BUG: Move defusedxml to optional dependencies (#12264)

Author: larsoner

doc/changes/v1.6.rst

@@ -4,6 +4,7 @@ Version 1.6.1 (unreleased)
 --------------------------
 
 - Fix bug with type hints in :func:`mne.io.read_raw_neuralynx` (:gh:`12236` by `Richard Höchenberger`_)
+- ``defusedxml`` is now an optional (rather than required) dependency and needed when reading EGI-MFF data, NEDF data, and BrainVision montages (:gh:`12264` by `Eric Larson`_)
 
 .. _changes_1_6_0:
 

mne/channels/_dig_montage_utils.py

@@ -13,9 +13,8 @@
 # Copyright the MNE-Python contributors.
 
 import numpy as np
-from defusedxml import ElementTree
 
-from ..utils import Bunch, _check_fname, warn
+from ..utils import Bunch, _check_fname, _soft_import, warn
 
 
 def _read_dig_montage_egi(
@@ -28,8 +27,8 @@ def _read_dig_montage_egi(
             "hsp, hpi, elp, point_names, fif must all be " "None if egi is not None"
         )
     _check_fname(fname, overwrite="read", must_exist=True)
-
-    root = ElementTree.parse(fname).getroot()
+    defusedxml = _soft_import("defusedxml", "reading EGI montages")
+    root = defusedxml.ElementTree.parse(fname).getroot()
     ns = root.tag[root.tag.index("{") : root.tag.index("}") + 1]
     sensors = root.find("%ssensorLayout/%ssensors" % (ns, ns))
     fids = dict()
@@ -76,8 +75,8 @@ def _read_dig_montage_egi(
 
 def _parse_brainvision_dig_montage(fname, scale):
     FID_NAME_MAP = {"Nasion": "nasion", "RPA": "rpa", "LPA": "lpa"}
-
-    root = ElementTree.parse(fname).getroot()
+    defusedxml = _soft_import("defusedxml", "reading BrainVision montages")
+    root = defusedxml.ElementTree.parse(fname).getroot()
     sensors = root.find("CapTrakElectrodeList")
 
     fids, dig_ch_pos = dict(), dict()

mne/channels/_standard_montage_utils.py

@@ -9,11 +9,10 @@
 from functools import partial
 
 import numpy as np
-from defusedxml import ElementTree
 
 from .._freesurfer import get_mni_fiducials
 from ..transforms import _sph_to_cart
-from ..utils import _pl, warn
+from ..utils import _pl, _soft_import, warn
 from . import __file__ as _CHANNELS_INIT_FILE
 from .montage import make_dig_montage
 
@@ -344,7 +343,8 @@ def _read_brainvision(fname, head_size):
     # standard electrode positions: X-axis from T7 to T8, Y-axis from Oz to
     # Fpz, Z-axis orthogonal from XY-plane through Cz, fit to a sphere if
     # idealized (when radius=1), specified in millimeters
-    root = ElementTree.parse(fname).getroot()
+    defusedxml = _soft_import("defusedxml", "reading BrainVision montages")
+    root = defusedxml.ElementTree.parse(fname).getroot()
     ch_names = [s.text for s in root.findall("./Electrode/Name")]
     theta = [float(s.text) for s in root.findall("./Electrode/Theta")]
     pol = np.deg2rad(np.array(theta))

mne/channels/tests/test_montage.py

@@ -513,6 +513,8 @@ def test_documented():
 )
 def test_montage_readers(reader, file_content, expected_dig, ext, warning, tmp_path):
     """Test that we have an equivalent of read_montage for all file formats."""
+    if file_content.startswith("<?xml"):
+        pytest.importorskip("defusedxml")
     fname = tmp_path / f"test.{ext}"
     with open(fname, "w") as fid:
         fid.write(file_content)
@@ -1067,6 +1069,7 @@ def test_fif_dig_montage(tmp_path):
 @testing.requires_testing_data
 def test_egi_dig_montage(tmp_path):
     """Test EGI MFF XML dig montage support."""
+    pytest.importorskip("defusedxml")
     dig_montage = read_dig_egi(egi_dig_montage_fname)
     fid, coord = _get_fid_coords(dig_montage.dig)
 
@@ -1123,6 +1126,7 @@ def _pop_montage(dig_montage, ch_name):
 @testing.requires_testing_data
 def test_read_dig_captrak(tmp_path):
     """Test reading a captrak montage file."""
+    pytest.importorskip("defusedxml")
     EXPECTED_CH_NAMES_OLD = [
         "AF3",
         "AF4",
@@ -1933,13 +1937,12 @@ def test_get_builtin_montages():
 def test_plot_montage():
     """Test plotting montage."""
     # gh-8025
+    pytest.importorskip("defusedxml")
     montage = read_dig_captrak(bvct_dig_montage_fname)
     montage.plot()
-    plt.close("all")
 
     f, ax = plt.subplots(1, 1)
     montage.plot(axes=ax)
-    plt.close("all")
 
     with pytest.raises(TypeError, match="must be an instance of Axes"):
         montage.plot(axes=101)

