Deploying to main from @ pyt-team/TopoModelX@106db16 🚀

pyt-team · Oct 21, 2024 · e29e8ad · e29e8ad
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diff --git a/topomodelx/.doctrees/environment.pickle b/topomodelx/.doctrees/environment.pickle
diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/cell/can_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/cell/can_train.ipynb
@@ -126,9 +126,9 @@
    ],
    "source": [
     "import numpy as np\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "from sklearn.model_selection import train_test_split\n",
-    "from toponetx.classes.cell_complex import CellComplex\n",
     "from torch_geometric.datasets import TUDataset\n",
     "from torch_geometric.utils.convert import to_networkx\n",
     "\n",
@@ -218,7 +218,7 @@
     "x_1_list = []\n",
     "y_list = []\n",
     "for graph in dataset:\n",
-    "    cell_complex = CellComplex(to_networkx(graph))\n",
+    "    cell_complex = tnx.CellComplex(to_networkx(graph))\n",
     "    cc_list.append(cell_complex)\n",
     "    x_0_list.append(graph.x)\n",
     "    x_1_list.append(graph.edge_attr)\n",

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/cell/ccxn_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/cell/ccxn_train.ipynb
@@ -58,7 +58,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "import toponetx.datasets as datasets\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "from sklearn.model_selection import train_test_split\n",
     "\n",
@@ -132,7 +132,7 @@
     }
    ],
    "source": [
-    "shrec, _ = datasets.mesh.shrec_16(size=\"small\")\n",
+    "shrec, _ = tnx.datasets.shrec_16(size=\"small\")\n",
     "\n",
     "shrec = {key: np.array(value) for key, value in shrec.items()}\n",
     "x_0s = shrec[\"node_feat\"]\n",

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/cell/cwn_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/cell/cwn_train.ipynb
@@ -66,7 +66,7 @@
    ],
    "source": [
     "import numpy as np\n",
-    "import toponetx.datasets as datasets\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "from sklearn.model_selection import train_test_split\n",
     "\n",
@@ -152,7 +152,7 @@
     }
    ],
    "source": [
-    "shrec, _ = datasets.mesh.shrec_16(size=\"small\")\n",
+    "shrec, _ = tnx.datasets.shrec_16(size=\"small\")\n",
     "\n",
     "shrec = {key: np.array(value) for key, value in shrec.items()}\n",
     "x_0s = shrec[\"node_feat\"]\n",

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/combinatorial/hmc_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/combinatorial/hmc_train.ipynb
@@ -133,8 +133,8 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
+    "import toponetx as tnx\n",
     "import torch\n",
-    "from toponetx.datasets.mesh import shrec_16\n",
     "from torch.utils.data import DataLoader, Dataset\n",
     "\n",
     "from topomodelx.nn.combinatorial.hmc import HMC"
@@ -338,7 +338,7 @@
     }
    ],
    "source": [
-    "shrec_training, shrec_testing = shrec_16()"
+    "shrec_training, shrec_testing = tnx.datasets.shrec_16()"
    ]
   },
   {
@@ -839,9 +839,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "venv_modelx",
+   "display_name": "venv",
    "language": "python",
-   "name": "venv_modelx"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -853,7 +853,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.3"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/hypergraph/dhgcn_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/hypergraph/dhgcn_train.ipynb
@@ -22,7 +22,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "import toponetx.datasets as datasets\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "from sklearn.model_selection import train_test_split\n",
     "\n",
@@ -98,7 +98,7 @@
     }
    ],
    "source": [
-    "shrec, _ = datasets.mesh.shrec_16(size=\"small\")\n",
+    "shrec, _ = tnx.datasets.mesh.shrec_16(size=\"small\")\n",
     "\n",
     "shrec = {key: np.array(value) for key, value in shrec.items()}\n",
     "x_0s = shrec[\"node_feat\"]\n",

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/hypergraph/hypergat_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/hypergraph/hypergat_train.ipynb
@@ -55,7 +55,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "import toponetx.datasets as datasets\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "from sklearn.model_selection import train_test_split\n",
     "\n",
@@ -112,7 +112,7 @@
     }
    ],
    "source": [
-    "shrec, _ = datasets.mesh.shrec_16(size=\"small\")\n",
+    "shrec, _ = tnx.datasets.shrec_16(size=\"small\")\n",
     "\n",
     "shrec = {key: np.array(value) for key, value in shrec.items()}\n",
     "x_0s = shrec[\"node_feat\"]\n",

