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Fixed pre-commit erros #46

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Merged
ramosv merged 1 commit into from
Mar 7, 2025
Merged

Fixed pre-commit erros #46

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1 change: 1 addition & 0 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ repos:
- id: mypy
name: Static type checking with MyPy
args: [--ignore-missing-imports]
fail_on_warning: false

- repo: local
hooks:
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5 changes: 2 additions & 3 deletions BioNeuralNet.ipynb
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Expand Up @@ -17,7 +17,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -46,8 +46,7 @@
"from bioneuralnet.utils import get_logger\n",
"\n",
"from bioneuralnet.external_tools import SmCCNet\n",
"from bioneuralnet.external_tools import WGCNA\n",
"from bioneuralnet.external_tools import Node2Vec"
"from bioneuralnet.external_tools import WGCNA"
]
},
{
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7 changes: 6 additions & 1 deletion docs/source/conf.py
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Expand Up @@ -48,4 +48,9 @@
"networkx": ("https://networkx.org/documentation/stable/", None),
}

autodoc_mock_imports = ["torch", "torch_geometric"]
autodoc_mock_imports = [
"torch",
"torch_geometric",
"bioneuralnet.external_tools",
"bioneuralnet.external_tools.node2vec",
]
4 changes: 2 additions & 2 deletions docs/source/examples/gnn_embedding_example.py
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Expand Up @@ -2,7 +2,7 @@
from bioneuralnet.datasets import DatasetLoader
from bioneuralnet.network_embedding import GNNEmbedding
from bioneuralnet.external_tools import SmCCNet
from bioneuralnet.utils import plot_embeddings
from bioneuralnet.metrics import plot_embeddings

# Load example synthetic dataset
loader = DatasetLoader("example1")
Expand Down Expand Up @@ -46,4 +46,4 @@

global_node_labels = embeddings._prepare_node_labels()
embeddings_array = embeddings_output.values
fig1 = plot_embeddings(embeddings_array, global_node_labels.to_frame(name="phenotype"), method="tsne")
fig1 = plot_embeddings(embeddings_array, global_node_labels)
2 changes: 2 additions & 0 deletions pytest.ini
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@@ -0,0 +1,2 @@
[pytest]
norecursedirs = docs/source/examples
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