os.path to pathlib

sappelhoff · sappelhoff · commit 75849ad0eb27 · 2024-11-21T10:32:51.000+01:00
diff --git a/examples/convert_eeg_to_bids.py b/examples/convert_eeg_to_bids.py
@@ -114,7 +114,7 @@
 
 # Get the electrode coordinates
 testing_data = mne.datasets.testing.data_path()
-captrak_path = op.join(testing_data, "montage", "captrak_coords.bvct")
+captrak_path = testing_data / "montage" / "captrak_coords.bvct"
 montage = mne.channels.read_dig_captrak(captrak_path)
 
 # Rename the montage channel names only for this example, because as said
@@ -165,7 +165,7 @@
 # .. warning:: Do not delete directories that may contain important data!
 #
 
-if op.exists(bids_root):
+if bids_root.exists():
     shutil.rmtree(bids_root)
 
 # %%
diff --git a/examples/convert_empty_room.py b/examples/convert_empty_room.py
@@ -41,9 +41,9 @@
 # And define the paths and event_id dictionary.
 
 data_path = sample.data_path()
-raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_raw.fif")
+raw_fname = data_path / "MEG" / "sample" / "sample_audvis_raw.fif"
 
-bids_root = op.join(data_path, "..", "MNE-sample-data-bids")
+bids_root = data_path / ".." / "MNE-sample-data-bids"
 
 # %%
 # To ensure the output path doesn't contain any leftover files from previous
@@ -52,7 +52,7 @@
 # .. warning:: Do not delete directories that may contain important data!
 #
 
-if op.exists(bids_root):
+if bids_root.exists():
     shutil.rmtree(bids_root)
 
 # %%
@@ -68,7 +68,7 @@
 
 # %%
 # Specify some empty room data and run BIDS conversion on it.
-er_raw_fname = op.join(data_path, "MEG", "sample", "ernoise_raw.fif")
+er_raw_fname = data_path / "MEG" / "sample" / "ernoise_raw.fif"
 er_raw = mne.io.read_raw_fif(er_raw_fname)
 er_raw.info["line_freq"] = 60  # specify power line frequency as req. by BIDS
 
diff --git a/examples/convert_group_studies.py b/examples/convert_group_studies.py
@@ -69,7 +69,7 @@
 # .. warning:: Do not delete directories that may contain important data!
 #
 
-if op.exists(bids_root):
+if bids_root.exists():
     shutil.rmtree(bids_root)
 
 # %%
diff --git a/examples/convert_ieeg_to_bids.py b/examples/convert_ieeg_to_bids.py
@@ -165,7 +165,7 @@
 # .. warning:: Do not delete directories that may contain important data!
 #
 
-if op.exists(bids_root):
+if bids_root.exists():
     shutil.rmtree(bids_root)
 
 # %%
@@ -330,7 +330,7 @@
 
 # ensure the output path doesn't contain any leftover files from previous
 # tests and example runs
-if op.exists(bids_root):
+if bids_root.exists():
     shutil.rmtree(bids_root)
 
 # load our raw data again
@@ -459,7 +459,7 @@
 
 # ensure the output path doesn't contain any leftover files from previous
 # tests and example runs
-if op.exists(bids_root):
+if bids_root.exists():
     shutil.rmtree(bids_root)
 
 # get a template mgz image to transform the montage to voxel coordinates
diff --git a/examples/convert_nirs_to_bids.py b/examples/convert_nirs_to_bids.py
@@ -116,7 +116,7 @@
 # .. warning:: Do not delete directories that may contain important data!
 #
 
-if op.exists(bids_root):
+if bids_root.exists():
     shutil.rmtree(bids_root)
 
 # %%
diff --git a/examples/mark_bad_channels.py b/examples/mark_bad_channels.py
@@ -61,7 +61,7 @@
 # .. warning:: Do not delete directories that may contain important data!
 #
 
-if op.exists(bids_root):
+if bids_root.exists():
     shutil.rmtree(bids_root)
 
 # %%
diff --git a/mne_bids/commands/tests/test_cli.py b/mne_bids/commands/tests/test_cli.py
@@ -23,7 +23,7 @@
 )
 
 data_path = testing.data_path(download=False)
-base_path = op.join(op.dirname(mne.__file__), "io")
+base_path = Path(mne.__file__).parent / "io"
 subject_id = "01"
 task = "testing"
 datatype = "meg"
diff --git a/mne_bids/tests/test_copyfiles.py b/mne_bids/tests/test_copyfiles.py
@@ -24,7 +24,7 @@
 from mne_bids.path import _parse_ext
 
 testing_path = testing.data_path(download=False)
-base_path = op.join(op.dirname(mne.__file__), "io")
+base_path = Path(mne.__file__).parent / "io"
 
