DOC: Move users docs from nipype to nipype_tutorial

[miykael]

Summary

PR miykael/nipype_tutorial#77 and miykael/nipype_tutorial#128 moved the content under User Guide already to the nipype_tutorial, but we haven't removed this content from nipype, yet. This PR takes care of that.

Deviation between the content

There are three sections that have been copied to the tutorial but either leads to errors or are still WIP:

Saving Workflows and Nodes to a file (experimental)

Running wf.export('special_workflow.py') in the notebook will lead to a TypeError: a bytes-like object is required, not 'str'. As the content of this section is still "experimental", I think it's ok if we leave it as WIP.

Running Nipype Interfaces from the command line (nipype_cmd)

The content between nipype and nipype_tutorial is identical. But currently, we're not running any tests, as the command nipype_cmd doesn't work inside the docker image. I haven't used nipype_cmd yet myself, but it seems nipype needs to be installed via apt install python-nipype for this to work?

Resource Scheduling and Profiling with Nipype

The content between nipype and nipype_tutorial is identical, but running the profiler within the docker image leads to the error AttributeError: 'list' object has no attribute 'startTime'. This is caused by the fact that the profiling information is not handed over as an object but as an object inside a list.

To consider

Removing the "User Docs" from nipype leads to new issues that need to be considered:

1. install.rst wasn't removed from doc/users as it is also needed in nipype's Quickstart section.
2. doc/users contains a folder examples that contains the workflow examples under Interfaces, Workflows and Examples. Once those workflows are included under niflows, this folder can be removed.
3. This PR inverts the order between the "Developer Guides" and the "Interfaces, Workflows and Examples" section, to this:
   
4. This PR puts the API and Developer Guide into two columns (see below). But the current setup has titles, as well as links to the corresponding sections. Should we take care of this?
   

[effigies]

Can we move this to nipype.github.io/tutorial? Not sure if we already had discussion there...

[miykael]

You're talking about the whole nipype_tutorial? Fine with me, but we haven't discussed it yet, or decided what to do.

[effigies]

Yeah.

[effigies]

This seems fine to me. Are there any outstanding issues? Can you merge master to get the latest version of testing in?

One quick note: nipype_cmd is now nipypecli. Not sure if that makes a difference for your notebook...

[effigies]

Actually, would you mind pushing a build of the docs to your gh-pages, so we can check them out on https://miykael.github.io/nipype?

[codecov-io]

Codecov Report

Merging #2726 into master will decrease coverage by 3.19%.
The diff coverage is n/a.

@@            Coverage Diff            @@
##           master    #2726     +/-   ##
=========================================
- Coverage   67.44%   64.24%   -3.2%     
=========================================
  Files         340      338      -2     
  Lines       43164    43102     -62     
  Branches     5351     5348      -3     
=========================================
- Hits        29110    27692   -1418     
- Misses      13355    14333    +978     
- Partials      699     1077    +378

Flag	Coverage Δ
#smoketests	?
#unittests	64.24% <ø> (-0.57%)	⬇️

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 46 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 39675df...93c475b. Read the comment docs.

[miykael]

I merged with master and renamed nipype_cmd to nipypecli. The newest version of the docs can be found on my gh-pages (https://miykael.github.io/nipype).

3 outstanding issues

Command line interface

If nipype_cmd is the same as nipypecli, does this mean that this content can be deleted?

Saving Workflows and Nodes to a file (experimental)

As mentioned above, this content is only in a WIP notebook and therefore not visible on the tutorial homepage. The problem is that wf.export('special_workflow.py') currently leads to an error in the notebook. Should we leave this as a WIP or remove the content?

Resource Scheduling and Profiling with Nipype

The resource profiler content is only as a WIP in the tutorial and doesn't work in the notebook, yet. I think this is addressed in #2571, but the proposed solution doesn't work in the container.

Mishap

Also, I unfortunately first updated the gh-pages from nipy/nipype. I didn't had a gh-pages branch yet, and so git checkout gh-pages put me directly on the upstream one... I'm really sorry for that and am happy to correct it, if necessary (gh-pages doesn't seem to be used anymore?). How can I revert my changes without bringing github down (again?)?

[effigies]

I reverted gh-pages to Satra's latest commit. Fortunately you didn't destroy the history.

Yes, nipype_cmd no longer exists. I don't know whether that information can be (usefully) updated for nipypecli or if it just needs deleting. I'm content to leave that decision to you.

I would leave the WIP notebooks as WIP at least until 2.0. Perhaps someone will fix the issues? I would go ahead and open issues for those notebooks here, as the fixes probably need to be done here.

Happy to be overruled by @satra on any and all points.

[effigies]

@miykael Are you happy with this at least for this release? We can open issues for any remaining things to fix in 1.1.5.

[miykael]

@effigies, yes. In my opinion it's good to go. Will keep track about any issues and open missing issues for the WIP on the tutrial homepage.