vbi 0.2.2__tar.gz → 0.3__tar.gz

vbi-0.3/PKG-INFO

@@ -0,0 +1,223 @@
+Metadata-Version: 2.4
+Name: vbi
+Version: 0.3
+Summary: Virtual brain inference.
+Author-email: Abolfazl Ziaeemehr <a.ziaeemehr@gmail.com>, Meysam Hashemi <meysam.hashemi@gmail.com>, Marmaduke Woodman <marmaduke.woodman@gmail.com>
+License: MIT
+Project-URL: homepage, https://ziaeemehr.github.io/vbi_paper/
+Project-URL: repository, https://github.com/Ziaeemehr/vbi_paper
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: wheel
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: numba
+Requires-Dist: h5py
+Requires-Dist: pandas
+Requires-Dist: networkx
+Requires-Dist: nbconvert
+Requires-Dist: matplotlib
+Requires-Dist: setuptools-scm
+Requires-Dist: tqdm
+Requires-Dist: autograd
+Requires-Dist: parameterized
+Requires-Dist: scikit-learn
+Requires-Dist: pytest
+Requires-Dist: swig
+Requires-Dist: rich
+Requires-Dist: corner
+Provides-Extra: light
+Provides-Extra: light-gpu
+Requires-Dist: cupy; extra == "light-gpu"
+Provides-Extra: inference
+Requires-Dist: sbi; extra == "inference"
+Requires-Dist: torch; extra == "inference"
+Provides-Extra: inference-gpu
+Requires-Dist: sbi; extra == "inference-gpu"
+Requires-Dist: torch; extra == "inference-gpu"
+Requires-Dist: cupy; extra == "inference-gpu"
+Provides-Extra: dev
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: numpydoc; extra == "docs"
+Requires-Dist: nbformat; extra == "docs"
+Requires-Dist: nbsphinx; extra == "docs"
+Requires-Dist: cloud_sptheme; extra == "docs"
+Requires-Dist: sphinx_bootstrap_theme; extra == "docs"
+Provides-Extra: all
+Requires-Dist: sbi; extra == "all"
+Requires-Dist: torch; extra == "all"
+Requires-Dist: cupy; extra == "all"
+Requires-Dist: pycatch22; extra == "all"
+Requires-Dist: sphinx; extra == "all"
+Requires-Dist: numpydoc; extra == "all"
+Requires-Dist: nbformat; extra == "all"
+Requires-Dist: nbsphinx; extra == "all"
+Requires-Dist: cloud_sptheme; extra == "all"
+Requires-Dist: sphinx_bootstrap_theme; extra == "all"
+Provides-Extra: all-docker
+Requires-Dist: sbi; extra == "all-docker"
+Requires-Dist: torch; extra == "all-docker"
+Requires-Dist: sphinx; extra == "all-docker"
+Requires-Dist: numpydoc; extra == "all-docker"
+Requires-Dist: nbformat; extra == "all-docker"
+Requires-Dist: nbsphinx; extra == "all-docker"
+Requires-Dist: cloud_sptheme; extra == "all-docker"
+Requires-Dist: sphinx_bootstrap_theme; extra == "all-docker"
+Provides-Extra: cu
+Requires-Dist: cupy; extra == "cu"
+Dynamic: license-file
+
+[![Test](https://github.com/ins-amu/vbi/actions/workflows/tests.yml/badge.svg)](https://github.com/ins-amu/vbi/actions/workflows/tests.yml)
+[![Documentation Status](https://readthedocs.org/projects/vbi/badge/?version=latest)](https://vbi.readthedocs.io/latest/)
+[![DOI](https://zenodo.org/badge/681090816.svg)](https://doi.org/10.5281/zenodo.14795543)
+[![Docker Build](https://github.com/ins-amu/vbi/actions/workflows/docker-image.yml/badge.svg)](https://github.com/ins-amu/vbi/actions/workflows/docker-image.yml)
+<!-- [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ins-amu/vbi/main?labpath=docs/examples/intro.ipynb) -->
+
+
+# VBI: Virtual Brain Inference
+---
+[Getting Started](https://github.com/ins-amu/vbi/tree/main/docs/examples) |
+[Documentation](https://vbi.readthedocs.io/latest/) | 
+
+<p align="center">
+<img src="https://github.com/Ziaeemehr/vbi_paper/blob/main/vbi_log.png"  width="250">
+</p>
+
+
+## Installation
+
+### Quick Start
+
+```bash
+# Create conda environment (recommended)
+conda create --name vbi python=3.10
+conda activate vbi
+
+
+# Install VBI
+export SKIP_CPP=1                  # To skip C++ compilation
+pip install vbi                    # Light version (CPU only)
+pip install vbi[inference]         # With parameter inference
+pip install vbi[inference-gpu]     # Full functionality with GPU support
+```
+
+### Installation Options
+
+- **`pip install vbi`** - Light version with CPU simulation only  
+- **`pip install vbi[inference]`** - Adds parameter inference capabilities  
+- **`pip install vbi[inference-gpu]`** - Full functionality with GPU acceleration  
+
+### Using Docker
+
+```bash
+# Quick start with pre-built image
+docker run --rm -it -p 8888:8888 ghcr.io/ins-amu/vbi:main
+
+# With GPU support
+docker run --gpus all --rm -it -p 8888:8888 ghcr.io/ins-amu/vbi:main
+```
+
+### Other Installation Methods
+
+For detailed installation instructions including:
+- **Installing from source**
+- **Windows-specific installation**  
+- **Building Docker locally**
+- **Platform-specific guides** (Google Colab, EBRAINS)
+- **Troubleshooting**
+
+See our comprehensive [Installation Guide](https://vbi.readthedocs.io/latest/installation.html) in the documentation.
