fix freeview

[stebo85]

[codecov[bot]]

Codecov Report

Merging #351 into master will decrease coverage by 24.96%. The diff coverage is n/a.

@@             Coverage Diff             @@
##           master     #351       +/-   ##
===========================================
- Coverage   74.63%   49.67%   -24.97%     
===========================================
  Files          35       35               
  Lines        1983     1983               
  Branches      260      260               
===========================================
- Hits         1480      985      -495     
- Misses        393      924      +531     
+ Partials      110       74       -36     

Impacted Files	Coverage Δ
neurodocker/interfaces/interfaces.py	73.09% <ø> (-3.51%)	:arrow_down:
neurodocker/tests/test_neurodocker.py	12.00% <0.00%> (-88.00%)	:arrow_down:
neurodocker/reprozip/tests/test_merge.py	20.83% <0.00%> (-72.92%)	:arrow_down:
neurodocker/reprozip/merge.py	17.17% <0.00%> (-71.72%)	:arrow_down:
neurodocker/reprozip/gentle/tests/test_minify.py	19.44% <0.00%> (-69.45%)	:arrow_down:
neurodocker/reprozip/trace.py	13.51% <0.00%> (-68.92%)	:arrow_down:
neurodocker/tests/test_parser.py	35.29% <0.00%> (-64.71%)	:arrow_down:
neurodocker/neurodocker.py	20.27% <0.00%> (-62.24%)	:arrow_down:
neurodocker/tests/test_utils.py	38.46% <0.00%> (-61.54%)	:arrow_down:
neurodocker/reprozip/gentle/trace.py	12.50% <0.00%> (-56.25%)	:arrow_down:
... and 9 more

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[Shotgunosine]

@kaczmarj Any chance of integrating this fix and cutting a new release of neurodocker? We've started using it for the neurodocker bids app and I'd like to build a version of the app for Freesurfer 7.1.0. Thanks!

[kaczmarj]

sorry for the delay folks. originally, i intended neurodocker to create docker images without gui capabilities, because gui applications are finicky in containers. but i see that this PR (and related gui PRs) would be useful.

i propose adding a flag to --freesurfer to install the gui-specific dependencies. i think this is a good idea because it would preserve the relatively small size of the recon-all minified containers, but would allow users to add gui dependencies for regular freesurfer installations.

[stebo85]

Dear @kaczmarj - a GUI flag is a great idea! Would it make sense to make it even more general and give every tool a GUI flag that we can then use in the recipes to add GUI components if needed? This would also apply to MrTrix, FSL, AFNI, MINC, MRIcron & SPM12 (which probably both don't make sense without the GUI flag :p)

[satra]

@stebo85 - do you have the bandwidth to attempt your suggestion, and rebase this on the current master?

[stebo85]

I can have a look at this after Christmas :)

[satra]

I can have a look at this after Christmas :)

that would be awesome.

[stebo85]

I will wait with implementing a GUI option until the neurodocker rewrite to use reproenv is completed.

[kaczmarj]

I will wait with implementing a GUI option until the neurodocker rewrite to use reproenv is completed.

@stebo85 - the rewrite is almost complete. I just have to add tests to make sure all of the templates are working properly. the code is in the branch refactor/migrate-to-reproenv. feel free to peruse and see how a gui option could be included.

my thought is to add an optional argument like gui and then include logic in the template to install the gui dependencies.

i also uploaded a docker image of the current version of the rewrite.

docker run --rm kaczmarj/neurodocker-reproenv:devs-only generate docker --help

[stebo85]

closing - GUI option is added in Neurodesk build