Merge remote-tracking branch 'upstream/main' into empty_epochs_msg

.circleci/config.yml

@@ -99,8 +99,10 @@ jobs:
             name: Install fonts needed for diagrams
             command: |
               mkdir -p $HOME/.fonts
+              echo "Source Code Pro"
               curl https://codeload.github.com/adobe-fonts/source-code-pro/tar.gz/2.038R-ro/1.058R-it/1.018R-VAR | tar xz -C $HOME/.fonts
-              curl https://codeload.github.com/adobe-fonts/source-sans-pro/tar.gz/3.028R | tar xz -C $HOME/.fonts
+              echo "Source Sans Pro"
+              curl https://codeload.github.com/adobe-fonts/source-sans/tar.gz/3.028R | tar xz -C $HOME/.fonts
               fc-cache -f
 
         # Load pip cache

.github/workflows/tests.yml

@@ -57,6 +57,9 @@ jobs:
         - os: macos-latest
           python: '3.8'
           kind: mamba
+        - os: windows-latest
+          python: '3.10'
+          kind: mamba
         - os: ubuntu-latest
           python: '3.8'
           kind: minimal
@@ -82,9 +85,9 @@ jobs:
       # Python (if conda)
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          activate-environment: ${{ env.CONDA_ACTIVATE_ENV }}
           python-version: ${{ env.PYTHON_VERSION }}
           environment-file: ${{ env.CONDA_ENV }}
+          activate-environment: mne
           miniforge-version: latest
           miniforge-variant: Mambaforge
           use-mamba: ${{ matrix.kind != 'conda' }}

azure-pipelines.yml

@@ -242,10 +242,8 @@ stages:
     variables:
       MNE_LOGGING_LEVEL: 'warning'
       MNE_FORCE_SERIAL: 'true'
-      OPENBLAS_NUM_THREADS: 1
-      MKL_NUM_THREADS: 2
+      OPENBLAS_NUM_THREADS: 2
       OMP_DYNAMIC: 'false'
-      MKL_DYNAMIC: 'false'
       PYTHONUNBUFFERED: 1
       PYTHONIOENCODING: 'utf-8'
       AZURE_CI_WINDOWS: 'true'
@@ -254,10 +252,6 @@ stages:
     strategy:
       maxParallel: 4
       matrix:
-        3.10 conda:
-          PLATFORM: 'x86-64'
-          TEST_MODE: 'conda'
-          PYTHON_VERSION: '3.10'
         3.9 pip:
           TEST_MODE: 'pip'
           PYTHON_VERSION: '3.9'
@@ -270,44 +264,16 @@ stages:
         versionSpec: $(PYTHON_VERSION)
         architecture: $(PYTHON_ARCH)
         addToPath: true
-      condition: in(variables['TEST_MODE'], 'pip', 'pip-pre')
       displayName: 'Get Python'
-    # https://docs.microsoft.com/en-us/azure/devops/pipelines/ecosystems/anaconda
-    # https://github.com/MicrosoftDocs/pipelines-anaconda
-    # https://github.com/ContinuumIO/anaconda-issues/issues/10949
-    - script: |
-        echo "##vso[task.prependpath]%CONDA%;%CONDA%\condabin;%CONDA%\Scripts;%CONDA%\Library\bin;%PROGRAMFILES%\Git\bin;%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;%PROGRAMFILES%\Git\usr\bin"
-      condition: in(variables['TEST_MODE'], 'conda')
-      displayName: Add conda to PATH, deal with Qt linking bug
     - bash: |
-        set -e
+        set -eo pipefail
         git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
         powershell gl-ci-helpers/appveyor/install_opengl.ps1
       displayName: Install OpenGL
-    - bash: |
-        set -e
-        ./tools/azure_dependencies.sh
-      condition: in(variables['TEST_MODE'], 'pip', 'pip-pre')
+    - bash: ./tools/azure_dependencies.sh
       displayName: Install dependencies with pip
-    - script: conda install -c conda-forge "mamba!=1.4.9"
-      condition: eq(variables['TEST_MODE'], 'conda')
-      displayName: Get mamba
-    - script: mamba env update --name base --file environment.yml
-      condition: eq(variables['TEST_MODE'], 'conda')
-      displayName: Setup MNE environment
-    # ipympl is not tested on Windows and even its installation interferes
-    # with basic matplotlib functionality so it must be uninstalled until fixed
-    - bash: |
-        set -e
-        mamba remove -c conda-forge --force -yq mne ipympl
-        rm /c/Miniconda/Scripts/mne.exe
-      condition: eq(variables['TEST_MODE'], 'conda')
-      displayName: Remove old MNE
     - script: pip install -e .
       displayName: 'Install MNE-Python dev'
-    - script: pip install --progress-bar off -e .[test]
-      condition: eq(variables['TEST_MODE'], 'conda')
-      displayName: Install testing requirements
     - script: mne sys_info -pd
       displayName: 'Print config'
     - script: python -c "import numpy; numpy.show_config()"

