Mounting niworkflows for development

If a local copy of niworkflows needs to be patched into the fmriprep docker container it needs to have an egg-info directory contains the package information needed by fmriprep to properly import niworkflows. The following commands will intialize your local copy of niworkflows with the needed package information:

~/projects/niworkflows $ docker run --rm -it --entrypoint=bash -v ~/projects/niworkflows:/root/src/src/niworkflows fmriprep

root@ad2c3ca4037e:~# cd /root/src/src/niworkflows/

root@ad2c3ca4037e:~/src/src/niworkflows# pip install -e .

Complete command I run to process ds054 with fmriprep using my own local copies of fmriprep and niworkflows code:

docker run --rm -v ~/projects/fmriprep:/root/src/fmriprep -v ~/cache/:/root/.cache/ -v ~/datasets/ds054/:/datasets/ds054 -v ~/dataset_processing/ds054_out/:/out/ -v ~/dataset_processing/ds054_work/:/work/ -v ~/projects/niworkflows/:/root/src/src/niworkflows fmriprep "-w /work/ /datasets/ds054 /out/ participant"