FIX: Some [skip circle]

Author: larsoner

mne/conftest.py

@@ -39,6 +39,7 @@
     Bunch,
     _assert_no_instances,
     _check_qt_version,
+    _chmod_rw_R,
     _pl,
     _record_warnings,
     _TempDir,
@@ -771,6 +772,7 @@ def subjects_dir_tmp(tmp_path):
     """Copy MNE-testing-data subjects_dir to a temp dir for manipulation."""
     for key in ("sample", "fsaverage"):
         shutil.copytree(op.join(subjects_dir, key), str(tmp_path / key))
+    _chmod_rw_R(tmp_path)
     return str(tmp_path)
 
 
@@ -788,6 +790,7 @@ def subjects_dir_tmp_few(tmp_path):
         shutil.copytree(
             test_path / "subjects" / "sample" / dirname, sample_path / dirname
         )
+    _chmod_rw_R(subjects_path)
     return subjects_path
 
 

mne/io/ctf/tests/test_ctf.py

@@ -32,7 +32,13 @@
 from mne.io.tests.test_raw import _test_raw_reader
 from mne.tests.test_annotations import _assert_annotations_equal
 from mne.transforms import apply_trans
-from mne.utils import _clean_names, _record_warnings, _stamp_to_dt, catch_logging
+from mne.utils import (
+    _clean_names,
+    _record_warnings,
+    _stamp_to_dt,
+    catch_logging,
+    copytree_rw,
+)
 
 ctf_dir = testing.data_path(download=False) / "CTF"
 ctf_fname_continuous = "testdata_ctf.ds"
@@ -75,7 +81,7 @@ def test_read_ctf(tmp_path):
     # Create a dummy .eeg file so we can test our reading/application of it
     os.mkdir(op.join(temp_dir, "randpos"))
     ctf_eeg_fname = op.join(temp_dir, "randpos", ctf_fname_catch)
-    shutil.copytree(op.join(ctf_dir, ctf_fname_catch), ctf_eeg_fname)
+    copytree_rw(op.join(ctf_dir, ctf_fname_catch), ctf_eeg_fname)
     with pytest.warns(RuntimeWarning, match="RMSP .* changed to a MISC ch"):
         raw = _test_raw_reader(read_raw_ctf, directory=ctf_eeg_fname)
     picks = pick_types(raw.info, meg=False, eeg=True)
@@ -689,7 +695,7 @@ def _bad_res4_grad_comp(dsdir):
 def test_missing_res4(tmp_path):
     """Test that res4 missing is handled gracefully."""
     use_ds = tmp_path / ctf_fname_continuous
-    shutil.copytree(ctf_dir / ctf_fname_continuous, tmp_path / ctf_fname_continuous)
+    copytree_rw(ctf_dir / ctf_fname_continuous, tmp_path / ctf_fname_continuous)
     read_raw_ctf(use_ds)
     os.remove(use_ds / (ctf_fname_continuous[:-2] + "meg4"))
     with pytest.raises(OSError, match="could not find the following"):

mne/io/egi/tests/test_egi.py

@@ -20,7 +20,7 @@
 from mne.io import read_evokeds_mff, read_raw_egi, read_raw_fif
 from mne.io.egi.egi import _combine_triggers
 from mne.io.tests.test_raw import _test_raw_reader
-from mne.utils import object_diff
+from mne.utils import _chmod_rw_R, object_diff
 
 base_dir = Path(__file__).parent / "data"
 egi_fname = base_dir / "test_egi.raw"
@@ -338,6 +338,7 @@ def test_io_egi_pns_mff(tmp_path):
     # EEG missing
     new_mff = tmp_path / "temp.mff"
     shutil.copytree(egi_mff_pns_fname, new_mff)
+    _chmod_rw_R(new_mff)
     read_raw_egi(new_mff, verbose="error")
     os.remove(new_mff / "info1.xml")
     os.remove(new_mff / "signal1.bin")
@@ -594,6 +595,7 @@ def test_egi_mff_bad_xml(tmp_path):
     """Test that corrupt XML files are gracefully handled."""
     pytest.importorskip("defusedxml")
     mff_fname = shutil.copytree(egi_mff_fname, tmp_path / "test_egi_bad_xml.mff")
+    _chmod_rw_R(mff_fname)
     bad_xml = mff_fname / "bad.xml"
     bad_xml.write_text("<foo>", encoding="utf-8")
     # Missing coordinate file

mne/io/fil/tests/test_fil.py

@@ -2,7 +2,6 @@
 # License: BSD-3-Clause
 # Copyright the MNE-Python contributors.
 