doc/_static/style.css

@@ -103,6 +103,22 @@ html[data-theme="dark"] img {
     color: var(--pst-color-link);
 }
 
+/* make versionadded smaller and inline with param name */
+/* don't do for deprecated / versionchanged; they have extra info (too long to fit) */
+div.versionadded > p {
+    margin-top: 0;
+    margin-bottom: 0;
+}
+div.versionadded {
+    margin: 0;
+    margin-left: 0.5rem;
+    display: inline-block;
+}
+/* when FF supports :has(), change to →  dd > p:has(+div.versionadded) */
+dd>p {
+    display: inline;
+}
+
 /* **************************************************** sphinx-gallery fixes */
 
 /* backreference links: restore hover decoration that SG removes */

doc/changes/latest.inc

@@ -43,6 +43,7 @@ Bugs
 - Extended test to highlight bug in :func:`mne.stats.permutation_t_test` (:gh:`11575` by :newcontrib:`Joshua Calder-Travis`)
 - Fix bug that used wrong indices for line/label styles (sometimes causing an ``IndexError``) in :meth:`mne.preprocessing.ICA.plot_sources` under certain conditions (:gh:`11808` by :newcontrib:`Joshua Calder-Travis`)
 - Fix bug with :func:`~mne.io.read_raw_snirf` to handle files with measurement time containing milliseconds (:gh:`11804` by :newcontrib:`Daniel Tse`)
+- Fix bug where :func:`mne.io.read_raw_cnt` imports unnecessary durations (:gh:`11828` by `Jacob Woessner`_)
 - Fix bug where :meth:`mne.viz.Brain.add_volume_labels` used an incorrect orientation (:gh:`11730` by `Alex Rockhill`_)
 - Fix bug with :func:`mne.forward.restrict_forward_to_label` where cortical patch information was not adjusted (:gh:`11694` by `Eric Larson`_)
 - Fix bug with PySide6 compatibility (:gh:`11721` by `Eric Larson`_)
@@ -52,11 +53,13 @@ Bugs
 - Fix bug with :func:`mne.io.read_raw_fil` where datasets without sensor positions would not import (:gh:`11733` by `George O'Neill`_)
 - Fix bug with :func:`mne.chpi.compute_chpi_snr` where cHPI being off for part of the recording or bad channels being defined led to an error or incorrect behavior (:gh:`11754`, :gh:`11755` by `Eric Larson`_)
 - Allow int-like for the argument ``id`` of `~mne.make_fixed_length_events` (:gh:`11748` by `Mathieu Scheltienne`_)
+- Fix bug where :func:`mne.io.read_raw_egi` did not properly set the EEG reference location for the reference channel itself (:gh:`11822` by `Eric Larson`_)
 - Fix bug with legacy :meth:`~mne.io.Raw.plot_psd` method where passed axes were not used (:gh:`11778` by `Daniel McCloy`_)
 - blink :class:`mne.Annotations` read in by :func:`mne.io.read_raw_eyelink` now begin with ``'BAD_'``, i.e. ``'BAD_blink'``, because ocular data are missing during blinks. (:gh:`11746` by `Scott Huberty`_)
 - Fix bug where :ref:`mne show_fiff` could fail with an ambiguous error if the file is corrupt (:gh:`11800` by `Eric Larson`_)
 - Fix bug where annotation FIF files lacked an end block tag (:gh:`11800` by `Eric Larson`_)
 - Fix display of :class:`~mne.Annotations` in `mne.preprocessing.ICA.plot_sources` when the ``raw`` has ``raw.first_samp != 0`` and doesn't have a measurement date (:gh:`11766` by `Mathieu Scheltienne`_)
+- Fix bug in read_raw_eyelink, where STATUS information of samples was always assumed to be in the file. Performance and memory improvements were also made. (:gh:`11823` by `Scott Huberty`_)
 
