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.github/workflows/autofix.yml

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@@ -21,4 +21,4 @@ jobs:
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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@7a166d7532b277f34e16238930461bf77f9d7ed8
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- uses: autofix-ci/action@c5b2d67aa2274e7b5a18224e8171550871fc7e4a

.github/workflows/codeql-analysis.yml

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@@ -44,7 +44,7 @@ jobs:
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# Initializes the CodeQL tools for scanning.
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- name: Initialize CodeQL
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uses: github/codeql-action/init@v4
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uses: github/codeql-action/init@v4.35.2
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with:
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languages: ${{ matrix.language }}
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# If you wish to specify custom queries, you can do so here or in a config file.
@@ -58,7 +58,7 @@ jobs:
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# Autobuild attempts to build any compiled languages (C/C++, C#, or Java).
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# If this step fails, then you should remove it and run the build manually (see below)
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- name: Autobuild
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uses: github/codeql-action/autobuild@v4
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uses: github/codeql-action/autobuild@v4.35.2
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# ℹ️ Command-line programs to run using the OS shell.
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# 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
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# ./location_of_script_within_repo/buildscript.sh
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- name: Perform CodeQL Analysis
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uses: github/codeql-action/analyze@v4
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uses: github/codeql-action/analyze@v4.35.2

.github/workflows/release.yml

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@@ -28,7 +28,7 @@ jobs:
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pip install build twine
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- run: python -m build --sdist --wheel
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- run: twine check --strict dist/*
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- uses: actions/upload-artifact@v6
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- uses: actions/upload-artifact@v7
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with:
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name: dist
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path: dist
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name: pypi
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url: https://pypi.org/p/mne
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steps:
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- uses: actions/download-artifact@v7
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- uses: actions/download-artifact@v8
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with:
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name: dist
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path: dist

.github/workflows/spec_zero.yml

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@@ -41,13 +41,17 @@ jobs:
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timeout-minutes: 10
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with:
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detached: true
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- uses: astral-sh/setup-uv@v7
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- uses: astral-sh/setup-uv@v8.1.0
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with:
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version: ">=0.9"
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activate-environment: true
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python-version: 3.12
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- run: uv pip install packaging requests tomlkit
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- run: python ./tools/dev/spec_zero_update_versions.py
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- name: Install dependencies
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run: uv pip install -e . packaging requests tomlkit
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- name: Update tracked dependencies
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run: python ./tools/dev/spec_zero_update_versions.py
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- name: Sync updated dependencies to README
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run: python tools/sync_dependencies.py
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- name: Create lockfile for old CI
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# uv pip compile requires setting the python version explicitly in the command :(
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run: |
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git config --global user.email "50266005+mne-bot@users.noreply.github.com"
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git config --global user.name "mne[bot]"
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git checkout -b spec_zero
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git add doc/changes/dev/dependency.rst # one new file, others changed
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if [ -f doc/changes/dev/dependency.rst ]; then
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git add doc/changes/dev/dependency.rst # one new file, others changed
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fi
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git commit -am "mne[bot]: Update dependency specifiers"
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git push origin spec_zero
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PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *It is very likely that \`tools/environment_old.yml\` needs to be updated.* <br> <br> *Adjustments may need to be made to shims in \`mne/fixes.py\` and elswhere in this or another PR. \`git grep TODO VERSION\` is a good starting point for finding potential updates.*")
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PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to shims in \`mne/fixes.py\` and elswhere in this or another PR. \`make -C tools/dev dep\` is a good starting point for finding potential updates.*")
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echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
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if: steps.status.outputs.dirty == 'true'

.github/workflows/tests.yml

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fi
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fi
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if: matrix.kind == 'conda' || matrix.kind == 'mamba'
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- uses: mamba-org/setup-micromamba@v2
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- uses: mamba-org/setup-micromamba@v3
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with:
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environment-file: ${{ env.CONDA_ENV }}
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environment-name: mne
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if: matrix.kind == 'conda' || matrix.kind == 'mamba'
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timeout-minutes: 20
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# Python (if old)
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- uses: astral-sh/setup-uv@v7
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- uses: astral-sh/setup-uv@v8.1.0
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with:
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version: ">=0.9"
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activate-environment: true
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path: ~/mne_data
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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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- uses: codecov/codecov-action@v5
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- uses: codecov/codecov-action@v6
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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if: success() || failure()

