10000 Merge remote-tracking branch 'upstream/main' into cola5 · larsoner/mne-python@46c193d · GitHub
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Merge remote-tracking branch 'upstream/main' into cola5
* upstream/main: (57 commits) Allow lasso selection sensors in a plot_evoked_topo (mne-tools#12071) MAINT: Fix doc build (mne-tools#13076) BUG: Improve sklearn compliance (mne-tools#13065) [pre-commit.ci] pre-commit autoupdate (mne-tools#13073) MAINT: Add Numba to 3.13 test (mne-tools#13075) Bump autofix-ci/action from ff86a557419858bb967097bfc916833f5647fa8c to 551dded8c6cc8a1054039c8bc0b8b48c51dfc6ef in the actions group (mne-tools#13071) [BUG] Correct annotation onset for exportation to EDF and EEGLAB (mne-tools#12656) New feature for removing heart artifacts from EEG or ESG data using a Principal Component Analysis - Optimal Basis Sets (PCA-OBS) algorithm (mne-tools#13037) [BUG] Fix taper weighting in computation of TFR multitaper power (mne-tools#13067) [FIX] Reading an EDF with preload=False and mixed frequency (mne-tools#13069) Fix evoked topomap colorbars, closes mne-tools#13050 (mne-tools#13063) [pre-commit.ci] pre-commit autoupdate (mne-tools#13060) BUG: Fix bug with interval calculation (mne-tools#13062) [DOC] extend documentation for add_channels (mne-tools#13051) Add `combine_tfr` to API (mne-tools#13054) Add `combine_spectrum()` function and allow `grand_average()` to support `Spectrum` data (mne-tools#13058) BUG: Fix bug with helium anon (mne-tools#13056) [ENH] Add option to store and return TFR taper weights (mne-tools#12910) BUG: viz plot window's 'title' argument showed no effect. (mne-tools#12828) MAINT: Ensure limited set of tests are skipped (mne-tools#13053) ...
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‎.circleci/config.yml

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- restore_cache:
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keys:
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- data-cache-phantom-kit
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- restore_cache:
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keys:
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- data-cache-ds004388
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- run:
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name: Get data
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# This limit could be increased, but this is helpful for finding slow ones
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name: Check sphinx log for warnings (which are treated as errors)
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when: always
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command: |
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! grep "^.* WARNING: .*$" sphinx_log.txt
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! grep "^.*\(WARNING\|ERROR\): " sphinx_log.txt
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key: data-cache-phantom-kit
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paths:
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- ~/mne_data/MNE-phantom-KIT-data # (1 G)
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- save_cache:
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key: data-cache-ds004388
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paths:
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- ~/mne_data/ds004388 # (1.8 G)
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‎.github/workflows/autofix.yml

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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persist-credentials: false
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- uses: actions/setup-python@v5
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with:
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python-version: '3.12'
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- run: pip install --upgrade towncrier pygithub gitpython numpy
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- run: python ./.github/actions/rename_towncrier/rename_towncrier.py
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- run: python ./tools/dev/ensure_headers.py
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- uses: autofix-ci/action@ff86a557419858bb967097bfc916833f5647fa8c
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- uses: autofix-ci/action@551dded8c6cc8a1054039c8bc0b8b48c51dfc6ef

‎.github/workflows/automerge.yml

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name: Bot auto-merge
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on: pull_request # yamllint disable-line rule:truthy
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jobs:
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autobot:
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permissions:
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contents: write
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pull-requests: write
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runs-on: ubuntu-latest
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# Names can be found with gh api /repos/mne-tools/mne-python/pulls/12998 -q .user.login for example
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if: (github.event.pull_request.user.login == 'dependabot[bot]' || github.event.pull_request.user.login == 'pre-commit-ci[bot]' || github.event.pull_request.user.login == 'github-actions[bot]') && github.repository == 'mne-tools/mne-python'
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steps:
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- name: Enable auto-merge for bot PRs
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run: gh pr merge --auto --squash "$PR_URL"
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env:
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PR_URL: ${{github.event.pull_request.html_url}}
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GH_TOKEN: ${{secrets.GITHUB_TOKEN}}