 API changes
 ~~~~~~~~~~~

doc/conf.py

@@ -16,11 +16,11 @@
 import numpy as np
 import matplotlib
 import sphinx
+from sphinx.domains.changeset import versionlabels
 from sphinx_gallery.sorting import FileNameSortKey, ExplicitOrder
 from numpydoc import docscrape
 
 import mne
-from mne.fixes import _compare_version
 from mne.tests.test_docstring_parameters import error_ignores
 from mne.utils import (
     linkcode_resolve,  # noqa, analysis:ignore
@@ -752,6 +752,10 @@ def append_attr_meth_examples(app, what, name, obj, options, lines):
 suppress_warnings = ["image.nonlocal_uri"]  # we intentionally link outside
 
 
+# -- Sphinx hacks / overrides ------------------------------------------------
+
+versionlabels["versionadded"] = sphinx.locale._("New in v%s")
+
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for

doc/install/mne_tools_suite.rst

@@ -51,22 +51,24 @@ MNE-Python, including packages for:
   (`alphaCSC`_)
 - independent component analysis (ICA) with good performance on real data
   (`PICARD`_)
+- automatic labeling of ICA components (`MNE-ICAlabel`_)
 - phase-amplitude coupling (`pactools`_)
 - representational similarity analysis (`rsa`_)
 - microstate analysis (`microstate`_)
 - connectivity analysis using dynamic imaging of coherent sources (DICS)
   (`conpy`_)
+- other connectivity algorithms (`MNE-Connectivity`_)
 - general-purpose statistical analysis of M/EEG data (`eelbrain`_)
 - post-hoc modification of linear models (`posthoc`_)
 - a python implementation of the Preprocessing Pipeline (PREP) for EEG data
   (`pyprep`_)
 - automatic multi-dipole localization and uncertainty quantification with
   the Bayesian algorithm SESAME (`sesameeg`_)
-- GLM and group level analysis of near-infrared spectroscopy data (`mne-nirs`_)
-- High-level EEG Python library for all kinds of EEG inverse solutions (`invertmeeg`_)
+- GLM and group level analysis of near-infrared spectroscopy data (`MNE-NIRS`_)
+- high-level EEG Python library for all kinds of EEG inverse solutions (`invertmeeg`_)
 - All-Resolutions Inference (ARI) for statistically valid circular inference
   and effect localization (`MNE-ARI`_)
-
+- real-time analysis (`MNE-Realtime`_)
 
 What should I install?
 ^^^^^^^^^^^^^^^^^^^^^^
@@ -109,6 +111,5 @@ Help with installation is available through the `MNE Forum`_. See the
 .. _posthoc: https://users.aalto.fi/~vanvlm1/posthoc/python/
 .. _pyprep: https://github.com/sappelhoff/pyprep
 .. _sesameeg: https://pybees.github.io/sesameeg
-.. _mne-nirs: https://github.com/mne-tools/mne-nirs
 .. _invertmeeg: https://github.com/LukeTheHecker/invert
 .. _MNE-ARI: https://github.com/john-veillette/mne_ari

doc/links.inc

@@ -23,6 +23,9 @@
 .. _`MNE-Realtime`: https://mne.tools/mne-realtime
 .. _`MNE-MATLAB git repository`: https://github.com/mne-tools/mne-matlab
 .. _`MNE-Docker`: https://github.com/mne-tools/mne-docker
+.. _`MNE-ICAlabel`: https://github.com/mne-tools/mne-icalabel
+.. _`MNE-Connectivity`: https://github.com/mne-tools/mne-connectivity
+.. _`MNE-NIRS`: https://github.com/mne-tools/mne-nirs
 .. _OpenMEEG: http://openmeeg.github.io
 .. _EOSS2: https://chanzuckerberg.com/eoss/proposals/improving-usability-of-core-neuroscience-analysis-tools-with-mne-python
