From fee87fd99cfe7c480fcbfbea0f5d3b156f5c7001 Mon Sep 17 00:00:00 2001 From: Devendra Govil Date: Tue, 26 Nov 2024 09:19:40 -0800 Subject: [PATCH 1/2] Trial --- trial.txt | 1 + 1 file changed, 1 insertion(+) create mode 100644 trial.txt diff --git a/trial.txt b/trial.txt new file mode 100644 index 00000000..a1bbd8eb --- /dev/null +++ b/trial.txt @@ -0,0 +1 @@ +Trying to see accesses \ No newline at end of file From b6c9e295d6bac55cd2eb5ee5ebca77f13e445d83 Mon Sep 17 00:00:00 2001 From: Devendra Govil Date: Mon, 2 Dec 2024 10:20:42 -0800 Subject: [PATCH 2/2] Changing the init files to import all models used in tutorials directly in repo. | Making required changes in tutorials as well --- topomodelx/nn/__init__.py | 66 +++++++++++++++++++ trial.txt | 1 - tutorials/cell/can_train.ipynb | 11 +++- tutorials/cell/ccxn_train.ipynb | 11 +++- tutorials/cell/cwn_train.ipynb | 2 +- tutorials/combinatorial/hmc_train.ipynb | 2 +- tutorials/hypergraph/allset_train.ipynb | 4 +- .../hypergraph/allset_transformer_train.ipynb | 4 +- tutorials/hypergraph/dhgcn_train.ipynb | 2 +- tutorials/hypergraph/hmpnn_train.ipynb | 11 +++- tutorials/hypergraph/hnhn_train.ipynb | 4 +- tutorials/hypergraph/hypergat_train.ipynb | 2 +- tutorials/hypergraph/hypersage_train.ipynb | 2 +- tutorials/hypergraph/unigcn_train.ipynb | 11 +++- tutorials/hypergraph/unigcnii_train.ipynb | 2 +- tutorials/hypergraph/unigin_train.ipynb | 2 +- tutorials/hypergraph/unisage_train.ipynb | 2 +- tutorials/simplicial/dist2cycle_train.ipynb | 2 +- tutorials/simplicial/hsn_train.ipynb | 2 +- tutorials/simplicial/san_train.ipynb | 2 +- tutorials/simplicial/sca_cmps_train.ipynb | 2 +- tutorials/simplicial/sccn_train.ipynb | 2 +- tutorials/simplicial/sccnn_train.ipynb | 2 +- tutorials/simplicial/scconv_train.ipynb | 2 +- tutorials/simplicial/scn2_train.ipynb | 2 +- tutorials/simplicial/scnn_train.ipynb | 2 +- tutorials/simplicial/scone_train.ipynb | 2 +- 27 files changed, 122 insertions(+), 37 deletions(-) delete mode 100644 trial.txt diff --git a/topomodelx/nn/__init__.py b/topomodelx/nn/__init__.py index b7cc10fe..cbf1db3d 100644 --- a/topomodelx/nn/__init__.py +++ b/topomodelx/nn/__init__.py @@ -1,3 +1,5 @@ +"All Models to be inherited in the namespace." +from .cell.can import CAN from .cell.can_layer import ( CANLayer, LiftLayer, @@ -6,7 +8,9 @@ MultiHeadLiftLayer, PoolLayer, ) +from .cell.ccxn import CCXN from .cell.ccxn_layer import CCXNLayer +from .cell.cwn import CWN from .cell.cwn_layer import ( CWNLayer, _CWNDefaultAggregate, @@ -14,6 +18,35 @@ _CWNDefaultSecondConv, _CWNDefaultUpdate, ) +from .combinatorial.hmc import HMC +from .combinatorial.hmc_layer import HBNS, HBS, HMCLayer +from .hypergraph.allset import AllSet +from .hypergraph.allset_layer import AllSetBlock, AllSetLayer +from .hypergraph.allset_transformer import AllSetTransformer +from .hypergraph.allset_transformer_layer import ( + AllSetTransformerBlock, + AllSetTransformerLayer, + MultiHeadAttention, +) +from .hypergraph.dhgcn import DHGCN +from .hypergraph.hmpnn import HMPNN +from .hypergraph.hnhn import HNHN +from .hypergraph.hypergat import HyperGAT +from .hypergraph.hypersage import HyperSAGE +from .hypergraph.unigcn import UniGCN +from .hypergraph.unigcnii import UniGCNII +from .hypergraph.unigin import UniGIN +from .hypergraph.unisage import UniSAGE +from .simplicial.dist2cycle import Dist2Cycle +from .simplicial.hsn import HSN +from .simplicial.san import SAN +from .simplicial.sca_cmps import SCACMPS +from .simplicial.sccn import SCCN +from .simplicial.sccnn import SCCNN +from .simplicial.scconv import SCConv +from .simplicial.scn2 import