mne/export/tests/test_export.py

@@ -459,6 +459,7 @@ def test_export_epochs_eeglab(tmp_path, preload):
 def test_export_evokeds_to_mff(tmp_path, fmt, do_history):
     """Test exporting evoked dataset to MFF."""
     pytest.importorskip("mffpy", "0.5.7")
+    pytest.importorskip("defusedxml")
     evoked = read_evokeds_mff(egi_evoked_fname)
     export_fname = tmp_path / "evoked.mff"
     history = [
@@ -515,6 +516,7 @@ def test_export_evokeds_to_mff(tmp_path, fmt, do_history):
 def test_export_to_mff_no_device():
     """Test no device type throws ValueError."""
     pytest.importorskip("mffpy", "0.5.7")
+    pytest.importorskip("defusedxml")
     evoked = read_evokeds_mff(egi_evoked_fname, condition="Category 1")
     evoked.info["device_info"] = None
     with pytest.raises(ValueError, match="No device type."):

mne/io/egi/egimff.py

@@ -10,7 +10,6 @@
 from pathlib import Path
 
 import numpy as np
-from defusedxml.minidom import parse
 
 from ..._fiff.constants import FIFF
 from ..._fiff.meas_info import _empty_info, _ensure_meas_date_none_or_dt, create_info
@@ -19,7 +18,7 @@
 from ...annotations import Annotations
 from ...channels.montage import make_dig_montage
 from ...evoked import EvokedArray
-from ...utils import _check_fname, _check_option, logger, verbose, warn
+from ...utils import _check_fname, _check_option, _soft_import, logger, verbose, warn
 from ..base import BaseRaw
 from .events import _combine_triggers, _read_events
 from .general import (
@@ -36,6 +35,9 @@
 
 def _read_mff_header(filepath):
     """Read mff header."""
+    _soft_import("defusedxml", "reading EGI MFF data")
+    from defusedxml.minidom import parse
+
     all_files = _get_signalfname(filepath)
     eeg_file = all_files["EEG"]["signal"]
     eeg_info_file = all_files["EEG"]["info"]
@@ -289,6 +291,9 @@ def _get_eeg_calibration_info(filepath, egi_info):
 
 def _read_locs(filepath, egi_info, channel_naming):
     """Read channel locations."""
+    _soft_import("defusedxml", "reading EGI MFF data")
+    from defusedxml.minidom import parse
+
     fname = op.join(filepath, "coordinates.xml")
     if not op.exists(fname):
         logger.warn("File coordinates.xml not found, not setting channel locations")

mne/io/egi/events.py

@@ -7,9 +7,8 @@
 from os.path import basename, join, splitext
 
 import numpy as np
-from defusedxml.ElementTree import parse
 
-from ...utils import logger
+from ...utils import _soft_import, logger
 
 
 def _read_events(input_fname, info):
@@ -82,7 +81,8 @@ def _read_mff_events(filename, sfreq):
 
 def _parse_xml(xml_file):
     """Parse XML file."""
-    xml = parse(xml_file)
+    defusedxml = _soft_import("defusedxml", "reading EGI MFF data")
+    xml = defusedxml.ElementTree.parse(xml_file)
     root = xml.getroot()
     return _xml2list(root)
 

mne/io/egi/general.py

@@ -6,13 +6,15 @@
 import re
 
 import numpy as np
-from defusedxml.minidom import parse
 
-from ...utils import _pl
+from ...utils import _pl, _soft_import
 
 
 def _extract(tags, filepath=None, obj=None):
     """Extract info from XML."""
+    _soft_import("defusedxml", "reading EGI MFF data")
+    from defusedxml.minidom import parse
+
     if obj is not None:
         fileobj = obj
     elif filepath is not None:
@@ -30,6 +32,9 @@ def _extract(tags, filepath=None, obj=None):
 
 def _get_gains(filepath):
     """Parse gains."""
+    _soft_import("defusedxml", "reading EGI MFF data")
+    from defusedxml.minidom import parse
+
     file_obj = parse(filepath)
     objects = file_obj.getElementsByTagName("calibration")
     gains = dict()
@@ -46,6 +51,9 @@ def _get_gains(filepath):
 
 def _get_ep_info(filepath):
     """Get epoch info."""
+    _soft_import("defusedxml", "reading EGI MFF data")
+    from defusedxml.minidom import parse
+
     epochfile = filepath + "/epochs.xml"
     epochlist = parse(epochfile)
     epochs = epochlist.getElementsByTagName("epoch")
@@ -123,6 +131,9 @@ def _get_blocks(filepath):
 
 def _get_signalfname(filepath):
     """Get filenames."""
+    _soft_import("defusedxml", "reading EGI MFF data")
+    from defusedxml.minidom import parse
+
     listfiles = os.listdir(filepath)
     binfiles = list(
         f for f in listfiles if "signal" in f and f[-4:] == ".bin" and f[0] != "."

