Fix deprecation warnings with newer versions of dependencies.

.circleci/config.yml

@@ -252,7 +252,7 @@ jobs:
           name: Check sphinx log for warnings (which are treated as errors)
           when: always
           command: |
-            ! grep "^.* WARNING: .*$" sphinx_log.txt
+            ! grep "^.* (WARNING|ERROR): .*$" sphinx_log.txt
       - run:
           name: Show profiling output
           when: always

.github/workflows/tests.yml

@@ -99,24 +99,22 @@ jobs:
           python-version: ${{ matrix.python }}
         if: startswith(matrix.kind, 'pip')
       # Python (if conda)
-      - name: Remove numba and dipy
-        run: |  # TODO: Remove when numba 0.59 and dipy 1.8 land on conda-forge
-          sed -i '/numba/d' environment.yml
-          sed -i '/dipy/d' environment.yml
-          sed -i 's/- mne$/- mne-base/' environment.yml
-        if: matrix.os == 'ubuntu-latest' && startswith(matrix.kind, 'conda') && matrix.python == '3.12'
+      - name: Fixes for conda
+        run: |
+          # For some reason on Linux we get crashes
+          if [[ "$RUNNER_OS" == "Linux" ]]; then
+            sed -i "/numba/d" environment.yml
+          elif [[ "$RUNNER_OS" == "macOS" ]]; then
+            sed -i "" "s/  - PySide6 .*/  - PySide6 <6.8/g" environment.yml
+          fi
+        if: matrix.kind == 'conda' || matrix.kind == 'mamba'
       - uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ${{ env.CONDA_ENV }}
           environment-name: mne
           create-args: >-
             python=${{ env.PYTHON_VERSION }}
-            mamba
-            nomkl
         if: ${{ !startswith(matrix.kind, 'pip') }}
-      # Make sure we have the right Python
-      - run: python -c "import platform; assert platform.machine() == 'arm64', platform.machine()"
-        if: matrix.os == 'macos-14'
       - run: ./tools/github_actions_dependencies.sh
       # Minimal commands on Linux (macOS stalls)
       - run: ./tools/get_minimal_commands.sh

doc/conf.py

@@ -666,6 +666,10 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     r"https://scholar.google.com/scholar\?cites=12188330066413208874&as_ylo=2014",
     r"https://scholar.google.com/scholar\?cites=1521584321377182930&as_ylo=2013",
     "https://www.research.chop.edu/imaging",
+    "http://prdownloads.sourceforge.net/optipng/optipng-0.7.8-win64.zip?download",
+    "https://sourceforge.net/projects/aespa/files/",
+    "https://sourceforge.net/projects/ezwinports/files/",
+    "https://www.mathworks.com/products/compiler/matlab-runtime.html",
     # 500 server error
     "https://openwetware.org/wiki/Beauchamp:FreeSurfer",
     # 503 Server error
@@ -688,6 +692,7 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     # SSL problems sometimes
     "http://ilabs.washington.edu",
     "https://psychophysiology.cpmc.columbia.edu",
+    "https://erc.easme-web.eu",
 ]
 linkcheck_anchors = False  # saves a bit of time
 linkcheck_timeout = 15  # some can be quite slow

doc/development/contributing.rst

@@ -1114,6 +1114,6 @@ it can serve as a useful example of what to expect from the PR review process.
 .. optipng
 
 .. _optipng: http://optipng.sourceforge.net/
-.. _optipng for Windows: http://prdownloads.sourceforge.net/optipng/optipng-0.7.7-win32.zip?download
+.. _optipng for Windows: http://prdownloads.sourceforge.net/optipng/optipng-0.7.8-win64.zip?download
 
 .. include:: ../links.inc

doc/install/installers.rst

@@ -86,7 +86,7 @@ Platform-specific installers
 
     .. We have to use a button-link here because button-ref doesn't properly nested parse the inline code
 
-    .. button-link:: ./ides.html
+    .. button-link:: ides.html
         :ref-type: ref
         :color: success
         :shadow:

environment.yml

@@ -23,11 +23,13 @@ dependencies:
   - joblib
   - jupyter
   - lazy_loader >=0.3
+  - mamba
   - matplotlib >=3.7
   - mffpy >=0.5.7
   - mne-qt-browser
   - nibabel
   - nilearn
+  - nomkl
   - numba
   - numpy >=1.25,<3
   - openmeeg >=2.5.5

mne/conftest.py

@@ -183,6 +183,10 @@ def pytest_configure(config):
     ignore:The (non_)?interactive_bk attribute was deprecated.*:
     # SWIG (via OpenMEEG)
     ignore:.*builtin type swigvarlink has no.*:DeprecationWarning
+    # eeglabio
+    ignore:numpy\.core\.records is deprecated.*:DeprecationWarning
+    # joblib
+    ignore:process .* is multi-threaded, use of fork/exec.*:DeprecationWarning
     """  # noqa: E501
     for warning_line in warning_lines.split("\n"):
         warning_line = warning_line.strip()

mne/datasets/sleep_physionet/_utils.py

@@ -2,6 +2,7 @@
 # License: BSD-3-Clause
 # Copyright the MNE-Python contributors.
 
