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"doc/changes/devel/13070.bugfix.rst": { + "a": 1, + "d": 0 + }, + "doc/changes/names.inc": { + "a": 1, + "d": 0 + }, + "mne/io/base.py": { + "a": 4, + "d": 1 + }, + "mne/io/fiff/tests/test_raw_fiff.py": { + "a": 10, + "d": 0 + } + } +} \ No newline at end of file diff --git a/doc/sphinxext/prs/13082.json b/doc/sphinxext/prs/13082.json new file mode 100644 index 00000000000..1eb2d448059 --- /dev/null +++ b/doc/sphinxext/prs/13082.json @@ -0,0 +1,35 @@ +{ + "merge_commit_sha": "3db12ff5357d4d6666f3d2257e91cee877e83234", + "authors": [ + { + "n": "Eric Larson", + "e": "larson.eric.d@gmail.com" + }, + { + "n": "autofix-ci[bot]", + "e": "114827586+autofix-ci[bot]@users.noreply.github.com" + } + ], + "changes": { + "doc/changes/devel/13082.bugfix.rst": { + "a": 1, + "d": 0 + }, + "examples/preprocessing/movement_detection.py": { + "a": 1, + "d": 0 + }, + "mne/conftest.py": { + "a": 1, + "d": 0 + }, + "mne/viz/_brain/tests/test_brain.py": { + "a": 0, + "d": 3 + }, + "mne/viz/backends/_pyvista.py": { + "a": 1, + "d": 1 + } + } +} \ No newline at end of file diff --git a/doc/sphinxext/prs/13084.json b/doc/sphinxext/prs/13084.json new file mode 100644 index 00000000000..c08d21af74b --- /dev/null +++ b/doc/sphinxext/prs/13084.json @@ -0,0 +1,35 @@ +{ + "merge_commit_sha": "d3d0bf520624a4eea2e8d34a927284c4bb19b87a", + "authors": [ + { + "n": "Lumberbot (aka Jack)", + "e": null + }, + { + "n": "Eric Larson", + "e": "larson.eric.d@gmail.com" + } + ], + "changes": { + "doc/changes/devel/13082.bugfix.rst": { + "a": 1, + "d": 0 + }, + "examples/preprocessing/movement_detection.py": { + "a": 1, + "d": 0 + }, + "mne/conftest.py": { + "a": 1, + "d": 0 + }, + "mne/viz/_brain/tests/test_brain.py": { + "a": 0, + "d": 3 + }, + "mne/viz/backends/_pyvista.py": { + "a": 1, + "d": 1 + } + } +} \ No newline at end of file diff --git a/doc/sphinxext/prs/13086.json b/doc/sphinxext/prs/13086.json new file mode 100644 index 00000000000..261d6a9a0e3 --- /dev/null +++ b/doc/sphinxext/prs/13086.json @@ -0,0 +1,23 @@ +{ + "merge_commit_sha": "631ddb3e9da67456947e23c6a070aa869d853a26", + "authors": [ + { + "n": "Marijn van Vliet", + "e": "w.m.vanvliet@gmail.com" + }, + { + "n": "Richard Höchenberger", + "e": "richard.hoechenberger@gmail.com" + } + ], + "changes": { + "mne/viz/_mpl_figure.py": { + "a": 2, + "d": 2 + }, + "tutorials/epochs/60_make_fixed_length_epochs.py": { + "a": 1, + "d": 1 + } + } +} \ No newline at end of file diff --git a/doc/sphinxext/prs/13087.json b/doc/sphinxext/prs/13087.json new file mode 100644 index 00000000000..1606b92a8c4 --- /dev/null +++ b/doc/sphinxext/prs/13087.json @@ -0,0 +1,19 @@ +{ + "merge_commit_sha": "4037ead8fe9ec27d7342263c574b99a7bc537104", + "authors": [ + { + "n": "Marijn van Vliet", + "e": "w.m.vanvliet@gmail.com" + } + ], + "changes": { + "mne/viz/_figure.py": { + "a": 1, + "d": 1 + }, + "mne/viz/_mpl_figure.py": { + "a": 2, + "d": 2 + } + } +} \ No newline at end of file diff --git a/doc/sphinxext/prs/13088.json b/doc/sphinxext/prs/13088.json new file mode 100644 index 00000000000..f23c44206b3 --- /dev/null +++ b/doc/sphinxext/prs/13088.json @@ -0,0 +1,23 @@ +{ + "merge_commit_sha": "45fb777fbc53c88888032d40a14940c985079a93", + "authors": [ + { + "n": "pre-commit-ci[bot]", + "e": "66853113+pre-commit-ci[bot]@users.noreply.github.com" + }, + { + "n": "Daniel McCloy", + "e": "dan@mccloy.info" + } + ], + "changes": { + ".pre-commit-config.yaml": { + "a": 2, + "d": 2 + }, + "mne/_fiff/proj.py": { + "a": 1, + "d": 1 + } + } +} \ No newline at end of file diff --git a/doc/sphinxext/prs/13089.json b/doc/sphinxext/prs/13089.json new file mode 100644 index 00000000000..b0ad8b2fce2 --- /dev/null +++ b/doc/sphinxext/prs/13089.json @@ -0,0 +1,23 @@ +{ + "merge_commit_sha": "715540a823ae5dec335bee0b2499f1f7183c19c4", + "authors": [ + { + "n": "Eric Larson", + "e": "larson.eric.d@gmail.com" + } + ], + "changes": { + "mne/viz/utils.py": { + "a": 1, + "d": 1 + }, + "tutorials/epochs/60_make_fixed_length_epochs.py": { + "a": 4, + "d": 5 + }, + "tutorials/evoked/10_evoked_overview.py": { + "a": 5, + "d": 6 + } + } +} \ No newline at end of file From fe3b79ca85f4767ee322e8a93c93c71d2171ed85 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Mon, 3 Feb 2025 14:25:23 -0500 Subject: [PATCH 2/7] FIX: CIs --- .mailmap | 2 ++ doc/sphinxext/credit_tools.py | 32 +++++++++++++++---------------- tools/install_pre_requirements.sh | 8 +++++++- 3 files changed, 25 insertions(+), 17 deletions(-) diff --git a/.mailmap b/.mailmap index 133eb2be306..b7d87833dcc 100644 --- a/.mailmap +++ b/.mailmap @@ -86,6 +86,7 @@ Eduard Ort examplename Ellen Lau ellenlau Emily Stephen Emily P. Stephen Emily Stephen emilyps14 +Emma Bailey <93327939+emma-bailey@users.noreply.github.com> emma-bailey <93327939+emma-bailey@users.noreply.github.com> Enrico Varano enricovara <69973551+enricovara@users.noreply.github.com> Enzo Altamiranda enzo Eric Larson Eric Larson @@ -315,6 +316,7 @@ Sara Sommariva sarasommariva Sebastien Treguer DataFox Sena Er <2799280+sena-neuro@users.noreply.github.com> Sena <2799280+sena-neuro@users.noreply.github.com> Senwen Deng <36327760+snwnde@users.noreply.github.com> Senwen DENG <36327760+snwnde@users.noreply.github.com> +Shristi Baral Shristi Baral Silvia Cotroneo <78911192+sfc-neuro@users.noreply.github.com> sfc-neuro <78911192+sfc-neuro@users.noreply.github.com> Simon Kern Simon Kern <14980558+skjerns@users.noreply.github.com> Simon Kern skjerns <14980558+skjerns@users.noreply.github.com> diff --git a/doc/sphinxext/credit_tools.py b/doc/sphinxext/credit_tools.py index e22bd0b5530..d3886b11200 100644 --- a/doc/sphinxext/credit_tools.py +++ b/doc/sphinxext/credit_tools.py @@ -39,6 +39,16 @@ # Allowed singletons single_names = "btkcodedev buildqa sviter Akshay".split() +# Surnames where we have more than one distinct contributor: +name_counts = dict( + Bailey=2, + Das=2, + Drew=2, + Li=2, + Peterson=2, + Wong=2, + Zhang=2, +) # Exceptions, e.g., abbrevitaions in first/last name or all-caps exceptions = [ "T. Wang", @@ -217,16 +227,6 @@ def generate_credit_rst(app=None, *, verbose=False): ) # Check for duplicate names based on last name, and also singleton names. - # Below are surnames where we have more than one distinct contributor: - name_counts = dict( - Das=2, - Drew=2, - Li=2, - Peterson=2, - Wong=2, - Zhang=2, - ) - # Below are allowed singleton names last_map = defaultdict(lambda: set()) bad_names = set() for these_stats in stats.values(): @@ -245,10 +245,11 @@ def generate_credit_rst(app=None, *, verbose=False): if len(names) > name_counts.get(last, 1): bad_names.append(f"Duplicates: {sorted(names)}") if bad_names: - raise RuntimeError( - "Unexpected possible duplicates or bad names found:\n" - + "\n".join(bad_names) + what = ( + "Unexpected possible duplicates or bad names found, " + f"consider modifying {'/'.join(Path(__file__).parts[-3:])}:\n" ) + raise RuntimeError(what + "\n".join(bad_names)) unknown_emails = set( email @@ -258,9 +259,8 @@ def generate_credit_rst(app=None, *, verbose=False): and "dependabot[bot]" not in email and "github-actions[bot]" not in email ) - assert len(unknown_emails) == 0, "Unknown emails\n" + "\n".join( - sorted(unknown_emails) - ) + what = "Unknown emails, consider adding to .mailmap:\n" + assert len(unknown_emails) == 0, what + "\n".join(sorted(unknown_emails)) logger.info("Biggest included commits/PRs:") commits = dict( diff --git a/tools/install_pre_requirements.sh b/tools/install_pre_requirements.sh index c717b1b477b..01bfc086fe5 100755 --- a/tools/install_pre_requirements.sh +++ b/tools/install_pre_requirements.sh @@ -27,9 +27,15 @@ python -m pip install $STD_ARGS --only-binary ":all:" --default-timeout=60 \ # statsmodels requires formulaic@main so we need to use --extra-index-url echo "statsmodels" +# https://github.com/statsmodels/statsmodels/issues/9501 +if [ "$PLATFORM" == "Windows" ]; then + STATS_VER=0.14.4 +else + STATS_VER=0.15.0.dev0 +fi python -m pip install $STD_ARGS --only-binary ":all:" \ --extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" \ - "statsmodels>=0.15.0.dev0" + "statsmodels>=$STATS_VER" # No Numba because it forces an old NumPy version From 0928b0ca3ba4f89d361c698776253544cfc50423 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Mon, 3 Feb 2025 14:28:45 -0500 Subject: [PATCH 3/7] FIX: Links, too [circle linkcheck] --- doc/changes/names.inc | 2 +- doc/conf.py | 3 ++- examples/io/read_xdf.py | 2 +- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/doc/changes/names.inc b/doc/changes/names.inc index 5a58ac0fa34..18753a0c872 100644 --- a/doc/changes/names.inc +++ b/doc/changes/names.inc @@ -256,7 +256,7 @@ .. _Romain Derollepot: https://github.com/rderollepot .. _Romain Trachel: https://fr.linkedin.com/in/trachelr .. _Roman Goj: https://romanmne.blogspot.co.uk -.. _Ross Maddox: https://www.urmc.rochester.edu/labs/maddox-lab.aspx +.. _Ross Maddox: https://medicine.umich.edu/dept/khri/ross-maddox-phd .. _Rotem Falach: https://github.com/Falach .. _Roy Eric Wieske: https://github.com/Randomidous .. _Sammi Chekroud: https://github.com/schekroud diff --git a/doc/conf.py b/doc/conf.py index f1b771571d6..eed98f49467 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -644,6 +644,7 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines): linkcheck_ignore = [ # will be compiled to regex # 403 Client Error: Forbidden "https://doi.org/10.1002/", # onlinelibrary.wiley.com/doi/10.1002/hbm + "https://doi.org/10.1016/", # neuroimage "https://doi.org/10.1021/", # pubs.acs.org/doi/abs "https://doi.org/10.1073/", # pnas.org "https://doi.org/10.1093/", # academic.oup.com/sleep/ @@ -667,7 +668,7 @@ 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/optipng-0.7.8-win64.zip?download", + "http://prdownloads.sourceforge.net/optipng", "https://sourceforge.net/projects/aespa/files/", "https://sourceforge.net/projects/ezwinports/files/", "https://www.mathworks.com/products/compiler/matlab-runtime.html", diff --git a/examples/io/read_xdf.py b/examples/io/read_xdf.py index 8ed69a3289b..4296167d493 100644 --- a/examples/io/read_xdf.py +++ b/examples/io/read_xdf.py @@ -8,7 +8,7 @@ Here we read some sample XDF data. Although we do not analyze it here, this recording is of a short parallel auditory response (pABR) experiment :footcite:`PolonenkoMaddox2019` and was provided by the `Maddox Lab -`__. +`__. """ # Authors: Clemens Brunner # Eric Larson From e16e8860eecddd6e0c990bdb3d27e3321f8e70ed Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Mon, 3 Feb 2025 14:30:10 -0500 Subject: [PATCH 4/7] FIX: What [circle linkcheck] --- examples/io/read_xdf.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/examples/io/read_xdf.py b/examples/io/read_xdf.py index 4296167d493..5457785f6ae 100644 --- a/examples/io/read_xdf.py +++ b/examples/io/read_xdf.py @@ -7,8 +7,7 @@ Here we read some sample XDF data. Although we do not analyze it here, this recording is of a short parallel auditory response (pABR) experiment -:footcite:`PolonenkoMaddox2019` and was provided by the `Maddox Lab -`__. +:footcite:`PolonenkoMaddox2019` and was provided by the `Maddox Lab `_. """ # Authors: Clemens Brunner # Eric Larson From 3b02eac82900a7915017b0ccbe6bb717e33189ae Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Mon, 3 Feb 2025 14:54:37 -0500 Subject: [PATCH 5/7] FIX: Link [circle linkcheck] --- doc/conf.py | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/conf.py b/doc/conf.py index eed98f49467..94916ade412 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -672,6 +672,7 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines): "https://sourceforge.net/projects/aespa/files/", "https://sourceforge.net/projects/ezwinports/files/", "https://www.mathworks.com/products/compiler/matlab-runtime.html", + "https://medicine.umich.edu/dept/khri/ross-maddox-phd", # 500 server error "https://openwetware.org/wiki/Beauchamp:FreeSurfer", # 503 Server error From 0b9bd3d83ba14031c6cea63bff8340a487d1ce29 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Mon, 3 Feb 2025 15:33:19 -0500 Subject: [PATCH 6/7] FIX: Linkin [circle linkcheck] --- examples/io/read_xdf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/io/read_xdf.py b/examples/io/read_xdf.py index 5457785f6ae..ee8524702a5 100644 --- a/examples/io/read_xdf.py +++ b/examples/io/read_xdf.py @@ -7,7 +7,7 @@ Here we read some sample XDF data. Although we do not analyze it here, this recording is of a short parallel auditory response (pABR) experiment -:footcite:`PolonenkoMaddox2019` and was provided by the `Maddox Lab `_. +:footcite:`PolonenkoMaddox2019` and was provided by the `Maddox Lab `_. """ # Authors: Clemens Brunner # Eric Larson From f28edb04c0ea225bb6fb9495cccb71d3251225aa Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Mon, 3 Feb 2025 15:57:41 -0500 Subject: [PATCH 7/7] FIX: One more [circle linkcheck] --- doc/conf.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/conf.py b/doc/conf.py index 94916ade412..a6c9579c133 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -696,6 +696,8 @@ 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", + # Not rendered by linkcheck builder + r"ides\.html", ] linkcheck_anchors = False # saves a bit of time linkcheck_timeout = 15 # some can be quite slow