[Docker] Install minimized version of FS6

[oesteban]

• Replaces the full installation of FS by a minimized version by @satra
• Depends on [ENH] Revise CircleCI settings #2022

[effigies]

I imagine you can safely remove all of the --excludes.

[satra]

this section should suffice:

https://github.com/nipy/mindboggle/blob/master/install/Dockerfile.mindboggle.base#L99

[effigies]

This install only includes files used to run recon-all? We have at least one case where we run a command not included in that set: mris_expand

[satra]

@effigies - do we actually have a test in circleci for nipype where this command is actually used?

[satra]

the intent of this at present is not to provide all things that are needed to run these individual packages or all of nipype, but primarily that all of the tests can be run.

[effigies]

I linked to the test. It runs the interface if FreeSurfer is installed.

Edit: I guess I don't know if Circle skips over the test, anyway.

[satra]

@effigies - ah thanks. i can update the tar ball to include that file.

[codecov-io]

Codecov Report

Merging #2024 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #2024   +/-   ##
=======================================
  Coverage   72.19%   72.19%           
=======================================
  Files        1132     1132           
  Lines       57012    57012           
  Branches     8162     8162           
=======================================
  Hits        41161    41161           
  Misses      14567    14567           
  Partials     1284     1284

Flag	Coverage Δ
#smoketests	72.19% <ø> (ø)	⬆️
#unittests	69.79% <ø> (ø)	⬆️

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[satra]

@effigies, @oesteban - here is the updated tarball: https://dl.dropbox.com/s/y3hvbdgfu4pfad8/recon-all-freesurfer6.min.tgz?dl=0

[satra]

@oesteban - can you retrigger the build? for some reason i can't. it looks like the failure came from the freesurfer test.

also i'm curious how docker handles things like a curl when the content of a URL changes but the URL is still the same. does it actually rerun it?

so to avoid confusion here is the new download link:

https://dl.dropbox.com/s/y3hvbdgfu4pfad8/recon-all-freesurfer6-1.min.tgz?dl=0

[satra]

@oesteban - i was able to update things in your branch and as a result the build re-triggered. added ants directly here to save time.

[oesteban]

Something is odd with freesurfer installation:

=================================== FAILURES ===================================

_____________________________ test_associated_file _____________________________



    @pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed")

    def test_associated_file():

        fssrc = FreeSurferSource(subjects_dir=fs.Info.subjectsdir(),

                                 subject_id='fsaverage', hemi='lh')

    

        fsavginfo = fssrc.run().outputs.get()

    

        # Pairs of white/pial files in the same directories

        for white, pial in [('lh.white', 'lh.pial'),

                            ('./lh.white', './lh.pial'),

                            (fsavginfo['white'], fsavginfo['pial'])]:

    

            # Unspecified paths, possibly with missing hemisphere information,

            # are equivalent to using the same directory and hemisphere

            for name in ('pial', 'lh.pial', pial):

                assert FSSurfaceCommand._associated_file(white, name) == pial

    

            # With path information, no changes are made

            for name in ('./pial', './lh.pial', fsavginfo['pial']):

>               assert FSSurfaceCommand._associated_file(white, name) == name



../../interfaces/freesurfer/tests/test_FSSurfaceCommand.py:50: 

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

../../interfaces/freesurfer/base.py:225: in _associated_file

    path, base = os.path.split(out_name)

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 



p = <undefined>



    def split(p):

        """Split a pathname.  Returns tuple "(head, tail)" where "tail" is

        everything after the final slash.  Either part may be empty."""

>       p = os.fspath(p)

E       TypeError: expected str, bytes or os.PathLike object, not _Undefined



/usr/local/miniconda/lib/python3.6/posixpath.py:105: TypeError

_______________________________ test_mrisexpand ________________________________



tmpdir = local('/tmp/pytest-of-root/pytest-0/test_mrisexpand0')



    @pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed")

    def test_mrisexpand(tmpdir):

        fssrc = FreeSurferSource(subjects_dir=fs.Info.subjectsdir(),

                                 subject_id='fsaverage', hemi='lh')

    

        fsavginfo = fssrc.run().outputs.get()

    

        # dt=60 to ensure very short runtime

        expand_if = fs.MRIsExpand(in_file=fsavginfo['smoothwm'],

                                  out_name='expandtmp',

                                  distance=1,

                                  dt=60)

    

        expand_nd = pe.Node(

            fs.MRIsExpand(in_file=fsavginfo['smoothwm'],

                          out_name='expandtmp',

                          distance=1,

                          dt=60),

            name='expand_node')

    

        # Interfaces should have same command line at instantiation

        orig_cmdline = 'mris_expand -T 60 {} 1 expandtmp'.format(fsavginfo['smoothwm'])

>       assert expand_if.cmdline == orig_cmdline



/src/nipype/nipype/interfaces/freesurfer/tests/test_utils.py:188: 

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

/src/nipype/nipype/interfaces/base.py:1673: in cmdline

    self._check_mandatory_inputs()

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 



self = <nipype.interfaces.freesurfer.utils.MRIsExpand object at 0x7f9be9611dd8>



    def _check_mandatory_inputs(self):

        """ Raises an exception if a mandatory input is Undefined

            """

        for name, spec in list(self.inputs.traits(mandatory=True).items()):

            value = getattr(self.inputs, name)

            self._check_xor(spec, name, value)

            if not isdefined(value) and spec.xor is None:

                msg = ("%s requires a value for input '%s'. "

                       "For a list of required inputs, see %s.help()" %

                       (self.__class__.__name__, name, self.__class__.__name__))

>               raise ValueError(msg)

E               ValueError: MRIsExpand requires a value for input 'in_file'. For a list of required inputs, see MRIsExpand.help()



/src/nipype/nipype/interfaces/base.py:969: ValueError

======== 2 failed, 2616 passed, 42 skipped, 7 xfailed in 652.87 seconds ========

[satra]

@oesteban - mris_expand is expecting a few additional files from fsaverage that are not required for recon-all. i will add them and update the tar file.

[satra]

@oesteban - just pushed an update - hopefully this will work