Backport PR #12661 on branch maint/1.7 (Fix EDF/BDF filter warning bu…

…g) (#12666) Co-authored-by: Clemens Brunner <clemens.brunner@gmail.com> Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
mne-tools · Jun 14, 2024 · 663d741 · 663d741
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diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -5,11 +5,9 @@ on: # yamllint disable-line rule:truthy
  release:
  types: [published]
  push:
- branches:
- - main
+ branches: ["main", "maint/*"]
  pull_request:
- branches:
- - main
+ branches: ["main", "maint/*"]
 
 permissions:
  contents: read

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,9 +1,9 @@
 cff-version: 1.2.0
 title: "MNE-Python"
 message: "If you use this software, please cite both the software itself, and the paper listed in the preferred-citation field."
-version: 1.7.0
-date-released: "2024-04-19"
-commit: a3743420a8eef774dafd2908f0de89c4d37fcd01
+version: 1.7.1
+date-released: "2024-06-14"
+commit: 7c00b56d077eaf6a2ca691eadd567d974865a03c
 doi: 10.5281/zenodo.592483
 keywords:
  - MEG

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -193,7 +193,7 @@ stages:
  displayName: 'PyQt6'
  - bash: |
  set -e
- python -m pip install "PySide6!=6.7.0"
+ python -m pip install "PySide6!=6.7.0,!=6.7.1"
  mne sys_info -pd
  mne sys_info -pd | grep "qtpy .* (PySide6=.*)$"
  PYTEST_QT_API=PySide6 pytest -m "not slowtest" ${TEST_OPTIONS}

diff --git a/codemeta.json b/codemeta.json
@@ -5,11 +5,11 @@
  "codeRepository": "git+https://github.com/mne-tools/mne-python.git",
  "dateCreated": "2010-12-26",
  "datePublished": "2014-08-04",
- "dateModified": "2024-04-19",
- "downloadUrl": "https://github.com/mne-tools/mne-python/archive/v1.7.0.zip",
+ "dateModified": "2024-06-14",
+ "downloadUrl": "https://github.com/mne-tools/mne-python/archive/v1.7.1.zip",
  "issueTracker": "https://github.com/mne-tools/mne-python/issues",
  "name": "MNE-Python",
- "version": "1.7.0",
+ "version": "1.7.1",
  "description": "MNE-Python is an open-source Python package for exploring, visualizing, and analyzing human neurophysiological data. It provides methods for data input/output, preprocessing, visualization, source estimation, time-frequency analysis, connectivity analysis, machine learning, and statistics.",
  "applicationCategory": "Neuroscience",
  "developmentStatus": "active",

diff --git a/doc/changes/devel/12633.bugfix.rst b/doc/changes/devel/12633.bugfix.rst
diff --git a/doc/changes/v1.7.rst b/doc/changes/v1.7.rst
@@ -1,3 +1,20 @@
+.. _changes_1_7_1:
+
+1.7.1 (2024-06-14)
+==================
+
+Bugfixes
+--------
+
+- Fix bug where :func:`mne.time_frequency.csd_multitaper`, :func:`mne.time_frequency.csd_fourier`, :func:`mne.time_frequency.csd_array_multitaper`, and :func:`mne.time_frequency.csd_array_fourier` would return cross-spectral densities with the ``fmin`` and ``fmax`` frequencies missing, by `Thomas Binns`_ (`#12633 <https://github.com/mne-tools/mne-python/pulls/12633>`__)
+- Fix incorrect RuntimeWarning (different channel filter settings) in EDF/BDF import, by `Clemens Brunner`_. (`#12661 <https://github.com/mne-tools/mne-python/pulls/12661>`__)
+
+Authors
+-------
+
+* Clemens Brunner
+* Thomas Binns
+
 .. _changes_1_7_0:
 
 1.7.0 (2024-04-19)

diff --git a/mne/conftest.py b/mne/conftest.py
@@ -200,6 +200,8 @@ def pytest_configure(config):
  ignore:np\.find_common_type is deprecated.*:DeprecationWarning
  # pyvista <-> NumPy 2.0
  ignore:__array_wrap__ must accept context and return_scalar arguments.*:DeprecationWarning
+ # sklearn
+ ignore:'multi_class' was deprecated.*:FutureWarning
  """ # noqa: E501
  for warning_line in warning_lines.split("\n"):
  warning_line = warning_line.strip()

diff --git a/mne/io/edf/edf.py b/mne/io/edf/edf.py
@@ -706,7 +706,7 @@ def _get_info(
  info["subject_info"]["weight"] = float(edf_info["subject_info"]["weight"])
 
