====== virtualenv ======
Run python code in a virtual environment to isolate specific dependencies from system (or other user or application) changes.

On [[:tools:rhea]], ''pyenv'' manages python versions and a plugin ''pyenv virtualenv'' manages virtual environments within those versions. Alternatives (not on rhea) include ''poetry'' and ''pipx''.

===== preproc =====

For [[::tools:preprocessfunctional]]'s 4dslicemotion, we need nipy. but nipy wont install on system python.

<code=bash>
pyenv virtualenv 3.10.12 preproc-3.10 # nipy doesn't install on 3.11
# pyenv versions |grep envs # points to /opt/ni_tools/pyenv/versions/3.10.12/envs/preproc-3.10
source /opt/ni_tools/pyenv/versions/3.10.12/envs/preproc-3.10/bin/activate
pip install git+https://github.com/nipy/nipy
pip install transforms3d
preprocessFunctional -check_dependencies
</code>


===== fmriprep =====
[[:tools:fmriprep]] can be run in a container or outside. to keep it's dependencies isolated:

<code=bash>
pyenv virtualenv 3.11.4 fmrirep-py3.11
pyenv local fmrirep-py3.11
pip install fmriprep
</code>