-import shutil
 from os import remove
 
 import pytest
@@ -14,6 +13,7 @@
 from mne.datasets import testing
 from mne.io import read_raw_fil
 from mne.io.fil.sensors import _get_pos_units
+from mne.utils import copytree_rw
 
 fil_path = testing.data_path(download=False) / "FIL"
 
@@ -161,7 +161,7 @@ def test_fil_complete():
 def test_fil_no_positions(tmp_path):
     """Test FIL reader in cases where a position file is missing."""
     test_path = tmp_path / "FIL"
-    shutil.copytree(fil_path, test_path)
+    copytree_rw(fil_path, test_path)
 
     posname = test_path / "sub-noise_ses-001_task-noise220622_run-001_positions.tsv"
     binname = test_path / "sub-noise_ses-001_task-noise220622_run-001_meg.bin"
@@ -179,7 +179,7 @@ def test_fil_no_positions(tmp_path):
 def test_fil_bad_channel_spec(tmp_path):
     """Test FIL reader when a bad channel is specified in channels.tsv."""
     test_path = tmp_path / "FIL"
-    shutil.copytree(fil_path, test_path)
+    copytree_rw(fil_path, test_path)
 
     channame = test_path / "sub-noise_ses-001_task-noise220622_run-001_channels.tsv"
     binname = test_path / "sub-noise_ses-001_task-noise220622_run-001_meg.bin"

mne/io/nirx/tests/test_nirx.py

@@ -4,7 +4,6 @@
 
 import datetime as dt
 import os
-import shutil
 
 import numpy as np
 import pytest
@@ -22,6 +21,7 @@
     source_detector_distances,
 )
 from mne.transforms import _get_trans, apply_trans
+from mne.utils import copytree_rw
 
 testing_path = data_path(download=False)
 fname_nirx_15_0 = testing_path / "NIRx" / "nirscout" / "nirx_15_0_recording"
@@ -246,7 +246,7 @@ def test_nirx_missing_warn():
 @requires_testing_data
 def test_nirx_missing_evt(tmp_path):
     """Test reading NIRX files when missing data."""
-    shutil.copytree(fname_nirx_15_2_short, str(tmp_path) + "/data/")
+    copytree_rw(fname_nirx_15_2_short, str(tmp_path) + "/data/")
     os.rename(
         tmp_path / "data" / "NIRS-2019-08-23_001.evt",
         tmp_path / "data" / "NIRS-2019-08-23_001.xxx",
@@ -259,7 +259,7 @@ def test_nirx_missing_evt(tmp_path):
 @requires_testing_data
 def test_nirx_dat_warn(tmp_path):
     """Test reading NIRX files when missing data."""
-    shutil.copytree(fname_nirx_15_2_short, str(tmp_path) + "/data/")
+    copytree_rw(fname_nirx_15_2_short, str(tmp_path) + "/data/")
     os.rename(
         tmp_path / "data" / "NIRS-2019-08-23_001.dat",
         tmp_path / "data" / "NIRS-2019-08-23_001.tmp",
@@ -461,7 +461,7 @@ def test_nirx_15_3_short():
 def test_locale_encoding(tmp_path):
     """Test NIRx encoding."""
     fname = tmp_path / "latin"
-    shutil.copytree(fname_nirx_15_2, fname)
+    copytree_rw(fname_nirx_15_2, fname)
     hdr_fname = fname / "NIRS-2019-10-02_003.hdr"
     hdr = list()
     with open(hdr_fname, "rb") as fid:

mne/io/persyst/tests/test_persyst.py

@@ -12,6 +12,7 @@
 from mne.datasets.testing import data_path, requires_testing_data
 from mne.io import read_raw_persyst
 from mne.io.tests.test_raw import _test_raw_reader
+from mne.utils import _chmod_rw_R
 
 testing_path = data_path(download=False)
 fname_lay = (
@@ -144,6 +145,7 @@ def test_persyst_moved_file(tmp_path):
     new_fname_lay = tmp_path / fname_lay.name
     new_fname_dat = tmp_path / fname_dat.name
     shutil.copy(fname_lay, new_fname_lay)
+    _chmod_rw_R(tmp_path)
 
