[BUG] Add overwrite to export_raw for EDF conversions (#930)

* Fix bug

* Add changelog

* Fix unit test and add doc string

* Fix

* Small change to test

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

doc/whats_new.rst

@@ -52,7 +52,7 @@ Requirements
 Bug fixes
 ^^^^^^^^^
 
-- ...
+- Forcing EDF conversion in :func:`mne_bids.write_raw_bids` properly uses the ``overwrite`` parameter now, by `Adam Li`_ (:gh:`930`)
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`
 

mne_bids/tests/test_write.py

@@ -20,6 +20,7 @@
 import json
 from pathlib import Path
 import codecs
+import warnings
 
 from pkg_resources import parse_version
 
@@ -2851,6 +2852,38 @@ def test_convert_eeg_formats(dir_name, format, fname, reader, tmp_path):
         raw.get_data(), raw2.get_data()[:, :orig_len], decimal=6)
 
 
+@requires_version('mne', '0.24')
+@requires_version('pybv', '0.6')
+@pytest.mark.parametrize(
+    'dir_name, format, fname, reader', test_converteeg_data)
+@pytest.mark.filterwarnings(
+    warning_str['channel_unit_changed'], warning_str['edfblocks'])
+def test_format_conversion_overwrite(dir_name, format, fname, reader,
+                                     tmp_path):
+    """Test that overwrite works when format is passed to write_raw_bids."""
+    bids_root = tmp_path / format
+    data_path = op.join(testing.data_path(), dir_name)
+    raw_fname = op.join(data_path, fname)
+
+    # the BIDS path for test datasets to get written to
+    bids_path = _bids_path.copy().update(root=bids_root, datatype='eeg')
+
+    raw = reader(raw_fname)
+    # drop 'misc' type channels when exporting
+    raw = raw.pick_types(eeg=True)
+    kwargs = dict(raw=raw, format=format, bids_path=bids_path, verbose=False)
+
+    with warnings.catch_warnings():
+        # ignore all warnings for this case to remove verbosity
+        # this unit test is not meant to test for warnings
+        warnings.filterwarnings('ignore')
+
+        # writing with the 'format' parameter should always work
+        # if overwrite is True
+        write_raw_bids(**kwargs)
+        write_raw_bids(**kwargs, overwrite=True)
+
+
 @requires_version('mne', '0.22')
 @pytest.mark.parametrize(
     'dir_name, format, fname, reader', test_converteeg_data)

mne_bids/write.py

@@ -960,7 +960,7 @@ def _write_raw_brainvision(raw, bids_fname, events, overwrite):
                       meas_date=meas_date)
 
 
-def _write_raw_edf(raw, bids_fname):
+def _write_raw_edf(raw, bids_fname, overwrite):
     """Store data as EDF.
 
     Parameters
@@ -969,9 +969,11 @@ def _write_raw_edf(raw, bids_fname):
         Raw data to save.
     bids_fname : str
         The output filename.
+    overwrite : bool
+        Whether to overwrite an existing file or not.
     """
     assert str(bids_fname).endswith('.edf')
-    raw.export(bids_fname)
+    raw.export(bids_fname, overwrite=overwrite)
 
 
 @verbose
@@ -1644,7 +1646,7 @@ def write_raw_bids(raw, bids_path, events_data=None, event_id=None,
                       if ext == '.pdf' else bids_path.fpath))
         elif bids_path.datatype in ['eeg', 'ieeg'] and format == 'EDF':
             warn('Converting data files to EDF format')
-            _write_raw_edf(raw, bids_path.fpath)
+            _write_raw_edf(raw, bids_path.fpath, overwrite=overwrite)
         else:
             warn('Converting data files to BrainVision format')
             bids_path.update(suffix=bids_path.datatype, extension='.vhdr')