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Update development environment docs #3188

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effigies opened this issue Dec 15, 2023 · 0 comments
Open

Update development environment docs #3188

effigies opened this issue Dec 15, 2023 · 0 comments

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@effigies
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Here's the workflow I use for development:

for REPO in nipreps/{fmriprep,smriprep,niworkflows,sdcflows}; do
    git clone https://github.com/$REPO
done
mamba env create -f fmriprep/env.yml
mamba env config vars set -n fmriprep FSLDIR=$CONDA_PREFIX
mamba activate fmriprep
pip install --no-deps -e ./fmriprep -e ./smriprep -e ./niworkflows -e ./sdcflows

Separately install AFNI, Connectome Workbench, FreeSurfer and msm.

Pretty much only use fmriprep-docker --patch to test fixes to specific released versions these days.

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