SCN2 +from .simplicial.scnn import SCNN +from .simplicial.scone import SCoNe __all__ = [ "LiftLayer", @@ -28,4 +61,37 @@ "_CWNDefaultSecondConv", "_CWNDefaultAggregate", "_CWNDefaultUpdate", + "CAN", + "CCXN", + "CWN", + "HBNS", + "HBS", + "HMCLayer", + "HMC", + "AllSetLayer", + "AllSetBlock", + "AllSetTransformerBlock", + "AllSetTransformerLayer", + "MultiHeadAttention", + "AllSet", + "AllSetTransformer", + "DHGCN", + "HMPNN", + "HNHN", + "HyperGAT", + "HyperSAGE", + "UniGCN", + "UniGCNII", + "UniGIN", + "UniSAGE", + "Dist2Cycle", + "HSN", + "SAN", + "SCACMPS", + "SCCN", + "SCCNN", + "SCConv", + "SCN2", + "SCNN", + "SCoNe", ] diff --git a/trial.txt b/trial.txt deleted file mode 100644 index a1bbd8eb..00000000 --- a/trial.txt +++ /dev/null @@ -1 +0,0 @@ -Trying to see accesses \ No newline at end of file diff --git a/tutorials/cell/can_train.ipynb b/tutorials/cell/can_train.ipynb index b9957dc4..7afc2097 100644 --- a/tutorials/cell/can_train.ipynb +++ b/tutorials/cell/can_train.ipynb @@ -132,7 +132,7 @@ "from torch_geometric.datasets import TUDataset\n", "from torch_geometric.utils.convert import to_networkx\n", "\n", - "from topomodelx.nn.cell.can import CAN\n", + "from topomodelx import CAN\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "torch.manual_seed(0)" @@ -592,7 +592,7 @@ ], "metadata": { "kernelspec": { - "display_name": "venv_tmx", + "display_name": "Python 3.12.7 64-bit", "language": "python", "name": "python3" }, @@ -606,7 +606,12 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.12.7" + }, + "vscode": { + "interpreter": { + "hash": "b0fa6594d8f4cbf19f97940f81e996739fb7646882a419484c72d19e05852a7e" + } } }, "nbformat": 4, diff --git a/tutorials/cell/ccxn_train.ipynb b/tutorials/cell/ccxn_train.ipynb index 2005fa75..9dd71a6b 100644 --- a/tutorials/cell/ccxn_train.ipynb +++ b/tutorials/cell/ccxn_train.ipynb @@ -62,7 +62,7 @@ "import torch\n", "from sklearn.model_selection import train_test_split\n", "\n", - "from topomodelx.nn.cell.ccxn import CCXN\n", + "from topomodelx import CCXN\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "torch.manual_seed(0)\n", @@ -645,7 +645,7 @@ ], "metadata": { "kernelspec": { - "display_name": "venv_modelx", + "display_name": "Python 3.12.7 64-bit", "language": "python", "name": "python3" }, @@ -659,7 +659,12 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.12.7" + }, + "vscode": { + "interpreter": { + "hash": "b0fa6594d8f4cbf19f97940f81e996739fb7646882a419484c72d19e05852a7e" + } } }, "nbformat": 4, diff --git a/tutorials/cell/cwn_train.ipynb b/tutorials/cell/cwn_train.ipynb index 55959c8d..3f450998 100644 --- a/tutorials/cell/cwn_train.ipynb +++ b/tutorials/cell/cwn_train.ipynb @@ -70,7 +70,7 @@ "import torch\n", "from sklearn.model_selection import train_test_split\n", "\n", - "from topomodelx.nn.cell.cwn import CWN\n", + "from topomodelx import CWN\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "torch.manual_seed(0)" diff --git a/tutorials/combinatorial/hmc_train.ipynb b/tutorials/combinatorial/hmc_train.ipynb index 9a6254df..97bd4485 100644 --- a/tutorials/combinatorial/hmc_train.ipynb +++ b/tutorials/combinatorial/hmc_train.ipynb @@ -137,7 +137,7 @@ "import torch\n", "from torch.utils.data import DataLoader, Dataset\n", "\n", - "from topomodelx.nn.combinatorial.hmc import HMC" + "from topomodelx import HMC" ] }, { diff --git a/tutorials/hypergraph/allset_train.ipynb b/tutorials/hypergraph/allset_train.ipynb index 528e71e0..526ad823 100644 --- a/tutorials/hypergraph/allset_train.ipynb +++ b/tutorials/hypergraph/allset_train.ipynb @@ -60,7 +60,7 @@ "import torch_geometric.datasets as