Metadata-Version: 2.3
Name: connectome_analysis
Version: 1.0.0
Summary: Methods for network analysis of graphs coming from brain models and activity on them
License: AGPL-3.0-or-later
Author: Daniela Egas Santander
Author-email: daniela.egas.math@gmail.com
Requires-Python: >=3.9,<3.13
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Typing :: Typed
Requires-Dist: bigrandomgraphs (>=0.0.4)
Requires-Dist: ipykernel (>=6.29.5,<7.0.0)
Requires-Dist: matplotlib
Requires-Dist: networkx
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: progressbar (==2.5)
Requires-Dist: pyflagser
Requires-Dist: pyflagsercount (>=0.2.41)
Requires-Dist: scikit-network
Requires-Dist: scipy
Requires-Dist: tables (>3.8)
Requires-Dist: tqdm
Project-URL: Documentation, https://openbraininstitute.github.io/connectome-analysis/
Project-URL: Homepage, https://openbraininstitute.github.io/connectome-analysis/
Project-URL: Repository, https://github.com/openbraininstitute/connectome-analysis.git
Description-Content-Type: text/markdown

# Connectome Analysis

#### General functions to analyze connectomes from a topological perspective.  

![](docs/banner_BPP_connalysis.jpg)

---

## Documentation 

See our [**documentation**](https://openbraininstitute.github.io/connectome-analysis/) for detailed explanations including examples and tutorials.

See our [**source code**](src/connalysis) for implementation details.

## User installation

```sh
pip install git+https://github.com/openbraininstitute/connectome-analysis.git
```

---

## Citation  

[![DOI:10.1101/2024.03.15.585196](http://img.shields.io/badge/DOI-10.1101/2024.03.15.585196-B31B1B.svg)](https://doi.org/10.1101/2024.03.15.585196)

If you use this software, kindly use the following BibTeX entry for citation:

```
@article{egas2024efficiency,
  title={Efficiency and reliability in biological neural network architectures},
  author={Egas Santander, Daniela and Pokorny, Christoph and Ecker, Andr{\'a}s and Lazovskis, J{\=a}nis and Santoro, Matteo and Smith, Jason P and Hess, Kathryn and Levi, Ran and Reimann, Michael W},
  journal={bioRxiv},
  pages={2024--03},
  year={2024},
  publisher={Cold Spring Harbor Laboratory},
  doi = {10.1101/2024.03.15.585196}
}
```

---
## Acknowledgements & Funding

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

Copyright (c) 2023-2024 Blue Brain Project / EPFL.<br>
Copyright (c) 2025 Open Brain Institute.

---

## Development installation

* Clone this repository
* Requirements:
  * [Poetry](https://python-poetry.org/)
  * [gcc](https://gcc.gnu.org/) 9+
  * [CMake](https://cmake.org/)
  * Python 3.9+

* Create a virtual environment and install the dependencies

```sh
poetry install
```

CMake may have difficulties to find the right compilers to compile the C++ code. 
If that is the case, you have to specify the path to the compilers yourself:

```sh
CC=/path/to/gcc CXX=/path/to/g++ poetry install
```

This is especially important on MacOS.

* Activate the virtual environment

```sh
poetry shell
```

* Testing

```sh
poetry run pytest tests
```

### Documentation

The documentation is automatically generated from the content of the [docs directory](./docs) and from the docstrings
 of the public signatures of the source code. The documentation is updated and published as a [Github project page
 ](https://pages.github.com/) automatically as part each release.

