added SPM12's new Normalize routine and updated version info and manual links

[miykael]

No description provided.

[coveralls]

Coverage remained the same when pulling 0e1b497 on miykael:master into 636f32a on nipy:master.

[satra]

we don't need to put opt or defaults anymore in description, the help generator automatically does this.

[satra]

looks good overall - could you please run through PEP8 fixes and make sure the tests pass. since this is a new interface, when you run make specs it will create a new test_auto_Normalize12.py file that should be added to the repo. (check using git status)

[miykael]

Thank you @satra for the feedback and sorry for the commit chaos, I had a bit of a mixup.
I've done PEP8 check for my changes as well as for some other parts of spm's preprocess.py and included the test_auto_Normalize12.py file.

But the running of make specs also generates a file called nipype/algorithms/tests/test_auto_Overlap.py. I don't see a direct link between my commit and this file, does it also have to be commited?

Here's the content of this file:

# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
from nipype.testing import assert_equal
from nipype.algorithms.misc import Overlap

def test_Overlap_inputs():
    input_map = dict(bg_overlap=dict(mandatory=True,
    usedefault=True,
    ),
    ignore_exception=dict(nohash=True,
    usedefault=True,
    ),
    mask_volume=dict(),
    out_file=dict(usedefault=True,
    ),
    vol_units=dict(mandatory=True,
    usedefault=True,
    ),
    volume1=dict(mandatory=True,
    ),
    volume2=dict(mandatory=True,
    ),
    weighting=dict(usedefault=True,
    ),
    )
    inputs = Overlap.input_spec()

    for key, metadata in input_map.items():
        for metakey, value in metadata.items():
            yield assert_equal, getattr(inputs.traits()[key], metakey), value

def test_Overlap_outputs():
    output_map = dict(dice=dict(),
    diff_file=dict(),
    jaccard=dict(),
    labels=dict(),
    roi_di=dict(),
    roi_ji=dict(),
    roi_voldiff=dict(),
    volume_difference=dict(),
    )
    outputs = Overlap.output_spec()

    for key, metadata in output_map.items():
        for metakey, value in metadata.items():
            yield assert_equal, getattr(outputs.traits()[key], metakey), value

[chrisgorgo]

Interesting. When I do make specs it does not generate this file. However I get a message that Overlap has a nonautotests. Presumably autotests are not generated if there are other tests for the class? right @satra?

$ make specs
Checking specs and autogenerating spec tests
python tools/checkspecs.py
141101-21:47:40,38 workflow DEBUG:
     networkx 1.4 dev or higher detected
Overlap has nonautotest
Overlap has nonautotest
Please install cfflib to use the connectome file format converter
BEDPOSTX has nonautotest
XFibres has nonautotest
FILMGLS has nonautotest
nipype.interfaces.slicer.surface:ModelMaker:Outputs:modelSceneFile:exists

[satra]

@miykael - could you please also update the CHANGES file with these lines:

* ENH: SPM12 Normalize interface (https://github.com/nipy/nipype/pull/986)
* FIX: Utility interface test dir (https://github.com/nipy/nipype/pull/986)
* FIX: IPython engine directory reset after crash (https://github.com/nipy/nipype/pull/987)

i know that last one didn't happen with this PR, but just getting things up to speed. we will try to adopt this style for any future merges.

[satra]

@miykael - can you merge my pull request too?

[miykael]

sorry, didn't see your merge. should be all done now.

[satra]

@chrisfilo - just to answer the question on nonautotest - for any interface if there is a test file in the tests directory named test_interfacename.py it will override the generation of the automatic test for that interface when make specs is run. this allows us to create specific tests for certain interfaces that are sensitive to versions of installed software.