ADD: method to merge reprozip pack files

[kaczmarj]

Adds the cli command neurodocker reprozip-merge to merge multiple pack files. Renames neurodocker reprozip to neurodocker reprozip-trace.

Related to nipy/nipype#2144.

Example

Given multiple ReproZip pack files (.rpz) in the current directory, merge pack files, and save merged pack file in the current directory:

docker run --rm -v $(pwd):/packs --workdir /packs kaczmarj/neurodocker reprozip-merge merged.rpz *.rpz

Create a Docker image from the merged pack file:

reprounzip docker setup merged.rpz merged

Run the new Docker image:

docker run --rm -it --entrypoint="/neurodocker/startup.sh" <reprounzip_docker_image>

[kaczmarj]

Also related to VIDA-NYU/reprozip#265

[schahid]

Hi, nice piece of work!. I am testing it. Please add perl installation while creating Docker file for Freesurfer. as perl is missing, so nu_correct can not be run.

[codecov-io]

Codecov Report

Merging #69 into master will decrease coverage by 6.67%.
The diff coverage is 13%.

@@ Coverage Diff @@ ## master #69 +/- ## ========================================== - Coverage 85.15% 78.48% -6.68%  ========================================== Files 32 34 +2 Lines 1354 1464 +110 Branches 121 132 +11 ========================================== - Hits 1153 1149 -4  - Misses 164 278 +114  Partials 37 37

Impacted Files	Coverage Δ
neurodocker/interfaces/__init__.py	100% <ø> (ø)	⬆️
neurodocker/reprozip/__init__.py	0% <0%> (ø)
neurodocker/reprozip/merge.py	0% <0%> (ø)
neurodocker/reprozip/trace.py	0% <0%> (ø)
neurodocker/neurodocker.py	89.69% <80%> (-1.22%)	⬇️

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[kaczmarj]

@schahid - can you please elaborate on your issue? are you using neurodocker to generate the freesurfer image? if so, can you share that command? you can submit a new issue and we can continue conversation there.