 additions and 57 deletions.
diff --git a/test/data/preprocess/test_preprocessor.py b/test/data/preprocess/test_preprocessor.py
@@ -23,11 +23,24 @@ def setup_method(self, mocker):
         )
 
         params = [
-            {"mock_inmemory_init": "torch_geometric.data.InMemoryDataset.__init__"},
-            {"mock_save_transform": (PreProcessor, "save_transform_parameters")},
+            {
+                "mock_inmemory_init": "torch_geometric.data.InMemoryDataset.__init__"
+            },
+            {
+                "mock_save_transform": (
+                    PreProcessor,
+                    "save_transform_parameters",
+                )
+            },
             {"mock_load": (PreProcessor, "load")},
-            {"mock_len": (PreProcessor, "__len__"), "init_args": {"return_value":3}},
-            {"mock_getitem": (PreProcessor, "get"), "init_args": {"return_value": "0"}},
+            {
+                "mock_len": (PreProcessor, "__len__"),
+                "init_args": {"return_value": 3},
+            },
+            {
+                "mock_getitem": (PreProcessor, "get"),
+                "init_args": {"return_value": "0"},
+            },
         ]
         self.flow_mocker = FlowMocker(mocker, params)
 
@@ -52,31 +65,32 @@ def test_init_with_transform(self, mocker):
         val_processed_paths = ["/some/path"]
         params = [
             {"assert_args": ("created_property", "processed_data_dir")},
-            {
-                "assert_args": ("created_property", "processed_data_dir")
-            },
+            {"assert_args": ("created_property", "processed_data_dir")},
             {
                 "mock_inmemory_init": "torch_geometric.data.InMemoryDataset.__init__",
-                "assert_args": ("called_once_with", ANY, None, ANY)
+                "assert_args": ("called_once_with", ANY, None, ANY),
             },
             {
                 "mock_processed_paths": (PreProcessor, "processed_paths"),
                 "init_args": {"property_val": val_processed_paths},
             },
             {
-                "mock_save_transform": (PreProcessor, "save_transform_parameters"),
-                "assert_args": ("created_property", "processed_paths")
+                "mock_save_transform": (
+                    PreProcessor,
+                    "save_transform_parameters",
+                ),
+                "assert_args": ("created_property", "processed_paths"),
             },
             {
                 "mock_load": (PreProcessor, "load"),
-                "assert_args": ("called_once_with", val_processed_paths[0])
+                "assert_args": ("called_once_with", val_processed_paths[0]),
             },
             {"mock_len": (PreProcessor, "__len__")},
             {"mock_getitem": (PreProcessor, "get")},
         ]
         self.flow_mocker = FlowMocker(mocker, params)
         self.preprocessor_with_tranform = PreProcessor(
-            self.dataset, self.data_dir,  self.transforms_config
+            self.dataset, self.data_dir, self.transforms_config
         )
         self.flow_mocker.assert_all(self.preprocessor_with_tranform)
 

diff --git a/topobenchmarkx/model/model.py b/topobenchmarkx/model/model.py
@@ -34,7 +34,9 @@ def __init__(
 
         # This line allows to access init params with 'self.hparams' attribute
         # also ensures init params will be stored in ckpt
-        self.save_hyperparameters(logger=False, ignore=["backbone","readout","feature_encoder"])
+        self.save_hyperparameters(
+            logger=False, ignore=["backbone", "readout", "feature_encoder"]
+        )
 
         self.feature_encoder = feature_encoder
         if backbone_wrapper is None:

diff --git a/topobenchmarkx/transforms/__init__.py b/topobenchmarkx/transforms/__init__.py
@@ -1,4 +1,4 @@
-from typing import Any  # noqa: I001
+from typing import Any
 
 from topobenchmarkx.transforms.data_manipulations import DATA_MANIPULATIONS
 from topobenchmarkx.transforms.feature_liftings import FEATURE_LIFTINGS

diff --git a/topobenchmarkx/transforms/data_manipulations/__init__.py b/topobenchmarkx/transforms/data_manipulations/__init__.py
@@ -1,6 +1,6 @@
 from .calculate_simplicial_curvature import (
     CalculateSimplicialCurvature,
-)  # noqa: I001
+)
 from .equal_gaus_features import EqualGausFeatures
 from .identity_transform import IdentityTransform
 from .infere_knn_connectivity import InfereKNNConnectivity