+import inspect
 import os
 import os.path as op
 
@@ -114,12 +115,16 @@ def _update_sleep_temazepam_records(fname=TEMAZEPAM_SLEEP_RECORDS):
     data = data.set_index(("Subject - age - sex", "Nr"))
     data.index.name = "subject"
     data.columns.names = [None, None]
+    kwargs = dict()
+    # TODO VERSION can be removed once we require Pandas 2.1
+    if "future_stack" in inspect.getfullargspec(pd.DataFrame.stack).args:
+        kwargs["future_stack"] = True
     data = (
         data.set_index(
             [("Subject - age - sex", "Age"), ("Subject - age - sex", "M1/F2")],
             append=True,
         )
-        .stack(level=0)
+        .stack(level=0, **kwargs)
         .reset_index()
     )
 

mne/decoding/base.py

@@ -85,7 +85,11 @@ def __sklearn_tags__(self):
         """Get sklearn tags."""
         from sklearn.utils import get_tags  # added in 1.6
 
-        return get_tags(self.model)
+        # fit method below does not allow sparse data via check_data, we could
+        # eventually make it smarter if we had to
+        tags = get_tags(self.model)
+        tags.input_tags.sparse = False
+        return tags
 
     def __getattr__(self, attr):
         """Wrap to model for some attributes."""

mne/decoding/transformer.py

@@ -238,7 +238,7 @@ def inverse_transform(self, epochs_data):
         return out
 
 
-class Vectorizer(TransformerMixin):
+class Vectorizer(TransformerMixin, BaseEstimator):
     """Transform n-dimensional array into 2D array of n_samples by n_features.
 
     This class reshapes an n-dimensional array into an n_samples * n_features
@@ -343,7 +343,7 @@ def inverse_transform(self, X):
 
 
 @fill_doc
-class PSDEstimator(TransformerMixin):
+class PSDEstimator(TransformerMixin, BaseEstimator):
     """Compute power spectral density (PSD) using a multi-taper method.
 
     Parameters
@@ -452,7 +452,7 @@ def transform(self, epochs_data):
 
 
 @fill_doc
-class FilterEstimator(TransformerMixin):
+class FilterEstimator(TransformerMixin, BaseEstimator):
     """Estimator to filter RtEpochs.
 
     Applies a zero-phase low-pass, high-pass, band-pass, or band-stop
@@ -743,7 +743,7 @@ def _apply_method(self, X, method):
 
 
 @fill_doc
-class TemporalFilter(TransformerMixin):
+class TemporalFilter(TransformerMixin, BaseEstimator):
     """Estimator to filter data array along the last dimension.
 
     Applies a zero-phase low-pass, high-pass, band-pass, or band-stop

mne/export/tests/test_export.py

@@ -145,7 +145,7 @@ def _create_raw_for_edf_tests(stim_channel_index=None):
 
 
 edfio_mark = pytest.mark.skipif(
-    not _check_edfio_installed(strict=False), reason="unsafe use of private module"
+    not _check_edfio_installed(strict=False), reason="requires edfio"
 )
 
 
@@ -476,7 +476,7 @@ def test_export_epochs_eeglab(tmp_path, preload):
     with ctx():
         epochs.export(temp_fname)
     epochs.drop_channels([ch for ch in ["epoc", "STI 014"] if ch in epochs.ch_names])
-    epochs_read = read_epochs_eeglab(temp_fname)
+    epochs_read = read_epochs_eeglab(temp_fname, verbose="error")  # head radius
     assert epochs.ch_names == epochs_read.ch_names
     cart_coords = np.array([d["loc"][:3] for d in epochs.info["chs"]])  # just xyz
     cart_coords_read = np.array([d["loc"][:3] for d in epochs_read.info["chs"]])

mne/fixes.py

@@ -720,3 +720,16 @@ def minimum_phase(h, method="homomorphic", n_fft=None, *, half=True):
 
     n_out = (n_half + len(h) % 2) if half else len(h)
     return h_minimum[:n_out]
+
+
+# SciPy 1.15 deprecates sph_harm for sph_harm_y and using it will trigger a
+# DeprecationWarning. This is a backport of the new function for older SciPy versions.
+def sph_harm_y(n, m, theta, phi, *, diff_n=0):
+    """Wrap scipy.special.sph_harm for sph_harm_y."""
+    # Can be removed once we no longer support scipy < 1.15.0
+    from scipy import special
+
+    if "sph_harm_y" in special.__dict__:
+        return special.sph_harm_y(n, m, theta, phi, diff_n=diff_n)
+    else:
+        return special.sph_harm(m, n, phi, theta)

mne/preprocessing/maxwell.py

@@ -10,7 +10,7 @@
 
 import numpy as np
 from scipy import linalg
-from scipy.special import lpmv, sph_harm
+from scipy.special import lpmv
 