 
 @testing.requires_testing_data
diff --git a/mne_bids/tests/test_dig.py b/mne_bids/tests/test_dig.py
@@ -9,6 +9,7 @@
 import os
 import os.path as op
 import warnings
+from pathlib import Path
 
 import mne
 import numpy as np
@@ -31,7 +32,7 @@
     template_to_head,
 )
 
-base_path = op.join(op.dirname(mne.__file__), "io")
+base_path = Path(mne.__file__).parent / "io"
 subject_id = "01"
 session_id = "01"
 run = "01"
diff --git a/mne_bids/tests/test_pick.py b/mne_bids/tests/test_pick.py
@@ -3,8 +3,6 @@
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause
 
-import os.path as op
-
 from mne.datasets import testing
 from mne.io import read_raw_fif
 
@@ -16,7 +14,7 @@
 @testing.requires_testing_data
 def test_coil_type():
     """Test the correct coil type is retrieved."""
-    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 = read_raw_fif(raw_fname)
     assert coil_type(raw.info, 0) == "meggradplanar"
     assert coil_type(raw.info, 2) == "megmag"
diff --git a/mne_bids/tests/test_report.py b/mne_bids/tests/test_report.py
@@ -3,7 +3,6 @@
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause
 
-import os.path as op
 import textwrap
 
 import mne
@@ -26,7 +25,7 @@
 
 # Get the MNE testing sample data
 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"
 
 warning_str = dict(
     channel_unit_changed="ignore:The unit for chann*.:RuntimeWarning:mne",
diff --git a/mne_bids/tests/test_utils.py b/mne_bids/tests/test_utils.py
@@ -22,7 +22,7 @@
     _infer_eeg_placement_scheme,
 )
 
-base_path = op.join(op.dirname(mne.__file__), "io")
+base_path = Path(mne.__file__).parent / "io"
 subject_id = "01"
 session_id = "01"
 run = "01"
diff --git a/mne_bids/tests/test_write.py b/mne_bids/tests/test_write.py
@@ -62,7 +62,7 @@
 )
 from mne_bids.write import _get_fid_coords
 
-base_path = op.join(op.dirname(mne.__file__), "io")
+base_path = Path(mne.__file__).parent / "io"
 subject_id = "01"
 subject_id2 = "02"
 session_id = "01"
@@ -475,8 +475,8 @@ def test_create_fif(_bids_validate, tmp_path):
     rng = np.random.RandomState(99)
     raw = mne.io.RawArray(rng.random((5, n_points)) * 1e-6, info)
     raw.info["line_freq"] = 60
-    raw.save(op.join(out_dir, "test-raw.fif"))
-    raw = _read_raw_fif(op.join(out_dir, "test-raw.fif"))
+    raw.save(out_dir / "test-raw.fif")
+    raw = _read_raw_fif(out_dir / "test-raw.fif")
     write_raw_bids(raw, bids_path, verbose=False, overwrite=True)
     _bids_validate(bids_root)
 
@@ -493,8 +493,8 @@ def test_line_freq(line_freq, _bids_validate, tmp_path):
     rng = np.random.RandomState(99)
     raw = mne.io.RawArray(rng.random((5, n_points)) * 1e-6, info)
 
-    raw.save(op.join(out_dir, "test-raw.fif"))
-    raw = _read_raw_fif(op.join(out_dir, "test-raw.fif"))
+    raw.save(out_dir / "test-raw.fif")
+    raw = _read_raw_fif(out_dir / "test-raw.fif")
     raw.info["line_freq"] = line_freq
     write_raw_bids(raw, bids_path, verbose=False, overwrite=True)
     _bids_validate(bids_root)
@@ -846,15 +846,13 @@ def test_fif(_bids_validate, tmp_path):
 def test_chpi(_bids_validate, tmp_path, fmt):
     """Test writing of cHPI information."""
     if fmt == "fif_no_chpi":
-        fif_raw_fname = op.join(
-            data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif"
-        )
+        fif_raw_fname = data_path / "MEG" / "sample" / "sample_audvis_trunc_raw.fif"
         raw = _read_raw_fif(fif_raw_fname)
     elif fmt == "fif":
-        fif_raw_fname = op.join(data_path, "SSS", "test_move_anon_raw.fif")
+        fif_raw_fname = data_path / "SSS" / "test_move_anon_raw.fif"
         raw = _read_raw_fif(fif_raw_fname, allow_maxshield="yes")
     elif fmt == "ctf":
-        ctf_raw_fname = op.join(data_path, "CTF", "testdata_ctf.ds")
+        ctf_raw_fname = data_path / "CTF" / "testdata_ctf.ds"
         raw = _read_raw_ctf(ctf_raw_fname)
     elif fmt == "kit":
         kit_data_path = op.join(base_path, "kit", "tests", "data")
@@ -1039,14 +1037,14 @@ def test_fif_exci(tmp_path):
 def test_kit(_bids_validate, tmp_path):
     """Test functionality of the write_raw_bids conversion for KIT data."""
     bids_root = tmp_path / "bids"
-    kit_path = op.join(base_path, "kit", "tests", "data")
-    raw_fname = op.join(kit_path, "test.sqd")
-    events_fname = op.join(kit_path, "test-eve.txt")
-    hpi_fname = op.join(kit_path, "test_mrk.sqd")
-    hpi_pre_fname = op.join(kit_path, "test_mrk_pre.sqd")
-    hpi_post_fname = op.join(kit_path, "test_mrk_post.sqd")
-    electrode_fname = op.join(kit_path, "test.elp")
-    headshape_fname = op.join(kit_path, "test.hsp")
+    kit_path = base_path / "kit" / "tests" / "data"
+    raw_fname = kit_path / "test.sqd"
+    events_fname = kit_path / "test-eve.txt"
+    hpi_fname = kit_path / "test_mrk.sqd"
+    hpi_pre_fname = kit_path / "test_mrk_pre.sqd"
+    hpi_post_fname = kit_path / "test_mrk_post.sqd"
+    electrode_fname = kit_path / "test.elp"
+    headshape_fname = kit_path / "test.hsp"
     event_id = dict(cond=128)
 
