Solve merge conflicts before release

.github/workflows/pre-commit.yml

@@ -33,6 +33,9 @@ jobs:
           python -m pip install --upgrade pip
           pip install -r requirements.txt
           pip install -r requirements-dev.txt
+          pip install torch
+          pip install torch_geometric
+        shell: bash
 
       - name: Verify pre-commit installation
         run: pre-commit --version

.gitignore

@@ -5,6 +5,7 @@ __pycache__/
 *.pyd
 env/
 venv/
+.test_env/
 ENV/
 env.bak/
 venv.bak/
@@ -16,6 +17,18 @@ bioneuralnet.egg-info
 /docker_files/
 .mypy_cache
 
+# Other example data and tests not needed in the repo.
+TOPMed_testing/
+TOPMed_notes/
+
+todo_slides.md
+test_notes.md
+todo.md
+test_release.md
+test_cuda_issues.md
+dpmon/
+dp/
+
 # Blocking sensitive file types globally
 *.csv
 *.RData
@@ -25,11 +38,6 @@ bioneuralnet.egg-info
 !bioneuralnet/datasets/example1/
 !bioneuralnet/datasets/example1/**/*.csv
 
-dpmon_output/
-todo.md
-ignore_dir/
-
-
 # Sphinx documentation build
 docs/build/
 

.readthedocs.yaml

@@ -1,7 +1,7 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
-# Required
+# The format is based on https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 
 build:

CHANGELOG.md

@@ -0,0 +1,37 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),  
+and this project adheres to [Semantic Versioning](https://semver.org/).
+
+## [0.2.0b2] - 2025-02-16
+
+### **Added**
+- **Hybrid Louvain Clustering**: New iterative Louvain clustering method with PageRank refinement.
+- **DatasetLoader Integration**: Standardized dataset loading for examples & tutorials.
+- **GNNEmbedding Improvements**: Enhanced tuning capabilities for better model selection.
+- **New Example Workflows**:
+  - **SmCCNet + GNN Embeddings + Subject Representation**
+  - **SmCCNet + DPMON for Disease Prediction**
+  - **Hybrid Louvain Clustering Example**
+- **Updated Tutorials**: Expanded documentation with `nbsphinx` support for `.ipynb` notebooks.
+
+### **Changed**
+- **FAQ Overhaul**: Simplified and updated FAQs based on new features.
+- **Improved Documentation**: Rewrote and updated multiple sections for better clarity.
+- **Updated README.md**:
+  - Improved feature descriptions.
+  - New **quick-start example** for SmCCNet + DPMON.
+  - Cleaner installation instructions.
+- **Refactored Examples**:
+  - Updated **clustering** and **embedding** workflows to match the latest API changes.
+
+### **Fixed**
+- **Bug Fixes**:
+  - Resolved incorrect handling of `tune=True` in Hybrid Louvain.
+  - Addressed inconsistencies in `GraphEmbedding` parameter parsing.
+  - Fixed dataset loading issues in example scripts.
+
+## **[Unreleased]**
+- Multi-Modal Integration