os.path to pathlib: part 1 / n

doc/sphinxext/gen_cli.py

@@ -7,11 +7,9 @@
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause
 
-import glob
-import os
 import shutil
 import sys
-from os import path as op
+from pathlib import Path
 
 import sphinx.util
 from mne.utils import hashfunc, run_subprocess
@@ -57,27 +55,22 @@ def setup(app):
 
 def generate_cli_rst(app=None):
     """Generate the command line interface docs."""
-    out_dir = op.abspath(op.join(op.dirname(__file__), "..", "generated"))
-    if not op.isdir(out_dir):
-        os.mkdir(out_dir)
-    out_fname = op.join(out_dir, "cli.rst.new")
+    out_dir = Path(__file__).resolve().parent.parent / "generated"
+    out_dir.mkdir(exist_ok=True)
+    out_fname = out_dir / "cli.rst.new"
 
-    cli_path = op.abspath(
-        op.join(os.path.dirname(__file__), "..", "..", "mne_bids", "commands")
-    )
-    fnames = sorted(
-        [op.basename(fname) for fname in glob.glob(op.join(cli_path, "mne_bids*.py"))]
-    )
+    cli_path = Path(__file__).resolve().parent.parent.parent / "mne_bids" / "commands"
+    fnames = sorted([fname.name for fname in cli_path.glob("mne_bids*.py")])
     iterator = sphinx.util.display.status_iterator(
         fnames, "generating MNE-BIDS cli help ... ", length=len(fnames)
     )
-    with open(out_fname, "w", encoding="utf-8") as f:
+    with out_fname.open("w", encoding="utf-8") as f:
         f.write(header)
         for fname in iterator:
             cmd_name = fname[:-3]
-            run_name = op.join(cli_path, fname)
+            run_name = cli_path / fname
             output, _ = run_subprocess(
-                [sys.executable, run_name, "--help"], verbose=False
+                [sys.executable, str(run_name), "--help"], verbose=False
             )
             output = output.splitlines()
 
@@ -118,12 +111,12 @@ def generate_cli_rst(app=None):
 def _replace_md5(fname):
     """Replace a file based on MD5sum."""
     # adapted from sphinx-gallery
-    assert fname.endswith(".new")
-    fname_old = fname[:-4]
-    if os.path.isfile(fname_old) and hashfunc(fname) == hashfunc(fname_old):
-        os.remove(fname)
+    assert fname.name.endswith(".new")
+    fname_old = fname.with_suffix("")
+    if fname_old.is_file() and hashfunc(fname) == hashfunc(fname_old):
+        fname.unlink()
     else:
-        shutil.move(fname, fname_old)
+        shutil.move(str(fname), str(fname_old))
 
 
 # This is useful for testing/iterating to see what the result looks like

examples/convert_eeg_to_bids.py

@@ -26,8 +26,8 @@
 
 # %%
 # We are importing everything we need for this example:
-import os.path as op
 import shutil
+from pathlib import Path
 
 import mne
 from mne.datasets import eegbci
@@ -66,8 +66,8 @@
 # of the directory tree.
 
 # get MNE directory with example data
-mne_data_dir = mne.get_config("MNE_DATASETS_EEGBCI_PATH")
-data_dir = op.join(mne_data_dir, "MNE-eegbci-data")
+mne_data_dir = Path(mne.get_config("MNE_DATASETS_EEGBCI_PATH"))
+data_dir = mne_data_dir / "MNE-eegbci-data"
 
 print_dir_tree(data_dir)
 
@@ -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
@@ -156,7 +156,7 @@
 
 # define a task name and a directory where to save the data to
 task = "RestEyesClosed"
-bids_root = op.join(mne_data_dir, "eegmmidb_bids_eeg_example")
+bids_root = mne_data_dir / "eegmmidb_bids_eeg_example"
 
 # %%
 # To ensure the output path doesn't contain any leftover files from previous
@@ -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)
 
 # %%
@@ -218,7 +218,7 @@
 #
 # If you are preparing a manuscript, please make sure to also cite MNE-BIDS
 # there.
-readme = op.join(bids_root, "README")
+readme = bids_root / "README"
 with open(readme, encoding="utf-8-sig") as fid:
     text = fid.read()
 print(text)

examples/convert_empty_room.py

@@ -28,7 +28,6 @@
 #
 # Let us first import mne_bids.
 
