vbi 0.1.3__tar.gz

vbi-0.1.3/.github/workflows/docker-image.yml

@@ -0,0 +1,51 @@
+name: build & push Docker image to ghcr
+
+on:
+  push:
+    # branches:
+    #   - main  # Runs when pushing to develop branch
+    tags:
+      - v*  # Runs when pushing tags starting with 'v'
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ins-amu/vbi  # Replace with your organization/package name
+
+jobs:
+  docker-build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.CR_PAT }}  # Use the PAT here
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=ref,event=branch
+            type=ref,event=tag
+
+        # Debugging Steps
+      - name: Debug Metadata
+        run: |
+          echo "Tags: ${{ steps.meta.outputs.tags }}"
+          echo "Labels: ${{ steps.meta.outputs.labels }}"
+
+      - name: Debug Docker Info
+        run: docker info
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

vbi-0.1.3/.github/workflows/tests.yml

@@ -0,0 +1,24 @@
+name: Test
+
+on: [push]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install .
+
+    - name: Compile C++ code
+      run: |
+        cd vbi/models/cpp/_src
+        make
+    - name: Run tests
+      run: |
+        python -m pytest

vbi-0.1.3/.gitignore

@@ -0,0 +1,45 @@
+*.pt
+*.txt
+*.png
+*.pdf
+__pycache__/
+build/
+_build/
+.vscode/
+vbi.egg-info/
+html/
+*/cpp/_src*.py
+*/cpp/_src/*.py
+.ipynb_checkpoints/
+latex/
+html/
+
+sbi-logs/
+e/
+e_*/
+_e/
+*/*/*/_src/*.py
+
+*_wrap.cpp
+*_wrap.cxx
+*.o
+*.dat
+*.so
+*.npz
+*.bin
+*.sh
+*.gz
+*.pickle
+*.jpeg
+*.pickle
+*.pkl
+.DS_Store
+.editorconfig
+*.mat
+*.csv
+*.json
+tt.ipynb
+*.egg
+examples_dev/
+
+vbi/models/cupy/_mpr.py

vbi-0.1.3/.readthedocs.yaml

@@ -0,0 +1,19 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+  apt_packages:
+    - swig
+    - build-essential
+
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+  - method: pip
+    path: .
+  - requirements: docs/requirements.txt

vbi-0.1.3/CONTRIBUTING.md

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+# Contributing to VBI
+
+Thank you for your interest in contributing to the VBI project! We welcome contributions in the form of bug reports, feature requests, and code contributions. Please follow the guidelines below to ensure a smooth contribution process.
+
+## Reporting Issues
+
+If you encounter any bugs or have feature requests, please open an issue on our [GitHub repository](https://github.com/ins-amu/vbi/issues). Provide as much detail as possible, including steps to reproduce the issue and any relevant logs or screenshots.
+
+## Code Contributions
+
+### Getting Started
+
+1. Fork the repository on GitHub.
+2. Clone your forked repository to your local machine:
+    ```sh
+    git clone https://github.com/your-username/vbi.git
+    cd vbi
+    ```
+3. Install the required dependencies:
+    ```sh
+    pip install .
+    # For development, install additional dependencies:
+    pip install -e .[all,dev,docs]
+    ```
+
+### Making Changes
+
+1. Create a new branch for your feature or bugfix:
+    ```sh
+    git checkout -b my-feature-branch
+    ```
+2. Make your changes in the codebase.
+3. Ensure your code follows our coding standards and includes tests for any new functionality.
+4. Run the tests to verify your changes:
+    ```sh
+    pytest
+    ```
+
+### Submitting a Pull Request
+
+1. Push your changes to your forked repository:
+    ```sh
+    git push origin my-feature-branch
+    ```
+2. Open a pull request on the original repository. Provide a clear description of your changes and any relevant issue numbers.
+
+### Code Review
+
+Your pull request will be reviewed by one of the project maintainers. Please be responsive to any feedback and make necessary changes. Once your pull request is approved, it will be merged into the main branch.
+
+## Coding Standards
+
+- Follow PEP 8 for Python code style.
+- Write clear and concise commit messages.
+- Include docstrings for all functions and classes.
+- Write tests for any new functionality or bugfixes.
+
+## Documentation
+
+If you are contributing to the documentation, make sure to update the relevant `.rst` files in the `docs` directory. You can build the documentation locally using:
+```sh
+cd docs
+make html
+```

vbi-0.1.3/LICENSE

@@ -0,0 +1,201 @@
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vbi-0.1.3/MANIFEST.in

@@ -0,0 +1,7 @@
+include LICENSE
+graft docs
+prune docs/_build
+graft vbi/models/cpp/_src
+graft vbi/dataset
+
+recursive-include vbi/feature_extraction *.json *.jar

vbi-0.1.3/PKG-INFO

@@ -0,0 +1,166 @@
+Metadata-Version: 2.4
+Name: vbi
+Version: 0.1.3
+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: sbi
+Requires-Dist: torch
+Requires-Dist: parameterized
+Requires-Dist: scikit-learn
+Requires-Dist: pycatch22
+Requires-Dist: pytest
+Requires-Dist: swig
+Requires-Dist: rich
+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: cu
+Requires-Dist: cupy; extra == "cu"
+Provides-Extra: all
+Requires-Dist: pytest; 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"
+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
+
+```bash
+    conda env create --name vbi python=3.10
+    conda activate vbi
+    git clone https://github.com/ins-amu/vbi.git
+    cd vbi
+    pip install .
+
+    # pip install -e .[all,dev,docs]
+```
+
+## Using Docker
+
+To use the Docker image, you can pull it from the GitHub Container Registry and run it as follows:
+
+```bash
+    # Get it without building anything locally
+    # without GPU
+    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
+
+
+    # or build it locally:
+    docker build -t vbi-project .                      # build
+    docker run --gpus all -it -p 8888:8888 vbi-project # use with gpu
+
+```    
+
+- Quick check :
+
+```python
+
+    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
+
+```
+
+
+## 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!
+
+
+## Citation
+
+```bibtex
+@article{VBI,
+  author = {Ziaeemehr, Abolfazl and Woodman, Marmaduke and Domide, Lia and Petkoski, Spase and Jirsa, Viktor and Hashemi, Meysam},
+  title = {Virtual Brain Inference (VBI): A flexible and integrative toolkit for efficient probabilistic inference on virtual brain models},
+  journal = {bioRxiv},
+  year = {2025},
+  doi = {10.1101/2025.01.21.633922},
+  url = {https://doi.org/10.1101/2025.01.21.633922},
+  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 and across 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.