.github/zizmor.yml

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@@ -3,3 +3,5 @@ rules:
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config:
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policies:
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"*": ref-pin
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secrets-outside-env:
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disable: true # TODO: Someday we should use envs for these

.mailmap

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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>
3+
Akhilesh S. Yadav <126486217+YadavAkhileshh@users.noreply.github.com> Akhilesh <126486217+YadavAkhileshh@users.noreply.github.com>
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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>
@@ -48,6 +49,7 @@ Christian Brodbeck <christianmbrodbeck@gmail.com> christianmbrodbeck <christianm
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Christian Mista <cmista@ingenieria.uner.edu.ar> cmista <79416030+cmista@users.noreply.github.com>
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Christina Zhao <zhaotc@uw.edu> ChristinaZhao <zhaotc@uw.edu>
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Christoph Dinh <chdinh@nmr.mgh.harvard.edu> Christoph Dinh <christoph.dinh@tu-ilmenau.de>
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Christoph Huber-Huber <christoph@huber-huber.at> CHH <christoph@huber-huber.at>
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Christopher J. Bailey <bailey.cj@gmail.com> Chris Bailey <bailey.cj@gmail.com>
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Claire Braboszcz <claire@guakamole.org> claire-braboszcz <claire@guakamole.org>
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Clemens Brunner <clemens.brunner@gmail.com>
@@ -108,6 +110,7 @@ Evgenii Kalenkovich <e.kalenkovich@gmail.com> kalenkovich <e.kalenkovich@gmail.c
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Evgeny Goldstein <84768107+evgenygoldstein@users.noreply.github.com> evgenygoldstein <84768107+evgenygoldstein@users.noreply.github.com>
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Ezequiel Mikulan <e.mikulan@gmail.com> ezemikulan <39155887+ezemikulan@users.noreply.github.com>
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Fahimeh Mamashli <33672431+fmamashli@users.noreply.github.com> fmamashli <33672431+fmamashli@users.noreply.github.com>
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Famous Raj Bhat <famousrajbhatt@gmail.com> Horizon_Architect_07 <famousrajbhatt@gmail.com>
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Fede Raimondo <federaimondo@gmail.com> Fede <slashack@gmail.com>
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Fede Raimondo <federaimondo@gmail.com> Fede Raimondo <federaimondo@gmail.com>
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Fede Raimondo <federaimondo@gmail.com> Fede Raimondo <fraimondo@dc.uba.ar>
@@ -130,6 +133,7 @@ Guillaume Dumas <deep@introspection.eu> deep-introspection <deep@introspection.e
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Guillaume Dumas <deep@introspection.eu> Guillaume Dumas <deep-introspection@users.noreply.github.com>
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Hakimeh Aslsardroud <hakimeh.aslsardroud@localhost>
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Hamid Maymandi <46011104+HamidMandi@users.noreply.github.com> Hamid <46011104+HamidMandi@users.noreply.github.com>
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Hansuja Budhiraja <hansujaigdtuwcseai@gmail.com> Hansuja <hansujaigdtuwcseai@gmail.com>
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Hasrat Ali Arzoo <hasrat407@gmail.com> hasrat17 <56307533+hasrat17@users.noreply.github.com>
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Hongjiang Ye <rubyyhj@gmail.com> YE Hongjiang <hongjiang.ye@outlook.com>
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Hongjiang Ye <rubyyhj@gmail.com> YE Hongjiang <rubyyhj@gmail.com>
@@ -247,6 +251,7 @@ Matti Hämäläinen <msh@nmr.mgh.harvard.edu> Matti Hämäläinen <msh@parsley.n
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Matti Hämäläinen <msh@nmr.mgh.harvard.edu> mshamalainen <msh@nmr.mgh.harvard.edu>
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Matti Toivonen <105695400+mattitoi@users.noreply.github.com> mattitoi <105695400+mattitoi@users.noreply.github.com>
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Maureen Shader <55732126+mshader@users.noreply.github.com> mshader <55732126+mshader@users.noreply.github.com>
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Melih Yayli <51379391+yaylim@users.noreply.github.com> yaylim <51379391+yaylim@users.noreply.github.com>
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Melih Yayli <melihyayli@hotmail.com>
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Michiru Kaneda <rcmdnk@gmail.com> rcmdnk <rcmdnk@gmail.com>
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Mikołaj Magnuski <mmagnuski@swps.edu.pl> Mikolaj Magnuski <mmagnuski@swps.edu.pl>
@@ -336,6 +341,7 @@ Simon Kern <simon.kern@online.de> skjerns <14980558+skjerns@users.noreply.github
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Simon Kern <simon.kern@online.de> skjerns <simon.kern@online.de>
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Sondre Foslien <sondre.foslien@gmail.com> sondrfos <sondre.foslien@gmail.com>
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Sophie Herbst <ksherbst@gmail.com>
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Srivarsha Chivukula <varshaa.1616@gmail.com> varshaa-1616 <varshaa.1616@gmail.com>
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Steinn Hauser Magnússon <hausersteinn@gmail.com> Steinn Magnusson <s.magnusson@senec.com>
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Steve Matindi <stevematindi@gmail.com> stevemats <stevematindi@gmail.com>
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Steven Bierer <neurolaunch@gmail.copm> Steven Bierer <40672003+NeuroLaunch@users.noreply.github.com>
@@ -364,7 +370,6 @@ Tziona NessAiver <tzionan@mail.tau.ac.il> TzionaN <tzionan@mail.tau.ac.il>
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user27182 <89109579+user27182@users.noreply.github.com>
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Valerii Chirkov <vagechirkov@gmail.com> Valerii <42982039+vagechirkov@users.noreply.github.com>
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Valerii Chirkov <vagechirkov@gmail.com> Valerii <vagechirkov@gmail.com>
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varshaa-1616 <varshaa.1616@gmail.com>
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Velu Prabhakar Kumaravel <veluprabhakarkumaravel@Velus-MBP.lan> Velu Prabhakar Kumaravel <veluprabhakarkumaravel@Velus-MBP.lan>
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Victoria Peterson <victoriapeterson09@gmail.com> vpeterson <victoriapeterson09@gmail.com>
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Wei Xu <weixu@mail.bnu.edu.cn> Wei <weixu@mail.bnu.edu.cn>

