Merge branch 'main' into fix-13845

Author: larsoner

.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@v4.35.2
       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@v4.35.2
 
     # 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@v4.35.2

.github/workflows/release.yml

@@ -28,7 +28,7 @@ jobs:
           pip install build twine
       - run: python -m build --sdist --wheel
       - run: twine check --strict dist/*
-      - uses: actions/upload-artifact@v6
+      - uses: actions/upload-artifact@v7
         with:
           name: dist
           path: dist
@@ -43,7 +43,7 @@ jobs:
       name: pypi
       url: https://pypi.org/p/mne
     steps:
-      - uses: actions/download-artifact@v7
+      - uses: actions/download-artifact@v8
         with:
           name: dist
           path: dist

.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

@@ -143,7 +143,7 @@ jobs:
             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
@@ -154,7 +154,7 @@ jobs:
         if: matrix.kind == 'conda' || matrix.kind == 'mamba'
         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
@@ -182,7 +182,7 @@ 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()

.github/zizmor.yml

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

.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: v0.15.4
+    rev: v0.15.11
     hooks:
       - id: ruff-check
         name: ruff lint mne
@@ -23,7 +23,7 @@ repos:
 
   # Codespell
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+    rev: v2.4.2
     hooks:
       - id: codespell
         additional_dependencies:
@@ -54,11 +54,11 @@ 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
-    rev: v0.24.3
+    rev: v0.24.4
     hooks:
       - id: toml-sort-fix
         files: pyproject.toml
@@ -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: v1.22.0
+    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