From 14938b9657b255a38aa96482a4aaf410e8865859 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 18 Dec 2024 19:34:52 +0000 Subject: [PATCH] MAINT: Update code credit [circle deploy] (#13038) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Eric Larson Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- azure-pipelines.yml | 3 +- doc/sphinxext/prs/13031.json | 35 ++++++++++++++++++ doc/sphinxext/prs/13032.json | 15 ++++++++ doc/sphinxext/prs/13035.json | 51 ++++++++++++++++++++++++++ doc/sphinxext/prs/13036.json | 27 ++++++++++++++ environment.yml | 2 +- mne/conftest.py | 4 +- tools/azure_dependencies.sh | 2 +- tools/circleci_dependencies.sh | 1 - tools/hooks/update_environment_file.py | 3 -- tutorials/time-freq/50_ssvep.py | 2 +- 11 files changed, 135 insertions(+), 10 deletions(-) create mode 100644 doc/sphinxext/prs/13031.json create mode 100644 doc/sphinxext/prs/13032.json create mode 100644 doc/sphinxext/prs/13035.json create mode 100644 doc/sphinxext/prs/13036.json diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 40e214102e1..3ca4177174f 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -171,8 +171,7 @@ stages: python -m pip install --progress-bar off --upgrade pip python -m pip install --progress-bar off --upgrade --pre --only-binary=\"numpy,scipy,matplotlib,vtk\" numpy scipy matplotlib vtk python -c "import vtk" - # Bug on 2.5.13 https://github.com/openmeeg/openmeeg/issues/700 - python -m pip install --progress-bar off --upgrade -ve .[full,test_extra] "openmeeg==2.5.12" + python -m pip install --progress-bar off --upgrade -ve .[full,test_extra] displayName: 'Install dependencies with pip' - bash: | set -e diff --git a/doc/sphinxext/prs/13031.json b/doc/sphinxext/prs/13031.json new file mode 100644 index 00000000000..428346e1b90 --- /dev/null +++ b/doc/sphinxext/prs/13031.json @@ -0,0 +1,35 @@ +{ + "merge_commit_sha": "5b06ca4bb8f9138bf4af85ea3171d95df07462c5", + "authors": [ + { + "n": "github-actions[bot]", + "e": "41898282+github-actions[bot]@users.noreply.github.com" + }, + { + "n": "Eric Larson", + "e": "larson.eric.d@gmail.com" + } + ], + "changes": { + ".github/workflows/credit.yml": { + "a": 2, + "d": 2 + }, + "doc/documentation/cited.rst": { + "a": 3, + "d": 3 + }, + "doc/sphinxext/prs/13029.json": { + "a": 91, + "d": 0 + }, + "doc/sphinxext/prs/6915.json": { + "a": 43, + "d": 0 + }, + "tools/dev/update_credit_json.py": { + "a": 3, + "d": 1 + } + } +} \ No newline at end of file diff --git a/doc/sphinxext/prs/13032.json b/doc/sphinxext/prs/13032.json new file mode 100644 index 00000000000..041aa7dfe1b --- /dev/null +++ b/doc/sphinxext/prs/13032.json @@ -0,0 +1,15 @@ +{ + "merge_commit_sha": "b38385ef90d0fd8214d54b15c5fd91333c3bc032", + "authors": [ + { + "n": "pre-commit-ci[bot]", + "e": "66853113+pre-commit-ci[bot]@users.noreply.github.com" + } + ], + "changes": { + ".pre-commit-config.yaml": { + "a": 2, + "d": 2 + } + } +} \ No newline at end of file diff --git a/doc/sphinxext/prs/13035.json b/doc/sphinxext/prs/13035.json new file mode 100644 index 00000000000..e9cf38b09c9 --- /dev/null +++ b/doc/sphinxext/prs/13035.json @@ -0,0 +1,51 @@ +{ + "merge_commit_sha": "dcd26258c5fd83fd3974d73ba2b1e2773c33bc3d", + "authors": [ + { + "n": "Mathieu Scheltienne", + "e": "mathieu.scheltienne@gmail.com" + }, + { + "n": "Eric Larson", + "e": "larson.eric.d@gmail.com" + } + ], + "changes": { + "environment.yml": { + "a": 1, + "d": 1 + }, + "mne/io/ant/ant.py": { + "a": 14, + "d": 12 + }, + "mne/io/ant/tests/test_ant.py": { + "a": 1, + "d": 1 + }, + "mne/preprocessing/tests/test_fine_cal.py": { + "a": 1, + "d": 1 + }, + "mne/utils/check.py": { + "a": 23, + "d": 24 + }, + "mne/utils/tests/test_check.py": { + "a": 7, + "d": 0 + }, + "pyproject.toml": { + "a": 1, + "d": 1 + }, + "tools/circleci_dependencies.sh": { + "a": 1, + "d": 6 + }, + "tutorials/intro/70_report.py": { + "a": 4, + "d": 5 + } + } +} \ No newline at end of file diff --git a/doc/sphinxext/prs/13036.json b/doc/sphinxext/prs/13036.json new file mode 100644 index 00000000000..6ce98904756 --- /dev/null +++ b/doc/sphinxext/prs/13036.json @@ -0,0 +1,27 @@ +{ + "merge_commit_sha": "41dbdd55eaff77314440ebc8700e0e58b1183113", + "authors": [ + { + "n": "Daniel McCloy", + "e": null + }, + { + "n": "autofix-ci[bot]", + "e": "114827586+autofix-ci[bot]@users.noreply.github.com" + } + ], + "changes": { + "doc/changes/devel/13036.bugfix.rst": { + "a": 1, + "d": 0 + }, + "mne/time_frequency/tests/test_spectrum.py": { + "a": 26, + "d": 0 + }, + "mne/viz/utils.py": { + "a": 3, + "d": 1 + } + } +} \ No newline at end of file diff --git a/environment.yml b/environment.yml index d3373f092eb..898132bc0a4 100644 --- a/environment.yml +++ b/environment.yml @@ -30,7 +30,7 @@ dependencies: - nilearn - numba - numpy >=1.23,<3 - - openmeeg =2.5.12=*_1 + - openmeeg >=2.5.5 - packaging - pandas - pillow diff --git a/mne/conftest.py b/mne/conftest.py index 5d3e033e095..d18b440dc9c 100644 --- a/mne/conftest.py +++ b/mne/conftest.py @@ -119,7 +119,7 @@ def pytest_configure(config): # we should remove them from here. # - This list should also be considered alongside reset_warnings in # doc/conf.py. - if os.getenv("MNE_IGNORE_WARNINGS_IN_TESTS", "") != "true": + if os.getenv("MNE_IGNORE_WARNINGS_IN_TESTS", "") not in ("true", "1"): first_kind = "error" else: first_kind = "always" @@ -180,6 +180,8 @@ def pytest_configure(config): ignore:The 'copy' argument in Quantity is deprecated.*: # debugpy uses deprecated matplotlib API ignore:The (non_)?interactive_bk attribute was deprecated.*: + # SWIG (via OpenMEEG) + ignore:.*builtin type swigvarlink has no.*:DeprecationWarning """ # noqa: E501 for warning_line in warning_lines.split("\n"): warning_line = warning_line.strip() diff --git a/tools/azure_dependencies.sh b/tools/azure_dependencies.sh index 17b5381d72f..56ec04b490d 100755 --- a/tools/azure_dependencies.sh +++ b/tools/azure_dependencies.sh @@ -5,7 +5,7 @@ SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd ) STD_ARGS="--progress-bar off --upgrade" python -m pip install $STD_ARGS pip setuptools wheel if [ "${TEST_MODE}" == "pip" ]; then - python -m pip install $STD_ARGS --only-binary="numba,llvmlite,numpy,scipy,vtk,dipy,openmeeg" -e .[test,full] "openmeeg==2.5.12" + python -m pip install $STD_ARGS --only-binary="numba,llvmlite,numpy,scipy,vtk,dipy,openmeeg" -e .[test,full] elif [ "${TEST_MODE}" == "pip-pre" ]; then ${SCRIPT_DIR}/install_pre_requirements.sh python -m pip install $STD_ARGS --pre -e .[test_extra] diff --git a/tools/circleci_dependencies.sh b/tools/circleci_dependencies.sh index 3f79ea750df..2ecc9718ab2 100755 --- a/tools/circleci_dependencies.sh +++ b/tools/circleci_dependencies.sh @@ -8,7 +8,6 @@ python -m pip install --upgrade --progress-bar off \ "git+https://github.com/sphinx-gallery/sphinx-gallery.git" \ "git+https://github.com/mne-tools/mne-bids.git" \ \ - "openmeeg<2.5.13" \ alphaCSC autoreject bycycle conpy emd fooof meggie \ mne-ari mne-bids-pipeline mne-faster mne-features \ mne-icalabel mne-lsl mne-microstates mne-nirs mne-rsa \ diff --git a/tools/hooks/update_environment_file.py b/tools/hooks/update_environment_file.py index bfedca39d1a..78df3eb5f9c 100755 --- a/tools/hooks/update_environment_file.py +++ b/tools/hooks/update_environment_file.py @@ -56,9 +56,6 @@ def split_dep(dep): # `environment.yaml` breaks the solver if package_name == "PySide6": version_spec = version_spec.replace("!=6.7.0,", "") - # openmeeg 2.5.12=*_2 is broken, so pin to 2.5.12=*_1 - if package_name == "openmeeg": - version_spec = "=2.5.12=*_1" # rstrip output line in case `version_spec` == "" line = f" - {package_name} {version_spec}".rstrip() # use pip for packages needing e.g. `platform_system` or `python_version` triaging diff --git a/tutorials/time-freq/50_ssvep.py b/tutorials/time-freq/50_ssvep.py index a0d130f1d35..a625a001d9e 100644 --- a/tutorials/time-freq/50_ssvep.py +++ b/tutorials/time-freq/50_ssvep.py @@ -641,7 +641,7 @@ def snr_spectrum(psd, noise_n_neighbor_freqs=1, noise_skip_neighbor_freqs=1): ].mean(axis=1) fig, ax = plt.subplots(1) -ax.boxplot(window_snrs, tick_labels=window_lengths, vert=True) +ax.boxplot(window_snrs, tick_labels=window_lengths, orientation="vertical") ax.set( title="Effect of trial duration on 12 Hz SNR", ylabel="Average SNR",