The recommended installation depends on your operating system. OSL can be installed from source using:

git clone https://github.com/OHBA-analysis/osl.git
cd osl
conda env create -f envs/<os>.yml
conda activate osl
pip install -e .

where the environment file <os>.yml can be:

• linux.yml for a generic linux machine.
• m1_mac.yml if you are using a modern Mac computer.
• hbaws.yml if you are using an OHBA workstation at Oxford.
• bmrc.yml if you are using the BMRC at Oxford.

Note, all of the above environments come with Jupyter Notebook installed. The hbaws.yml and m1_mac.yml environments also comes with Spyder installed.

If you installed osl using the instructions above then to completely remove it simply delete the conda environment and delete the repo on your local machine:

conda env remove -n osl
rm -rf osl

Run tests:

cd osl
pytest tests

or to run a specific test:

cd osl/tests
pytest test_file_handling.py

Build documentation:

python setup.py build_sphinx

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