‎.github/workflows/check_changelog.yml

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types: [opened, synchronize, labeled, unlabeled]
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contents: read
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‎.github/workflows/circle_artifacts.yml

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on: [status] # yamllint disable-line rule:truthy
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contents: read
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statuses: write
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‎.github/workflows/codeql-analysis.yml

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# Initializes the CodeQL tools for scanning.
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- name: Initialize CodeQL
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# If you wish to specify custom queries, you can do so here or in a config file.
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# By default, queries listed here will override any specified in a config file.
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# Prefix the list here with "+" to use these queries and those in the config file.
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# Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
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# Autobuild attempts to build any compiled languages (C/C++, C#, or Java).
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# ℹ️ Command-line programs to run using the OS shell.
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# If the Autobuild fails above, remove it and uncomment the following three lines.
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# If the Autobuild fails above, remove it and uncomment the following three lines.
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# modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
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‎.github/workflows/credit.yml

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PR_NUM=$(gh pr create --base main --head credit --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }})." --label "no-changelog-entry-needed")
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‎.github/workflows/release.yml

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‎.github/workflows/tests.yml

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kind: pip
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- uses: pyvista/setup-headless-display-action@v3
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wm: false
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sed -i '/numba/d' environment.yml
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sed -i '/dipy/d' environment.yml
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sed -i 's/- mne$/- mne-base/' environment.yml
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- name: Fixes for conda
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run: |
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# For some reason on Linux we get crashes
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if [[ "$RUNNER_OS" == "Linux" ]]; then
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sed -i "/numba/d" environment.yml
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elif [[ "$RUNNER_OS" == "macOS" ]]; then
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sed -i "" "s/ - PySide6 .*/ - PySide6 <6.8/g" environment.yml
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fi
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if: matrix.kind == 'conda' || matrix.kind == 'mamba'
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mamba
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- run: ./tools/github_actions_dependencies.sh
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- run: bash ./tools/github_actions_dependencies.sh
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- run: bash ./tools/get_minimal_commands.sh
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- run: bash ./tools/github_actions_infos.sh
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- run: bash ./tools/github_actions_download.sh
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- run: bash ./tools/github_actions_test.sh # for some reason on macOS we need to run "bash X" in order for a failed test run to show up
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‎.mailmap

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@@ -2,6 +2,7 @@ Adam Li <adam2392@gmail.com> Adam Li <adam2392@Adams-MBP-2.home>
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Adam Li <adam2392@gmail.com> Adam Li <adam2392@new-host-2.home>
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Alan Leggitt <leggitta3@gmail.com> leggitta <leggitta3@gmail.com>
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Alessandro Tonin <alessandro.tonin@wysscenter.ch> Lychfindel <58313635+Lychfindel@users.noreply.github.com>
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Alex Lepauvre <alex.lepauvre@ae.mpg.de> Alex lepauvre <alex.lepauvre@ae.mpg.de>
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Alex Rockhill <aprockhill206@gmail.com> Alex <aprockhill206@gmail.com>
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Alex Rockhill <aprockhill206@gmail.com> Alex <aprockhill@mailbox.org>
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Alex Rockhill <aprockhill206@gmail.com> Alex Rockhill <aprock@uw.edu>
@@ -356,4 +357,4 @@ Yousra Bekhti <yousra.bekhti@gmail.com> Yousra BEKHTI <yousra.bekhti@gmail.com>
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Yousra Bekhti <yousra.bekhti@gmail.com> yousrabk <yousra.bekhti@gmail.com>
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Zhi Zhang <850734033@qq.com> ZHANG Zhi <850734033@qq.com>
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Zhi Zhang <850734033@qq.com> ZHANG Zhi <zhi271.zhang@connect.polyu.hk>
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Ziyi ZENG <ziyizeng@link.cuhk.edu.cn>
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Ziyi ZENG <ziyizeng@link.cuhk.edu.cn> ZIYI ZENG <CME1909120@XMU.EDU.MY>

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