Setting up environment with VS Code

Software

1. Install VS code
2. Install Docker

Virtual environment

Create and Activate the new virtual environment see venv

GIT

Clone https://github.com/Australian-Imaging-Service/pipelines

VS code

1. Select the Python interpreter from venv (using cmd+shift+p -> Select: Python interpreter)
2. Check that the virtual environment is activated
3. In the test explorer tab, choose "Configure Python tests" and select Pytest

Licenses

Some of the packages used in pipelines require a license

• Freesurfer license can be obtained via Freesurfer registration
• The fMRIPrep pipeline uses a combination of tools from well-known software packages, including FSL, ANTs, FreeSurfer and AFNI. As such, it also requires a Freesurfer license

At the root of Pipelines project, create a licenses directory and upload the required licenses there

Optional

1. Clone other (AIS) GitHub repositories to be able to modify them
2. In order to use the project in editable mode (i.e. setuptools "develop mode") from a local project path, use pip install -e /path/to/your/repo