OSL: Electrophysiological Data Analysis Toolbox

Tools for analysing electrophysiological (M/EEG) data.

Documentation: https://osl-ephys.readthedocs.io/en/latest/.

Installation

We recommend installing osl-ephys in a conda environment.

Conda / mamba

Miniforge (conda) can be installed with:

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh
rm Miniforge3-$(uname)-$(uname -m).sh

Mamba (mamba) can be installed with:

conda install -n base -c conda-forge mamba

osl-ephys

osl-ephys can be installed from source code in a conda environment using the following.

git clone https://github.com/OHBA-analysis/osl-ephys.git
cd osl-ephys
mamba env create -f envs/osle.yml
conda activate osle
pip install -e .

Note, on a headless server you may need to set the following environment variable:

export PYVISTA_OFF_SCREEN=true

Oxford-specific computers

If you are installing on an OHBA workstation computer (hbaws) use:

git clone https://github.com/OHBA-analysis/osl-ephys.git
cd osl-ephys
mamba env create -f envs/hbaws.yml
conda activate osle
pip install -e .

Or on the BMRC cluster:

git clone https://github.com/OHBA-analysis/osl-ephys.git
cd osl-ephys
mamba env create -f envs/bmrc.yml
conda activate osle
pip install -e .

Remember to set the following environment variable:

export PYVISTA_OFF_SCREEN=true

Removing osl-ephys

Simply remove the conda environment and delete the repository:

conda env remove -n osle
rm -rf osl-ephys

For developers

Install all the requirements:

pip install -r requirements.txt

Run tests:

cd osl_ephys
pytest tests

or to run a specific test:

cd osl_ephys/tests
pytest test_file_handling.py

Build documentation locally:

sphinx-build -b html doc/source build

Compiled docs can be found in doc/build/html/index.html.