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

* upstream/main: (25 commits)
  DOC: Exclude some implicit refs in doc build (mne-tools#10433)
  MAINT: Better issue forms (mne-tools#11101)
  [FIX] Typo in example (mne-tools#11118)
  [MRG] Improve interpolation of bridged electrodes (mne-tools#11094)
  BUG: Spectrum deprecation cleanup [circle deploy] (mne-tools#11115)
  Add API entry list and map (mne-tools#10999)
  Add legacy decorator (mne-tools#11097)
  [ENH, MRG] Add time-frequency epoch source estimation (mne-tools#11095)
  Revert "Add error message when conversion of EEG locs to [circle deploy] (mne-tools#11104)
  MRG: Fixes for mne-tools#11090 (mne-tools#11108)
  add test for edf units param (mne-tools#11105)
  BUG: Improve logic for bti (mne-tools#11102)
  add spectrum class (mne-tools#10184)
  ENH : add units parameter to read_raw_edf in case units is missing from the file (mne-tools#11099)
  ENH: Add temperature and galvanic (mne-tools#11090)
  Add error message when conversion of EEG locs to head space fails (mne-tools#11080)
  DOC: removed unnecessary line in PSF example (mne-tools#11085)
  FIX: Update helmet during ICP (mne-tools#11084)
  Fix various typos (mne-tools#11086)
  DOC: Rel
  ...

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,65 @@
+name: 🐛 Bug report
+
+# See the json schema to help you create / update this form
+# https://json.schemastore.org/github-issue-forms.json
+
+description: Tell us about errors in our computations or plots.
+
+labels: ["BUG"]
+
+body:
+
+  - type: markdown
+    attributes:
+      value: |
+        Please use the [MNE-Python forum](https://mne.discourse.group/) to ask (and answer)
+        concrete technical questions or about usage of MNE-Python.
+        Use this form *only* if you think there is a bug in MNE-Python code.
+
+  - type: textarea
+    attributes:
+      label: Description of the problem
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Steps to reproduce
+      description: |
+        Paste here a code snippet or minimal working example
+        ([MWE](https://en.wikipedia.org/wiki/Minimal_Working_Example))
+        to replicate your problem, using one of the
+        [datasets shipped with MNE-Python](https://mne.tools/dev/overview/datasets_index.html),
+        preferably the one called [sample](https://mne.tools/dev/overview/datasets_index.html#sample).
+      render: Python
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Link to data
+      description: |
+        If you couldn't replicate on a built-in dataset, provide a link to a
+        small, anonymized portion of your data that does yield the error.
+
+  - type: textarea
+    attributes:
+      label: Expected results
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Actual results
+      description: |
+        Please provide the actual output, traceback, screenshot, or another description of the results.
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Additional information
+      description: |
+        Tell us about your system: paste the output of `mne.sys_info()` here.
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -1,5 +1,5 @@
 blank_issues_enabled: true
 contact_links:
-  - name: Forum
-    url: https://mne.discourse.group
-    about: For questions about analysis and usage, and announcements of interest to the neuroimaging community
+  - name: 💬 MNE-Python forum
+    url: https://mne.discourse.group/
+    about: Use the [MNE-Python forum](https://mne.discourse.group/) to ask (and answer) concrete technical questions or about usage of MNE-Python

