From c28d77914344f770b6698e39bd7303934147636a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 8 Sep 2025 09:10:16 +0000 Subject: [PATCH 1/5] Bump actions/setup-python from 5 to 6 in the actions group Bumps the actions group with 1 update: [actions/setup-python](https://github.com/actions/setup-python). Updates `actions/setup-python` from 5 to 6 - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v5...v6) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions ... Signed-off-by: dependabot[bot] --- .github/workflows/autofix.yml | 2 +- .github/workflows/credit.yml | 2 +- .github/workflows/release.yml | 2 +- .github/workflows/tests.yml | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/autofix.yml b/.github/workflows/autofix.yml index 6d82b9d71f9..b41e636bf5f 100644 --- a/.github/workflows/autofix.yml +++ b/.github/workflows/autofix.yml @@ -15,7 +15,7 @@ jobs: - uses: actions/checkout@v5 with: persist-credentials: false - - uses: actions/setup-python@v5 + - uses: actions/setup-python@v6 with: python-version: '3.12' - run: pip install --upgrade towncrier pygithub gitpython numpy diff --git a/.github/workflows/credit.yml b/.github/workflows/credit.yml index 895a0fea588..5e538f6a974 100644 --- a/.github/workflows/credit.yml +++ b/.github/workflows/credit.yml @@ -20,7 +20,7 @@ jobs: - uses: actions/checkout@v5 with: persist-credentials: true - - uses: actions/setup-python@v5 + - uses: actions/setup-python@v6 with: python-version: '3.12' - run: pip install pygithub -e . diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 892f73bb809..47adf707d36 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -19,7 +19,7 @@ jobs: - uses: actions/checkout@v5 with: persist-credentials: false - - uses: actions/setup-python@v5 + - uses: actions/setup-python@v6 with: python-version: '3.10' - name: Install dependencies diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 5a3b310b2fd..8f173768b2e 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -28,7 +28,7 @@ jobs: - uses: actions/checkout@v5 with: persist-credentials: false - - uses: actions/setup-python@v5 + - uses: actions/setup-python@v6 with: python-version: '3.13' - uses: pre-commit/action@v3.0.1 @@ -118,7 +118,7 @@ jobs: pyvista: false wm: false # Python (if pip) - - uses: actions/setup-python@v5 + - uses: actions/setup-python@v6 with: python-version: ${{ matrix.python }} if: startswith(matrix.kind, 'pip') From 064e1b190b8e640811ce628af86d1810dec95e9a Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Mon, 8 Sep 2025 09:37:27 -0400 Subject: [PATCH 2/5] FIX: Bins --- mne/_ola.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mne/_ola.py b/mne/_ola.py index e43e7cd3d31..939aff39646 100644 --- a/mne/_ola.py +++ b/mne/_ola.py @@ -309,7 +309,7 @@ def __init__( # Create our window boundaries window_name = window if isinstance(window, str) else "custom" self._window = get_window( - window, self._n_samples, fftbins=(self._n_samples - 1) % 2 + window, self._n_samples, fftbins=bool((self._n_samples - 1) % 2) ) self._window /= _check_cola( self._window, self._n_samples, self._step, window_name, tol=tol From 85f5c6fedcdd58d631e79550b5d8dfb4c3eb4bb4 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Mon, 8 Sep 2025 09:50:59 -0400 Subject: [PATCH 3/5] MAINT: Fix links [circle linkcheck] --- doc/changes/names.inc | 2 +- doc/conf.py | 5 ++--- doc/sphinxext/related_software.py | 4 ++++ 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/doc/changes/names.inc b/doc/changes/names.inc index 6d22340c78c..38c240d69d7 100644 --- a/doc/changes/names.inc +++ b/doc/changes/names.inc @@ -112,7 +112,7 @@ .. _Harrison Ritz: https://github.com/harrisonritz .. _Hasrat Ali Arzoo: https://github.com/hasrat17 .. _Henrich Kolkhorst: https://github.com/hekolk -.. _Hongjiang Ye: https://github.com/hongjiang-ye +.. _Hongjiang Ye: https://github.com/ye-hongjiang .. _Hubert Banville: https://github.com/hubertjb .. _Hyonyoung Shin: https://github.com/mcvain .. _Hüseyin Orkun Elmas: https://github.com/HuseyinOrkun diff --git a/doc/conf.py b/doc/conf.py index 2ea68ec8d0a..dc989108a69 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -664,6 +664,7 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines): "https://doi.org/10.1167/", # jov.arvojournals.org "https://doi.org/10.1177/", # journals.sagepub.com "https://doi.org/10.3109/", # www.tandfonline.com + "https://doi.org/10.3390/", # mdpi.com "https://hms.harvard.edu/", # doc/funding.rst "https://stackoverflow.com/questions/21752259/python-why-pickle", # doc/help/faq "https://www.biorxiv.org/content/10.1101/", # biorxiv.org @@ -672,9 +673,7 @@ 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", - "https://sourceforge.net/projects/aespa/files/", - "https://sourceforge.net/projects/ezwinports/files/", + r"https://.