Bump conda-incubator/setup-miniconda from 2 to 3 (mne-tools#12260)

Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]>
snwnde · Mar 20, 2024 · 1fe18e6 · 1fe18e6
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -90,7 +90,7 @@ jobs:
           python-version: ${{ matrix.python }}
         if: startswith(matrix.kind, 'pip')
       # Python (if conda)
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ env.PYTHON_VERSION }}
           environment-file: ${{ env.CONDA_ENV }}

diff --git a/.gitignore b/.gitignore
@@ -71,6 +71,8 @@ doc/*.dat
 doc/fil-result
 doc/optipng.exe
 sg_execution_times.rst
+sg_api_usage.rst
+sg_api_unused.dot
 cover
 *.html
 

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -108,7 +108,7 @@ stages:
           - bash: |
               set -e
               python -m pip install --progress-bar off --upgrade pip
-              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git@main" pyvista scikit-learn pytest-error-for-skips python-picard "PyQt6!=6.5.1" "PyQt6-Qt6!=6.6.1" qtpy nibabel sphinx-gallery
+              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git@main" pyvista scikit-learn pytest-error-for-skips python-picard "PyQt6!=6.5.1,!=6.6.1" "PyQt6-Qt6!=6.6.1" qtpy nibabel sphinx-gallery
               python -m pip uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e .[test]
             displayName: 'Install dependencies with pip'
@@ -187,7 +187,7 @@ stages:
             displayName: 'Get test data'
           - bash: |
               set -e
-              python -m pip install PyQt6 "PyQt6-Qt6!=6.6.1"
+              python -m pip install "PyQt6!=6.6.1" "PyQt6-Qt6!=6.6.1"
               LD_DEBUG=libs python -c "from PyQt6.QtWidgets import QApplication, QWidget; app = QApplication([]); import matplotlib; matplotlib.use('QtAgg'); import matplotlib.pyplot as plt; plt.figure()"
           - bash: |
               mne sys_info -pd

diff --git a/doc/api/realtime.rst b/doc/api/realtime.rst
@@ -1,5 +1,6 @@
+.. include:: ../links.inc
 
 Realtime
 ========
 
-Realtime functionality has moved to the standalone module :mod:`mne_realtime`.
+Realtime functionality has moved to the standalone module `MNE-LSL`_.
diff --git a/doc/changes/v0.23.rst b/doc/changes/v0.23.rst
@@ -246,7 +246,7 @@ Bugs
 
 - Fix bug with :func:`mne.grow_labels` where ``overlap=False`` could run forever or raise an error (:gh:`9317` by `Eric Larson`_)
 
-- Fix compatibility bugs with :mod:`mne_realtime` (:gh:`8845` by `Eric Larson`_)
+- Fix compatibility bugs with ``mne_realtime`` (:gh:`8845` by `Eric Larson`_)
 
 - Fix bug with `mne.viz.Brain` where non-inflated surfaces had an X-offset imposed by default (:gh:`8794` by `Eric Larson`_)
 

