|Deletions are marked like this.||Additions are marked like this.|
|Line 1:||Line 1:|
|Line 13:||Line 12:|
=== Developing and Using the FreeSurfer Python Library ===
The freesurfer python library source, which contains general utilities and various submodules like `gems` and `samseg`, is developed in the repository under `repo/python/freesurfer`. In order to utilize this library for your own local development, you must point your `PYTHONPATH` at it:
This allows you to import your working version of the freesurfer library in any script or python interpreter. Alternatively, there is a nightly build of the freesurfer module, enabling import of the package without cloning or installing the full freesurfer repository. To access this, add the following to your `PYTHONPATH`. Currently, we build for python `3.5-3.8`.
FreeSurfer and LCN Python Development
To facilitate straightforward and reproducible python development in the lab, a local conda distribution for internal developers is installed at /autofs/cluster/freesurfer/python/linux. To use this version, make sure all calls to python or python3 point to this install by adding the following to your PATH:
Keep in mind there's also a python3 link in /usr/pubsw/bin, so it's important that /autofs/cluster/freesurfer/python/linux/bin comes before that in your PATH. If you want a python package installed into this distribution, email Andrew.
NOTE: This "lab" conda install is meant for quick access to python utilities. If you're a frequent python developer who uses multiple package versions or environments, please install your own local conda distribution. It will give you full access and control of the installed packages.