Merge branch 'main' into issue-13767

Author: nordme

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,9 +1,23 @@
 <!--
 
-Thanks for contributing a pull request! Please make sure you have read the
-[contribution guidelines](https://mne.tools/dev/development/contributing.html)
+Thanks for contributing a pull request! Please make sure you have read
+[CONTRIBUTING.md](https://github.com/mne-tools/mne-python/blob/main/CONTRIBUTING.md)
+and the [detailed contribution guidelines](https://mne.tools/dev/development/contributing.html)
 before submitting.
 
+If you used AI to help prepare this pull request, please pay special attention to
+our **Policy on AI Assistance in Contributions** in
+[CONTRIBUTING.md](https://github.com/mne-tools/mne-python/blob/main/CONTRIBUTING.md).
+Here are some examples of what we expect for "tool, manner, and scope" disclosure:
+
+- "I implemented the code changes myself, and Claude Sonnet 4.6 wrote the test."
+- "I prompted Gemini 3.1 Pro to get a first draft implementation, then refined it
+  manually until I was satisfied."
+- "I wrote the code and asked Kimi K2.5 to write the docstring for me."
+- "I fed GPT 5.4 the paper where the algorithm is described, and asked it to implement
+  it for me. Then I had it write an example script using the `sample` dataset, and I
+  wrote the narrative text of the tutorial myself."
+
 Please be aware that we are a loose team of volunteers so patience is
 necessary. Assistance handling other issues is very welcome. We value
 all user contributions, no matter how minor they are. If we are slow to

.github/workflows/autofix.yml

@@ -21,4 +21,4 @@ jobs:
       - run: pip install --upgrade towncrier pygithub gitpython numpy
       - run: python ./.github/actions/rename_towncrier/rename_towncrier.py
       - run: python ./tools/dev/ensure_headers.py
-      - uses: autofix-ci/action@7a166d7532b277f34e16238930461bf77f9d7ed8
+      - uses: autofix-ci/action@c5b2d67aa2274e7b5a18224e8171550871fc7e4a

.github/workflows/codeql-analysis.yml

@@ -44,7 +44,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v4
+      uses: github/codeql-action/init@v4.35.3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -58,7 +58,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v4
+      uses: github/codeql-action/autobuild@v4.35.3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -71,4 +71,4 @@ jobs:
     #   ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v4
+      uses: github/codeql-action/analyze@v4.35.3

.github/workflows/spec_zero.yml

@@ -41,13 +41,17 @@ jobs:
         timeout-minutes: 10
         with:
           detached: true
-      - uses: astral-sh/setup-uv@v7
+      - uses: astral-sh/setup-uv@v8.1.0
         with:
           version: ">=0.9"
           activate-environment: true
           python-version: 3.12
-      - run: uv pip install packaging requests tomlkit
-      - run: python ./tools/dev/spec_zero_update_versions.py
+      - name: Install dependencies
+        run: uv pip install -e . packaging requests tomlkit
+      - name: Update tracked dependencies
+        run: python ./tools/dev/spec_zero_update_versions.py
+      - name: Sync updated dependencies to README
+        run: python tools/sync_dependencies.py
       - name: Create lockfile for old CI
         # uv pip compile requires setting the python version explicitly in the command :(
         run: |
@@ -72,9 +76,11 @@ jobs:
           git config --global user.email "50266005+mne-bot@users.noreply.github.com"
           git config --global user.name "mne[bot]"
           git checkout -b spec_zero
-          git add doc/changes/dev/dependency.rst  # one new file, others changed
+          if [ -f doc/changes/dev/dependency.rst ]; then
+            git add doc/changes/dev/dependency.rst  # one new file, others changed
+          fi
           git commit -am "mne[bot]: Update dependency specifiers"
           git push origin spec_zero
-          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.*")
+          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.*")
           echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
         if: steps.status.outputs.dirty == 'true'