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/hypergraph/unigcn_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/hypergraph/unigcn_train.ipynb
@@ -7,9 +7,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import toponetx as tnx\n",
     "import torch\n",
     "from sklearn.model_selection import train_test_split\n",
-    "from toponetx.classes.simplicial_complex import SimplicialComplex\n",
     "from torch_geometric.datasets import TUDataset\n",
     "from torch_geometric.utils.convert import to_networkx\n",
     "\n",
@@ -83,7 +83,7 @@
     "x_1_list = []\n",
     "y_list = []\n",
     "for graph in dataset:\n",
-    "    hg = SimplicialComplex(to_networkx(graph)).to_hypergraph()\n",
+    "    hg = tnx.SimplicialComplex(to_networkx(graph)).to_hypergraph()\n",
     "    hg_list.append(hg)\n",
     "    x_1_list.append(graph.x.to(device))\n",
     "    y_list.append(graph.y.to(device))\n",

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/hypergraph/unigin_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/hypergraph/unigin_train.ipynb
@@ -6,9 +6,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import toponetx as tnx\n",
     "import torch\n",
     "from sklearn.model_selection import train_test_split\n",
-    "from toponetx.classes.simplicial_complex import SimplicialComplex\n",
     "from torch_geometric.datasets import TUDataset\n",
     "from torch_geometric.utils.convert import to_networkx\n",
     "\n",
@@ -78,7 +78,7 @@
     "x_1_list = []\n",
     "y_list = []\n",
     "for graph in dataset:\n",
-    "    hg = SimplicialComplex(to_networkx(graph)).to_hypergraph()\n",
+    "    hg = tnx.SimplicialComplex(to_networkx(graph)).to_hypergraph()\n",
     "    hg_list.append(hg)\n",
     "    x_1_list.append(graph.x.to(device))\n",
     "    y_list.append(graph.y.to(device))\n",

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/dist2cycle_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/dist2cycle_train.ipynb
@@ -34,7 +34,7 @@
    "source": [
     "import numpy as np\n",
     "import numpy.linalg as npla\n",
-    "import toponetx.datasets.graph as graph\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "\n",
     "from topomodelx.nn.simplicial.dist2cycle import Dist2Cycle\n",
@@ -72,7 +72,7 @@
     }
    ],
    "source": [
-    "dataset = graph.karate_club(complex_type=\"simplicial\")\n",
+    "dataset = tnx.datasets.karate_club(complex_type=\"simplicial\")\n",
     "print(dataset)"
    ]
   },

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/hsn_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/hsn_train.ipynb
@@ -38,7 +38,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "import toponetx.datasets.graph as graph\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "\n",
     "from topomodelx.nn.simplicial.hsn import HSN\n",
@@ -75,7 +75,7 @@
     }
    ],
    "source": [
-    "dataset = graph.karate_club(complex_type=\"simplicial\")\n",
+    "dataset = tnx.datasets.karate_club(complex_type=\"simplicial\")\n",
     "print(dataset)"
    ]
   },

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/san_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/san_train.ipynb
@@ -86,7 +86,7 @@
    ],
    "source": [
     "import numpy as np\n",
-    "import toponetx.datasets.graph as graph\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "\n",
     "from topomodelx.nn.simplicial.san import SAN\n",
@@ -149,7 +149,7 @@
     }
    ],
    "source": [
-    "dataset = graph.karate_club(complex_type=\"simplicial\")\n",
+    "dataset = tnx.datasets.karate_club(complex_type=\"simplicial\")\n",
     "print(dataset)"
    ]
   },

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/sca_cmps_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/sca_cmps_train.ipynb
@@ -38,7 +38,7 @@
    ],
    "source": [
     "import numpy as np\n",
-    "import toponetx.datasets.graph as graph\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "\n",
     "from topomodelx.nn.simplicial.sca_cmps import SCACMPS\n",
@@ -100,7 +100,7 @@
     }
    ],
    "source": [
-    "dataset = graph.karate_club(complex_type=\"simplicial\")\n",
+    "dataset = tnx.datasets.karate_club(complex_type=\"simplicial\")\n",
     "print(dataset)"
    ]
   },

