FIX: corrects readthedocs build error

[miykael]

Closes #2713.

Small PR that takes care of the readthedocs build error mentioned under #2713.

The problem was that matplotlib version 3.0.0 doesn't include the sphinxext.only_directives anymore.

[codecov-io]

Codecov Report

Merging #2723 into master will decrease coverage by 3.32%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #2723      +/-   ##
==========================================
- Coverage    67.6%   64.28%   -3.33%     
==========================================
  Files         340      338       -2     
  Lines       43153    43102      -51     
  Branches     5351     5348       -3     
==========================================
- Hits        29174    27707    -1467     
- Misses      13277    14314    +1037     
- Partials      702     1081     +379

Flag	Coverage Δ
#smoketests	?
#unittests	64.28% <ø> (-0.8%)	⬇️

Impacted Files	Coverage Δ
nipype/interfaces/nilearn.py	40% <0%> (-56.67%)	⬇️
nipype/utils/spm_docs.py	25.92% <0%> (-44.45%)	⬇️
nipype/interfaces/freesurfer/base.py	49.59% <0%> (-30.9%)	⬇️
nipype/utils/logger.py	59.7% <0%> (-29.86%)	⬇️
nipype/algorithms/rapidart.py	35.39% <0%> (-29.21%)	⬇️
nipype/interfaces/spm/base.py	58.41% <0%> (-29.05%)	⬇️
nipype/utils/provenance.py	55.73% <0%> (-28.99%)	⬇️
nipype/interfaces/fsl/model.py	55.26% <0%> (-25.35%)	⬇️
nipype/testing/fixtures.py	77.33% <0%> (-21.34%)	⬇️
nipype/interfaces/matlab.py	64.64% <0%> (-21.22%)	⬇️
... and 43 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 88de9f8...912039e. Read the comment docs.

[miykael]

All the errors on circleci seem to be due to the spm version issue mentioned under ReproNim/neurodocker#227.

This PR updates pybids version to 0.6.5 with 46cbed6, but I wasn't able to update neurodocker to 0.4.1 here? How do I get the new/corresponding sha256?

Also, can somebody help me to understand why the tests on travis were failing?

[effigies]

The Travis tests are failing because of a coverage change in the pre-release. I think @adelavega can point to the issue, if needed.

[effigies]

In any event, those pre-release checks shouldn't block merging, if that's the only thing holding you back right now. I think the solution is just to wait for a new coverage RC and Travis will fix itself.

[miykael]

The main issue that I've tried to solve in this PR as well (I perhaps should rather create a new PR to do so), is to update neurodocker to 0.4.0. But this opens up questions, about FreeSurfer installation and license file, etc.

[effigies]

From the builds:

Step 11/18 : ENV FREESURFER_HOME="/opt/freesurfer-6.0.0"     PATH="/opt/freesurfer-6.0.0/bin:$PATH"
...
Step 13/18 : RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
 ---> Running in 590ff37e749b
sh: 1: cannot create /opt/freesurfer/license.txt: Directory nonexistent
The command '/bin/sh -c echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh' returned a non-zero code: 2

Let's update the B64-encoded script to target $FREESURFER_HOME/license_file.txt. Unless the preferred method will be to require users to pass their own license file in?

[effigies]

Looks like this is being used prior to the definition of PYTHON_VERSION_* (L102).

[miykael]

I will revert all the commits concerning docker/generate_dockerfiles.sh as they will be taken care of with #2707.