more again

mne_bids/commands/tests/test_cli.py

@@ -54,7 +54,7 @@ def check_usage(module, force_help=False):
 def test_raw_to_bids(tmp_path):
     """Test mne_bids raw_to_bids."""
     output_path = str(tmp_path)
-    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
     # Check that help is printed
     check_usage(mne_bids_raw_to_bids)
 
@@ -150,7 +150,7 @@ def test_mark_bad_channels_single_file(tmp_path):
 
     # Create test dataset.
     output_path = str(tmp_path)
-    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
     events_fname = op.join(
         data_path, "MEG", "sample", "sample_audvis_trunc_raw-eve.fif"
     )
@@ -237,7 +237,7 @@ def test_mark_bad_channels_multiple_files(tmp_path):
 
     # Create test dataset.
     output_path = str(tmp_path)
-    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
     events_fname = op.join(
         data_path, "MEG", "sample", "sample_audvis_trunc_raw-eve.fif"
     )
@@ -344,7 +344,7 @@ def test_count_events(tmp_path):
 
     # Create test dataset.
     output_path = str(tmp_path)
-    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
 
     raw = mne.io.read_raw(raw_fname)
     raw.info["line_freq"] = 60.0
@@ -393,7 +393,7 @@ def test_inspect(tmp_path):
     subject = "01"
     task = "test"
     datatype = "meg"
-    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
 
     raw = mne.io.read_raw(raw_fname)
     raw.info["line_freq"] = 60.0

mne_bids/tests/test_copyfiles.py

@@ -188,8 +188,8 @@ def test_copyfile_edfbdf_uppercase(tmp_path):
 
     # Test regular copying
     for ext in [".edf", ".bdf"]:
-        raw_fname = op.join(data_path, "test" + ext)
-        new_name = op.join(bids_root, "test_copy" + ext.upper())
+        raw_fname = data_path / f"test{ext}"
+        new_name = bids_root / f"test_copy{ext.upper()}"
 
         with pytest.warns(RuntimeWarning, match="Upper-case extension"):
             copyfile_edf(raw_fname, new_name)
@@ -203,8 +203,8 @@ def test_copyfile_edfbdf_uppercase(tmp_path):
 def test_copyfile_eeglab(tmp_path, fname):
     """Test the copying of EEGlab set and fdt files."""
     bids_root = str(tmp_path)
-    data_path = op.join(testing_path, "EEGLAB")
-    raw_fname = op.join(data_path, fname)
+    data_path = testing_path / "EEGLAB"
+    raw_fname = data_path / fname
     new_name = op.join(bids_root, f"CONVERTED_{fname}.set")
 
     # IO error testing
@@ -227,10 +227,10 @@ def test_copyfile_kit(tmp_path):
     """Test copying and renaming KIT files to a new location."""
     output_path = str(tmp_path)
     data_path = base_path / "kit" / "tests" / "data"
-    raw_fname = op.join(data_path, "test.sqd")
-    hpi_fname = op.join(data_path, "test_mrk.sqd")
-    electrode_fname = op.join(data_path, "test.elp")
-    headshape_fname = op.join(data_path, "test.hsp")
+    raw_fname = data_path / "test.sqd"
+    hpi_fname = data_path / "test_mrk.sqd"
+    electrode_fname = data_path / "test.elp"
+    headshape_fname = data_path / "test.hsp"
     subject_id = "01"
     session_id = "01"
     run = "01"

mne_bids/tests/test_dig.py

@@ -49,7 +49,7 @@
 
 def _load_raw():
     """Load the sample raw data."""
-    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
     raw = mne.io.read_raw(raw_fname)
     raw.drop_channels(raw.info["bads"])
     raw.info["line_freq"] = 60
@@ -338,11 +338,11 @@ def test_convert_montage():
     raw = _load_raw()
     montage = raw.get_montage()
     trans = mne.read_trans(
-        op.join(data_path, "MEG", "sample", "sample_audvis_trunc-trans.fif")
+        data_path / "MEG" / "sample" / "sample_audvis_trunc-trans.fif"
     )
     montage.apply_trans(trans)
 