 from .. import __version__
 from .._fiff.compensator import make_compensator
@@ -24,7 +24,7 @@
 from ..annotations import _annotations_starts_stops
 from ..bem import _check_origin
 from ..channels.channels import _get_T1T2_mag_inds, fix_mag_coil_types
-from ..fixes import _safe_svd, bincount
+from ..fixes import _safe_svd, bincount, sph_harm_y
 from ..forward import _concatenate_coils, _create_meg_coils, _prep_meg_channels
 from ..io import BaseRaw, RawArray
 from ..surface import _normalize_vectors
@@ -436,7 +436,7 @@ def _prep_maxwell_filter(
     # we purposefully stay away from shorthand notation in both and use
     # explicit terms (like 'azimuth' and 'polar') to avoid confusion.
     # See mathworld.wolfram.com/SphericalHarmonic.html for more discussion.
-    # Our code follows the same standard that ``scipy`` uses for ``sph_harm``.
+    # Our code follows the same standard that ``scipy`` uses for ``sph_harm_y``.
 
     # triage inputs ASAP to avoid late-thrown errors
     _validate_type(raw, BaseRaw, "raw")
@@ -1487,7 +1487,7 @@ def _sss_basis_basic(exp, coils, mag_scale=100.0, method="standard"):
             S_in_out = list()
             grads_in_out = list()
             # Same spherical harmonic is used for both internal and external
-            sph = sph_harm(order, degree, az, pol)
+            sph = sph_harm_y(degree, order, pol, az)
             sph_norm = _sph_harm_norm(order, degree)
             # Compute complex gradient for all integration points
             # in spherical coordinates (Eq. 6). The gradient for rad, az, pol

mne/preprocessing/tests/test_maxwell.py

@@ -11,14 +11,14 @@
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
 from scipy import sparse
-from scipy.special import sph_harm
 
 import mne
 from mne import compute_raw_covariance, concatenate_raws, pick_info, pick_types
 from mne._fiff.constants import FIFF
 from mne.annotations import _annotations_starts_stops
 from mne.chpi import filter_chpi, read_head_pos
 from mne.datasets import testing
+from mne.fixes import sph_harm_y
 from mne.forward import _prep_meg_channels, use_coil_def
 from mne.io import (
     BaseRaw,
@@ -431,9 +431,9 @@ def test_spherical_conversions():
     az, pol = np.meshgrid(np.linspace(0, 2 * np.pi, 30), np.linspace(0, np.pi, 20))
     for degree in range(1, int_order):
         for order in range(0, degree + 1):
-            sph = sph_harm(order, degree, az, pol)
+            sph = sph_harm_y(degree, order, pol, az)
             # ensure that we satisfy the conjugation property
-            assert_allclose(_sh_negate(sph, order), sph_harm(-order, degree, az, pol))
+            assert_allclose(_sh_negate(sph, order), sph_harm_y(degree, -order, pol, az))
             # ensure our conversion functions work
             sph_real_pos = _sh_complex_to_real(sph, order)
             sph_real_neg = _sh_complex_to_real(sph, -order)

mne/transforms.py

@@ -12,14 +12,13 @@
 import numpy as np
 from scipy import linalg
 from scipy.spatial.distance import cdist
-from scipy.special import sph_harm
 
 from ._fiff.constants import FIFF
 from ._fiff.open import fiff_open
 from ._fiff.tag import read_tag
 from ._fiff.write import start_and_end_file, write_coord_trans
 from .defaults import _handle_default
-from .fixes import _get_img_fdata, jit
+from .fixes import _get_img_fdata, jit, sph_harm_y
 from .utils import (
     _check_fname,
     _check_option,
@@ -926,7 +925,7 @@ def _compute_sph_harm(order, az, pol):
     # _deg_ord_idx(0, 0) = -1 so we're actually okay to use it here
     for degree in range(order + 1):
         for order_ in range(degree + 1):
-            sph = sph_harm(order_, degree, az, pol)
+            sph = sph_harm_y(degree, order_, pol, az)
             out[:, _deg_ord_idx(degree, order_)] = _sh_complex_to_real(sph, order_)
             if order_ > 0:
                 out[:, _deg_ord_idx(degree, -order_)] = _sh_complex_to_real(

tools/github_actions_dependencies.sh

@@ -23,7 +23,7 @@ if [ ! -z "$CONDA_ENV" ]; then
 elif [[ "${MNE_CI_KIND}" == "pip" ]]; then
 	# Only used for 3.13 at the moment, just get test deps plus a few extras
 	# that we know are available
-	INSTALL_ARGS="nibabel scikit-learn numpydoc PySide6 mne-qt-browser"
+	INSTALL_ARGS="nibabel scikit-learn numpydoc PySide6 mne-qt-browser pandas h5io mffpy defusedxml"
 	INSTALL_KIND="test"
 else
 	test "${MNE_CI_KIND}" == "pip-pre"