Merge pull request #103 from UCD-BDLab/quick-start-for-biologists

v1.2.2 release: Updated docs + depedency bug fix

Author: ramosv

CHANGELOG.md

@@ -5,6 +5,18 @@ 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/).
 
+## [1.2.2] - 2025-12-29
+
+### Documentation
+- **Updated Index**: index now includes tables with examples for feature selection.
+- **Getting Started for Biologists**: An updated page which leverages google colab for a more user friendly walkthrough of BioNeuralNet.
+
+### Ray Tune Patch
+- **Ray tune**: Updated from `ray[tune,train]>=2.46.0` to `ray[tune,train]>=2.46.0, <2.53.0` due to an recent release on December 20, 2025 which breaks some functionality. This temporately fixes the issue.
+
+### New DPMON param: `tune_trails`
+- This parameter gives users the ability to dictate how many ray tune trials to run. This works alongside the Dynamic Sampling from `v1.2.1`.
+
 ## [1.2.1] - 2025-11-30
 
 ### Dependencies
@@ -227,4 +239,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/).
 - **Bug Fixes**:
   - Resolved incorrect handling of `tune=True` in Hybrid Louvain.
   - Addressed inconsistencies in `GraphEmbedding` parameter parsing.
-  - Fixed dataset loading issues in example scripts.
+  - Fixed dataset loading issues in example scripts.

README.md

@@ -8,7 +8,7 @@
 [![Documentation](https://img.shields.io/badge/docs-read%20the%20docs-blue.svg)](https://bioneuralnet.readthedocs.io/en/latest/)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17503083.svg)](https://doi.org/10.5281/zenodo.17503083)
 
-## Welcome to BioNeuralNet 1.2.1
+## Welcome to BioNeuralNet 1.2.2
 
 ![BioNeuralNet Logo](assets/LOGO_TB.png)
 

bioneuralnet/__init__.py

@@ -23,7 +23,7 @@
 * `utils`: Utilities for logging, reproducibility, graph generation, and data processing.
 """
 
-__version__ = "1.2.1"
+__version__ = "1.2.2"
 
 # submodules to enable direct imports such as `from bioneuralnet import utils`
 from . import utils

bioneuralnet/downstream_task/dpmon.py

@@ -69,6 +69,7 @@ class DPMON:
         lr (float): Learning rate for the optimizer.
         weight_decay (float): L2 weight decay (regularization) coefficient.
         tune (bool): If True, perform hyperparameter tuning before final training.
+        tune_trails (int): Number of trials to perform if tune=True.
         gpu (bool): If True, use GPU if available.
         cv (bool): If True, use K-fold cross-validation; otherwise use repeated train/test splits.
         cuda (int): CUDA device index to use when gpu=True.
@@ -98,6 +99,7 @@ def __init__(
         lr: float = 1e-1,
         weight_decay: float = 1e-4,
         tune: bool = False,
+        tune_trails: int = 10,
         gpu: bool = False,
         cv: bool = False,
         cuda: int = 0,
@@ -156,6 +158,7 @@ def __init__(
         self.lr = lr
         self.weight_decay = weight_decay
         self.tune = tune
+        self.tune_trails = tune_trails
         self.gpu = gpu
         self.cuda = cuda
         self.seed = seed
@@ -205,6 +208,7 @@ def run(self) -> Tuple[pd.DataFrame, object, torch.Tensor | None]:
             "gpu": self.gpu,
             "cuda": self.cuda,
             "tune": self.tune,
+            "tune_trials": self.tune_trails,
             "seed": self.seed,
             "seed_trials": self.seed_trials,
             "cv": self.cv,
@@ -892,8 +896,8 @@ def short_dirname_creator(trial):
 
     gpu_per_trial = 0.05 if use_gpu else 0.0
 
-    num_samples = 50
-    max_retries = 5
+    num_samples = dpmon_params['tune_trials']
+    max_retries = 4
 
     seed_trials = dpmon_params.get("seed_trials", False)
 
@@ -916,6 +920,7 @@ def short_dirname_creator(trial):
                 config=pipeline_configs,
                 num_samples=num_samples,
                 verbose=0,
+                log_to_file=True,
                 scheduler=scheduler,
                 stop=stopper,
                 name="tune_dp",

docs/source/Quick_Start.ipynb

@@ -19,7 +19,6 @@ bioneuralnet.clustering.correlated\_louvain
    .. autosummary::
 
       ASHAScheduler
-      Any
       CLIReporter
       CorrelatedLouvain
       PCA

docs/source/_autosummary/bioneuralnet.clustering.correlated_louvain.rst

@@ -17,7 +17,6 @@ bioneuralnet.clustering.correlated\_pagerank
    .. autosummary::
 
       ASHAScheduler
-      Any
       CLIReporter
       CorrelatedPageRank
       PCA

docs/source/_autosummary/bioneuralnet.clustering.correlated_pagerank.rst

@@ -21,7 +21,6 @@ bioneuralnet.downstream\_task.subject\_representation
    .. autosummary::
 
       ASHAScheduler
-      Any
       AutoEncoder
       CLIReporter
       PCA

docs/source/_autosummary/bioneuralnet.downstream_task.subject_representation.rst

@@ -15,7 +15,6 @@ bioneuralnet.external\_tools.smccnet
 
    .. autosummary::
 
-      Any
       Path
       SmCCNet