-    subjects_dir = op.join(data_path, "subjects")
+    subjects_dir = data_path / "subjects"
     # test read
     with pytest.raises(RuntimeError, match="incorrectly formatted"):
         convert_montage_to_mri(montage, "foo", subjects_dir)

mne_bids/tests/test_path.py

@@ -53,7 +53,7 @@
 def return_bids_test_dir(tmp_path_factory):
     """Return path to a written test BIDS dir."""
     bids_root = str(tmp_path_factory.mktemp("mnebids_utils_test_bids_ds"))
-    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
 
     event_id = {
         "Auditory/Left": 1,
@@ -66,8 +66,8 @@ def return_bids_test_dir(tmp_path_factory):
     events_fname = op.join(
         data_path, "MEG", "sample", "sample_audvis_trunc_raw-eve.fif"
     )
-    cal_fname = op.join(data_path, "SSS", "sss_cal_mgh.dat")
-    crosstalk_fname = op.join(data_path, "SSS", "ct_sparse.fif")
+    cal_fname = data_path / "SSS" / "sss_cal_mgh.dat"
+    crosstalk_fname = data_path / "SSS" / "ct_sparse.fif"
 
     raw = mne.io.read_raw_fif(raw_fname)
     raw.info["line_freq"] = 60
@@ -1127,7 +1127,7 @@ def test_find_matching_paths(return_bids_test_dir):
 @testing.requires_testing_data
 def test_find_empty_room(return_bids_test_dir, tmp_path):
     """Test reading of empty room data."""
-    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
     bids_root = tmp_path / "bids"
     bids_root.mkdir()
 
@@ -1269,7 +1269,7 @@ def test_find_empty_room(return_bids_test_dir, tmp_path):
 @testing.requires_testing_data
 def test_find_emptyroom_ties(tmp_path):
     """Test that we receive a warning on a date tie."""
-    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
 
     bids_root = str(tmp_path)
     bids_path = _bids_path.copy().update(root=bids_root, datatype="meg")
@@ -1283,7 +1283,7 @@ def test_find_emptyroom_ties(tmp_path):
 
     raw = _read_raw_fif(raw_fname)
 
-    er_raw_fname = op.join(data_path, "MEG", "sample", "ernoise_raw.fif")
+    er_raw_fname = data_path / "MEG" / "sample" / "ernoise_raw.fif"
     raw.copy().crop(0, 10).save(er_raw_fname, overwrite=True)
     er_raw = _read_raw_fif(er_raw_fname)
     raw.set_meas_date(meas_date)
@@ -1306,7 +1306,7 @@ def test_find_emptyroom_ties(tmp_path):
 @testing.requires_testing_data
 def test_find_emptyroom_no_meas_date(tmp_path):
     """Test that we warn if measurement date can be read or inferred."""
-    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
 
     bids_root = str(tmp_path)
     bids_path = _bids_path.copy().update(root=bids_root)
@@ -1324,7 +1324,7 @@ def test_find_emptyroom_no_meas_date(tmp_path):
     er_basename = er_bids_path.basename
     raw = _read_raw_fif(raw_fname)
 
-    er_raw_fname = op.join(data_path, "MEG", "sample", "ernoise_raw.fif")
+    er_raw_fname = data_path / "MEG" / "sample" / "ernoise_raw.fif"
     raw.copy().crop(0, 10).save(er_raw_fname, overwrite=True)
     er_raw = _read_raw_fif(er_raw_fname)
     er_raw.set_meas_date(er_meas_date)

mne_bids/tests/test_read.py

@@ -63,10 +63,10 @@
 
 # Get the MNE testing sample data - USA
 data_path = testing.data_path(download=False)
-raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
 