geom_datasets\n", "from torch_geometric.utils import to_undirected\n", "\n", - "from topomodelx.nn.hypergraph.allset import AllSet\n", + "from topomodelx import AllSet\n", "\n", "torch.manual_seed(0)" ] @@ -533,7 +533,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.9.6" }, "vscode": { "interpreter": { diff --git a/tutorials/hypergraph/allset_transformer_train.ipynb b/tutorials/hypergraph/allset_transformer_train.ipynb index a7ed18bc..04ce4a86 100644 --- a/tutorials/hypergraph/allset_transformer_train.ipynb +++ b/tutorials/hypergraph/allset_transformer_train.ipynb @@ -94,7 +94,7 @@ "import torch_geometric.datasets as geom_datasets\n", "from torch_geometric.utils import to_undirected\n", "\n", - "from topomodelx.nn.hypergraph.allset_transformer import AllSetTransformer\n", + "from topomodelx import AllSetTransformer\n", "\n", "torch.manual_seed(0)" ] @@ -515,7 +515,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.9.6" }, "vscode": { "interpreter": { diff --git a/tutorials/hypergraph/dhgcn_train.ipynb b/tutorials/hypergraph/dhgcn_train.ipynb index a15d0a74..acd14c3d 100644 --- a/tutorials/hypergraph/dhgcn_train.ipynb +++ b/tutorials/hypergraph/dhgcn_train.ipynb @@ -26,7 +26,7 @@ "import torch\n", "from sklearn.model_selection import train_test_split\n", "\n", - "from topomodelx.nn.hypergraph.dhgcn import DHGCN\n", + "from topomodelx import DHGCN\n", "from topomodelx.utils.sparse import from_sparse" ] }, diff --git a/tutorials/hypergraph/hmpnn_train.ipynb b/tutorials/hypergraph/hmpnn_train.ipynb index 6f429a52..f8f334b3 100644 --- a/tutorials/hypergraph/hmpnn_train.ipynb +++ b/tutorials/hypergraph/hmpnn_train.ipynb @@ -28,7 +28,7 @@ "import torch_geometric.datasets as geom_datasets\n", "from sklearn.metrics import accuracy_score\n", "\n", - "from topomodelx.nn.hypergraph.hmpnn import HMPNN\n", + "from topomodelx import HMPNN\n", "\n", "torch.manual_seed(0)" ] @@ -327,7 +327,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Python 3.12.7 64-bit", "language": "python", "name": "python3" }, @@ -341,7 +341,12 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.12.7" + }, + "vscode": { + "interpreter": { + "hash": "b0fa6594d8f4cbf19f97940f81e996739fb7646882a419484c72d19e05852a7e" + } } }, "nbformat": 4, diff --git a/tutorials/hypergraph/hnhn_train.ipynb b/tutorials/hypergraph/hnhn_train.ipynb index 83a07aca..b7a11e00 100644 --- a/tutorials/hypergraph/hnhn_train.ipynb +++ b/tutorials/hypergraph/hnhn_train.ipynb @@ -59,7 +59,7 @@ "import torch_geometric.datasets as geom_datasets\n", "from torch_geometric.utils import to_undirected\n", "\n", - "from topomodelx.nn.hypergraph.hnhn import HNHN\n", + "from topomodelx import HNHN\n", "\n", "torch.manual_seed(0)" ] @@ -529,7 +529,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.6" + "version": "3.9.6" }, "vscode": { "interpreter": { diff --git a/tutorials/hypergraph/hypergat_train.ipynb b/tutorials/hypergraph/hypergat_train.ipynb index cc7bdf59..88e0b0cd 100644 --- a/tutorials/hypergraph/hypergat_train.ipynb +++ b/tutorials/hypergraph/hypergat_train.ipynb @@ -59,7 +59,7 @@ "import torch\n", "from sklearn.model_selection import train_test_split\n", "\n", - "from topomodelx.nn.hypergraph.hypergat import HyperGAT\n", + "from topomodelx import HyperGAT\n", "from topomodelx.utils.sparse import from_sparse" ] }, diff --git a/tutorials/hypergraph/hypersage_train.ipynb b/tutorials/hypergraph/hypersage_train.ipynb index 4514fcd4..4601a40b 100644 --- a/tutorials/hypergraph/hypersage_train.ipynb +++ b/tutorials/hypergraph/hypersage_train.ipynb @@ -62,7 +62,7 @@ "import torch_geometric.datasets as geom_datasets\n", "from