diff --git a/doc/changes/v0.24.rst b/doc/changes/v0.24.rst
@@ -37,7 +37,7 @@ Enhancements
 ~~~~~~~~~~~~
 .. - Add something cool (:gh:`9192` **by new contributor** |New Contributor|_)
 
-- Add `pooch` to system information reports (:gh:`9801` **by new contributor** |Joshua Teves|_)
+- Add ``pooch`` to system information reports (:gh:`9801` **by new contributor** |Joshua Teves|_)
 
 - Get annotation descriptions from the name field of SNIRF stimulus groups when reading SNIRF files via `mne.io.read_raw_snirf` (:gh:`9575` **by new contributor** |Darin Erat Sleiter|_)
 

diff --git a/doc/conf.py b/doc/conf.py
@@ -172,18 +172,14 @@
     "patsy": ("https://patsy.readthedocs.io/en/latest", None),
     "pyvista": ("https://docs.pyvista.org", None),
     "imageio": ("https://imageio.readthedocs.io/en/latest", None),
-    "mne_realtime": ("https://mne.tools/mne-realtime", None),
     "picard": ("https://pierreablin.github.io/picard/", None),
-    "qdarkstyle": ("https://qdarkstylesheet.readthedocs.io/en/latest", None),
     "eeglabio": ("https://eeglabio.readthedocs.io/en/latest", None),
     "dipy": (
         "https://dipy.org/documentation/1.7.0/",
         "https://dipy.org/documentation/1.7.0/objects.inv/",
     ),
-    "pooch": ("https://www.fatiando.org/pooch/latest/", None),
     "pybv": ("https://pybv.readthedocs.io/en/latest/", None),
     "pyqtgraph": ("https://pyqtgraph.readthedocs.io/en/latest/", None),
-    "openmeeg": ("https://openmeeg.github.io", None),
 }
 
 
@@ -400,6 +396,10 @@
     "CoregistrationUI",
     "IntracranialElectrodeLocator",
     "mne_qt_browser.figure.MNEQtBrowser",
+    # pooch, since its website is unreliable and users will rarely need the links
+    "pooch.Unzip",
+    "pooch.Untar",
+    "pooch.HTTPDownloader",
 }
 numpydoc_validate = True
 numpydoc_validation_checks = {"all"} | set(error_ignores)

diff --git a/doc/install/mne_tools_suite.rst b/doc/install/mne_tools_suite.rst
@@ -100,7 +100,6 @@ Help with installation is available through the `MNE Forum`_. See the
 .. _MNELAB: https://github.com/cbrnr/mnelab
 .. _autoreject: https://autoreject.github.io/
 .. _alphaCSC: https://alphacsc.github.io/
-.. _picard: https://pierreablin.github.io/picard/
 .. _pactools: https://pactools.github.io/
 .. _rsa: https://github.com/wmvanvliet/mne-rsa
 .. _microstate: https://github.com/wmvanvliet/mne_microstates

diff --git a/doc/links.inc b/doc/links.inc
@@ -26,6 +26,7 @@
 .. _`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
+.. _PICARD: https://pierreablin.github.io/picard/
 .. _OpenMEEG: https://openmeeg.github.io
 .. _openneuro-py: https://pypi.org/project/openneuro-py
 .. _EOSS2: https://chanzuckerberg.com/eoss/proposals/improving-usability-of-core-neuroscience-analysis-tools-with-mne-python

diff --git a/mne/bem.py b/mne/bem.py
@@ -415,8 +415,8 @@ def make_bem_solution(surfs, *, solver="mne", verbose=None):
     surfs : list of dict
         The BEM surfaces to use (from :func:`mne.make_bem_model`).
     solver : str
-        Can be ``'mne'`` (default) to use MNE-Python, or ``'openmeeg'`` to use
-        the :doc:`OpenMEEG <openmeeg:index>` package.
+        Can be ``'mne'`` (default) to use MNE-Python, or ``'openmeeg'`` to use the
+        `OpenMEEG <https://openmeeg.github.io>`__ package.
 
         .. versionadded:: 1.2
     %(verbose)s

diff --git a/mne/datasets/_fetch.py b/mne/datasets/_fetch.py
@@ -56,7 +56,7 @@ def fetch_dataset(
         What to do after downloading the file. ``"unzip"`` and ``"untar"`` will
         decompress the downloaded file in place; for custom extraction (e.g.,
         only extracting certain files from the archive) pass an instance of
-        :class:`pooch.Unzip` or :class:`pooch.Untar`. If ``None`` (the
+        ``pooch.Unzip`` or ``pooch.Untar``. If ``None`` (the
         default), the files are left as-is.
     path : None | str
         Directory in which to put the dataset. If ``None``, the dataset
@@ -87,10 +87,10 @@ def fetch_dataset(
         Default is ``False``.
     auth : tuple | None
         Optional authentication tuple containing the username and
-        password/token, passed to :class:`pooch.HTTPDownloader` (e.g.,
+        password/token, passed to ``pooch.HTTPDownloader`` (e.g.,
         ``auth=('foo', 012345)``).
     token : str | None
-        Optional authentication token passed to :class:`pooch.HTTPDownloader`.
+        Optional authentication token passed to ``pooch.HTTPDownloader``.
 
     Returns
     -------

diff --git a/mne/decoding/transformer.py b/mne/decoding/transformer.py
@@ -492,10 +492,9 @@ class FilterEstimator(TransformerMixin):
 
     Notes
     -----
-    This is primarily meant for use in conjunction with
-    :class:`mne_realtime.RtEpochs`. In general it is not recommended in a
