MAINT: Revisions after previous maintenance commit (#83)

[oesteban]

Revise #83 and fix the two outstanding issues:

• Outdated requirements.txt file when generating docs.
• Inconsistent handling of the --output-spaces section, as a result of copy&paste from fMRIPrep.

[pull-assistant]

Best reviewed: commit by commit

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Optimal code review plan

     docs: update dependencies in docs/requirements.txt

     fix: update the --output-spaces option to be more consistent

     fix(docs,workflow): include @josephmje's suggestions

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[ghost]

Warnings are found on analyzing the commit 03b0302.

1 warning:

• ⚠️ Goodcheck

We recommend to address them as possible, for example, update outdated dependencies, fix the tool's configuration, configure sider.yml, turn off unused tools, and so on.

If you are struggling with these errors or warnings, feel free to ask us via chat. 💬

[oesteban]

for some obscure reason, circle has stopped to build my PRs :(

[codecov]

Codecov Report

Merging #85 into master will increase coverage by 0.24%.
The diff coverage is 22.22%.

@@            Coverage Diff             @@
##           master      #85      +/-   ##
==========================================
+ Coverage   52.61%   52.85%   +0.24%     
==========================================
  Files          16       16              
  Lines         899      893       -6     
  Branches      110      109       -1     
==========================================
- Hits          473      472       -1     
+ Misses        425      420       -5     
  Partials        1        1

Impacted Files	Coverage Δ
dmriprep/workflows/base.py	28.57% <0%> (-1.01%)	⬇️
dmriprep/cli/run.py	31.15% <33.33%> (+0.58%)	⬆️

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[arokem]

for some obscure reason, circle has stopped to build my PRs :(

That's annoying.

@josephmje : is your PR #81 rebased on current master? Maybe there's a difference between these two PRs that explains why one is tested and the other isn't?

[josephmje]

for some obscure reason, circle has stopped to build my PRs :(

That's annoying.

@josephmje : is your PR #81 rebased on current master? Maybe there's a difference between these two PRs that explains why one is tested and the other isn't?

Yes, I rebased earlier this morning.

[josephmje]

With the new version of smriprep, many of the output_spaces arguments need to be changed to spaces.

eg.

TypeError: init_anat_preproc_wf() got an unexpected keyword argument 'output_spaces'

[josephmje]

I forgot that the documentation used a different set of package versions. That explains why we were still getting nipype errors.

[oesteban]

@josephmje have you rebased to this one? should I just merge and check whether I successfully addressed all issues?

[josephmje]

@josephmje have you rebased to this one? should I just merge and check whether I successfully addressed all issues?

I haven't rebased to this one but I did test locally. The pinned versions are working well. I left a comment about the "orig" space. Also, in the call to init_anat_preproc_wf(), the output_spaces argument should be changed to spaces.

[oesteban]

Seems like unfollowing and following from my repo did the trick (regarding to CircleCI).