torch_geometric.utils import to_undirected\n", "\n", - "from topomodelx.nn.hypergraph.hypersage import HyperSAGE\n", + "from topomodelx import HyperSAGE\n", "\n", "torch.manual_seed(0)" ] diff --git a/tutorials/hypergraph/unigcn_train.ipynb b/tutorials/hypergraph/unigcn_train.ipynb index 40c55387..de9a57f7 100644 --- a/tutorials/hypergraph/unigcn_train.ipynb +++ b/tutorials/hypergraph/unigcn_train.ipynb @@ -13,7 +13,7 @@ "from torch_geometric.datasets import TUDataset\n", "from torch_geometric.utils.convert import to_networkx\n", "\n", - "from topomodelx.nn.hypergraph.unigcn import UniGCN\n", + "from topomodelx import UniGCN\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "torch.manual_seed(0)" @@ -328,7 +328,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Python 3.12.7 64-bit", "language": "python", "name": "python3" }, @@ -342,7 +342,12 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.12.7" + }, + "vscode": { + "interpreter": { + "hash": "b0fa6594d8f4cbf19f97940f81e996739fb7646882a419484c72d19e05852a7e" + } } }, "nbformat": 4, diff --git a/tutorials/hypergraph/unigcnii_train.ipynb b/tutorials/hypergraph/unigcnii_train.ipynb index 712c4174..18737e25 100644 --- a/tutorials/hypergraph/unigcnii_train.ipynb +++ b/tutorials/hypergraph/unigcnii_train.ipynb @@ -25,7 +25,7 @@ "import torch_geometric.datasets as geom_datasets\n", "from torch_geometric.utils import to_undirected\n", "\n", - "from topomodelx.nn.hypergraph.unigcnii import UniGCNII\n", + "from topomodelx import UniGCNII\n", "\n", "torch.manual_seed(0)" ] diff --git a/tutorials/hypergraph/unigin_train.ipynb b/tutorials/hypergraph/unigin_train.ipynb index b8293db8..94b8fcd4 100644 --- a/tutorials/hypergraph/unigin_train.ipynb +++ b/tutorials/hypergraph/unigin_train.ipynb @@ -12,7 +12,7 @@ "from torch_geometric.datasets import TUDataset\n", "from torch_geometric.utils.convert import to_networkx\n", "\n", - "from topomodelx.nn.hypergraph.unigin import UniGIN\n", + "from topomodelx import UniGIN\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "torch.manual_seed(0)" diff --git a/tutorials/hypergraph/unisage_train.ipynb b/tutorials/hypergraph/unisage_train.ipynb index 78ffa263..81da95bd 100644 --- a/tutorials/hypergraph/unisage_train.ipynb +++ b/tutorials/hypergraph/unisage_train.ipynb @@ -12,7 +12,7 @@ "import torch_geometric.datasets as geom_datasets\n", "from torch_geometric.utils import to_undirected\n", "\n", - "from topomodelx.nn.hypergraph.unisage import UniSAGE\n", + "from topomodelx import UniSAGE\n", "\n", "torch.manual_seed(0)" ] diff --git a/tutorials/simplicial/dist2cycle_train.ipynb b/tutorials/simplicial/dist2cycle_train.ipynb index 94c85ef7..698668f2 100644 --- a/tutorials/simplicial/dist2cycle_train.ipynb +++ b/tutorials/simplicial/dist2cycle_train.ipynb @@ -37,7 +37,7 @@ "import toponetx as tnx\n", "import torch\n", "\n", - "from topomodelx.nn.simplicial.dist2cycle import Dist2Cycle\n", + "from topomodelx import Dist2Cycle\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "%load_ext autoreload\n", diff --git a/tutorials/simplicial/hsn_train.ipynb b/tutorials/simplicial/hsn_train.ipynb index 5c6fdc96..b6f99d64 100644 --- a/tutorials/simplicial/hsn_train.ipynb +++ b/tutorials/simplicial/hsn_train.ipynb @@ -41,7 +41,7 @@ "import toponetx as tnx\n", "import torch\n", "\n", - "from topomodelx.nn.simplicial.hsn import HSN\n", + "from topomodelx import HSN\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "%load_ext autoreload\n", diff --git a/tutorials/simplicial/san_train.ipynb b/tutorials/simplicial/san_train.ipynb index 290d440e..7f2f456c 100644 --- a/tutorials/simplicial/san_train.ipynb +++ b/tutorials/simplicial/san_train.ipynb @@ -89,7 +89,7 @@ "import toponetx as tnx\n", "import torch\n", "\n", - "from topomodelx.nn.simplicial.san import SAN\n", + "from topomodelx import SAN\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "%load_ext autoreload\n", diff --git a/tutorials/simplicial/sca_cmps_train.ipynb b/tutorials/simplicial/sca_cmps_train.ipynb index 343cf5a4..29690749 100644 --- a/tutorials/simplicial/sca_cmps_train.ipynb +++ b/tutorials/simplicial/sca_cmps_train.ipynb @@ -41,7 +41,7 @@ "import toponetx as tnx\n", "import torch\n", "\n", - "from topomodelx.nn.simplicial.sca_cmps import SCACMPS\n", + "from topomodelx import SCACMPS\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "%load_ext autoreload\n", diff --git a/tutorials/simplicial/sccn_train.ipynb b/tutorials/simplicial/sccn_train.ipynb index e12635c1..e410105d 100644 --- a/tutorials/simplicial/sccn_train.ipynb +++ b/tutorials/simplicial/sccn_train.ipynb @@ -43,7 +43,7 @@ "import toponetx as tnx\n", "import torch\n", "\n", - "from topomodelx.nn.simplicial.sccn import SCCN\n", + "from topomodelx import SCCN\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "%load_ext autoreload\n", diff --git a/tutorials/simplicial/sccnn_train.ipynb b/tutorials/simplicial/sccnn_train.ipynb index 27c14178..9aad27ba 100644 --- a/tutorials/simplicial/sccnn_train.ipynb +++ b/tutorials/simplicial/sccnn_train.ipynb @@ -77,7 +77,7 @@ "import torch\n", "from sklearn.model_selection import train_test_split\n", "\n", - "from topomodelx.nn.simplicial.sccnn import SCCNN\n", + "from topomodelx import SCCNN\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "%load_ext autoreload\n", diff --git a/tutorials/simplicial/scconv_train.ipynb b/tutorials/simplicial/scconv_train.ipynb index 45204349..8f9f5ac2 100644 --- a/tutorials/simplicial/scconv_train.ipynb +++ b/tutorials/simplicial/scconv_train.ipynb @@ -78,7 +78,7 @@ "import torch\n", "from scipy.sparse import coo_matrix, diags\n", "\n", - "from topomodelx.nn.simplicial.scconv import SCConv\n", + "from topomodelx import SCConv\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "%load_ext autoreload\n", diff --git a/tutorials/simplicial/scn2_train.ipynb b/tutorials/simplicial/scn2_train.ipynb index b42778f5..e24025ab 100644 --- a/tutorials/simplicial/scn2_train.ipynb +++ b/tutorials/simplicial/scn2_train.ipynb @@ -39,7 +39,7 @@ "import torch\n", "from sklearn.model_selection import train_test_split\n", "\n", - "from topomodelx.nn.simplicial.scn2 import SCN2\n", + "from topomodelx import SCN2\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "%load_ext autoreload\n", diff --git a/tutorials/simplicial/scnn_train.ipynb b/tutorials/simplicial/scnn_train.ipynb index 9c518696..07250c0a 100644 --- a/tutorials/simplicial/scnn_train.ipynb +++ b/tutorials/simplicial/scnn_train.ipynb @@ -67,7 +67,7 @@ "import torch\n", "from sklearn.model_selection import train_test_split\n", "\n", - "from topomodelx.nn.simplicial.scnn import SCNN\n", + "from topomodelx import SCNN\n", "from topomodelx.utils.sparse import from_sparse\n", "\n", "%load_ext autoreload\n", diff --git a/tutorials/simplicial/scone_train.ipynb b/tutorials/simplicial/scone_train.ipynb index 3d8b023a..bb32681f 100644 --- a/tutorials/simplicial/scone_train.ipynb +++ b/tutorials/simplicial/scone_train.ipynb @@ -63,7 +63,7 @@ "from torch.utils.data import DataLoader, random_split\n", "from torch.utils.data.dataset import Dataset\n", "\n", - "from topomodelx.nn.simplicial.scone import SCoNe\n", + "from topomodelx import SCoNe\n", "\n", "%load_ext autoreload\n", "%autoreload 2"