  # Filter settings
- if filt_ch_idxs := [x for x in sel if x not in stim_channel_idxs]:
+ if filt_ch_idxs := [x for x in range(len(sel)) if x not in stim_channel_idxs]:
  _set_prefilter(info, edf_info, filt_ch_idxs, "highpass")
  _set_prefilter(info, edf_info, filt_ch_idxs, "lowpass")
 
@@ -951,6 +951,7 @@ def _read_edf_header(
  edf_info["units"] = np.array(edf_info["units"], float)
 
  ch_names = [ch_names[idx] for idx in sel]
+ ch_types = [ch_types[idx] for idx in sel]
  units = [units[idx] for idx in sel]
 
  if not exclude_after_unique:

diff --git a/mne/io/edf/tests/test_edf.py b/mne/io/edf/tests/test_edf.py
@@ -175,26 +175,24 @@ def test_bdf_data():
  # XXX BDF data for these is around 0.01 when it should be in the uV range,
  # probably some bug
  test_scaling = False
- with pytest.warns(RuntimeWarning, match="Channels contain different"):
- raw_py = _test_raw_reader(
- read_raw_bdf,
- input_fname=bdf_path,
- eog=eog,
- misc=misc,
- exclude=["M2", "IEOG"],
- test_scaling=test_scaling,
- )
+ raw_py = _test_raw_reader(
+ read_raw_bdf,
+ input_fname=bdf_path,
+ eog=eog,
+ misc=misc,
+ exclude=["M2", "IEOG"],
+ test_scaling=test_scaling,
+ )
  assert len(raw_py.ch_names) == 71
- with pytest.warns(RuntimeWarning, match="Channels contain different"):
- raw_py = _test_raw_reader(
- read_raw_bdf,
- input_fname=bdf_path,
- montage="biosemi64",
- eog=eog,
- misc=misc,
- exclude=["M2", "IEOG"],
- test_scaling=test_scaling,
- )
+ raw_py = _test_raw_reader(
+ read_raw_bdf,
+ input_fname=bdf_path,
+ montage="biosemi64",
+ eog=eog,
+ misc=misc,
+ exclude=["M2", "IEOG"],
+ test_scaling=test_scaling,
+ )
  assert len(raw_py.ch_names) == 71
  assert "RawEDF" in repr(raw_py)
  picks = pick_types(raw_py.info, meg=False, eeg=True, exclude="bads")

diff --git a/mne/io/fiff/tests/test_raw_fiff.py b/mne/io/fiff/tests/test_raw_fiff.py
@@ -60,7 +60,6 @@
 fif_bad_marked_fname = base_dir / "test_withbads_raw.fif"
 bad_file_works = base_dir / "test_bads.txt"
 bad_file_wrong = base_dir / "test_wrong_bads.txt"
-hp_fname = base_dir / "test_chpi_raw_hp.txt"
 hp_fif_fname = base_dir / "test_chpi_raw_sss.fif"
 
 
@@ -695,12 +694,14 @@ def test_bids_split_files(tmp_path):
  with pytest.raises(ValueError, match="Passing a BIDSPath"):
  raw.save(bids_path, **save_kwargs)
  bids_path.split = None
- want_paths = [Path(bids_path.copy().update(split=ii).fpath) for ii in range(1, 3)]
+ want_paths = [
+ Path(bids_path.copy().update(split=f"{ii:02d}").fpath) for ii in range(1, 3)
+ ]
  for want_path in want_paths:
  assert not want_path.is_file()
  raw.save(bids_path, **save_kwargs)
  for want_path in want_paths:
- assert want_path.is_file()
+ assert want_path.is_file(), want_path
 
 
 def _err(*args, **kwargs):

diff --git a/pyproject.toml b/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
 [project]
 name = "mne"
 description = "MNE-Python project for MEG and EEG data analysis."
-version = "1.7.0"
+version = "1.7.1"
 authors = [
  { name = "Alexandre Gramfort", email = "alexandre.gramfort@inria.fr" },
 ]

diff --git a/tools/generate_codemeta.py b/tools/generate_codemeta.py
@@ -98,7 +98,8 @@ def parse_name(name):
 args = ["git", "shortlog", "-nse"]
 result = subprocess.run(args, capture_output=True, text=True)
 lines = result.stdout.strip().split("\n")
-all_names = [parse_name(line) for line in lines if "[bot]" not in line]
+exclude = ["[bot]", "Lumberbot (aka Jack)"]
+all_names = [parse_name(line) for line in lines if not any(x in line for x in exclude)]
 
 
 # CONSTRUCT JSON AUTHORS LIST