diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 9685dc88a00..ba23d92367d 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -114,6 +114,9 @@ jobs: mamba nomkl if: ${{ !startswith(matrix.kind, 'pip') }} + # unknown error on macOS conda + - run: conda remove -y openmeeg + if: startswith(matrix.os, 'macos') && matrix.kind == 'mamba' - run: ./tools/github_actions_dependencies.sh # Minimal commands on Linux (macOS stalls) - run: ./tools/get_minimal_commands.sh diff --git a/doc/conf.py b/doc/conf.py index 7dd6ec90d4f..96028fb9045 100644 --- a/doc/conf.py +++ b/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 diff --git a/doc/development/contributing.rst b/doc/development/contributing.rst index 07c28f55d3d..011fd3c11f4 100644 --- a/doc/development/contributing.rst +++ b/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 diff --git a/doc/install/installers.rst b/doc/install/installers.rst index 5b7eeba5203..533c0207963 100644 --- a/doc/install/installers.rst +++ b/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: diff --git a/mne/conftest.py b/mne/conftest.py index fc3bc3b7a53..6eea624467a 100644 --- a/mne/conftest.py +++ b/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() diff --git a/mne/datasets/sleep_physionet/_utils.py b/mne/datasets/sleep_physionet/_utils.py index b97d0611591..7fbcca3a2d7 100644 --- a/mne/datasets/sleep_physionet/_utils.py +++ b/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() ) diff --git a/mne/export/tests/test_export.py b/mne/export/tests/test_export.py index 706a83476e4..bb3787be8b9 100644 --- a/mne/export/tests/test_export.py +++ b/mne/export/tests/test_export.py @@ -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"]])