 .. _EOSS4: https://chanzuckerberg.com/eoss/proposals/building-pediatric-and-clinical-data-pipelines-for-mne-python/

mne/channels/montage.py

@@ -1171,25 +1171,22 @@ def _backcompat_value(pos, ref_pos):
     chs = [info["chs"][ii] for ii in picks]
     non_names = [info["chs"][ii]["ch_name"] for ii in non_picks]
     del picks
-    ref_pos = [ch["loc"][3:6] for ch in chs]
+    ref_pos = np.array([ch["loc"][3:6] for ch in chs])
 
     # keep reference location from EEG-like channels if they
     # already exist and are all the same.
-    custom_eeg_ref_dig = False
     # Note: ref position is an empty list for fieldtrip data
-    if ref_pos:
-        if (
-            all([np.equal(ref_pos[0], pos).all() for pos in ref_pos])
-            and not np.equal(ref_pos[0], [0, 0, 0]).all()
-        ):
-            eeg_ref_pos = ref_pos[0]
-            # since we have an EEG reference position, we have
-            # to add it into the info['dig'] as EEG000
-            custom_eeg_ref_dig = True
-    if not custom_eeg_ref_dig:
+    if len(ref_pos) and ref_pos[0].any() and (ref_pos[0] == ref_pos).all():
+        eeg_ref_pos = ref_pos[0]
+        # since we have an EEG reference position, we have
+        # to add it into the info['dig'] as EEG000
+        custom_eeg_ref_dig = True
+    else:
         refs = set(ch_pos) & {"EEG000", "REF"}
         assert len(refs) <= 1
         eeg_ref_pos = np.zeros(3) if not refs else ch_pos.pop(refs.pop())
+        custom_eeg_ref_dig = False
+    del ref_pos
 
     # This raises based on info being subset/superset of montage
     info_names = [ch["ch_name"] for ch in chs]

mne/conftest.py

@@ -163,6 +163,10 @@ def pytest_configure(config):
         warning_line = warning_line.strip()
         if warning_line and not warning_line.startswith("#"):
             config.addinivalue_line("filterwarnings", warning_line)
+    # TODO: Fix this with casts?
+    # https://github.com/numpy/numpy/pull/22449
+    if check_version("numpy", "1.26"):
+        np.set_printoptions(legacy="1.25")
 
 
 # Have to be careful with autouse=True, but this is just an int comparison

mne/cov.py

@@ -382,7 +382,15 @@ def plot_topomap(
         %(sphere_topomap_auto)s
         %(image_interp_topomap)s
         %(extrapolate_topomap)s
+
+            .. versionchanged:: 0.21
+
+               - The default was changed to ``'local'`` for MEG sensors.
+               - ``'local'`` was changed to use a convex hull mask
+               - ``'head'`` was changed to extrapolate out to the clipping circle.
         %(border_topomap)s
+
+            .. versionadded:: 0.20
         %(res_topomap)s
         %(size_topomap)s
         %(cmap_topomap)s

mne/io/base.py

@@ -170,6 +170,8 @@ class BaseRaw(
           (only needed for types that support on-demand disk reads)
     """
 
+    _extra_attributes = ()
+
     @verbose
     def __init__(
         self,

mne/io/brainvision/brainvision.py

@@ -61,6 +61,8 @@ class RawBrainVision(BaseRaw):
     mne.io.Raw : Documentation of attributes and methods.
     """
 
+    _extra_attributes = ("impedances",)
+
     @verbose
     def __init__(
         self,

mne/io/bti/bti.py

@@ -1086,7 +1086,7 @@ def __init__(