-import os.path as op
 import shutil
 from datetime import datetime, timezone
 
@@ -41,9 +40,9 @@
 # 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.parent / "MNE-sample-data-bids"
 
 # %%
 # To ensure the output path doesn't contain any leftover files from previous
@@ -52,7 +51,7 @@
 # .. 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 +67,7 @@
 
 # %%
 # 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
 

examples/convert_group_studies.py

@@ -17,8 +17,8 @@
 # %%
 # Let us import ``mne_bids``
 
-import os.path as op
 import shutil
+from pathlib import Path
 
 import mne
 from mne.datasets import eegbci
@@ -53,14 +53,15 @@
     eegbci.load_data(subjects=subject_id, runs=runs, update_path=True)
 
 # get path to MNE directory with the downloaded example data
-mne_data_dir = mne.get_config("MNE_DATASETS_EEGBCI_PATH")
-data_dir = op.join(mne_data_dir, "MNE-eegbci-data")
+data_dir = eegbci.data_path
+mne_data_dir = Path(mne.get_config("MNE_DATASETS_EEGBCI_PATH"))
+data_dir = mne_data_dir / "MNE-eegbci-data"
 
 # %%
 # Let us loop over the subjects and create BIDS-compatible folder
 
 # Make a path where we can save the data to
-bids_root = op.join(mne_data_dir, "eegmmidb_bids_group_conversion")
+bids_root = mne_data_dir / "eegmmidb_bids_group_conversion"
 
 # %%
 # To ensure the output path doesn't contain any leftover files from previous
@@ -69,7 +70,7 @@
 # .. warning:: Do not delete directories that may contain important data!
 #
 
-if op.exists(bids_root):
+if bids_root.exists():
     shutil.rmtree(bids_root)
 
 # %%

examples/convert_ieeg_to_bids.py

@@ -45,8 +45,8 @@
 
 # %%
 
-import os.path as op
 import shutil
+from pathlib import Path
 
 import mne
 import nibabel as nib
@@ -77,9 +77,9 @@
 
 # The electrode coords data are in the tsv file format
 # which is easily read in using numpy
-raw = mne.io.read_raw_fif(op.join(misc_path, "seeg", "sample_seeg_ieeg.fif"))
+raw = mne.io.read_raw_fif(misc_path / "seeg" / "sample_seeg_ieeg.fif")
 raw.info["line_freq"] = 60  # specify power line frequency as required by BIDS
-subjects_dir = op.join(misc_path, "seeg")  # Freesurfer recon-all directory
+subjects_dir = misc_path / "seeg"  # Freesurfer recon-all directory
 
 # %%
 # When the locations of the channels in this dataset were found in
@@ -153,10 +153,10 @@
 task = "motor"
 
 # get MNE-Python directory w/ example data
-mne_data_dir = mne.get_config("MNE_DATASETS_MISC_PATH")
+mne_data_dir = Path(mne.get_config("MNE_DATASETS_MISC_PATH"))
 
 # There is the root directory for where we will write our data.
-bids_root = op.join(mne_data_dir, "ieeg_bids")
+bids_root = mne_data_dir / "ieeg_bids"
 
 # %%
 # To ensure the output path doesn't contain any leftover files from previous
@@ -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)
 
 # %%
@@ -182,7 +182,7 @@
 # plot T1 to show that it is ACPC-aligned
 # note that the origin is centered on the anterior commissure (AC)
 # with the y-axis passing through the posterior commissure (PC)
-T1_fname = op.join(subjects_dir, "sample_seeg", "mri", "T1.mgz")
+T1_fname = subjects_dir / "sample_seeg" / "mri" / "T1.mgz"
 fig = plot_anat(T1_fname, cut_coords=(0, 0, 0))
 fig.axes["x"].ax.annotate(
     "AC",
@@ -295,7 +295,7 @@
 # We can see that the appropriate citations are already written in the README.
 # If you are preparing a manuscript, please make sure to also cite MNE-BIDS
 # there.
-readme = op.join(bids_root, "README")
+readme = bids_root / "README"
 with open(readme, encoding="utf-8-sig") as fid:
     text = fid.read()
 print(text)
@@ -330,11 +330,11 @@
 
