From 8a3ee08eaf38b5e539ff1369c6db10c7121fb9f5 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 21 Jan 2025 13:40:25 -0500 Subject: [PATCH 1/7] MAINT: Add Numba to 3.13 test --- tools/github_actions_dependencies.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index cebd2caefa7..d47d9070f8b 100755 --- a/tools/github_actions_dependencies.sh +++ b/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 pandas h5io mffpy defusedxml" + INSTALL_ARGS="nibabel scikit-learn numpydoc PySide6 mne-qt-browser pandas h5io mffpy defusedxml numba" INSTALL_KIND="test" else test "${MNE_CI_KIND}" == "pip-pre" From 1f5619acf1c472854f2c31c8f0d030aa6da5a488 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 21 Jan 2025 13:55:36 -0500 Subject: [PATCH 2/7] FIX: Ref --- mne/export/_export.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/mne/export/_export.py b/mne/export/_export.py index 835eb9f8513..5626c6aae2b 100644 --- a/mne/export/_export.py +++ b/mne/export/_export.py @@ -27,9 +27,10 @@ def export_raw( .. warning:: When exporting ``Raw`` with annotations, ``raw.info["meas_date"]`` must be the same as ``raw.annotations.orig_time``. This guarantees that the annotations are - in the same reference frame as the samples. - When `Raw.first_time` is not zero (e.g., after cropping), the onsets are - automatically corrected so that onsets are always relative to the first sample. + in the same reference frame as the samples. When + :property:`Raw.first_time ` is not zero (e.g., after + cropping), the onsets are automatically corrected so that onsets are always + relative to the first sample. Parameters ---------- From a6229b6e248f05bed86e1334d18f3f6464b78976 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 21 Jan 2025 14:16:00 -0500 Subject: [PATCH 3/7] FIX: More --- doc/changes/devel/12656.bugfix.rst | 2 +- mne/export/_export.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/changes/devel/12656.bugfix.rst b/doc/changes/devel/12656.bugfix.rst index b3a0c62539a..3f32dbd23e5 100644 --- a/doc/changes/devel/12656.bugfix.rst +++ b/doc/changes/devel/12656.bugfix.rst @@ -1 +1 @@ -Fix bug where :func:`mne.export.export_raw` does not correct for recording start time (`raw.first_time`) when exporting Raw instances to EDF or EEGLAB formats, by `Qian Chu`_. \ No newline at end of file +Fix bug where :func:`mne.export.export_raw` does not correct for recording start time (:attr:`raw.first_time `) when exporting Raw instances to EDF or EEGLAB formats, by `Qian Chu`_. \ No newline at end of file diff --git a/mne/export/_export.py b/mne/export/_export.py index 5626c6aae2b..7e2057562c7 100644 --- a/mne/export/_export.py +++ b/mne/export/_export.py @@ -28,7 +28,7 @@ def export_raw( When exporting ``Raw`` with annotations, ``raw.info["meas_date"]`` must be the same as ``raw.annotations.orig_time``. This guarantees that the annotations are in the same reference frame as the samples. When - :property:`Raw.first_time ` is not zero (e.g., after + :attr:`Raw.first_time ` is not zero (e.g., after cropping), the onsets are automatically corrected so that onsets are always relative to the first sample. From 5e7650bfe94ace3a1b45f8538b52731c17bad78d Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 21 Jan 2025 14:17:10 -0500 Subject: [PATCH 4/7] FIX: Better --- mne/utils/docs.