.github/workflows/tests.yml

@@ -30,7 +30,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.13'
+          python-version: '3.14'
       - uses: pre-commit/action@v3.0.1
       - run: pip install mypy numpy scipy vulture
       - run: mypy
@@ -76,15 +76,12 @@ jobs:
           - os: ubuntu-latest
             python: '3.13'
             kind: conda
-          - os: macos-latest  # arm64 (Apple Silicon): Sequoia
-            python: '3.13'
-            kind: mamba
-          - os: macos-15-intel  # intel: Sequoia
+          - os: macos-latest  # arm64
+            python: '3.14'
+            kind: pip
+          - os: macos-15-intel  # Intel
             python: '3.13'
-            kind: mamba
-          - os: windows-latest
-            python: '3.11'
-            kind: mamba
+            kind: pip
           - os: ubuntu-latest
             python: '3.12'
             kind: minimal
@@ -122,47 +119,34 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python }}
-        if: startswith(matrix.kind, 'pip')
+        if: startswith(matrix.kind, 'pip') || matrix.kind == 'minimal'
+        id: setup-python
+      # Workaround macOS path behavior with login shells (which puts system Python first)
+      - run: echo "export PATH=\"$(dirname ${{ steps.setup-python.outputs.python-path }}):$PATH\"" | tee -a ~/.bash_profile  # zizmor: ignore[template-injection]
+        if: startswith(matrix.kind, 'pip') && startswith(matrix.os, 'macos')
       # Python (if conda)
-      - name: Fixes for conda
-        run: |
-          # For some reason on Linux we get crashes
-          if [[ "$RUNNER_OS" == "Linux" ]]; then
-            sed -i "/numba/d" environment.yml
-          fi
-          # And on Windows and macOS PySide6.9.0 segfaults
-          if [[ "$RUNNER_OS" == "macOS" ]]; then
-            sed -i "" "s/  - PySide6 .*/  - PySide6 =6.9.2/g" environment.yml
-            sed -i "" "s/  - vtk .*/  - vtk =9.5.1/g" environment.yml
-
-          else
-            sed -i "s/  - PySide6 .*/  - PySide6 =6.9.2/g" environment.yml
-            sed -i "s/  - vtk .*/  - vtk =9.5.1/g" environment.yml
-            if [[ "$RUNNER_OS" == "Windows" ]]; then
-              echo "MNE_IS_OSMESA=true" | tee -a $GITHUB_ENV
-            fi
-          fi
-        if: matrix.kind == 'conda' || matrix.kind == 'mamba'
-      - uses: mamba-org/setup-micromamba@v2
+      - uses: mamba-org/setup-micromamba@v3
         with:
           environment-file: ${{ env.CONDA_ENV }}
           environment-name: mne
-          log-level: ${{ runner.debug == '1' && 'debug' || 'info' }}
+          log-level: 'info'
           create-args: >-
             python=${{ env.PYTHON_VERSION }}
             -v
-        if: matrix.kind == 'conda' || matrix.kind == 'mamba'
+        if: matrix.kind == 'conda'
         timeout-minutes: 20
       # Python (if old)
-      - uses: astral-sh/setup-uv@v7
+      - uses: astral-sh/setup-uv@v8.1.0
         with:
           version: ">=0.9"
           activate-environment: true
           cache-dependency-glob: |
             **/pylock.ci-old.toml
           python-version: ${{ matrix.python }}
         if: matrix.kind == 'old'
+      - run: bash ./tools/github_actions_verify_python.sh "${{ matrix.python }}"
       - run: bash ./tools/github_actions_dependencies.sh
+        timeout-minutes: 10
       - run: python ./tools/github_actions_check_old_env.py
         if: matrix.kind == 'old'
       # Minimal commands on Linux (macOS stalls)
@@ -182,7 +166,7 @@ jobs:
           path: ~/mne_data
       - run: bash ./tools/github_actions_download.sh
       - 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
-      - uses: codecov/codecov-action@v5
+      - uses: codecov/codecov-action@v6
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
         if: success() || failure()