 # Data with cHPI info
-raw_fname_chpi = op.join(data_path, "SSS", "test_move_anon_raw.fif")
+raw_fname_chpi = data_path / "SSS" / "test_move_anon_raw.fif"
 
 # Tiny BIDS testing dataset
 mne_bids_root = Path(mne_bids.__file__).parents[1]
@@ -229,7 +229,7 @@ def test_get_head_mri_trans(tmp_path):
     events_fname = op.join(
         data_path, "MEG", "sample", "sample_audvis_trunc_raw-eve.fif"
     )
-    subjects_dir = op.join(data_path, "subjects")
+    subjects_dir = data_path / "subjects"
 
     # Drop unknown events.
     events = mne.read_events(events_fname)
@@ -253,7 +253,7 @@ def test_get_head_mri_trans(tmp_path):
 
     # Get the T1 weighted MRI data file ... test write_anat with a nibabel
     # image instead of a file path
-    t1w_mgh = op.join(data_path, "subjects", "sample", "mri", "T1.mgz")
+    t1w_mgh = data_path / "subjects" / "sample" / "mri" / "T1.mgz"
     t1w_mgh = nib.load(t1w_mgh)
 
     landmarks = get_anat_landmarks(
@@ -278,7 +278,7 @@ def test_get_head_mri_trans(tmp_path):
     raw.info["dig"][0]["r"] = np.full(3, np.nan)
     sh.rmtree(anat_dir)
     bad_landmarks = get_anat_landmarks(
-        t1w_mgh, raw.info, trans, "sample", op.join(data_path, "subjects")
+        t1w_mgh, raw.info, trans, "sample", data_path / "subjects"
     )
     write_anat(t1w_mgh, bids_path=t1w_bids_path, landmarks=bad_landmarks)
     with pytest.raises(RuntimeError, match="AnatomicalLandmarkCoordinates"):
@@ -873,7 +873,7 @@ def test_handle_eeg_coords_reading(tmp_path):
         root=tmp_path,
     )
 
-    raw_fname = op.join(data_path, "EDF", "test_reduced.edf")
+    raw_fname = data_path / "EDF" / "test_reduced.edf"
     raw = _read_raw_edf(raw_fname)
 
     # ensure we are writing 'eeg' data
@@ -933,7 +933,7 @@ def test_handle_eeg_coords_reading(tmp_path):
 @testing.requires_testing_data
 def test_handle_ieeg_coords_reading(bids_path, tmp_path):
     """Test reading iEEG coordinates from BIDS files."""
-    raw_fname = op.join(data_path, "EDF", "test_reduced.edf")
+    raw_fname = data_path / "EDF" / "test_reduced.edf"
     bids_fname = bids_path.copy().update(
         datatype="ieeg", suffix="ieeg", extension=".edf", root=tmp_path
     )
@@ -1105,7 +1105,7 @@ def test_get_head_mri_trans_ctf(fname, tmp_path):
     """Test getting a trans object from BIDS data in CTF."""
     nib = pytest.importorskip("nibabel")
 
-    ctf_data_path = op.join(data_path, "CTF")
+    ctf_data_path = data_path / "CTF"
     raw_ctf_fname = op.join(ctf_data_path, fname)
     raw_ctf = _read_raw_ctf(raw_ctf_fname, clean_names=True)
     bids_path = _bids_path.copy().update(root=tmp_path, datatype="meg", suffix="meg")
@@ -1116,7 +1116,7 @@ def test_get_head_mri_trans_ctf(fname, tmp_path):
 
