[pull] main from mne-tools:main

.github/workflows/credit.yml

@@ -40,6 +40,6 @@ jobs:
           git checkout -b credit
           git commit -am "MAINT: Update code credit"
           git push origin credit
-          PR_NUM=$(gh pr create --base main --head credit --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }})." --label "no-changelog-entry-needed")
+          PR_NUM=$(gh pr create --base main --head credit --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to `doc/changes/credit_tools.py` or `.mailmap` etc. to get CircleCI to pass.*" --label "no-changelog-entry-needed")
           echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
         if: steps.status.outputs.dirty == 'true'

.github/workflows/spec_zero.yml

@@ -57,6 +57,6 @@ jobs:
           git checkout -b spec_zero
           git commit -am "MAINT: Update dependency specifiers"
           git push origin spec_zero
-          PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }})." --label "no-changelog-entry-needed")
+          PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to shims in mne/fixes.py in this or another PR. `git grep TODO VERSION` is a good starting point for finding potential updates.*" --label "no-changelog-entry-needed")
           echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
         if: steps.status.outputs.dirty == 'true'

doc/changes/dev/13448.newfeature.rst

@@ -0,0 +1 @@
+Add support for Nihon Kohden EEG-1200A V01.00, by `Eric Larson`_.

doc/changes/dev/13458.apichange.rst

@@ -0,0 +1 @@
+Add ``encoding`` parameter to :func:`mne.io.read_raw_nihon` for better handling of annotation decoding, by `Tom Ma`_.

environment.yml

@@ -45,11 +45,11 @@ dependencies:
   - PySide6 !=6.9.1
   - python-neo
   - python-picard
-  - pyvista >=0.32,!=0.35.2,!=0.38.0,!=0.38.1,!=0.38.2,!=0.38.3,!=0.38.4,!=0.38.5,!=0.38.6,!=0.42.0
-  - pyvistaqt >=0.4
+  - pyvista >=0.42.1
+  - pyvistaqt >=0.11
   - qdarkstyle !=3.2.2
   - qtpy
-  - scikit-learn >=1.3.0
+  - scikit-learn >=1.3
   - scipy >=1.11
   - sip
   - snirf

mne/io/artemis123/tests/test_artemis123.py

@@ -41,14 +41,14 @@ def _assert_trans(actual, desired, dist_tol=0.017, angle_tol=5.0):
     assert angle <= angle_tol, f"{angle:0.3f} > {angle_tol:0.3f}° rotation"
 
 
-@pytest.mark.timeout(60)  # ~25 s on Travis Linux OpenBLAS
 @testing.requires_testing_data
 def test_artemis_reader():
     """Test reading raw Artemis123 files."""
     _test_raw_reader(
         read_raw_artemis123,
         input_fname=short_hpi_1kz_fname,
         pos_fname=dig_fname,
+        add_head_trans=False,
         verbose="error",
     )
 

mne/io/eeglab/tests/test_eeglab.py

@@ -9,6 +9,7 @@
 
 import numpy as np
 import pytest
+from flaky import flaky
 from numpy.testing import (
     assert_allclose,
     assert_array_almost_equal,
@@ -23,7 +24,6 @@
 from mne.channels import read_custom_montage
 from mne.datasets import testing
 from mne.io import read_raw_eeglab
-from mne.io.eeglab import _eeglab as eeglab_mod
 from mne.io.eeglab._eeglab import _readmat
 from mne.io.eeglab.eeglab import _dol_to_lod, _get_montage_information
 from mne.io.tests.test_raw import _test_raw_reader
@@ -769,25 +769,20 @@ def test_eeglab_drop_nan_annotations(tmp_path):
         raw = read_raw_eeglab(file_path, preload=True)
 
 
+@flaky
 @testing.requires_testing_data
 @pytest.mark.timeout(10)
-def test_io_set_preload_false_is_faster(monkeypatch):
+@pytest.mark.slowtest  # has the advantage of not running on macOS where it errs a lot
+def test_io_set_preload_false_is_faster():
     """Using preload=False should skip the expensive data read branch."""
-    real_loadmat = eeglab_mod.loadmat
-    call_counts = {"n": 0}
-
-    def counting_loadmat(*args, **kwargs):
-        call_counts["n"] += 1
-        return real_loadmat(*args, **kwargs)
-
-    monkeypatch.setattr(eeglab_mod, "loadmat", counting_loadmat)
+    # warm start
+    read_raw_eeglab(raw_fname_mat, preload=False)
 
     durations = {}
-    with _record_warnings():
-        for preload in (False, True):
-            start = time.perf_counter()
-            _ = read_raw_eeglab(raw_fname_mat, preload=preload)
-            durations[preload] = time.perf_counter() - start
+    for preload in (True, False):
+        start = time.perf_counter()
+        _ = read_raw_eeglab(raw_fname_mat, preload=preload)
+        durations[preload] = time.perf_counter() - start
 