.mailmap

@@ -1,5 +1,6 @@
 Adam Li <adam2392@gmail.com> Adam Li <adam2392@Adams-MBP-2.home>
 Adam Li <adam2392@gmail.com> Adam Li <adam2392@new-host-2.home>
+Akhilesh S. Yadav <126486217+YadavAkhileshh@users.noreply.github.com> Akhilesh <126486217+YadavAkhileshh@users.noreply.github.com>
 Alan Leggitt <leggitta3@gmail.com> leggitta <leggitta3@gmail.com>
 Alessandro Tonin <alessandro.tonin@wysscenter.ch> Lychfindel <58313635+Lychfindel@users.noreply.github.com>
 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
 Christian Mista <cmista@ingenieria.uner.edu.ar> cmista <79416030+cmista@users.noreply.github.com>
 Christina Zhao <zhaotc@uw.edu> ChristinaZhao <zhaotc@uw.edu>
 Christoph Dinh <chdinh@nmr.mgh.harvard.edu> Christoph Dinh <christoph.dinh@tu-ilmenau.de>
+Christoph Huber-Huber <christoph@huber-huber.at> CHH <christoph@huber-huber.at>
 Christopher J. Bailey <bailey.cj@gmail.com> Chris Bailey <bailey.cj@gmail.com>
 Claire Braboszcz <claire@guakamole.org> claire-braboszcz <claire@guakamole.org>
 Clemens Brunner <clemens.brunner@gmail.com>
@@ -108,6 +110,7 @@ Evgenii Kalenkovich <e.kalenkovich@gmail.com> kalenkovich <e.kalenkovich@gmail.c
 Evgeny Goldstein <84768107+evgenygoldstein@users.noreply.github.com> evgenygoldstein <84768107+evgenygoldstein@users.noreply.github.com>
 Ezequiel Mikulan <e.mikulan@gmail.com> ezemikulan <39155887+ezemikulan@users.noreply.github.com>
 Fahimeh Mamashli <33672431+fmamashli@users.noreply.github.com> fmamashli <33672431+fmamashli@users.noreply.github.com>
+Famous Raj Bhat <famousrajbhatt@gmail.com> Horizon_Architect_07 <famousrajbhatt@gmail.com>
 Fede Raimondo <federaimondo@gmail.com> Fede <slashack@gmail.com>
 Fede Raimondo <federaimondo@gmail.com> Fede Raimondo <federaimondo@gmail.com>
 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
 Guillaume Dumas <deep@introspection.eu> Guillaume Dumas <deep-introspection@users.noreply.github.com>
 Hakimeh Aslsardroud <hakimeh.aslsardroud@localhost>
 Hamid Maymandi <46011104+HamidMandi@users.noreply.github.com> Hamid <46011104+HamidMandi@users.noreply.github.com>
+Hansuja Budhiraja <hansujaigdtuwcseai@gmail.com> Hansuja <hansujaigdtuwcseai@gmail.com>
 Hasrat Ali Arzoo <hasrat407@gmail.com> hasrat17 <56307533+hasrat17@users.noreply.github.com>
 Hongjiang Ye <rubyyhj@gmail.com> YE Hongjiang <hongjiang.ye@outlook.com>
 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
 Matti Hämäläinen <msh@nmr.mgh.harvard.edu> mshamalainen <msh@nmr.mgh.harvard.edu>
 Matti Toivonen <105695400+mattitoi@users.noreply.github.com> mattitoi <105695400+mattitoi@users.noreply.github.com>
 Maureen Shader <55732126+mshader@users.noreply.github.com> mshader <55732126+mshader@users.noreply.github.com>
+Melih Yayli <51379391+yaylim@users.noreply.github.com> yaylim <51379391+yaylim@users.noreply.github.com>
 Melih Yayli <melihyayli@hotmail.com>
 Michiru Kaneda <rcmdnk@gmail.com> rcmdnk <rcmdnk@gmail.com>
 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
 Simon Kern <simon.kern@online.de> skjerns <simon.kern@online.de>
 Sondre Foslien <sondre.foslien@gmail.com> sondrfos <sondre.foslien@gmail.com>
 Sophie Herbst <ksherbst@gmail.com>
+Srivarsha Chivukula <varshaa.1616@gmail.com> varshaa-1616 <varshaa.1616@gmail.com>
 Steinn Hauser Magnússon <hausersteinn@gmail.com> Steinn Magnusson <s.magnusson@senec.com>
 Steve Matindi <stevematindi@gmail.com> stevemats <stevematindi@gmail.com>
 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>
 user27182 <89109579+user27182@users.noreply.github.com>
 Valerii Chirkov <vagechirkov@gmail.com> Valerii <42982039+vagechirkov@users.noreply.github.com>
 Valerii Chirkov <vagechirkov@gmail.com> Valerii <vagechirkov@gmail.com>
-varshaa-1616 <varshaa.1616@gmail.com>
 Velu Prabhakar Kumaravel <veluprabhakarkumaravel@Velus-MBP.lan> Velu Prabhakar Kumaravel <veluprabhakarkumaravel@Velus-MBP.lan>
 Victoria Peterson <victoriapeterson09@gmail.com> vpeterson <victoriapeterson09@gmail.com>
 Wei Xu <weixu@mail.bnu.edu.cn> Wei <weixu@mail.bnu.edu.cn>

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.8
+    rev: v0.15.12
     hooks:
       - id: ruff-check
         name: ruff lint mne
@@ -54,7 +54,7 @@ repos:
     rev: v6.0.0
     hooks:
       - id: file-contents-sorter
-        files: ^doc/changes/names.inc|^.mailmap|^doc/sphinxext/related_software.txt
+        files: ^doc/changes/names.inc|^.mailmap|^doc/sphinxext/related_software.txt|^ignore_words.txt
         args: ["--ignore-case"]
 
   - repo: https://github.com/pappasam/toml-sort
@@ -71,28 +71,16 @@ repos:
         language: python
         entry: ./tools/hooks/update_environment_file.py
         files: '^(pyproject.toml|tools/hooks/update_environment_file.py)$'
-  - repo: local
-    hooks:
-      - id: dependency-sync
-        name: Copy core dependencies from pyproject.toml to README.rst
-        language: python
-        entry: ./tools/hooks/sync_dependencies.py
-        files: '^(pyproject.toml|tools/hooks/sync_dependencies.py)$'
-        additional_dependencies: ["mne==1.11.0"]
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.23.1
+    rev: v1.24.1
     hooks:
       - id: zizmor
         args: [--fix]
         # We correctly use pull_request_trigger, and need Zizmor 2.0+ to configure the ignore
         exclude: ^.github/workflows/automerge.yml
 
-# these should *not* be run on CIs:
-ci:
-  skip: [dependency-sync]  # needs MNE to work, which exceeds the free tier space alloc.
-
 # The following are too slow to run on local commits, so let's only run on CIs:
 #
 #   - repo: https://github.com/pre-commit/mirrors-mypy