+
+### Quick Verification
+
+```python
+import vbi
+vbi.tests()
+vbi.test_imports()
+```
+
+**Example output:**
+```
+              Dependency Check              
+                                         
+  Package      Version       Status        
+━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 
+  vbi          v0.2.1        ✅ Available  
+  numpy        1.24.4        ✅ Available  
+  scipy        1.10.1        ✅ Available  
+  matplotlib   3.7.5         ✅ Available  
+  sbi          0.22.0        ✅ Available  
+  torch        2.4.1+cu121   ✅ Available  
+  cupy         12.3.0        ✅ Available  
+                                          
+  Torch GPU available: True
+  Torch device count: 1
+  Torch CUDA version: 12.1
+  CuPy GPU available: True
+  CuPy device count: 1
+```
+
+## Getting Started
+
+- **📚 [Documentation](https://vbi.readthedocs.io/latest/)** - Complete guides and API reference
+- **🎯 [Examples](https://github.com/ins-amu/vbi/tree/main/docs/examples)** - Jupyter notebooks with tutorials
+- **🚀 [Quick Start](https://vbi.readthedocs.io/latest/examples_overview.html)** - Choose your computational backend
+
+
+## Feedback and Contributions
+
+We welcome contributions to the VBI project! If you have suggestions, bug reports, or feature requests, please open an issue on our [GitHub repository](https://github.com/ins-amu/vbi/issues). To contribute code, fork the repository, create a new branch for your feature or bugfix, and submit a pull request. Make sure to follow our coding standards and include tests for your changes. For detailed guidelines, please refer to our [CONTRIBUTING.md](https://github.com/ins-amu/vbi/blob/main/CONTRIBUTING.md) file. Thank you for helping us improve VBI!
+
+
+## GDPR Compliance
+
+VBI itself does not collect, store, or transmit personal data.  
+Users may provide their own datasets locally; in such cases, the responsibility for GDPR compliance lies with the user and their execution environment.  
+
+For details, see [GDPR_COMPLIANCE.md](GDPR_COMPLIANCE.md).
+
+
+## Citation
+
+```bibtex
+@article{VBI, 
+title={Virtual Brain Inference (VBI): A flexible and integrative toolkit for efficient probabilistic inference on virtual brain models},
+author={Ziaeemehr, Abolfazl and Woodman, Marmaduke and Domide, Lia and Petkoski, Spase and Jirsa, Viktor and Hashemi, Meysam},
+DOI={10.7554/elife.106194.1}, 
+url={http://dx.doi.org/10.7554/eLife.106194.1}, 
+publisher={eLife Sciences Publications, Ltd}, 
+year={2025}, 
+abstract = {Network neuroscience has proven essential for understanding the principles and mechanisms
+underlying complex brain (dys)function and cognition. In this context, whole-brain network modeling–
+also known as virtual brain modeling–combines computational models of brain dynamics (placed at each network node)
+with individual brain imaging data (to coordinate and connect the nodes), advancing our understanding of
+the complex dynamics of the brain and its neurobiological underpinnings. However, there remains a critical
+need for automated model inversion tools to estimate control (bifurcation) parameters at large scales
+associated with neuroimaging modalities, given their varying spatio-temporal resolutions.
+This study aims to address this gap by introducing a flexible and integrative toolkit for efficient Bayesian inference
+on virtual brain models, called Virtual Brain Inference (VBI). This open-source toolkit provides fast simulations,
+taxonomy of feature extraction, efficient data storage and loading, and probabilistic machine learning algorithms,
+enabling biophysically interpretable inference from non-invasive and invasive recordings.
