From 2eeeaba5a510f97742d83e4d4444baef083d9bb8 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 3 Feb 2026 12:25:41 -0500 Subject: [PATCH 1/5] MAINT: Work around pandas deprecation --- doc/sphinxext/mne_doc_utils.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/sphinxext/mne_doc_utils.py b/doc/sphinxext/mne_doc_utils.py index 2cc089666ee..ff1a8b18920 100644 --- a/doc/sphinxext/mne_doc_utils.py +++ b/doc/sphinxext/mne_doc_utils.py @@ -72,6 +72,8 @@ def reset_warnings(gallery_conf, fname): r"open_text is deprecated\. Use files", # dipy etc. "The `disp` and `iprint` options of the L-BFGS-B solver", + # statsmodels<->pandas + "Substitution is deprecated and will be removed", ): warnings.filterwarnings( # deal with other modules having bad imports "ignore", message=f".*{key}.*", category=DeprecationWarning From dd61a91c59c2c5cfc98f1b998cd5938c310d5659 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 3 Feb 2026 14:26:27 -0500 Subject: [PATCH 2/5] FIX: Working [circle linkcheck] --- doc/links.inc | 2 +- mne/conftest.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/links.inc b/doc/links.inc index 7a6f7afc39f..bdc37b0dab5 100644 --- a/doc/links.inc +++ b/doc/links.inc @@ -40,7 +40,7 @@ .. _fwer: https://en.wikipedia.org/wiki/Family-wise_error_rate .. _fdr: https://en.wikipedia.org/wiki/False_discovery_rate .. _ft_cluster: http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test -.. _ft_cluster_effect_size: https://mailman.science.ru.nl/pipermail/fieldtrip/2017-September/024644.html +.. _ft_cluster_effect_size: https://mailman.science.ru.nl/pipermail/fieldtrip/2017-September/011773.html .. _ft_exch: https://mailman.science.ru.nl/pipermail/fieldtrip/2008-October/001794.html diff --git a/mne/conftest.py b/mne/conftest.py index b1d18d6805f..782f15775a9 100644 --- a/mne/conftest.py +++ b/mne/conftest.py @@ -180,6 +180,7 @@ def pytest_configure(config: pytest.Config): ignore:\n*Pyarrow will become a required dependency of pandas.*:DeprecationWarning ignore:np\.find_common_type is deprecated.*:DeprecationWarning ignore:Python binding for RankQuantileOptions.*: + ignore:Substitution is deprecated and will be removed.*:DeprecationWarning # pyvista <-> NumPy 2.0 ignore:__array_wrap__ must accept context and return_scalar arguments.*:DeprecationWarning # pyvista <-> VTK dev From 813b5a49a4a1152d36d151855d24538bcdbfe7f2 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Wed, 4 Feb 2026 09:56:25 -0500 Subject: [PATCH 3/5] FIX: More --- mne/conftest.py | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/mne/conftest.py b/mne/conftest.py index 782f15775a9..a1e6a21ec48 100644 --- a/mne/conftest.py +++ b/mne/conftest.py @@ -19,6 +19,7 @@ import numpy as np import pytest +from packaging.version import Version from pytest import StashKey, register_assert_rewrite # Any `assert` statements in our testing functions should be verbose versions @@ -180,7 +181,6 @@ def pytest_configure(config: pytest.Config): ignore:\n*Pyarrow will become a required dependency of pandas.*:DeprecationWarning ignore:np\.find_common_type is deprecated.*:DeprecationWarning ignore:Python binding for RankQuantileOptions.*: - ignore:Substitution is deprecated and will be removed.*:DeprecationWarning # pyvista <-> NumPy 2.0 ignore:__array_wrap__ must accept context and return_scalar arguments.*:DeprecationWarning # pyvista <-> VTK dev @@ -216,6 +216,20 @@ def pytest_configure(config: pytest.Config): warning_line = warning_line.strip() if warning_line and not warning_line.startswith("#"): config.addinivalue_line("filterwarnings", warning_line) + try: + import pandas + except Exception: + pass + else: + if Version(pandas.__version__) >= Version("3.1.0.dev0"): + # TODO VERSION once statsmodels dev has updated for pip-pre + # (failing as of 2026/02/04) + config.addinivalue_line( + "filterwarnings", + "ignore:" + ".+ is deprecated and will be removed in a future version.*:" + "pandas.errors.Pandas4Warning", + ) def pytest_collection_modifyitems(items: list[pytest.Item]): From 66407209a8a4aa7b1ec02ff6c2295abd1d782f37 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Wed, 4 Feb 2026 09:57:43 -0500 Subject: [PATCH 4/5] FIX: Linkcheck [circle linkcheck] --- doc/changes/names.inc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/changes/names.inc b/doc/changes/names.inc index b684d067a1d..3d74b32d150 100644 --- a/doc/changes/names.inc +++ b/doc/changes/names.inc @@ -337,7 +337,7 @@ .. _Tom Ma: https://github.com/myd7349 .. _Tom Stone: https://github.com/tomdstone .. _Tommy Clausner: https://github.com/TommyClausner -.. _Toomas Erik Anijärv: https://www.toomaserikanijarv.com/ +.. _Toomas Erik Anijärv: https://github.com/teanijarv .. _Tristan Stenner: https://github.com/tstenner/ .. _Tziona NessAiver: https://github.com/TzionaN .. _user27182: https://github.com/user27182 From fc67fdd7825a300cedc6053f8789332012422932 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Wed, 4 Feb 2026 10:47:57 -0500 Subject: [PATCH 5/5] FIX: Link [circle linkcheck] --- doc/conf.py | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/conf.py b/doc/conf.py index 35ad9e5f40b..90f826b1ea6 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -726,6 +726,7 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines): "http://ilabs.washington.edu", "https://psychophysiology.cpmc.columbia.edu", "https://erc.easme-web.eu", + "https://www.crnl.fr", # Not rendered by linkcheck builder r"ides\.html", ]