-    normal processing pipeline as it may result in edge artifacts. Use with
-    caution.
+    This is primarily meant for use in realtime applications.
+    In general it is not recommended in a normal processing pipeline as it may result
+    in edge artifacts. Use with caution.
     """
 
     def __init__(

diff --git a/mne/forward/_make_forward.py b/mne/forward/_make_forward.py
@@ -661,7 +661,7 @@ def make_forward_solution(
     followed by :func:`mne.convert_forward_solution`.
 
     .. note::
-        If the BEM solution was computed with :doc:`OpenMEEG <openmeeg:index>`
+        If the BEM solution was computed with `OpenMEEG <https://openmeeg.github.io>`__
         in :func:`mne.make_bem_solution`, then OpenMEEG will automatically
         be used to compute the forward solution.
 

diff --git a/mne/utils/docs.py b/mne/utils/docs.py
@@ -4532,7 +4532,7 @@ def _reflow_param_docstring(docstring, has_first_line=True, width=75):
 theme : str | path-like
     Can be "auto", "light", or "dark" or a path-like to a
     custom stylesheet. For Dark-Mode and automatic Dark-Mode-Detection,
-    :mod:`qdarkstyle` and
+    `qdarkstyle <https://github.com/ColinDuquesnoy/QDarkStyleSheet>`__ and
     `darkdetect <https://github.com/albertosottile/darkdetect>`__,
     respectively, are required.\
     If None (default), the config option {config_option} will be used,

diff --git a/mne/viz/ica.py b/mne/viz/ica.py
@@ -855,8 +855,8 @@ def _plot_ica_sources_evoked(evoked, picks, exclude, title, show, ica, labels=No
         lines[-1].set_pickradius(3.0)
 
     ax.set(title=title, xlim=times[[0, -1]], xlabel="Time (ms)", ylabel="(NA)")
-    if len(exclude) > 0:
-        plt.legend(loc="best")
+    if len(lines):
+        ax.legend(lines, exclude_labels, loc="best")
 
     texts.append(
         ax.text(

diff --git a/pyproject.toml b/pyproject.toml
@@ -59,7 +59,7 @@ hdf5 = ["h5io", "pymatreader"]
 full = [
     "mne[hdf5]",
     "qtpy",
-    "PyQt6",
+    "PyQt6!=6.6.1",
     "PyQt6-Qt6!=6.6.1",
     "pyobjc-framework-Cocoa>=5.2.0; platform_system=='Darwin'",
     "sip",

diff --git a/tools/azure_dependencies.sh b/tools/azure_dependencies.sh
@@ -6,11 +6,11 @@ if [ "${TEST_MODE}" == "pip" ]; then
 	python -m pip install --only-binary="numba,llvmlite,numpy,scipy,vtk" -e .[test,full]
 elif [ "${TEST_MODE}" == "pip-pre" ]; then
 	STD_ARGS="$STD_ARGS --pre"
-	python -m pip install $STD_ARGS --only-binary ":all:" --extra-index-url "https://www.riverbankcomputing.com/pypi/simple" PyQt6 PyQt6-sip PyQt6-Qt6 "PyQt6-Qt6!=6.6.1"
+	python -m pip install $STD_ARGS --only-binary ":all:" --extra-index-url "https://www.riverbankcomputing.com/pypi/simple" "PyQt6!=6.6.1" PyQt6-sip PyQt6-Qt6 "PyQt6-Qt6!=6.6.1"
 	echo "Numpy etc."
 	# See github_actions_dependencies.sh for comments
 	python -m pip install $STD_ARGS --only-binary "numpy" numpy
-	python -m pip install $STD_ARGS --only-binary ":all:" --extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" "numpy>=2.0.0.dev0" "scipy>=1.12.0.dev0" scikit-learn matplotlib pandas statsmodels
+	python -m pip install $STD_ARGS --only-binary ":all:" --extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" "numpy>=2.0.0.dev0" "scipy>=1.12.0.dev0" scikit-learn matplotlib statsmodels
 	# echo "dipy"
 	# python -m pip install $STD_ARGS --only-binary ":all:" --extra-index-url "https://pypi.anaconda.org/scipy-wheels-nightly/simple" dipy
 	# echo "h5py"

diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh
@@ -22,10 +22,10 @@ else
 	echo "Numpy"
 	pip uninstall -yq numpy
 	echo "PyQt6"
-	pip install $STD_ARGS --only-binary ":all:" --default-timeout=60 --extra-index-url https://www.riverbankcomputing.com/pypi/simple PyQt6 "PyQt6-Qt6!=6.6.1"
+	pip install $STD_ARGS --only-binary ":all:" --default-timeout=60 --extra-index-url https://www.riverbankcomputing.com/pypi/simple "PyQt6!=6.6.1" "PyQt6-Qt6!=6.6.1"
 	echo "NumPy/SciPy/pandas etc."
-	pip install $STD_ARGS --only-binary ":all:" --default-timeout=60 --extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" "numpy>=2.0.0.dev0" "scipy>=1.12.0.dev0" scikit-learn matplotlib pillow pandas statsmodels
-	# No dipy, h5py, openmeeg, python-picard (needs numexpr) until they update to NumPy 2.0 compat
+	pip install $STD_ARGS --only-binary ":all:" --default-timeout=60 --extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" "numpy>=2.0.0.dev0" "scipy>=1.12.0.dev0" scikit-learn matplotlib pillow statsmodels
+	# No pandas, dipy, h5py, openmeeg, python-picard (needs numexpr) until they update to NumPy 2.0 compat
 	INSTALL_KIND="test_extra"
 	# echo "dipy"
 	# pip install $STD_ARGS --only-binary ":all:" --default-timeout=60 --extra-index-url "https://pypi.anaconda.org/scipy-wheels-nightly/simple" dipy