diff --git a/topobenchmarkx/transforms/liftings/graph2hypergraph/khop.py b/topobenchmarkx/transforms/liftings/graph2hypergraph/khop.py
@@ -1,4 +1,4 @@
-import torch  # noqa: I001
+import torch
 import torch_geometric
 
 from topobenchmarkx.transforms.liftings.graph2hypergraph import (

diff --git a/topobenchmarkx/transforms/liftings/graph2hypergraph/knn.py b/topobenchmarkx/transforms/liftings/graph2hypergraph/knn.py
@@ -1,4 +1,4 @@
-import torch  # noqa: I001
+import torch
 import torch_geometric
 
 from topobenchmarkx.transforms.liftings.graph2hypergraph import (

diff --git a/topobenchmarkx/transforms/liftings/graph2simplicial/clique.py b/topobenchmarkx/transforms/liftings/graph2simplicial/clique.py
@@ -1,4 +1,4 @@
-from itertools import combinations  # noqa: I001
+from itertools import combinations
 from typing import Any
 
 import networkx as nx

diff --git a/topobenchmarkx/transforms/liftings/graph2simplicial/khop.py b/topobenchmarkx/transforms/liftings/graph2simplicial/khop.py
@@ -1,4 +1,4 @@
-import random  # noqa: I001
+import random
 from itertools import combinations
 from typing import Any
 

