[MRG] _part- -> _split- to conform with BIDS (#417)

* improve citation info

* _part- -> _split- to conform with BIDS

* fix comments

* add whatsnew [skip ci]

* move changelog to API section

* bump validator version

.travis.yml

@@ -36,7 +36,7 @@ matrix:
 env:
   global:
     # can be "stable", or anything that can be used with git checkout
-    - VALIDATOR_VERSION="8887074e5f5f48a768842ffcf96fb2952dbe0e38"
+    - VALIDATOR_VERSION="e457907ca9af4c32aede828117ea5a43737b4597"
     # can be any branch of MNE-Python (e.g., "maint/0.18", "master", ...)
 
 before_install:

README.rst

@@ -210,17 +210,19 @@ Please see our `contributing guide <https://github.com/mne-tools/mne-bids/blob/m
 Cite
 ----
 
-If you use ``mne-bids`` in your work, please cite:
+If you use ``mne-bids`` in your work, please cite our
+`publication in JOSS <https://doi.org/10.21105/joss.01896>`_.
 
 .. code-block:: Text
 
     Appelhoff, S., Sanderson, M., Brooks, T., Vliet, M., Quentin, R., Holdgraf, C.,
     Chaumon, M., Mikulan, E., Tavabi, K., Höchenberger, R., Welke, D., Brunner, C.,
     Rockhill, A., Larson, E., Gramfort, A. and Jas, M. (2019). MNE-BIDS: Organizing
     electrophysiological data into the BIDS format and facilitating their analysis.
-    Journal of Open Source Software 4: (1896).
+    Journal of Open Source Software 4: (1896). https://doi.org/10.21105/joss.01896
 
-and one of the following papers, depending on which modality you used:
+and one of the following papers to credit BIDS, depending on which modality you
+used:
 
 `MEG <http://doi.org/10.1038/sdata.2018.110>`_
 ##############################################
@@ -231,7 +233,7 @@ and one of the following papers, depending on which modality you used:
    Henson, R. N., Jas, M., Litvak, V., Moreau, J., Oostenveld, R., Schoffelen, J.,
    Tadel, F., Wexler, J., Baillet, S. (2018). MEG-BIDS, the brain imaging data
    structure extended to magnetoencephalography. Scientific Data, 5, 180110.
-   http://doi.org/10.1038/sdata.2018.110
+   https://doi.org/10.1038/sdata.2018.110
 
 
 `EEG <https://doi.org/10.1038/s41597-019-0104-8>`_

appveyor.yml

@@ -4,7 +4,7 @@ environment:
         # latter case, you MUST adjust VALIDATOR_EXECUTABLE to the following value:
         # "C:\\projects\\mne-bids\\bids-validator\\bids-validator\\bin\\bids-validator"
         # ... whereas for "stable", VALIDATOR_EXECUTABLE MUST be set to "n/a"
-        VALIDATOR_VERSION: "8887074e5f5f48a768842ffcf96fb2952dbe0e38"
+        VALIDATOR_VERSION: "e457907ca9af4c32aede828117ea5a43737b4597"
         # can be any branch of MNE-Python (e.g., "maint/0.18", "master", ...)
         MNE_VERSION: "maint/0.20"
         VALIDATOR_EXECUTABLE: "C:\\projects\\mne-bids\\bids-validator\\bids-validator\\bin\\bids-validator"

doc/whats_new.rst

@@ -41,6 +41,7 @@ API
 - :func:`read_raw_bids` now expects `bids_basename` as the first argument and gains a `kind` parameter. The name of the file to read will be inferred automatically, and can no longer be passed to the function directly. This ensures better API consistency with :func:`write_raw_bids`, by `Richard Höchenberger`_ (`#410 <https://github.com/mne-tools/mne-bids/pull/410>`_)
 - :func:`get_matched_empty_room` now expects `bids_basename` as the first argument and returns the `bids_basename` of the best-matching empty-room recording (instead of its filename before). The `bids_fname` argument has been dropped, by `Richard Höchenberger`_ (`#410 <https://github.com/mne-tools/mne-bids/pull/410>`_)
 - :func:`get_head_mri_trans` now expects `bids_basename` as the first argument. The `bids_fname` argument has been dropped, by `Richard Höchenberger`_ (`#410 <https://github.com/mne-tools/mne-bids/pull/410>`_)
+- BIDS conformity: The ``_part-%d`` entity is now called ``_split-`` throughout BIDS, MNE, and MNE-BIDS, by `Stefan Appelhoff`_ (`#417 <https://github.com/mne-tools/mne-bids/pull/417>`_)
 
