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| 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`: | If you're a frequent python developer who uses multiple package versions or environments, please install your own local [[https://docs.conda.io/en/latest/miniconda.html|mini-conda distribution]]. It will give you full access and control of the installed packages. To facilitate quick access to python utilities 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`: |
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| 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 [[https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html|conda distribution]]. It will give you full access and control of the installed packages. === 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: {{{ export PYTHONPATH=/path/to/your/freesurfer-repository/python:$PYTHONPATH }}} This allows you to import your working version of the freesurfer library in any script or python interpreter. Alternatively, there is a nightly build of the freesurfer module, enabling import of the package without cloning or installing the full freesurfer repository. To access this, add the following to your `PYTHONPATH`. Currently, we build for python `3.5-3.8`. {{{ export PYTHONPATH=/autofs/cluster/freesurfer/python/fsmodule:$PYTHONPATH }}} |
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 [[avnish.kumar@mgh.harvard.edu|Avnish]]. |
FreeSurfer and LCN Python Development
If you're a frequent python developer who uses multiple package versions or environments, please install your own local mini-conda distribution. It will give you full access and control of the installed packages.
To facilitate quick access to python utilities 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:
export PATH=/autofs/cluster/freesurfer/python/linux/bin:$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 Avnish.