diff --git a/tutorials/tutorial_lifting.ipynb b/tutorials/tutorial_lifting.ipynb
@@ -31,27 +31,29 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from omegaconf import OmegaConf\n",
     "from itertools import combinations\n",
     "from typing import Any\n",
-    "import networkx as nx\n",
-    "from toponetx.classes import SimplicialComplex\n",
     "\n",
+    "import lightning as pl\n",
+    "import networkx as nx\n",
     "import torch\n",
     "import torch_geometric\n",
-    "import lightning as pl\n",
+    "from omegaconf import OmegaConf\n",
+    "from topomodelx.nn.simplicial.scn2 import SCN2\n",
+    "from toponetx.classes import SimplicialComplex\n",
     "\n",
     "from topobenchmarkx.data.load import GraphLoader\n",
     "from topobenchmarkx.data.preprocess import PreProcessor\n",
     "from topobenchmarkx.dataloader import TBXDataloader\n",
-    "from topobenchmarkx.nn.encoders import AllCellFeatureEncoder\n",
-    "from topobenchmarkx.nn.readouts import PropagateSignalDown\n",
-    "from topomodelx.nn.simplicial.scn2 import SCN2\n",
-    "from topobenchmarkx.nn.wrappers.simplicial import SCNWrapper\n",
     "from topobenchmarkx.evaluator import TBXEvaluator\n",
     "from topobenchmarkx.loss import TBXLoss\n",
     "from topobenchmarkx.model import TBXModel\n",
-    "from topobenchmarkx.transforms.liftings.graph2simplicial import Graph2SimplicialLifting"
+    "from topobenchmarkx.nn.encoders import AllCellFeatureEncoder\n",
+    "from topobenchmarkx.nn.readouts import PropagateSignalDown\n",
+    "from topobenchmarkx.nn.wrappers.simplicial import SCNWrapper\n",
+    "from topobenchmarkx.transforms.liftings.graph2simplicial import (\n",
+    "    Graph2SimplicialLifting,\n",
+    ")"
    ]
   },
   {
@@ -75,50 +77,50 @@
    "outputs": [],
    "source": [
     "loader_config = {\n",
-    "    'data_domain': 'graph',\n",
-    "    'data_type': 'TUDataset',\n",
-    "    'data_name': 'MUTAG',\n",
-    "    'data_dir': './data/MUTAG/',\n",
+    "    \"data_domain\": \"graph\",\n",
+    "    \"data_type\": \"TUDataset\",\n",
+    "    \"data_name\": \"MUTAG\",\n",
+    "    \"data_dir\": \"./data/MUTAG/\",\n",
     "}\n",
     "\n",
-    "transform_config = { 'clique_lifting':\n",
-    "    {'_target_': '__main__.SimplicialCliquesLEQLifting',\n",
-    "     'transform_name': 'SimplicialCliquesLEQLifting',\n",
-    "    'transform_type': 'lifting',\n",
-    "    'complex_dim': 3,}\n",
+    "transform_config = { \"clique_lifting\":\n",
+    "    {\"_target_\": \"__main__.SimplicialCliquesLEQLifting\",\n",
+    "     \"transform_name\": \"SimplicialCliquesLEQLifting\",\n",
+    "    \"transform_type\": \"lifting\",\n",
+    "    \"complex_dim\": 3,}\n",
     "}\n",
     "\n",
     "split_config = {\n",
-    "    'learning_setting': 'inductive',\n",
-    "    'split_type': 'k-fold',\n",
-    "    'data_seed': 0,\n",
-    "    'data_split_dir': './data/MUTAG/splits/',\n",
-    "    'k': 10,\n",
+    "    \"learning_setting\": \"inductive\",\n",
+    "    \"split_type\": \"k-fold\",\n",
+    "    \"data_seed\": 0,\n",
+    "    \"data_split_dir\": \"./data/MUTAG/splits/\",\n",
+    "    \"k\": 10,\n",
     "}\n",
     "\n",
     "in_channels = 7\n",
     "out_channels = 2\n",
     "dim_hidden = 128\n",
     "\n",
     "wrapper_config = {\n",
-    "    'out_channels': dim_hidden,\n",
-    "    'num_cell_dimensions': 3,\n",
+    "    \"out_channels\": dim_hidden,\n",
+    "    \"num_cell_dimensions\": 3,\n",
     "}\n",
     "\n",
     "readout_config = {\n",
-    "    'readout_name': 'PropagateSignalDown',\n",
-    "    'num_cell_dimensions': 1,\n",
-    "    'hidden_dim': dim_hidden,\n",
-    "    'out_channels': out_channels,\n",
-    "    'task_level': 'graph',\n",
-    "    'pooling_type': 'sum',\n",
+    "    \"readout_name\": \"PropagateSignalDown\",\n",
+    "    \"num_cell_dimensions\": 1,\n",
+    "    \"hidden_dim\": dim_hidden,\n",
+    "    \"out_channels\": out_channels,\n",
+    "    \"task_level\": \"graph\",\n",
+    "    \"pooling_type\": \"sum\",\n",
     "}\n",
     "\n",
-    "loss_config = {'task': 'classification', 'loss_type': 'cross_entropy'}\n",
+    "loss_config = {\"task\": \"classification\", \"loss_type\": \"cross_entropy\"}\n",
     "\n",
-    "evaluator_config = {'task': 'classification', \n",
-    "                    'num_classes': out_channels, \n",
-    "                    'classification_metrics': ['accuracy', 'precision', 'recall']}\n",
+    "evaluator_config = {\"task\": \"classification\",\n",
+    "                    \"num_classes\": out_channels,\n",
+    "                    \"classification_metrics\": [\"accuracy\", \"precision\", \"recall\"]}\n",
     "\n",
     "loader_config = OmegaConf.create(loader_config)\n",
     "transform_config = OmegaConf.create(transform_config)\n",
@@ -222,7 +224,7 @@
    "source": [
     "from topobenchmarkx.transforms import TRANSFORMS\n",
     "\n",
-    "TRANSFORMS['SimplicialCliquesLEQLifting'] = SimplicialCliquesLEQLifting"
+    "TRANSFORMS[\"SimplicialCliquesLEQLifting\"] = SimplicialCliquesLEQLifting"
    ]
   },
   {
@@ -367,7 +369,7 @@
     }
    ],
    "source": [
-    "trainer = pl.Trainer(max_epochs=200, accelerator='gpu', enable_progress_bar=False)\n",
+    "trainer = pl.Trainer(max_epochs=200, accelerator=\"gpu\", enable_progress_bar=False)\n",
     "\n",
     "trainer.fit(model, datamodule)\n",
     "train_metrics = trainer.callback_metrics"
@@ -395,7 +397,7 @@
    ],
    "source": [
     "for key in train_metrics:\n",
-    "    print(key,':    ', train_metrics[key].item())"
+    "    print(key,\":    \", train_metrics[key].item())"
    ]
   },
   {