vbi 0.2.1__tar.gz → 0.3__tar.gz

{vbi-0.2.1/vbi.egg-info → vbi-0.3}/PKG-INFO

@@ -1,13 +1,14 @@
 Metadata-Version: 2.4
 Name: vbi
-Version: 0.2.1
+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-Expression: Apache-2.0
+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
@@ -23,14 +24,23 @@ Requires-Dist: nbconvert
 Requires-Dist: matplotlib
 Requires-Dist: setuptools-scm
 Requires-Dist: tqdm
-Requires-Dist: sbi
-Requires-Dist: torch
+Requires-Dist: autograd
 Requires-Dist: parameterized
 Requires-Dist: scikit-learn
-Requires-Dist: pycatch22
 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"
@@ -39,17 +49,28 @@ 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: cu
-Requires-Dist: cupy; extra == "cu"
 Provides-Extra: all
-Requires-Dist: pytest; 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"
-Requires-Dist: cupy; 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)
@@ -69,75 +90,84 @@ Dynamic: license-file
 </p>
 
 
-## installation
+## Installation
+
+### Quick Start
 
 ```bash
-    conda env create --name vbi python=3.10
-    conda activate vbi
-    # from pip: Recommended
-    pip install vbi
-    # from source: More recent update
-    git clone https://github.com/ins-amu/vbi.git
-    cd vbi
-    pip install .
-
-    # pip install -e .[all,dev,docs]
-    
-    # To skip C++ compilation, use the following environment variable and install from source:
-    SKIP_CPP=1 pip install -e . 
+# 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
 ```
 
-## Using Docker
+### 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  
 
-To use the Docker image, you can pull it from the GitHub Container Registry and run it as follows:
+### Using Docker
 
 ```bash
-    # Get it without building anything locally
-    # without GPU
-    docker run --rm -it -p 8888:8888 ghcr.io/ins-amu/vbi:main
+# Quick start with pre-built image
+docker run --rm -it -p 8888:8888 ghcr.io/ins-amu/vbi:main
 
-    # with GPU
-    docker run --gpus all --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
 
-    # or build it locally:
-    docker build -t vbi-project .                      # build
-    docker run --gpus all -it -p 8888:8888 vbi-project # use with gpu
+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 check :
+### Quick Verification
 
 ```python
+import vbi
+vbi.tests()
+vbi.test_imports()
+```
 
-    import vbi
-    vbi.tests()
-    vbi.test_imports()
-
-    
-  #              Dependency Check              
-  #                                         
-  #  Package      Version       Status        
-  #━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 
-  #  vbi          v0.1.3        ✅ 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
-  #  CUDA Version: 11.8
-  #  Device Name: NVIDIA RTX A5000
-  #  Total Memory: 23.68 GB
-  #  Compute Capability: 8.6
-
+**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
@@ -145,6 +175,14 @@ To use the Docker image, you can pull it from the GitHub Container Registry and
 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

{vbi-0.2.1 → vbi-0.3}/README.md

@@ -15,75 +15,84 @@
 </p>
 
 
-## installation
+## Installation
+
+### Quick Start
 
 ```bash
-    conda env create --name vbi python=3.10
-    conda activate vbi
-    # from pip: Recommended
-    pip install vbi
-    # from source: More recent update
-    git clone https://github.com/ins-amu/vbi.git
-    cd vbi
-    pip install .
-
-    # pip install -e .[all,dev,docs]
-    
-    # To skip C++ compilation, use the following environment variable and install from source:
-    SKIP_CPP=1 pip install -e . 
+# 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
 ```
 
-## Using Docker
+### 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  
 
-To use the Docker image, you can pull it from the GitHub Container Registry and run it as follows:
+### Using Docker
 
 ```bash
-    # Get it without building anything locally
-    # without GPU
-    docker run --rm -it -p 8888:8888 ghcr.io/ins-amu/vbi:main
+# Quick start with pre-built image
+docker run --rm -it -p 8888:8888 ghcr.io/ins-amu/vbi:main
 
-    # with GPU
-    docker run --gpus all --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
 
-    # or build it locally:
-    docker build -t vbi-project .                      # build
-    docker run --gpus all -it -p 8888:8888 vbi-project # use with gpu
+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 check :
+### Quick Verification
 
 ```python
+import vbi
+vbi.tests()
+vbi.test_imports()
+```
 
-    import vbi
-    vbi.tests()
-    vbi.test_imports()
-
-    
-  #              Dependency Check              
-  #                                         
-  #  Package      Version       Status        
-  #━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 
-  #  vbi          v0.1.3        ✅ 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
-  #  CUDA Version: 11.8
-  #  Device Name: NVIDIA RTX A5000
-  #  Total Memory: 23.68 GB
-  #  Compute Capability: 8.6
-
+**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
@@ -91,6 +100,14 @@ To use the Docker image, you can pull it from the GitHub Container Registry and
 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

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