.github/ISSUE_TEMPLATE/documentation.yml

@@ -0,0 +1,26 @@
+name: 📄 Documentation
+
+# See the json schema to help you create / update this form
+# https://json.schemastore.org/github-issue-forms.json
+
+description: Tell us about tutorials you wish we had in our docs, ideas for improving existing tutorials, terms missing from our glossary, or parts of our docstrings that are confusing or inaccurate.
+
+labels: ["DOC"]
+
+body:
+
+  - type: markdown
+    attributes:
+      value: |
+        Please make the issue title a succinct description of your proposed change.
+        For example: "add 'foo' to the glossary" or "add my favorite visualization to
+        the ERP tutorial".
+
+  - type: textarea
+    attributes:
+      label: Proposed documentation enhancement
+      description: |
+        Describe your proposed enhancement in detail. If you are requesting a new
+        glossary term, please include a proposed definition.
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,51 @@
+name: 🛠️ Feature request
+
+# See the json schema to help you create / update this form
+# https://json.schemastore.org/github-issue-forms.json
+
+description: Tell us about algorithms, visualizations, or other functionality you wish MNE-Python included.
+
+labels: ["ENH"]
+
+body:
+
+  - type: markdown
+    attributes:
+      value: |
+        Please use the [MNE-Python forum](https://mne.discourse.group/) to ask (and answer)
+        concrete technical questions or about usage of MNE-Python.
+        Use this form *only* if you want to suggest new features.
+
+  - type: textarea
+    attributes:
+      label: Describe the new feature or enhancement
+      description: |
+        Please provide a clear and concise description of what you want to add or change.
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Describe your proposed implementation
+      description: |
+        Describe how you think the feature or improvement should be implemented (e.g.,
+        as a new method on an existing class? as new capability added to an existing
+        method?)
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Describe possible alternatives
+      description: |
+        If you've suggested an implementation above, list here any alternative
+        implementations you can think of, and brief comments explaining why the chosen
+        implementation is better.
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Additional context
+      description: |
+        Add any other context or screenshots about the feature request here.

Makefile

@@ -1,4 +1,4 @@
-# simple makefile to simplify repetetive build env management tasks under posix
+# simple makefile to simplify repetitive build env management tasks under posix
 
 PYTHON ?= python
 PYTESTS ?= py.test

doc/_includes/channel_types.rst

@@ -65,4 +65,8 @@ ias            Internal Active Shielding data
 
 syst           System status channel information
                (Triux systems only)
+
+temperature    Temperature                               Degrees Celsius
+
+gsr            Galvanic skin response                    Siemens
 =============  ========================================= =================

doc/_static/style.css

@@ -327,3 +327,6 @@ ul.icon-bullets {
 img.hidden {
     visibility: hidden;
 }
+td.justify {
+    text-align-last: justify;
+}

doc/changes/latest.inc

@@ -23,6 +23,7 @@ Current (1.2.dev0)
 