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/mne/utils/docs.py b/mne/utils/docs.py index 683704c4bc6..694ec848a94 100644 --- a/mne/utils/docs.py +++ b/mne/utils/docs.py @@ -1504,9 +1504,10 @@ def _reflow_param_docstring(docstring, has_first_line=True, width=75): docdict["export_fmt_support_raw"] = """\ Supported formats: - - BrainVision (``.vhdr``, ``.vmrk``, ``.eeg``, uses `pybv `_) - - EEGLAB (``.set``, uses :mod:`eeglabio`) - - EDF (``.edf``, uses `edfio `_) + +- BrainVision (``.vhdr``, ``.vmrk``, ``.eeg``, uses `pybv `_) +- EEGLAB (``.set``, uses :mod:`eeglabio`) +- EDF (``.edf``, uses `edfio `_) """ # noqa: E501 docdict["export_warning"] = """\ From 45057188837944210c4141f55c2e38d759e03347 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 21 Jan 2025 14:33:34 -0500 Subject: [PATCH 5/7] FIX: Maybe --- mne/export/_export.py | 1 + 1 file changed, 1 insertion(+) diff --git a/mne/export/_export.py b/mne/export/_export.py index 7e2057562c7..4b93fda917e 100644 --- a/mne/export/_export.py +++ b/mne/export/_export.py @@ -22,6 +22,7 @@ def export_raw( """Export Raw to external formats. %(export_fmt_support_raw)s + %(export_warning)s .. warning:: From 2778b5956f684cbdc934ef6e10920e6adc3028ae Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 21 Jan 2025 14:50:08 -0500 Subject: [PATCH 6/7] FIX: More --- mne/utils/docs.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/mne/utils/docs.py b/mne/utils/docs.py index 694ec848a94..54cc6845e58 100644 --- a/mne/utils/docs.py +++ b/mne/utils/docs.py @@ -1494,12 +1494,14 @@ def _reflow_param_docstring(docstring, has_first_line=True, width=75): docdict["export_fmt_support_epochs"] = """\ Supported formats: - - EEGLAB (``.set``, uses :mod:`eeglabio`) + +- EEGLAB (``.set``, uses :mod:`eeglabio`) """ docdict["export_fmt_support_evoked"] = """\ Supported formats: - - MFF (``.mff``, uses :func:`mne.export.export_evokeds_mff`) + +- MFF (``.mff``, uses :func:`mne.export.export_evokeds_mff`) """ docdict["export_fmt_support_raw"] = """\ From 571dc35bf4f663f583e722adbdd9e2fc015d5f46 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 21 Jan 2025 16:07:36 -0500 Subject: [PATCH 7/7] FIX: More --- mne/forward/tests/test_make_forward.py | 2 +- mne/preprocessing/tests/test_fine_cal.py | 2 +- tools/github_actions_env_vars.sh | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/mne/forward/tests/test_make_forward.py b/mne/forward/tests/test_make_forward.py index 37ec6e041b5..a357c5779c9 100644 --- a/mne/forward/tests/test_make_forward.py +++ b/mne/forward/tests/test_make_forward.py @@ -482,7 +482,7 @@ def test_make_forward_solution_openmeeg(n_layers): eeg_atol=100, meg_corr_tol=0.98, eeg_corr_tol=0.98, - meg_rdm_tol=0.1, + meg_rdm_tol=0.11, eeg_rdm_tol=0.2, ) diff --git a/mne/preprocessing/tests/test_fine_cal.py b/mne/preprocessing/tests/test_fine_cal.py index 45971620db5..8b45208e848 100644 --- a/mne/preprocessing/tests/test_fine_cal.py +++ b/mne/preprocessing/tests/test_fine_cal.py @@ -231,7 +231,7 @@ def test_fine_cal_systems(system, tmp_path): err_limit = 6000 n_ref = 28 corrs = (0.19, 0.41, 0.49) - sfs = [0.5, 0.7, 0.9, 1.5] + sfs = [0.5, 0.7, 0.9, 1.55] corr_tol = 0.55 elif system == "fil": raw = read_raw_fil(fil_fname, verbose="error") diff --git a/tools/github_actions_env_vars.sh b/tools/github_actions_env_vars.sh index 8accf72a11a..9f424ae5f48 100755 --- a/tools/github_actions_env_vars.sh +++ b/tools/github_actions_env_vars.sh @@ -28,7 +28,7 @@ else # conda-like echo "MNE_LOGGING_LEVEL=warning" | tee -a $GITHUB_ENV echo "MNE_QT_BACKEND=PySide6" | tee -a $GITHUB_ENV # TODO: Also need "|unreliable on GitHub Actions conda" on macOS, but omit for now to make sure the failure actually shows up - echo "MNE_TEST_ALLOW_SKIP=.*(Requires (spm|brainstorm) dataset|CUDA not|PySide6 causes segfaults).*" | tee -a $GITHUB_ENV + echo "MNE_TEST_ALLOW_SKIP=.*(Requires (spm|brainstorm) dataset|CUDA not|PySide6 causes segfaults|Accelerate|Flakey verbose behavior).*" | tee -a $GITHUB_ENV fi fi set +x