delaynet 0.3.2
Delay Propagation in Transportation Networks
License: BSD-3-Clause
Requires Python: >=3.11
Keywords: Delay Propagation, Transportation Networks, Information Flow, Information Theory

<div style="text-align: center; max-width: 700px; margin: 0 auto;">
  <a href="https://delaynet.readthedocs.io/">
    <picture>
      <source media="(prefers-color-scheme: light)" srcset="https://raw.githubusercontent.com/cbueth/delaynet/refs/heads/main/docs/_static/dn_banner.png">
      <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/cbueth/delaynet/refs/heads/main/docs/_static/dn_banner_dark.png">
      <img src="https://raw.githubusercontent.com/cbueth/delaynet/refs/heads/main/docs/_static/dn_banner.png" style="max-width: 80%; height: auto;" alt="delaynet logo">
    </picture>
  </a>
</div>

<div align="center">

<a href="">[![Documentation](https://readthedocs.org/projects/delaynet/badge/)](https://delaynet.readthedocs.io/)</a>
<a href="">[![PyPI Version](https://badge.fury.io/py/delaynet.svg)](https://pypi.org/project/delaynet/)</a>
<a href="">[![Python Version](https://img.shields.io/pypi/pyversions/delaynet)](https://pypi.org/project/delaynet/)</a>
<a href="">[![Anaconda Version](https://anaconda.org/conda-forge/delaynet/badges/version.svg)](https://anaconda.org/conda-forge/delaynet)</a>

</div>

<div align="center">

<a href="">[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16875272.svg)](https://doi.org/10.5281/zenodo.16875272)</a>
<a href="">[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)</a>
<a href="">[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-1.2-4baaaa.svg)](CODE_OF_CONDUCT.md)</a>

</div>

<div align="center">

<a href="">[![pipeline status](https://gitlab.ifisc.uib-csic.es/carlson/delaynet/badges/main/pipeline.svg)](https://gitlab.ifisc.uib-csic.es/carlson/delaynet/-/commits/main)</a>
<a href="">[![coverage report](https://gitlab.ifisc.uib-csic.es/carlson/delaynet/badges/main/coverage.svg)](https://gitlab.ifisc.uib-csic.es/carlson/delaynet/-/jobs)</a>

</div>

Python package to reconstruct and analyse delay functional networks from time series.
It provides tools for data preparation and detrending, multiple connectivity measures
(e.g. Granger causality, transfer entropy, correlations), optimal-lag network
reconstruction, and network analysis.

### Features

- Connectivity measures with hypothesis testing and optimal-lag reconstruction
- Network analysis: betweenness, eigenvector centrality, link density, transitivity,
  reciprocity, isolated nodes, global efficiency
- Null-model normalisation for metrics: report z-scores vs directed G(n,m) random
  graphs (igraph-based; binary-only; on-the-fly generation)
- Comprehensive documentation and examples
- Tested across multiple Python versions with high coverage

---

For details on how to use this package, see the
[Guide](https://delaynet.readthedocs.io/en/latest/guide/) or
the [Documentation](https://delaynet.readthedocs.io/en/latest/).

## Setup

This package can be installed from PyPI using pip:

```bash
pip install delaynet  # when public on PyPI
```

This will automatically install all the necessary dependencies as specified in the
`pyproject.toml` file. It is recommended to use a virtual environment, e.g., using
`conda`, `mamba` or `micromamba` (they can be used interchangeably).

```bash
micromamba create -n delay_net -c conda-forge python
micromamba activate delay_net
pip install delaynet  # or `micromamba install delaynet` when on conda-forge
```

### Quickstart

```python
import numpy as np
import delaynet as dn

# Generate toy data: 5 nodes, 300 time points
rng = np.random.default_rng(1520)
data = rng.standard_normal((300, 5))

# Compute a connectivity p-value and lag for one pair
pval, lag = dn.connectivity(data[:, 0], data[:, 1], metric="gc", lag_steps=10)
print(f"GC p-value={pval:.3g}, best lag={lag}")

# Reconstruct a delay network (p-value matrix and lag matrix)
weights, lags = dn.reconstruct_network(data, connectivity_measure="gc", lag_steps=5)
print(weights.shape, lags.shape)
```

## Development Setup

For development, we recommend using [`uv`](https://docs.astral.sh/uv/)  or `micromamba`
to create a virtual environment.
After cloning the repository, navigate to the root folder and
create the environment.
When using `uv`, the environment can be created with the following command:

```bash
uv sync
```

Or, if you prefer to use `micromamba`,
with the desired Python version and the dependencies.

```bash
micromamba create -n delay_net -c conda-forge -f requirements.txt
micromamba activate delay_net
```

Either way, using `pip` to install the package in editable mode will also install the
development dependencies.

```bash
pip install -e ".[all]"
```

Or, to let `micromamba` handle the dependencies, use the `requirements.txt` file

```bash
micromamba install --file requirements.txt
pip install --no-build-isolation --no-deps -e .
```

Now, the package can be imported and used in the python environment, from anywhere on
the system if the environment is activated.

## Set up Jupyter kernel

If you want to use `delaynet` with its environment `delay_net` in Jupyter, run:

```bash
pip install --user ipykernel
python -m ipykernel install --user --name=delay_net
```

This allows you to run Jupyter with the kernel `delay_net` (Kernel > Change Kernel >
im_env)

## Acknowledgments

This project has received funding from the European Research Council (ERC) under the
European Union's Horizon 2020 research and innovation programme (grant agreement No
851255).
This work was partially supported by the María de Maeztu project CEX2021-001164-M funded
by the MICIU/AEI/10.13039/501100011033 and FEDER, EU.

Copyright (c) 2024, delaynet Developers.
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:

1. Redistributions of source code must retain the above copyright
   notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above
   copyright notice, this list of conditions and the following
   disclaimer in the documentation and/or other materials provided
   with the distribution.

3. Neither the name of the copyright holder nor the names of its
   contributors may be used to endorse or promote products derived
   from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.