 Enhancements
 ~~~~~~~~~~~~
+- Add ``vmin`` and ``vmax`` parameters to :meth:`mne.Evoked.animate_topomap` (:gh:`11073` by :newcontrib:`Mats van Es`)
 - EEGLAB files (saved as MAT versions less than v7.3) can now be imported with :func:`mne.io.read_raw_eeglab` without the optional dependency ``pymatreader`` (:gh:`11006` by `Clemens Brunner`_)
 - Add eight source estimate comparison metrics to new submodule :mod:`mne.simulation.metrics` (:gh:`6233` by `Kostiantyn Maksymenko`_ and `Alex Gramfort`_)
 - Add :func:`mne.time_frequency.csd_tfr` to compute cross-spectral density from :class:`mne.time_frequency.EpochsTFR` (:gh:`10986` by `Alex Rockhill`_)
@@ -32,17 +33,28 @@ Enhancements
 - Add ``starting_affine`` keyword argument to :func:`mne.transforms.compute_volume_registration` to initialize an alignment with an affine (:gh:`11020` by `Alex Rockhill`_)
 - The ``trans`` parameter in :func:`mne.make_field_map` now accepts a :class:`~pathlib.Path` object, and uses standardised loading logic (:gh:`10784` by :newcontrib:`Andrew Quinn`)
 - Add HTML representation for `~mne.Evoked` in Jupyter Notebooks (:gh:`11075` by `Valerii Chirkov`_ and `Andrew Quinn`_)
+- Add support for ``temperature`` and ``gsr`` (galvanic skin response, i.e., electrodermal activity) channel types (:gh:`11090`, :gh:`11108` by `Eric Larson`_ and `Richard Höchenberger`_)
 - Allow :func:`mne.beamformer.make_dics` to take ``pick_ori='vector'`` to compute vector source estimates (:gh:`19080` by `Alex Rockhill`_)
+- Add ``units`` parameter to :func:`mne.io.read_raw_edf` in case units are missing from the file (:gh:`11099` by `Alex Gramfort`_)
+- Add ``on_missing`` functionality to all of our classes that have a ``drop_channels`` method, to control what happens when channel names are not in the object (:gh:`11077` by `Andrew Quinn`_)
+- Improve interpolation of bridged electrodes with `~mne.preprocessing.interpolate_bridged_electrodes` (:gh:`11094` by `Mathieu Scheltienne`_)
+- Add :func:`mne.minimum_norm.apply_inverse_tfr_epochs` to apply inverse methods to time-frequency resolved epochs (:gh:`11095` by `Alex Rockhill`_)
 
 Bugs
 ~~~~
+- Fix bug in :func:`mne.io.read_raw_eeglab` where unlabeled fiducials causde reading errors (:gh:`11074` by :newcontrib:`Sebastiaan Mathot`)
 - Fix bug in :func:`mne.time_frequency.read_csd` that returned ``projs`` as a list of dict instead of :class:`mne.Projection` (:gh:`11072` by :newcontrib:`Chetan Gohil`)
 - Fix bug in :func:`mne.decoding.TimeFrequency` that prevented cloning if constructor arguments were modified (:gh:`11004` by :newcontrib:`Daniel Carlström Schad`)
 - Fix bug in :class:`mne.viz.Brain` constructor where the first argument was named ``subject_id`` instead of ``subject`` (:gh:`11049` by `Eric Larson`_)
+- Fix bug in :ref:`mne coreg` where the MEG helmet position was not updated during ICP fitting (:gh:`11084` by `Eric Larson`_)
 - Document ``height`` and ``weight`` keys of  ``subject_info`` entry in :class:`mne.Info` (:gh:`11019` by :newcontrib:`Sena Er`)
-- Fixed bug in :func:`mne.viz.plot_filter` when plotting filters created using ``output='ba'`` mode with ``compensation`` turned on. (by `Marian Dovgialo`_)
+- Fix bug in :func:`mne.viz.plot_filter` when plotting filters created using ``output='ba'`` mode with ``compensation`` turned on. (:gh:`11040` by `Marian Dovgialo`_)
+- Fix bug in :func:`mne.io.read_raw_bti` where EEG, EMG, and H/VEOG channels were not detected properly, and many non-ECG channels were called ECG. The logic has been improved, and any channels of unknown type are now labeled as ``misc`` (:gh:`11102` by `Eric Larson`_)
+- Fix bug in :func:`mne.viz.plot_topomap` when providing ``sphere="eeglab"`` (:gh:`11081` by `Mathieu Scheltienne`_)
 