+Through in-silico testing, we demonstrate the accuracy and reliability of inference for commonly used
+whole-brain network models and their associated neuroimaging data. VBI shows potential to improve hypothesis
+evaluation in network neuroscience through uncertainty quantification, and contribute to advances in precision
+medicine by enhancing the predictive power of virtual brain models.}
+}
+```
+
+This research has received funding from:
+
+- EU's Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreements:
+  - No. 101147319 (EBRAINS 2.0 Project)
+  - No. 101137289 (Virtual Brain Twin Project)
+  - No. 101057429 (project environMENTAL)
+- Government grant managed by the Agence Nationale de la Recherche:
+  - Reference ANR-22-PESN-0012 (France 2030 program)
+
+The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

vbi-0.3/README.md

@@ -0,0 +1,148 @@
+[![Test](https://github.com/ins-amu/vbi/actions/workflows/tests.yml/badge.svg)](https://github.com/ins-amu/vbi/actions/workflows/tests.yml)
+[![Documentation Status](https://readthedocs.org/projects/vbi/badge/?version=latest)](https://vbi.readthedocs.io/latest/)
+[![DOI](https://zenodo.org/badge/681090816.svg)](https://doi.org/10.5281/zenodo.14795543)
+[![Docker Build](https://github.com/ins-amu/vbi/actions/workflows/docker-image.yml/badge.svg)](https://github.com/ins-amu/vbi/actions/workflows/docker-image.yml)
+<!-- [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ins-amu/vbi/main?labpath=docs/examples/intro.ipynb) -->
+
+
+# VBI: Virtual Brain Inference
+---
+[Getting Started](https://github.com/ins-amu/vbi/tree/main/docs/examples) |
+[Documentation](https://vbi.readthedocs.io/latest/) | 
+
+<p align="center">
+<img src="https://github.com/Ziaeemehr/vbi_paper/blob/main/vbi_log.png"  width="250">
+</p>
+
+
+## Installation
+
+### Quick Start
+
+```bash
+# Create conda environment (recommended)
+conda create --name vbi python=3.10
+conda activate vbi
+
+
+# Install VBI
+export SKIP_CPP=1                  # To skip C++ compilation
+pip install vbi                    # Light version (CPU only)
+pip install vbi[inference]         # With parameter inference
+pip install vbi[inference-gpu]     # Full functionality with GPU support
+```
+
+### Installation Options
+
+- **`pip install vbi`** - Light version with CPU simulation only  
+- **`pip install vbi[inference]`** - Adds parameter inference capabilities  
+- **`pip install vbi[inference-gpu]`** - Full functionality with GPU acceleration  
+
+### Using Docker
+
+```bash
+# Quick start with pre-built image
+docker run --rm -it -p 8888:8888 ghcr.io/ins-amu/vbi:main
+
+# With GPU support
+docker run --gpus all --rm -it -p 8888:8888 ghcr.io/ins-amu/vbi:main
+```
+
+### Other Installation Methods
+
+For detailed installation instructions including:
+- **Installing from source**
+- **Windows-specific installation**  
+- **Building Docker locally**
+- **Platform-specific guides** (Google Colab, EBRAINS)
+- **Troubleshooting**
+
+See our comprehensive [Installation Guide](https://vbi.readthedocs.io/latest/installation.html) in the documentation.
+
+### Quick Verification
+
+```python
+import vbi
+vbi.tests()
+vbi.test_imports()
+```
+
+**Example output:**
+```
+              Dependency Check              
+                                         
+  Package      Version       Status        
+━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 
+  vbi          v0.2.1        ✅ Available  
+  numpy        1.24.4        ✅ Available  
+  scipy        1.10.1        ✅ Available  
+  matplotlib   3.7.5         ✅ Available  
+  sbi          0.22.0        ✅ Available  
+  torch        2.4.1+cu121   ✅ Available  
+  cupy         12.3.0        ✅ Available  
+                                          
+  Torch GPU available: True
+  Torch device count: 1
+  Torch CUDA version: 12.1
+  CuPy GPU available: True
+  CuPy device count: 1
+```
+
+## Getting Started
+
+- **📚 [Documentation](https://vbi.readthedocs.io/latest/)** - Complete guides and API reference
+- **🎯 [Examples](https://github.com/ins-amu/vbi/tree/main/docs/examples)** - Jupyter notebooks with tutorials
+- **🚀 [Quick Start](https://vbi.readthedocs.io/latest/examples_overview.html)** - Choose your computational backend
+
+
+## Feedback and Contributions
+
+We welcome contributions to the VBI project! If you have suggestions, bug reports, or feature requests, please open an issue on our [GitHub repository](https://github.com/ins-amu/vbi/issues). To contribute code, fork the repository, create a new branch for your feature or bugfix, and submit a pull request. Make sure to follow our coding standards and include tests for your changes. For detailed guidelines, please refer to our [CONTRIBUTING.md](https://github.com/ins-amu/vbi/blob/main/CONTRIBUTING.md) file. Thank you for helping us improve VBI!