 # 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
-raw = mne.io.read_raw_fif(op.join(misc_path, "seeg", "sample_seeg_ieeg.fif"))
+raw = mne.io.read_raw_fif(misc_path / "seeg" / "sample_seeg_ieeg.fif")
 raw.info["line_freq"] = 60  # specify power line frequency as required by BIDS
 
 # get Talairach transform
@@ -459,19 +459,19 @@
 
 # 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
-subjects_dir = op.join(mne.datasets.sample.data_path(), "subjects")
-template_T1 = nib.load(op.join(subjects_dir, "fsaverage", "mri", "T1.mgz"))
+subjects_dir = mne.datasets.sample.data_path() / "subjects"
+template_T1 = nib.load(subjects_dir / "fsaverage" / "mri" / "T1.mgz")
 
 # get voxels to surface RAS and scanner RAS transforms
 vox_mri_t = template_T1.header.get_vox2ras_tkr()  # surface RAS
 vox_ras_t = template_T1.header.get_vox2ras()  # scanner RAS
 
 raw = mne.io.read_raw_fif(
-    op.join(misc_path, "seeg", "sample_seeg_ieeg.fif")  # load our raw data again
+    misc_path / "seeg" / "sample_seeg_ieeg.fif"  # load our raw data again
 )
 montage = raw.get_montage()  # get the original montage
 montage.apply_trans(trans)  # head->mri

examples/convert_mne_sample.py

@@ -23,7 +23,6 @@
 # sample data, and then finally the MNE-BIDS functions we need for this example
 
 import json
-import os.path as op
 import shutil
 from pprint import pprint
 
@@ -58,10 +57,10 @@
     "Button": 32,
 }
 
-raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_raw.fif")
-er_fname = op.join(data_path, "MEG", "sample", "ernoise_raw.fif")  # empty room
-events_fname = op.join(data_path, "MEG", "sample", "sample_audvis_raw-eve.fif")
-output_path = op.join(data_path, "..", "MNE-sample-data-bids")
+raw_fname = data_path / "MEG" / "sample" / "sample_audvis_raw.fif"
+er_fname = data_path / "MEG" / "sample" / "ernoise_raw.fif"  # empty room
+events_fname = data_path / "MEG" / "sample" / "sample_audvis_raw-eve.fif"
+output_path = data_path.parent / "MNE-sample-data-bids"
 
 # %%
 # To ensure the output path doesn't contain any leftover files from previous
@@ -70,7 +69,7 @@
 # .. warning:: Do not delete directories that may contain important data!
 #
 
-if op.exists(output_path):
+if output_path.exists():
     shutil.rmtree(output_path)
 
 # %%
@@ -122,8 +121,8 @@
 # are required when processing Elekta/Neuromag/MEGIN data using MaxFilter®.
 # Let's store these data in appropriate places, too.
 
-cal_fname = op.join(data_path, "SSS", "sss_cal_mgh.dat")
-ct_fname = op.join(data_path, "SSS", "ct_sparse_mgh.fif")
+cal_fname = data_path / "SSS" / "sss_cal_mgh.dat"
+ct_fname = data_path / "SSS" / "ct_sparse_mgh.fif"
 
 write_meg_calibration(cal_fname, bids_path)
 write_meg_crosstalk(ct_fname, bids_path)
@@ -174,7 +173,7 @@
 # The README created by :func:`write_raw_bids` also takes care of the citation
 # for mne-bids. If you are preparing a manuscript, please make sure to also
 # cite MNE-BIDS there.
-readme = op.join(output_path, "README")
+readme = output_path / "README"
 with open(readme, encoding="utf-8-sig") as fid:
     text = fid.read()
 print(text)