 .. _changes_0_4:
 

mne_bids/tests/test_utils.py

@@ -273,11 +273,11 @@ def test_parse_ext():
 
 
 @pytest.mark.parametrize('fname', [
-    'sub-01_ses-02_task-test_run-3_part-01_meg.fif',
-    'sub-01_ses-02_task-test_run-3_part-01.fif',
-    'sub-01_ses-02_task-test_run-3_part-01',
+    'sub-01_ses-02_task-test_run-3_split-01_meg.fif',
+    'sub-01_ses-02_task-test_run-3_split-01.fif',
+    'sub-01_ses-02_task-test_run-3_split-01',
     ('/bids_root/sub-01/ses-02/meg/' +
-     'sub-01_ses-02_task-test_run-3_part-01_meg.fif'),
+     'sub-01_ses-02_task-test_run-3_split-01_meg.fif'),
 ])
 def test_parse_bids_filename(fname):
     """Test parsing entities from a bids filename."""
@@ -286,9 +286,9 @@ def test_parse_bids_filename(fname):
     assert params['ses'] == '02'
     assert params['run'] == '3'
     assert params['task'] == 'test'
-    assert params['part'] == '01'
+    assert params['split'] == '01'
     assert list(params.keys()) == ['sub', 'ses', 'task', 'acq', 'run', 'proc',
-                                   'space', 'recording', 'part', 'kind']
+                                   'space', 'recording', 'split', 'kind']
 
 
 def test_age_on_date():

mne_bids/tests/test_write.py

@@ -327,14 +327,14 @@ def test_fif(_bids_validate):
 
     assert op.exists(op.join(bids_root, 'participants.tsv'))
 
-    # asserting that single fif files do not include the part key
+    # asserting that single fif files do not include the split key
     files = glob(op.join(bids_output_path, 'sub-' + subject_id2,
                          'ses-' + subject_id2, 'meg', '*.fif'))
     for ii, FILE in enumerate(files):
-        assert 'part' not in FILE
+        assert 'split' not in FILE
     assert ii < 1
 
-    # check that split files have part key
+    # check that split files have split key
     raw = mne.io.read_raw_fif(raw_fname)
     data_path3 = _TempDir()
     raw_fname3 = op.join(data_path3, 'sample_audvis_raw.fif')
@@ -348,7 +348,7 @@ def test_fif(_bids_validate):
     files = glob(op.join(bids_output_path, 'sub-' + subject_id3,
                          'ses-' + subject_id3, 'meg', '*.fif'))
     for FILE in files:
-        assert 'part' in FILE
+        assert 'split' in FILE
 
     # test unknown extension
     raw = mne.io.read_raw_fif(raw_fname)

mne_bids/utils.py

@@ -363,7 +363,7 @@ def _parse_ext(raw_fname, verbose=False):
 def _parse_bids_filename(fname, verbose):
     """Get dict from BIDS fname."""
     keys = ['sub', 'ses', 'task', 'acq', 'run', 'proc', 'run', 'space',
-            'recording', 'part', 'kind']
+            'recording', 'split', 'kind']
     params = {key: None for key in keys}
     idx_key = 0
     for match in re.finditer(param_regex, op.basename(fname)):

mne_bids/write.py

@@ -721,7 +721,7 @@ def _write_raw_fif(raw, bids_fname):
         split_naming = 'bids'
         raw.save(bids_fname, split_naming=split_naming, overwrite=True)
     else:
-        # This ensures that single FIF files do not have the part param
+        # This ensures that single FIF files do not have the split param
         raw.save(bids_fname, split_naming='neuromag', overwrite=True)