+
+
+## GDPR Compliance
+
+VBI itself does not collect, store, or transmit personal data.  
+Users may provide their own datasets locally; in such cases, the responsibility for GDPR compliance lies with the user and their execution environment.  
+
+For details, see [GDPR_COMPLIANCE.md](GDPR_COMPLIANCE.md).
+
+
+## Citation
+
+```bibtex
+@article{VBI, 
+title={Virtual Brain Inference (VBI): A flexible and integrative toolkit for efficient probabilistic inference on virtual brain models},
+author={Ziaeemehr, Abolfazl and Woodman, Marmaduke and Domide, Lia and Petkoski, Spase and Jirsa, Viktor and Hashemi, Meysam},
+DOI={10.7554/elife.106194.1}, 
+url={http://dx.doi.org/10.7554/eLife.106194.1}, 
+publisher={eLife Sciences Publications, Ltd}, 
+year={2025}, 
+abstract = {Network neuroscience has proven essential for understanding the principles and mechanisms
+underlying complex brain (dys)function and cognition. In this context, whole-brain network modeling–
+also known as virtual brain modeling–combines computational models of brain dynamics (placed at each network node)
+with individual brain imaging data (to coordinate and connect the nodes), advancing our understanding of
+the complex dynamics of the brain and its neurobiological underpinnings. However, there remains a critical
+need for automated model inversion tools to estimate control (bifurcation) parameters at large scales
+associated with neuroimaging modalities, given their varying spatio-temporal resolutions.
+This study aims to address this gap by introducing a flexible and integrative toolkit for efficient Bayesian inference
+on virtual brain models, called Virtual Brain Inference (VBI). This open-source toolkit provides fast simulations,
+taxonomy of feature extraction, efficient data storage and loading, and probabilistic machine learning algorithms,
+enabling biophysically interpretable inference from non-invasive and invasive recordings.
+Through in-silico testing, we demonstrate the accuracy and reliability of inference for commonly used
+whole-brain network models and their associated neuroimaging data. VBI shows potential to improve hypothesis
+evaluation in network neuroscience through uncertainty quantification, and contribute to advances in precision
+medicine by enhancing the predictive power of virtual brain models.}
+}
+```
+
+This research has received funding from:
+
+- EU's Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreements:
+  - No. 101147319 (EBRAINS 2.0 Project)
+  - No. 101137289 (Virtual Brain Twin Project)
+  - No. 101057429 (project environMENTAL)
+- Government grant managed by the Agence Nationale de la Recherche:
+  - Reference ANR-22-PESN-0012 (France 2030 program)
+
+The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

vbi-0.3/docs/API.rst

@@ -0,0 +1,250 @@
+.. raw:: html
+
+   <link rel="stylesheet" type="text/css" href="_static/custom.css">
+
+
+API and documentation
+=====================
+
+
+C++ models
+-------------------------
+
+
+vbi.models.cpp.jansen_rit
+~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cpp.jansen_rit
+        :members:
+        :undoc-members:
+
+vbi.models.cpp.km
+~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cpp.km
+        :members:
+        :undoc-members:
+
+vbi.models.cpp.mpr 
+~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cpp.mpr
+        :members:
+        :undoc-members:
+
+vbi.models.cpp.vep 
+~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cpp.vep
+        :members:
+        :undoc-members:
+
+vbi.models.cpp.wc 
+~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cpp.wc
+        :members:
+        :undoc-members:
+
+vbi.models.cpp.damp_oscillator
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cpp.damp_oscillator
+        :members:
+        :undoc-members:
+
+
+Cupy models 
+-----------
+
+vbi.models.cupy.mpr 
+~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cupy.mpr
+        :members:
+        :undoc-members:
+
+vbi.models.cupy.ghb
+~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cupy.ghb
+        :members:
+        :undoc-members:
+
+vbi.models.cupy.jansen_rit
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cupy.jansen_rit
+        :members:
+        :undoc-members:
+
+vbi.models.cupy.utils 
+~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cupy.utils
+        :members:
+        :undoc-members:
+
+vbi.models.cupy.bold
+~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cupy.bold
+        :members:
+        :undoc-members:
+
+vbi.models.cupy.km
+~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cupy.km
+        :members:
+        :undoc-members:
+
+vbi.models.cupy.mpr_modified_bold
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cupy.mpr_modified_bold
+        :members:
+        :undoc-members:
+
+.. vbi.models.cupy.mpr_multi_gpu
+.. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+..     .. automodule:: vbi.models.cupy.mpr_multi_gpu
+..         :members:
+..         :undoc-members:
+
+vbi.models.cupy.wilson_cowan
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cupy.wilson_cowan
+        :members:
+        :undoc-members:
+
+vbi.models.cupy.ww
+~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.cupy.ww
+        :members:
+        :undoc-members:
+
+
+Numba models 
+------------
+
+vbi.models.numba.damp_oscillator
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.numba.damp_oscillator
+        :members:
+        :undoc-members:
+
+vbi.models.numba.ghb
+~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.numba.ghb
+        :members:
+        :undoc-members:
+
+vbi.models.numba.jansen_rit
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.numba.jansen_rit
+        :members:
+        :undoc-members:
+
+vbi.models.numba.mpr
+~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.numba.mpr
+        :members:
+        :undoc-members:
+
+vbi.models.numba.vep
+~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.numba.vep
+        :members:
+        :undoc-members:
+
+vbi.models.numba.wilson_cowan
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.numba.wilson_cowan
+        :members:
+        :undoc-members:
+
+vbi.models.numba.ww
+~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.numba.ww
+        :members:
+        :undoc-members:
+
+
+PyTorch models 
+--------------
+
+vbi.models.pytorch.ww_sde_kong
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.pytorch.ww_sde_kong
+        :members:
+        :undoc-members:
+
+
+TVB-K models 
+------------
+
+vbi.models.tvbk.tvbk_wrapper
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.tvbk.tvbk_wrapper
+        :members:
+        :undoc-members:
+
+vbi.models.tvbk.utils
+~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.models.tvbk.utils
+        :members:
+        :undoc-members:
+
+
+Core VBI modules
+----------------
+
+vbi.inference
+~~~~~~~~~~~~~
+    .. automodule:: vbi.inference
+        :members:
+        :undoc-members:
+
+vbi.utils
+~~~~~~~~~
+    .. automodule:: vbi.utils
+        :members:
+        :undoc-members:
+
+vbi.optional_deps
+~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.optional_deps
+        :members:
+        :undoc-members:
+
+
+Feature extraction
+------------------
+
+vbi.feature_extraction.calc_features
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.feature_extraction.calc_features
+        :members:
+        :undoc-members:
+
+vbi.feature_extraction.features
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.feature_extraction.features
+        :members:
+        :undoc-members:
+
+vbi.feature_extraction.features_settings
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.feature_extraction.features_settings
+        :members:
+        :undoc-members:
+
+vbi.feature_extraction.features_utils
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.feature_extraction.features_utils
+        :members:
+        :undoc-members:
+
+vbi.feature_extraction.utility
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.feature_extraction.utility
+        :members:
+        :undoc-members:
+
+
+Dataset
+-------------------------
+
+vbi.dataset
+~~~~~~~~~~~~~~~~~~~~~~~~~
+    .. automodule:: vbi.dataset
+        :members:
+        :undoc-members:

vbi-0.3/docs/Examples.rst

@@ -0,0 +1,39 @@
+.. raw:: html
+
+   <link rel="stylesheet" type="text/css" href="_static/custom.css">
+
+Examples (Legacy)
+=================
+
+.. note::
+   This page contains the complete list of examples. For better organization, see:
+   
+   - :doc:`examples_overview` - Simulation examples organized by backend
+   - :doc:`inference_examples` - Inference methods and tutorials
+
+Complete Example List
+---------------------
+
+.. toctree::
+   :maxdepth: 2
+
+   examples/intro
+   examples/intro_feature
+   examples/distributions
+   examples/do_cpp
+   examples/do_nb
+   examples/vep_sde
+   examples/vep_sde_numba
+   examples/mpr_sde_cupy
+   examples/mpr_sde_numba
+   examples/mpr_sde_cpp
+   examples/mpr_tvbk
+   examples/jansen_rit_sde_cpp
+   examples/jansen_rit_sde_cupy
+   examples/jansen_rit_sde_numba
+   examples/ww_sde_torch_kong
+   examples/ghb_sde_cupy
+   examples/wilson_cowan_cupy
+   examples/wilson_cowan_sde_numba
+   examples/ww_full_sde_cupy
+   examples/ww_full_sde_numba