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/sccn_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/sccn_train.ipynb
@@ -40,7 +40,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "import toponetx.datasets.graph as graph\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "\n",
     "from topomodelx.nn.simplicial.sccn import SCCN\n",
@@ -79,7 +79,7 @@
     }
    ],
    "source": [
-    "dataset = graph.karate_club(complex_type=\"simplicial\", feat_dim=2)\n",
+    "dataset = tnx.datasets.karate_club(complex_type=\"simplicial\", feat_dim=2)\n",
     "print(dataset)"
    ]
   },

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/sccnn_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/sccnn_train.ipynb
@@ -73,7 +73,7 @@
    ],
    "source": [
     "import numpy as np\n",
-    "import toponetx.datasets as datasets\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "from sklearn.model_selection import train_test_split\n",
     "\n",
@@ -112,7 +112,7 @@
     }
    ],
    "source": [
-    "shrec, _ = datasets.mesh.shrec_16(size=\"small\")\n",
+    "shrec, _ = tnx.datasets.shrec_16(size=\"small\")\n",
     "shrec = {key: np.array(value) for key, value in shrec.items()}\n",
     "x_0s = shrec[\"node_feat\"]\n",
     "x_1s = shrec[\"edge_feat\"]\n",
@@ -499,8 +499,6 @@
     }
    ],
    "source": [
-    "import toponetx.datasets.graph as graph\n",
-    "\n",
     "%load_ext autoreload\n",
     "%autoreload 2"
    ]
@@ -533,7 +531,7 @@
     }
    ],
    "source": [
-    "dataset = graph.karate_club(complex_type=\"simplicial\")\n",
+    "dataset = tnx.datasets.karate_club(complex_type=\"simplicial\")\n",
     "print(dataset)\n",
     "max_rank = dataset.dim\n",
     "print(max_rank)"

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/scconv_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/scconv_train.ipynb
@@ -74,7 +74,7 @@
    ],
    "source": [
     "import numpy as np\n",
-    "import toponetx.datasets.graph as graph\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "from scipy.sparse import coo_matrix, diags\n",
     "\n",
@@ -138,7 +138,7 @@
     }
    ],
    "source": [
-    "dataset = graph.karate_club(complex_type=\"simplicial\")\n",
+    "dataset = tnx.datasets.karate_club(complex_type=\"simplicial\")\n",
     "print(dataset)"
    ]
   },

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/scn2_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/scn2_train.ipynb
@@ -35,7 +35,7 @@
    ],
    "source": [
     "import numpy as np\n",
-    "import toponetx.datasets as datasets\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "from sklearn.model_selection import train_test_split\n",
     "\n",
@@ -91,7 +91,7 @@
     }
    ],
    "source": [
-    "shrec, _ = datasets.mesh.shrec_16(size=\"small\")\n",
+    "shrec, _ = tnx.datasets.shrec_16(size=\"small\")\n",
     "\n",
     "shrec = {key: np.array(value) for key, value in shrec.items()}\n",
     "x_0s = shrec[\"node_feat\"]\n",

diff --git a/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/scnn_train.ipynb b/topomodelx/.doctrees/nbsphinx/notebooks/simplicial/scnn_train.ipynb
@@ -63,7 +63,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "import toponetx.datasets as datasets\n",
+    "import toponetx as tnx\n",
     "import torch\n",
     "from sklearn.model_selection import train_test_split\n",
     "\n",
@@ -102,7 +102,7 @@
     }
    ],
    "source": [
-    "shrec, _ = datasets.mesh.shrec_16(size=\"small\")\n",
+    "shrec, _ = tnx.datasets.shrec_16(size=\"small\")\n",
     "\n",
     "shrec = {key: np.array(value) for key, value in shrec.items()}\n",
     "\n",
@@ -381,15 +381,6 @@
     "# 2. Node Classification "
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 10,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import toponetx.datasets.graph as graph"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -413,7 +404,7 @@
     }
    ],
    "source": [
-    "dataset = graph.karate_club(complex_type=\"simplicial\")\n",
+    "dataset = tnx.datasets.karate_club(complex_type=\"simplicial\")\n",
     "print(dataset)\n",
     "\n",
     "# Maximal simplex order\n",