From 633fe425286249ccadf2df3d3c944a35f9c72b08 Mon Sep 17 00:00:00 2001 From: Vicente Date: Wed, 25 Mar 2026 11:51:09 -0600 Subject: [PATCH 1/2] added tqdm due to error from read the docs build --- docs/requirements.txt | 1 + docs/source/gnns.rst | 21 --------------------- requirements.txt | 1 + setup.cfg | 1 + 4 files changed, 3 insertions(+), 21 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index ce36eae..03d55ab 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -7,3 +7,4 @@ nbsphinx myst_nb furo sphinx-copybutton +tqdm diff --git a/docs/source/gnns.rst b/docs/source/gnns.rst index 9e957e8..79e1b47 100644 --- a/docs/source/gnns.rst +++ b/docs/source/gnns.rst @@ -94,25 +94,4 @@ How DPMON Utilizes GNN Embeddings `View full-size image: Disease Prediction (DPMON) `_ -Example Code: Training a GNN Embedding Model --------------------------------------------- -Below is a simplified example showing how to train GNN embeddings guided by phenotype correlations: - -.. code-block:: python - - from bioneuralnet.network_embedding import GNNEmbedding - import pandas as pd - - gnn = GNNEmbedding( - adjacency_matrix=adjacency_matrix, - omics_data=omics_data, - phenotype_data=phenotype_data, - clinical_data=clinical_data, - phenotype_col='finalgold_visit', - model_type='GAT', - hidden_dim=64 - ) - gnn.fit() - node_embeds = gnn.embed() - Return to :doc:`../index` diff --git a/requirements.txt b/requirements.txt index 938730c..df5a749 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,5 +8,6 @@ python-louvain pydantic ray[tune] statsmodels +tqdm # torch # torch_geometric diff --git a/setup.cfg b/setup.cfg index bfa623d..7d93340 100644 --- a/setup.cfg +++ b/setup.cfg @@ -33,6 +33,7 @@ install_requires = networkx>=3.4.2 pydantic>=2.12.5 ray[tune]>=2.46.0 + tqdm>=4.66.0 [options.packages.find] where = . From fe77798eb14abb3608298a7dd20c9864a4a5301f Mon Sep 17 00:00:00 2001 From: Vicente Date: Wed, 25 Mar 2026 11:52:00 -0600 Subject: [PATCH 2/2] removed old reference from manifest --- MANIFEST.in | 1 - 1 file changed, 1 deletion(-) diff --git a/MANIFEST.in b/MANIFEST.in index d4a6972..ef3d1d2 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -16,7 +16,6 @@ recursive-include bioneuralnet/datasets/example *.csv recursive-include bioneuralnet/datasets/brca *.csv recursive-include bioneuralnet/datasets/lgg *.csv recursive-include bioneuralnet/datasets/kipan *.csv -recursive-include bioneuralnet/datasets/paad *.csv # Include documentation source files prune docs