osl 0.1.1

OHBA Software Library

OHBA Software Library (OSL) in Python

Python version of https://github.com/OHBA-analysis/osl-core.

Installation

The recommended installation depends on your operating system. If you are installing on a Mac or Linux machine, we recommend:

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

Here, the -e indicates we have installed in 'editable mode'. This means if we execute git pull or make any local modifications these changes will be reflected when we import the package.

If you use the OHBA workstation (hbaws) with TigerVNC, we recommend:

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

On remote servers without displays specific package versions are required (related to source reconstruction visualisation). The following can be used to install on machines without a display:

git clone https://github.com/OHBA-analysis/oslpy.git
cd oslpy
conda env create -f envs/headless-server.yml
conda activate osl
pip install -e .

If you use the BMRC server, we recommend:

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

If you use the OHBA workstation (hbaws) via the terminal only, we recommend:

git clone https://github.com/OHBA-analysis/oslpy.git
cd oslpy
conda env create -f envs/hbaws-no-display.yml
conda activate osl-nd
pip install -e .

For Developers

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.