esi-syncopy 2023.9

Systems Neuroscience Computing in Python

Syncopy aims to be a user-friendly toolkit for large-scale electrophysiology data-analysis in Python. We strive to achieve the following goals:

1. Syncopy is a fully open source Python environment for electrophysiology data analysis.

2. Syncopy is scalable and built for very large datasets. It automatically makes use of available computing resources and is developed with built-in parallelism in mind.

3. Syncopy is compatible with FieldTrip. Data and results can be loaded into MATLAB and Python, and parameter names and function call syntax are as similar as possible.

Syncopy is developed at the Ernst Strüngmann Institute (ESI) gGmbH for Neuroscience in Cooperation with Max Planck Society and released free of charge under the BSD 3-Clause “New” or “Revised” License.

Installation

We recommend to install SynCoPy into a new conda environment:

1. Install the Anaconda Distribution for your Operating System if you do not yet have it.

2. Start a new terminal.

   • You can do this by starting `Anaconda navigator`, selecting `Environments` in the left tab, selecting the `base (root)` environment, and clicking the green play button and then `Open Terminal`.

   • Alternatively, under Linux, you can just type `bash` in your active terminal to start a new session.

You should see a terminal with a command prompt that starts with `(base)`, indicating that you are in the conda `base` environment.

Now we create a new environment named `syncopy` and install syncopy into this environment:

conda create -y --name syncopy
conda activate syncopy
conda install -y -c conda-forge esi-syncopy

Getting Started

Please visit our online documentation.

git clone https://github.com/esi-neuroscience/syncopy.git
cd syncopy/
conda env create --name syncopy-dev --file syncopy.yml
conda activate syncopy-dev
pip install -e .

python -m pytest -k "not parallel"