.pre-commit-config.yaml

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repos:
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# Ruff mne
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.15.4
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rev: v0.15.11
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hooks:
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- id: ruff-check
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name: ruff lint mne
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# Codespell
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- repo: https://github.com/codespell-project/codespell
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rev: v2.4.1
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rev: v2.4.2
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hooks:
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- id: codespell
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additional_dependencies:
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rev: v6.0.0
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hooks:
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- id: file-contents-sorter
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files: ^doc/changes/names.inc|^.mailmap|^doc/sphinxext/related_software.txt
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files: ^doc/changes/names.inc|^.mailmap|^doc/sphinxext/related_software.txt|^ignore_words.txt
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args: ["--ignore-case"]
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- repo: https://github.com/pappasam/toml-sort
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rev: v0.24.3
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rev: v0.24.4
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hooks:
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- id: toml-sort-fix
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files: pyproject.toml
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language: python
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entry: ./tools/hooks/update_environment_file.py
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files: '^(pyproject.toml|tools/hooks/update_environment_file.py)$'
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- repo: local
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hooks:
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- id: dependency-sync
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name: Copy core dependencies from pyproject.toml to README.rst
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language: python
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entry: ./tools/hooks/sync_dependencies.py
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files: '^(pyproject.toml|tools/hooks/sync_dependencies.py)$'
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additional_dependencies: ["mne==1.11.0"]
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# zizmor
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- repo: https://github.com/woodruffw/zizmor-pre-commit
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rev: v1.22.0
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rev: v1.24.1
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hooks:
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- id: zizmor
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args: [--fix]
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# We correctly use pull_request_trigger, and need Zizmor 2.0+ to configure the ignore
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exclude: ^.github/workflows/automerge.yml
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# these should *not* be run on CIs:
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ci:
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skip: [dependency-sync] # needs MNE to work, which exceeds the free tier space alloc.
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# The following are too slow to run on local commits, so let's only run on CIs:
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#
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# - repo: https://github.com/pre-commit/mirrors-mypy

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