 API changes
 ~~~~~~~~~~~
 - The ``bands`` parameter of :meth:`mne.Epochs.plot_psd_topomap` now accepts :class:`dict` input; legacy :class:`tuple` input is supported, but discouraged for new code (:gh:`11050` by `Daniel McCloy`_)
 - The ``show_toolbar`` argument to :class:`mne.viz.Brain` is being removed by deprecation (:gh:`11049` by `Eric Larson`_)
+- New classes :class:`~mne.time_frequency.Spectrum` and :class:`~mne.time_frequency.EpochsSpectrum`, created via new methods :meth:`Raw.compute_psd()<mne.io.Raw.compute_psd>`, :meth:`Epochs.compute_psd()<mne.Epochs.compute_psd>`, and :meth:`Evoked.compute_psd()<mne.Evoked.compute_psd>` (:gh:`10184` by `Daniel McCloy`_)
+- The PSD functions that operate on Raw/Epochs/Evoked instances (``mne.time_frequency.psd_welch`` and ``mne.time_frequency.psd_multitaper``) are deprecated; for equivalent functionality create :class:`~mne.time_frequency.Spectrum` or :class:`~mne.time_frequency.EpochsSpectrum` objects instead and then run ``spectrum.get_data(return_freqs=True)`` (:gh:`10184` by `Daniel McCloy`_)

doc/changes/names.inc

@@ -296,6 +296,8 @@
 
 .. _Mathurin Massias: https://mathurinm.github.io/
 
+.. _Mats van Es: https://github.com/matsvanes
+
 .. _Matt Boggess: https://github.com/mattboggess
 
 .. _Matt Courtemanche: https://github.com/mjcourte
@@ -412,6 +414,8 @@
 
 .. _Scott Huberty:  https://orcid.org/0000-0003-2637-031X
 
+.. _Sebastiaan Mathot: http://www.cogsci.nl/smathot
+
 .. _Sebastian Castano: https://github.com/jscastanoc
 
 .. _Sebastian Major: https://github.com/major-s

doc/conf.py

@@ -236,6 +236,8 @@
     'Transform': 'mne.transforms.Transform',
     'Coregistration': 'mne.coreg.Coregistration',
     'Figure3D': 'mne.viz.Figure3D',
+    'Spectrum': 'mne.time_frequency.Spectrum',
+    'EpochsSpectrum': 'mne.time_frequency.EpochsSpectrum',
     # dipy
     'dipy.align.AffineMap': 'dipy.align.imaffine.AffineMap',
     'dipy.align.DiffeomorphicMap': 'dipy.align.imwarp.DiffeomorphicMap',
@@ -465,6 +467,41 @@ def __call__(self, gallery_conf, fname, when):
     'matplotlib_animations': True,
     'compress_images': compress_images,
     'filename_pattern': '^((?!sgskip).)*$',
+    'exclude_implicit_doc': {
+        r'mne\.io\.read_raw_fif', r'mne\.io\.Raw', r'mne\.Epochs',
+        r'mne.datasets.*',
+    },
+    'api_usage_ignore': (
+        '('
+        '.*__.*__|'  # built-ins
+        '.*Base.*|.*Array.*|mne.Vector.*|mne.Mixed.*|mne.Vol.*|'  # inherited
+        'mne.coreg.Coregistration.*|'  # GUI
+        # common
+        '.*utils.*|.*verbose()|.*copy()|.*update()|.*save()|'
+        '.*get_data()|'
+        # mixins
+        '.*add_channels()|.*add_reference_channels()|'
+        '.*anonymize()|.*apply_baseline()|.*apply_function()|'
+        '.*apply_hilbert()|.*as_type()|.*decimate()|'
+        '.*drop()|.*drop_channels()|.*drop_log_stats()|'
+        '.*export()|.*get_channel_types()|'
+        '.*get_montage()|.*interpolate_bads()|.*next()|'
+        '.*pick()|.*pick_channels()|.*pick_types()|'
+        '.*plot_sensors()|.*rename_channels()|'
+        '.*reorder_channels()|.*savgol_filter()|'
+        '.*set_eeg_reference()|.*set_channel_types()|'
+        '.*set_meas_date()|.*set_montage()|.*shift_time()|'
+        '.*time_as_index()|.*to_data_frame()|'
+        # dictionary inherited
+        '.*clear()|.*fromkeys()|.*get()|.*items()|'
+        '.*keys()|.*pop()|.*popitem()|.*setdefault()|'
+        '.*values()|'
+        # sklearn inherited
+        '.*apply()|.*decision_function()|.*fit()|'
+        '.*fit_transform()|.*get_params()|.*predict()|'
+        '.*predict_proba()|.*set_params()|.*transform()|'
+        # I/O, also related to mixins
+        '.*.remove.*|.*.write.*)')
 }
 # Files were renamed from plot_* with:
 # find . -type f -name 'plot_*.py' -exec sh -c 'x="{}"; xn=`basename "${x}"`; git mv "$x" `dirname "${x}"`/${xn:5}' \;  # noqa