mne/io/egi/tests/test_egi.py

@@ -70,6 +70,7 @@
 )
 def test_egi_mff_pause(fname, skip_times, event_times):
     """Test EGI MFF with pauses."""
+    pytest.importorskip("defusedxml")
     if fname == egi_pause_w1337_fname:
         # too slow to _test_raw_reader
         raw = read_raw_egi(fname).load_data()
@@ -129,6 +130,7 @@ def test_egi_mff_pause(fname, skip_times, event_times):
 )
 def test_egi_mff_pause_chunks(fname, tmp_path):
     """Test that on-demand of all short segments works (via I/O)."""
+    pytest.importorskip("defusedxml")
     fname_temp = tmp_path / "test_raw.fif"
     raw_data = read_raw_egi(fname, preload=True).get_data()
     raw = read_raw_egi(fname)
@@ -142,6 +144,7 @@ def test_egi_mff_pause_chunks(fname, tmp_path):
 @requires_testing_data
 def test_io_egi_mff():
     """Test importing EGI MFF simple binary files."""
+    pytest.importorskip("defusedxml")
     # want vars for n chans
     n_ref = 1
     n_eeg = 128
@@ -258,6 +261,7 @@ def test_io_egi():
 @requires_testing_data
 def test_io_egi_pns_mff(tmp_path):
     """Test importing EGI MFF with PNS data."""
+    pytest.importorskip("defusedxml")
     raw = read_raw_egi(egi_mff_pns_fname, include=None, preload=True, verbose="error")
     assert "RawMff" in repr(raw)
     pns_chans = pick_types(raw.info, ecg=True, bio=True, emg=True)
@@ -314,6 +318,7 @@ def test_io_egi_pns_mff(tmp_path):
 @pytest.mark.parametrize("preload", (True, False))
 def test_io_egi_pns_mff_bug(preload):
     """Test importing EGI MFF with PNS data (BUG)."""
+    pytest.importorskip("defusedxml")
     egi_fname_mff = testing_path / "EGI" / "test_egi_pns_bug.mff"
     with pytest.warns(RuntimeWarning, match="EGI PSG sample bug"):
         raw = read_raw_egi(
@@ -356,6 +361,7 @@ def test_io_egi_pns_mff_bug(preload):
 @requires_testing_data
 def test_io_egi_crop_no_preload():
     """Test crop non-preloaded EGI MFF data (BUG)."""
+    pytest.importorskip("defusedxml")
     raw = read_raw_egi(egi_mff_fname, preload=False)
     raw.crop(17.5, 20.5)
     raw.load_data()
@@ -383,6 +389,8 @@ def test_io_egi_crop_no_preload():
 def test_io_egi_evokeds_mff(idx, cond, tmax, signals, bads):
     """Test reading evoked MFF file."""
     pytest.importorskip("mffpy", "0.5.7")
+
+    pytest.importorskip("defusedxml")
     # expected n channels
     n_eeg = 256
     n_ref = 1
@@ -468,6 +476,7 @@ def test_read_evokeds_mff_bad_input():
 @requires_testing_data
 def test_egi_coord_frame():
     """Test that EGI coordinate frame is changed to head."""
+    pytest.importorskip("defusedxml")
     info = read_raw_egi(egi_mff_fname).info
     want_idents = (
         FIFF.FIFFV_POINT_LPA,
@@ -505,6 +514,7 @@ def test_egi_coord_frame():
 )
 def test_meas_date(fname, timestamp, utc_offset):
     """Test meas date conversion."""
+    pytest.importorskip("defusedxml")
     raw = read_raw_egi(fname, verbose="warning")
     dt = datetime.strptime(timestamp, "%Y-%m-%dT%H:%M:%S.%f%z")
     measdate = dt.astimezone(timezone.utc)
@@ -526,6 +536,7 @@ def test_meas_date(fname, timestamp, utc_offset):
 )
 def test_set_standard_montage_mff(fname, standard_montage):
     """Test setting a standard montage."""
+    pytest.importorskip("defusedxml")
     raw = read_raw_egi(fname, verbose="warning")
     n_eeg = int(standard_montage.split("-")[-1])
     n_dig = n_eeg + 3

mne/io/nedf/nedf.py

@@ -6,11 +6,10 @@
 from datetime import datetime, timezone
 
 import numpy as np
-from defusedxml import ElementTree
 
 from ..._fiff.meas_info import create_info
 from ..._fiff.utils import _mult_cal_one
-from ...utils import _check_fname, verbose, warn
+from ...utils import _check_fname, _soft_import, verbose, warn
 from ..base import BaseRaw
 
 
@@ -52,6 +51,7 @@ def _parse_nedf_header(header):
     n_samples : int
         The number of data samples.
     """
+    defusedxml = _soft_import("defusedxml", "reading NEDF data")
     info = {}
     # nedf files have three accelerometer channels sampled at 100Hz followed
     # by five EEG samples + TTL trigger sampled at 500Hz
@@ -69,7 +69,7 @@ def _parse_nedf_header(header):
     headerend = header.find(b"\0")
     if headerend == -1:
         raise RuntimeError("End of header null not found")
-    headerxml = ElementTree.fromstring(header[:headerend])
+    headerxml = defusedxml.ElementTree.fromstring(header[:headerend])
     nedfversion = headerxml.findtext("NEDFversion", "")
     if nedfversion not in ["1.3", "1.4"]:
         warn("NEDFversion unsupported, use with caution")