*\.sourceforge\.net/", "https://www.mathworks.com/products/compiler/matlab-runtime.html", "https://medicine.umich.edu/dept/khri/ross-maddox-phd", # TODO https://github.com/mne-tools/curry-python-reader/issues/5 diff --git a/doc/sphinxext/related_software.py b/doc/sphinxext/related_software.py index 8cbc91be4ff..eff1a18dee7 100644 --- a/doc/sphinxext/related_software.py +++ b/doc/sphinxext/related_software.py @@ -74,6 +74,10 @@ "Summary": "DICOM to NIfTI converter", }, # TODO: these do not set a valid homepage or documentation page on PyPI + "picard": { # https://github.com/mind-inria/picard/issues/60 + "Home-page": "https://github.com/mind-inria/picard", + "Summary": "Preconditioned ICA for Real Data", + }, "eeg_positions": { "Home-page": "https://eeg-positions.readthedocs.io", "Summary": "Compute and plot standard EEG electrode positions.", From aba32acbdf1040561e3c87395b21330d8833f7c3 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Mon, 8 Sep 2025 10:35:09 -0400 Subject: [PATCH 4/5] FIX: Maybe [circle linkcheck] --- doc/conf.py | 4 ++++ doc/sphinxext/related_software.py | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index dc989108a69..07242cbc5c9 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -673,7 +673,11 @@ 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", + "https://sourceforge.net/projects/aespa/files/", + "https://sourceforge.net/projects/ezwinports/files/", r"https://.*\.sourceforge\.net/", + "https://www.cogsci.nl/smathot", "https://www.mathworks.com/products/compiler/matlab-runtime.html", "https://medicine.umich.edu/dept/khri/ross-maddox-phd", # TODO https://github.com/mne-tools/curry-python-reader/issues/5 diff --git a/doc/sphinxext/related_software.py b/doc/sphinxext/related_software.py index eff1a18dee7..4d6105a83a9 100644 --- a/doc/sphinxext/related_software.py +++ b/doc/sphinxext/related_software.py @@ -74,7 +74,7 @@ "Summary": "DICOM to NIfTI converter", }, # TODO: these do not set a valid homepage or documentation page on PyPI - "picard": { # https://github.com/mind-inria/picard/issues/60 + "python-picard": { # https://github.com/mind-inria/picard/issues/60 "Home-page": "https://github.com/mind-inria/picard", "Summary": "Preconditioned ICA for Real Data", }, From 80a91a7061151f428a9ceadf2be3f75bdcfaaf42 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Mon, 8 Sep 2025 11:25:33 -0400 Subject: [PATCH 5/5] FIX: More [circle linkcheck] --- doc/conf.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index 07242cbc5c9..415f1bf46cc 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -650,10 +650,11 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines): "https://doi.org/10.1073/", # pnas.org "https://doi.org/10.1080/", # www.tandfonline.com "https://doi.org/10.1088/", # www.tandfonline.com + "https://doi.org/10.1090/", # ams.org "https://doi.org/10.1093/", # academic.oup.com/sleep/ "https://doi.org/10.1098/", # royalsocietypublishing.org "https://doi.org/10.1101/", # www.biorxiv.org - "https://doi.org/10.1103", # journals.aps.org/rmp + "https://doi.org/10.1103/", # journals.aps.org/rmp "https://doi.org/10.1111/", # onlinelibrary.wiley.com/doi/10.1111/psyp "https://doi.org/10.1126/", # www.science.org "https://doi.org/10.1137/", # epubs.siam.org @@ -663,6 +664,7 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines): "https://doi.org/10.1162/", # direct.mit.edu/neco/article/ "https://doi.org/10.1167/", # jov.arvojournals.org "https://doi.org/10.1177/", # journals.sagepub.com + "https://doi.org/10.1523/", # jneurosci.org "https://doi.org/10.3109/", # www.tandfonline.com "https://doi.org/10.3390/", # mdpi.com "https://hms.harvard.edu/", # doc/funding.rst