[FIX] add "USER root" to top of every Dockerfile

[jdkent]

ref #249

first pass at forcing the user to be root.
Not going to say that this fixes #249 because this does not cover singularity builds.

I'm also unsure how this will interact with #270 if you want to primarily interact with the container as a user (not root).

[jdkent]

ping to see if anyone can review this pull request.

[kaczmarj]

sorry for the delay @jdkent - things were busy at school. i will test out this pr tomorrow. i'll check for interactions with #270

[codecov-io]

Codecov Report

❗ No coverage uploaded for pull request base (master@702fe0f). Click here to learn what that means.
The diff coverage is 37.14%.

@@            Coverage Diff            @@
##             master     #306   +/-   ##
=========================================
  Coverage          ?   68.69%           
=========================================
  Files             ?       33           
  Lines             ?     1853           
  Branches          ?      241           
=========================================
  Hits              ?     1273           
  Misses            ?      490           
  Partials          ?       90

Impacted Files	Coverage Δ
neurodocker/generators/singularity.py	29.54% <ø> (ø)
neurodocker/interfaces/tests/test_miniconda.py	70% <ø> (ø)
neurodocker/__init__.py	80% <100%> (ø)
neurodocker/_version.py	36.46% <36.46%> (ø)

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 702fe0f...fdee517. Read the comment docs.

[kaczmarj]

@jdkent - i added a commit to implement similar behavior for singularity recipes. now this should fix #249 . once the tests pass, i will merge unless you have reservations.

i spoke too soon... i'll figure out why the tests are failing.

[jdkent]

The singularity issue for the miniconda test appears to be related to ContinuumIO/anaconda-issues#11163

[jdkent]

changed the singularity test to work with a previous version of miniconda, I suppose building a singularity with a newer version of miniconda will be defunct until some upstream changes are put into place.

@kaczmarj I believe this ready for review.

[kaczmarj]

Thank you so much for figuring out the issue. It was bugging me and I could not find the cause... my Google fu is not powerful enough yet. I will review tonight. Best, Jakub

…

On Jan 9, 2020, at 3:32 AM, James Kent ***@***.***> wrote: changed the singularity test to work with a previous version of miniconda, I suppose building a singularity with a newer version of miniconda will be defunct until some upstream changes are put into place. @kaczmarj I believe this ready for review. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[kaczmarj]

thank you @jdkent