     # preload=True should not be faster than preload=False (timings may vary
     # across systems, so avoid strict thresholds)

mne/io/nihon/nihon.py

@@ -23,7 +23,9 @@ def _ensure_path(fname):
 
 
 @fill_doc
-def read_raw_nihon(fname, preload=False, verbose=None) -> "RawNihon":
+def read_raw_nihon(
+    fname, preload=False, *, encoding="utf-8", verbose=None
+) -> "RawNihon":
     """Reader for an Nihon Kohden EEG file.
 
     Parameters
@@ -32,6 +34,9 @@ def read_raw_nihon(fname, preload=False, verbose=None) -> "RawNihon":
         Path to the Nihon Kohden data file (``.EEG``).
     preload : bool
         If True, all data are loaded at initialization.
+    %(encoding_nihon)s
+
+        .. versionadded:: 1.11
     %(verbose)s
 
     Returns
@@ -44,7 +49,7 @@ def read_raw_nihon(fname, preload=False, verbose=None) -> "RawNihon":
     --------
     mne.io.Raw : Documentation of attributes and methods of RawNihon.
     """
-    return RawNihon(fname, preload, verbose)
+    return RawNihon(fname, preload, encoding=encoding, verbose=verbose)
 
 
 _valid_headers = [
@@ -57,7 +62,7 @@ def read_raw_nihon(fname, preload=False, verbose=None) -> "RawNihon":
     "EEG-2100  V02.00",
     "DAE-2100D V01.30",
     "DAE-2100D V02.00",
-    # 'EEG-1200A V01.00',  # Not working for the moment.
+    "EEG-1200A V01.00",
 ]
 
 
@@ -66,8 +71,10 @@ def _read_nihon_metadata(fname):
     fname = _ensure_path(fname)
     pnt_fname = fname.with_suffix(".PNT")
     if not pnt_fname.exists():
-        warn("No PNT file exists. Metadata will be blank")
-        return metadata
+        pnt_fname = fname.with_suffix(".pnt")
+        if not pnt_fname.exists():
+            warn("No PNT file exists. Metadata will be blank")
+            return metadata
     logger.info("Found PNT file, reading metadata.")
     with open(pnt_fname) as fid:
         version = np.fromfile(fid, "|S16", 1).astype("U16")[0]
@@ -315,7 +322,7 @@ def _parse_sub_event_log(sub_event_log):
     return t_sub_desc, t_sub_onset
 
 
-def _read_nihon_annotations(fname):
+def _read_nihon_annotations(fname, encoding="utf-8"):
     fname = _ensure_path(fname)
     log_fname = fname.with_suffix(".LOG")
     if not log_fname.exists():
@@ -346,15 +353,10 @@ def _read_nihon_annotations(fname):
                     t_onset += t_sub_onset
 
                 t_desc = t_desc.rstrip(b"\x00")
-                for enc in _encodings:
-                    try:
-                        t_desc = t_desc.decode(enc)
-                    except UnicodeDecodeError:
-                        pass
-                    else:
-                        break
-                else:
-                    warn(f"Could not decode log as one of {_encodings}")
+                try:
+                    t_desc = t_desc.decode(encoding)
+                except UnicodeDecodeError:
+                    warn(f"Could not decode log as {encoding}")
                     continue
 
                 all_onsets.append(t_onset)
@@ -414,6 +416,9 @@ class RawNihon(BaseRaw):
         Path to the Nihon Kohden data ``.eeg`` file.
     preload : bool
         If True, all data are loaded at initialization.
+    %(encoding_nihon)s
+
+        .. versionadded:: 1.11
     %(verbose)s
 
     See Also
@@ -422,7 +427,7 @@ class RawNihon(BaseRaw):
     """
 
     @verbose
-    def __init__(self, fname, preload=False, verbose=None):
+    def __init__(self, fname, preload=False, *, encoding="utf-8", verbose=None):
         fname = _check_fname(fname, "read", True, "fname")
         data_name = fname.name
         logger.info(f"Loading {data_name}")
@@ -468,7 +473,7 @@ def __init__(self, fname, preload=False, verbose=None):
         )
 
         # Get annotations from LOG file
-        annots = _read_nihon_annotations(fname)
+        annots = _read_nihon_annotations(fname, encoding)
 