     # Get the T1 weighted MRI data file ... test write_anat with a nibabel
     # image instead of a file path
-    t1w_mgh = op.join(data_path, "subjects", "sample", "mri", "T1.mgz")
+    t1w_mgh = data_path / "subjects" / "sample" / "mri" / "T1.mgz"
     t1w_mgh = nib.load(t1w_mgh)
 
     t1w_bids_path = BIDSPath(
@@ -1127,7 +1127,7 @@ def test_get_head_mri_trans_ctf(fname, tmp_path):
         raw_ctf.info,
         trans,
         fs_subject="sample",
-        fs_subjects_dir=op.join(data_path, "subjects"),
+        fs_subjects_dir=data_path / "subjects",
     )
     write_anat(t1w_mgh, bids_path=t1w_bids_path, landmarks=landmarks)
 
@@ -1136,7 +1136,7 @@ def test_get_head_mri_trans_ctf(fname, tmp_path):
         bids_path=bids_path,
         extra_params=dict(clean_names=True),
         fs_subject="sample",
-        fs_subjects_dir=op.join(data_path, "subjects"),
+        fs_subjects_dir=data_path / "subjects",
     )
 
     assert_almost_equal(trans["trans"], estimated_trans["trans"])

mne_bids/tests/test_update.py

@@ -43,7 +43,7 @@
 def _get_bids_test_dir(tmp_path_factory):
     """Return path to a written test BIDS dir."""
     bids_root = str(tmp_path_factory.mktemp("mnebids_utils_test_bids_ds"))
-    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
 
     event_id = {
         "Auditory/Left": 1,
@@ -56,8 +56,8 @@ def _get_bids_test_dir(tmp_path_factory):
     events_fname = op.join(
         data_path, "MEG", "sample", "sample_audvis_trunc_raw-eve.fif"
     )
-    cal_fname = op.join(data_path, "SSS", "sss_cal_mgh.dat")
-    crosstalk_fname = op.join(data_path, "SSS", "ct_sparse.fif")
+    cal_fname = data_path / "SSS" / "sss_cal_mgh.dat"
+    crosstalk_fname = data_path / "SSS" / "ct_sparse.fif"
 
     raw = mne.io.read_raw_fif(raw_fname)
     raw.info["line_freq"] = 60
@@ -316,7 +316,7 @@ def test_readme_conflicts(extension, _get_bids_test_dir):
         root=_get_bids_test_dir,
     )
 
-    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
     raw = mne.io.read_raw_fif(raw_fname)
 
     write_raw_bids(raw, bids_path, overwrite=False)
@@ -341,7 +341,7 @@ def test_multiple_readmes_invalid(_get_bids_test_dir):
         root=_get_bids_test_dir,
     )
 
-    raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")
+    raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
     raw = mne.io.read_raw_fif(raw_fname)
 
     with pytest.raises(RuntimeError, match="Multiple README files found"):

mne_bids/tests/test_utils.py

@@ -3,7 +3,6 @@
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause
 
-import os.path as op
 from datetime import datetime
 from pathlib import Path
 
@@ -150,16 +149,16 @@ def test_infer_eeg_placement_scheme():
     """Test inferring a correct EEG placement scheme."""
     # no eeg channels case (e.g., MEG data)
     data_path = base_path / "bti" / "tests" / "data"
-    raw_fname = op.join(data_path, "test_pdf_linux")
-    config_fname = op.join(data_path, "test_config_linux")
-    headshape_fname = op.join(data_path, "test_hs_linux")
+    raw_fname = data_path / "test_pdf_linux"
+    config_fname = data_path / "test_config_linux"
+    headshape_fname = data_path / "test_hs_linux"
     raw = mne.io.read_raw_bti(raw_fname, config_fname, headshape_fname)
     placement_scheme = _infer_eeg_placement_scheme(raw)
     assert placement_scheme == "n/a"
 
     # 1020 case
     data_path = base_path / "brainvision" / "tests" / "data"
-    raw_fname = op.join(data_path, "test.vhdr")
+    raw_fname = data_path / "test.vhdr"
     raw = mne.io.read_raw_brainvision(raw_fname)
     placement_scheme = _infer_eeg_placement_scheme(raw)
     assert placement_scheme == "based on the extended 10/20 system"