     kit_bids_path = _bids_path.copy().update(
@@ -1061,7 +1059,7 @@ def test_kit(_bids_validate, tmp_path):
     )
 
     _bids_validate(bids_root)
-    assert op.exists(bids_root / "participants.tsv")
+    assert (bids_root / "participants.tsv").exists()
     read_raw_bids(bids_path=kit_bids_path)
 
     # ensure the marker file is produced in the right place
@@ -1075,7 +1073,7 @@ def test_kit(_bids_validate, tmp_path):
         datatype="meg",
         root=bids_root,
     )
-    assert op.exists(marker_fname)
+    assert marker_fname.exists()
 
     # test anonymize
     output_path = _test_anonymize(
@@ -1091,7 +1089,7 @@ def test_kit(_bids_validate, tmp_path):
     assert "STI 014" not in data["name"]
 
     # ensure the marker file is produced in the right place
-    assert op.exists(marker_fname)
+    assert marker_fname.exists()
 
     # test attempts at writing invalid event data
     event_data = np.loadtxt(events_fname)
@@ -1147,11 +1145,11 @@ def test_kit(_bids_validate, tmp_path):
         )
 
     # check that everything works with MRK markers, and CON files
-    kit_path = op.join(data_path, "KIT")
-    raw_fname = op.join(kit_path, "data_berlin.con")
-    hpi_fname = op.join(kit_path, "MQKIT_125.mrk")
-    electrode_fname = op.join(kit_path, "MQKIT_125.elp")
-    headshape_fname = op.join(kit_path, "MQKIT_125.hsp")
+    kit_path = data_path / "KIT"
+    raw_fname = kit_path / "data_berlin.con"
+    hpi_fname = kit_path / "MQKIT_125.mrk"
+    electrode_fname = kit_path / "MQKIT_125.elp"
+    headshape_fname = kit_path / "MQKIT_125.hsp"
     bids_root = tmp_path / "bids_kit_mrk"
     kit_bids_path = _bids_path.copy().update(
         acquisition=None, root=bids_root, suffix="meg"

Original file line number	Diff line number	Diff line change
`@@ -69,7 +69,7 @@`
`69`	`69`	`# .. warning:: Do not delete directories that may contain important data!`
`70`	`70`	`#`
`71`	`71`
`72`		`-if op.exists(bids_root):`
	`72`	`+if bids_root.exists():`
`73`	`73`	`shutil.rmtree(bids_root)`
`74`	`74`
`75`	`75`	`# %%`
Original file line number	Diff line number	Diff line change
`@@ -116,7 +116,7 @@`
`116`	`116`	`# .. warning:: Do not delete directories that may contain important data!`
`117`	`117`	`#`
`118`	`118`
`119`		`-if op.exists(bids_root):`
	`119`	`+if bids_root.exists():`
`120`	`120`	`shutil.rmtree(bids_root)`
`121`	`121`
`122`	`122`	`# %%`
Original file line number	Diff line number	Diff line change
`@@ -61,7 +61,7 @@`
`61`	`61`	`# .. warning:: Do not delete directories that may contain important data!`
`62`	`62`	`#`
`63`	`63`
`64`		`-if op.exists(bids_root):`
	`64`	`+if bids_root.exists():`
`65`	`65`	`shutil.rmtree(bids_root)`
`66`	`66`
`67`	`67`	`# %%`
Original file line number	Diff line number	Diff line change
`@@ -23,7 +23,7 @@`
`23`	`23`	`)`
`24`	`24`
`25`	`25`	`data_path = testing.data_path(download=False)`
`26`		`-base_path = op.join(op.dirname(mne.__file__), "io")`
	`26`	`+base_path = Path(mne.__file__).parent / "io"`
`27`	`27`	`subject_id = "01"`
`28`	`28`	`task = "testing"`
`29`	`29`	`datatype = "meg"`