         # Annotate acquisition skips
         controlblock = header["controlblocks"][0]

mne/time_frequency/tests/test_tfr.py

@@ -614,6 +614,7 @@ def test_tfr_decim_and_shift_time(epochs, method, freqs, decim):
     assert_array_equal(freqs, tfr.freqs)
 
 
+@pytest.mark.slowtest
 @pytest.mark.parametrize("inst", ("raw_tfr", "epochs_tfr", "average_tfr"))
 def test_tfr_io(inst, average_tfr, request, tmp_path):
     """Test TFR I/O."""

mne/utils/docs.py

@@ -1285,6 +1285,11 @@ def _reflow_param_docstring(docstring, has_first_line=True, width=75):
     encoding according to the EDF+ standard).
 """
 
+docdict["encoding_nihon"] = """
+encoding : str
+    Text encoding of Nihon Kohden annotations. See :ref:`standard-encodings`.
+"""
+
 docdict["encoding_nirx"] = """
 encoding : str
     Text encoding of the NIRX header file. See :ref:`standard-encodings`.

mne/viz/backends/_pyvista.py

@@ -212,7 +212,8 @@ def __init__(
     ):
         from .._3d import _get_3d_option
 
-        _require_version("pyvista", "use 3D rendering", "0.32")
+        # TODO VERSION change whenever PyVista min gets updated:
+        _require_version("pyvista", "use 3D rendering", "0.42")
         multi_samples = _get_3d_option("multi_samples")
         # multi_samples > 1 is broken on macOS + Intel Iris + volume rendering
         if platform.system() == "Darwin":

pyproject.toml

@@ -23,11 +23,11 @@ dependencies = [
   "decorator",
   "jinja2",
   "lazy_loader >= 0.3",
-  "matplotlib >= 3.8",  # released: 2023/09/15
-  "numpy >= 1.26,<3",  # released: 2023/09/16
+  "matplotlib >= 3.8",  # released 2023-09-15, will become 3.9 on 2026-05-15
+  "numpy >= 1.26, < 3",  # released 2023-09-16, will become 2.0 on 2026-06-16
   "packaging",
   "pooch >= 1.5",
-  "scipy >= 1.11",  # released: 2023/06/25
+  "scipy >= 1.11",  # released 2023-06-28, will become 1.12 on 2026-01-19
   "tqdm",
 ]
 description = "MNE-Python project for MEG and EEG data analysis."
@@ -78,7 +78,7 @@ doc = [
   "sphinx-gallery >= 0.16",
   "sphinx_copybutton",
   "sphinxcontrib-bibtex >= 2.5",
-  "sphinxcontrib-towncrier >=0.5.0a0",
+  "sphinxcontrib-towncrier >= 0.5.0a0",
   "sphinxcontrib-youtube",
 ]
 full = ["mne[full-no-qt]", "PyQt6 != 6.6.0", "PyQt6-Qt6 != 6.6.0, != 6.7.0"]
@@ -112,17 +112,17 @@ full-no-qt = [
   "nilearn",
   "numba",
   "openmeeg >= 2.5.7",
-  "pandas >= 2.1",  # released: 2023/08/30
+  "pandas >= 2.1",  # released 2023-08-30, will become 2.2 on 2026-01-19
   "pillow",  # for `Brain.save_image` and `mne.Report`
   "pyarrow",  # only needed to avoid a deprecation warning in pandas
   "pybv",
   "pyobjc-framework-Cocoa >= 5.2.0; platform_system == 'Darwin'",
   "python-picard",
-  "pyvista >= 0.32, != 0.35.2, != 0.38.0, != 0.38.1, != 0.38.2, != 0.38.3, != 0.38.4, != 0.38.5, != 0.38.6, != 0.42.0",
-  "pyvistaqt >= 0.4",
+  "pyvista >= 0.42.1",  # released 2023-09-06, will become 0.43 on 2025-12-06
+  "pyvistaqt >= 0.11",  # released 2023-06-30, no newer version available
   "qdarkstyle != 3.2.2",
   "qtpy",
-  "scikit-learn >=1.3.0",  # released: 2023/06/30
+  "scikit-learn >= 1.3",  # released 2023-06-30, will become 1.4 on 2026-01-17
   "sip",
   "snirf",
   "statsmodels",
@@ -152,7 +152,7 @@ test = [
   "pytest-timeout",
   "ruff",
   "toml-sort",
-  "tomli; python_version<'3.11'",
+  "tomli; python_version < '3.11'",
   "twine",
   "vulture",
   "wheel",