     # original file read should work
     read_raw_persyst(fname_lay)

mne/io/snirf/tests/test_snirf.py

@@ -28,7 +28,7 @@
     source_detector_distances,
 )
 from mne.transforms import _get_trans, apply_trans
-from mne.utils import catch_logging
+from mne.utils import _chmod_rw_R, catch_logging
 
 testing_path = data_path(download=False)
 # SfNIRS files
@@ -252,8 +252,9 @@ def test_snirf_against_nirx():
 @requires_testing_data
 def test_snirf_nonstandard(tmp_path):
     """Test custom tags."""
-    shutil.copy(sfnirs_homer_103_wShort, str(tmp_path) + "/mod.snirf")
     fname = str(tmp_path) + "/mod.snirf"
+    shutil.copy(sfnirs_homer_103_wShort, fname)
+    _chmod_rw_R(tmp_path)
     # Manually mark up the file to match MNE-NIRS custom tags
     with h5py.File(fname, "r+") as f:
         f.create_dataset("nirs/metaDataTags/middleName", data=[b"X"])
@@ -287,8 +288,9 @@ def test_snirf_nonstandard(tmp_path):
 @requires_testing_data
 def test_snirf_empty_landmark_labels(tmp_path):
     """Test reading SNIRF files with empty landmarkLabels (gh-13627)."""
-    shutil.copy(sfnirs_homer_103_wShort, tmp_path / "empty_labels.snirf")
     fname = tmp_path / "empty_labels.snirf"
+    shutil.copy(sfnirs_homer_103_wShort, fname)
+    _chmod_rw_R(tmp_path)
 
     # Modify file to have landmarkPos3D but empty/scalar landmarkLabels
     with h5py.File(fname, "r+") as f:
@@ -586,6 +588,7 @@ def test_sample_rate_jitter(tmp_path):
     # Create a clean copy and ensure it loads without error
     new_file = tmp_path / "snirf_nirsport2_2019.snirf"
     copy2(snirf_nirsport2_20219, new_file)
+    _chmod_rw_R(tmp_path)
     read_raw_snirf(new_file)
 
     # Edit the file and add jitter within tolerance (0.99%)

mne/tests/test_bem.py

@@ -44,6 +44,7 @@
 from mne.surface import _get_ico_surface, read_surface
 from mne.transforms import translation
 from mne.utils import (
+    _chmod_rw_R,
     _record_warnings,
     catch_logging,
     check_version,
@@ -231,6 +232,7 @@ def test_bem_model_topology(tmp_path):
             subjects_dir / "sample" / "bem" / fname,
             tmp_path / "foo" / "bem" / fname,
         )
+    _chmod_rw_R(tmp_path)
     outer_fname = tmp_path / "foo" / "bem" / "outer_skull.surf"
     rr, tris = read_surface(outer_fname)
     tris = tris[:-1]

mne/utils/__init__.pyi

@@ -56,6 +56,7 @@ __all__ = [
     "_check_stc_units",
     "_check_subject",
     "_check_time_format",
+    "_chmod_rw_R",
     "_clean_names",
     "_click_ch_name",
     "_compute_row_norms",
@@ -202,6 +203,7 @@ from ._logging import (
 )
 from ._testing import (
     ArgvSetter,
+    _chmod_rw_R,
     _click_ch_name,
     _raw_annot,
     _TempDir,

mne/utils/_testing.py

@@ -6,6 +6,7 @@
 
 import inspect
 import os
+import shutil
 import sys
 import tempfile
 import traceback
@@ -417,3 +418,23 @@ def assert_trans_allclose(actual, desired, dist_tol=0.0, angle_tol=0.0):
         f"{1000 * dist:0.3f} > {1000 * dist_tol:0.3f} mm translation"
     )
     assert angle <= angle_tol, f"{angle:0.3f} > {angle_tol:0.3f}° rotation"
+
+
+def _chmod_rw_R(path):
+    assert os.path.isdir(path), f"Expected a directory, got {path}"
+    os.chmod(path, 0o700 | os.stat(path).st_mode)
+    for root, dirs, files in os.walk(path):
+        for name in files:
+            this_name = os.path.join(root, name)
+            os.chmod(this_name, 0o600 | os.stat(this_name).st_mode)
+        for name in dirs:
+            this_name = os.path.join(root, name)
+            os.chmod(this_name, 0o770 | os.stat(this_name).st_mode)
+
+
+def copytree_rw(src, dst):
+    """Copy a directory tree and make it read/write."""
+    assert os.path.isdir(src), f"Expected a directory, got {src}"
+    shutil.copytree(src, dst)
+    _chmod_rw_R(dst)
+    return dst