Make pybids tutorial notebook great again

[yarikoptic]

ATM it is broken at layout.get(type='T1w', subject='01') puking with

~/proj/bids/pybids > cat pybids-tut.py          
import bids.layout   
import bids.tests
import os
layout = bids.layout.BIDSLayout(os.path.join(bids.tests.get_test_data_path(), '7t_trt'))
print(layout.get()[10])

print(layout.get(type='T1w', subject='01'))

~/proj/bids/pybids > python pybids-tut.py
File(filename='/home/yoh/proj/bids/pybids/bids/tests/data/7t_trt/sub-01/ses-1/fmap/sub-01_ses-1_run-2_phasediff.json', datatype='fmap', session='1', run=2, suffix='phasediff', subject='01')
Traceback (most recent call last):
  File "pybids-tut.py", line 7, in <module>
    print(layout.get(type='T1w', subject='01'))
  File "/home/yoh/proj/bids/pybids/bids/layout/layout.py", line 288, in get
    **md_kwargs)
  File "/home/yoh/proj/bids/pybids/bids/layout/layout.py", line 524, in search
    self.index_file(f)
  File "/home/yoh/proj/bids/pybids/bids/layout/layout.py", line 465, in index_file
    if f.path in self.file_index and not overwrite:
AttributeError: 'File' object has no attribute 'path'

blind attempt to fix in grabbit which somewhat brakes API (.filename of the namedtuple File becomes just the filename, not .path) is not sufficient alone, but I didn't want to dive deeper before decision on that one was made

[tyarkoni]

See #259; closing here. The fix is to use suffix instead of type.

[yarikoptic]

oy... What should type reflect then? If it must not be present at all, at least at pybids level, then it might better to explicitly check if it is given and puke with an informative message (instead of delaying and exploding deep inside the guts)

[tyarkoni]

type is gone--it was inconsistent with the naming conventions used in the spec. I agree it would probably be a good idea to spit out a more informative error. Want to open a PR for that? :)

[yarikoptic]

Ok will do

[tyarkoni]

Also, see the Changelog for a summary of most (all?) of the breaking changes. I think the entity renaming and the path specification are the two major ones, but there might be other things we should probably flag.