MAINT: Sort dependencies alphabetically

[oesteban]

Splitting up #2959 in digestible bits.

This would be great to merge quickly if possible.

Summary

Fixes # .

List of changes proposed in this PR (pull-request)

Acknowledgment

• (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

[effigies]

This is fine by me, but I think the idea was to give a rough order of perceived importance of the dependency. Is the change just to make it easier to search and see if a dependency is or isn't in the list?

[oesteban]

Is the change just to make it easier to search and see if a dependency is or isn't in the list?

Yes, that is the idea.

@satra, I'd say to remove those dependencies in a separate PR, just in case tests start failing...

@kaczmarj any fast way to instruct neurodocker to run all pip installs with --no-cache-dir?
EDIT: it is actually conda, not pip.

[satra]

I'd say to remove those dependencies in a separate PR, just in case tests start failing

unfortunately i don't think we have a test for this. which i'll try to add. however this is not about removing, but the order of listing the dependencies. so neurdflib has to come after prov.

right now the tests are failing for other reasons.

[effigies]

This might be fixed by using a newer neurodocker.

[kaczmarj]

@oesteban - neurodocker should include some conda clean call after conda install. at least version 0.5.0 does. is the cache present in the container?

[codecov-io]

Codecov Report

Merging #2961 into master will decrease coverage by 3.36%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #2961      +/-   ##
==========================================
- Coverage    67.6%   64.24%   -3.37%     
==========================================
  Files         344      342       -2     
  Lines       43797    43743      -54     
  Branches     5471     5468       -3     
==========================================
- Hits        29609    28101    -1508     
- Misses      13478    14554    +1076     
- Partials      710     1088     +378

Flag	Coverage Δ
#smoketests	?
#unittests	64.24% <100%> (-0.8%)	⬇️

Impacted Files	Coverage Δ
nipype/info.py	88.23% <100%> (-5.8%)	⬇️
nipype/interfaces/nilearn.py	40% <0%> (-56.67%)	⬇️
nipype/utils/spm_docs.py	25.92% <0%> (-44.45%)	⬇️
nipype/interfaces/freesurfer/base.py	50% <0%> (-30.51%)	⬇️
nipype/utils/logger.py	59.7% <0%> (-29.86%)	⬇️
nipype/algorithms/rapidart.py	35% <0%> (-29.42%)	⬇️
nipype/interfaces/spm/base.py	57.94% <0%> (-29.14%)	⬇️
nipype/utils/provenance.py	55.73% <0%> (-28.35%)	⬇️
nipype/interfaces/fsl/model.py	55.26% <0%> (-25.35%)	⬇️
nipype/testing/fixtures.py	77.33% <0%> (-21.34%)	⬇️
... and 42 more

---

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 b1eb3ee...772d0c8. Read the comment docs.

[oesteban]

@kaczmarj 0.5.0 is failing too

[kaczmarj]

@oesteban - i will try to look into this tomorrow

[effigies]

The issue is caused by conda/conda-package-handling#34. We need to set the working directory to something owned by the neuro user.

[effigies]

Need to restore neurdflib to post-prov. Updating the RTD requirements while we're at it.

Build failure addressed in #2789.
Please revert Neurodocker 0.5.0 update or remove it in a rebase; nipype builds don't work with it. See #2963 (comment).

[oesteban]

@effigies, I added your suggestions within the merge upstream/master commit. I hope that's fine.

[effigies]

Seems fine. @satra, any concerns apart from prov before neurdflib?

[satra]

@effigies - looks good to me. the one thing about rtd is that it was limited to the dependencies required for doc building, but it's fine to have everything. we should definitely check, once this is merged that rtd does build.

[effigies]

Docs built fine. https://readthedocs.org/projects/nipype/builds/9387007/

Somewhat unclear why they aren't built with every commit to master. I had to manually trigger the build.

[satra]

i clicked on a few buttons (specifically enabled github integration - which i thought was already enabled). let's see if that makes a difference.