             sort_by_ch_name=sort_by_ch_name,
             eog_ch=eog_ch,
         )
-        self.bti_ch_labels = [c["chan_label"] for c in bti_info["chs"]]
+        bti_info["bti_ch_labels"] = [c["chan_label"] for c in bti_info["chs"]]
         # make Raw repr work if we have a BytesIO as input
         if isinstance(pdf_fname, BytesIO):
             pdf_fname = repr(pdf_fname)

mne/io/bti/tests/test_bti.py

@@ -285,10 +285,12 @@ def test_info_no_rename_no_reorder_no_pdf():
         preload=True,
     )
 
-    sort_idx = [raw1.bti_ch_labels.index(ch) for ch in raw2.bti_ch_labels]
+    bti_ch_labels_1 = raw1._raw_extras[0]["bti_ch_labels"]
+    bti_ch_labels_2 = raw2._raw_extras[0]["bti_ch_labels"]
+    sort_idx = [bti_ch_labels_1.index(ch) for ch in bti_ch_labels_2]
     raw1._data = raw1._data[sort_idx]
     assert_array_equal(raw1._data, raw2._data)
-    assert_array_equal(raw2.bti_ch_labels, raw2.ch_names)
+    assert_array_equal(bti_ch_labels_2, raw2.ch_names)
 
 
 def test_no_conversion():

mne/io/cnt/cnt.py

@@ -145,9 +145,9 @@ def _update_bad_span_onset(accept_reject, onset, duration, description):
             event_type=type(my_events[0]),
             data_format=data_format,
         )
-        duration = np.array(
-            [getattr(e, "Latency", 0.0) for e in my_events], dtype=float
-        )
+        # There is a Latency field but it's not useful for durations, see
+        # https://github.com/mne-tools/mne-python/pull/11828
+        duration = np.zeros(len(my_events), dtype=float)
         accept_reject = _accept_reject_function(
             np.array([e.KeyPad_Accept for e in my_events])
         )

mne/io/ctf/ctf.py

@@ -193,9 +193,8 @@ def __init__(
         )
         annot = marker_annot if annot is None else annot + marker_annot
         self.set_annotations(annot)
-
         if clean_names:
-            self._clean_names()
+            _clean_names_inst(self)
 
     def _read_segment_file(self, data, idx, fi, start, stop, cals, mult):
         """Read a chunk of raw data."""
@@ -222,15 +221,14 @@ def _read_segment_file(self, data, idx, fi, start, stop, cals, mult):
                 _mult_cal_one(data_view, this_data, idx, cals, mult)
                 offset += n_read
 
-    def _clean_names(self):
-        """Clean up CTF suffixes from channel names."""
-        mapping = dict(zip(self.ch_names, _clean_names(self.ch_names)))
-
-        self.rename_channels(mapping)
 
-        for comp in self.info["comps"]:
-            for key in ("row_names", "col_names"):
-                comp["data"][key] = _clean_names(comp["data"][key])
+def _clean_names_inst(inst):
+    """Clean up CTF suffixes from channel names."""
+    mapping = dict(zip(inst.ch_names, _clean_names(inst.ch_names)))
+    inst.rename_channels(mapping)
+    for comp in inst.info["comps"]:
+        for key in ("row_names", "col_names"):
+            comp["data"][key] = _clean_names(comp["data"][key])
 
 
 def _get_sample_info(fname, res4, system_clock):

mne/io/egi/egi.py

@@ -178,6 +178,8 @@ def read_raw_egi(
 class RawEGI(BaseRaw):
     """Raw object from EGI simple binary file."""
 
+    _extra_attributes = ("event_id",)
+
     @verbose
     def __init__(
         self,