Merge remote-tracking branch 'upstream/main' into cnt-overflow-fix

* upstream/main: (83 commits)
  [pre-commit.ci] pre-commit autoupdate (mne-tools#13818)
  MAINT: Update dependency specifiers (mne-tools#13814)
  FIX: correct sensor name ordering in plot_topomap when using Info object (mne-tools#13686)
  ENH: Add support for plotting ICA source timecourses in Report.add_ica (mne-tools#13697)
  fixed some info fields in MEG interpolation across sensor types using… (mne-tools#13759)
  [dependabot]: Bump the actions group with 2 updates (mne-tools#13817)
  DOC: Fix type annotation for order parameter in Epochs.plot() (mne-tools#13639)
  Add pybispectra as related software (mne-tools#13812)
  ENH: Add initial BCI2000 .dat reader (preload-only) (mne-tools#13699)
  BUG: Fix bug with fwd.info["dev_head_t"] setting (mne-tools#13619)
  MAINT: Remove tomli, tomlsort, and ruff from `test` group (mne-tools#13809)
  MAINT: Make sys_info more robust (mne-tools#13810)
  ENH: Replace custom _whosmat_hdf5 with pymatreader.whosmat (mne-tools#13753)
  MAINT: Install SciPy pre (mne-tools#13807)
  ENH: add cmap parameter to Evoked.animate_topomap (mne-tools#13756)
  ENH: expose font_file in Brain.add_text (mne-tools#13778)
  Replacing abstractclassmethod with abstractmethod (mne-tools#13806)
  FIX: short-circuit n_jobs=None to n_jobs=1 without Parallel setup (mne-tools#13777)
  MAINT: Update code credit (mne-tools#13805)
  Fix top and bottom clipping in raw.plot() (mne-tools#13787)
  ...

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@635ffb0c9798bd160680f18fd73371e355b85f27
+      - uses: autofix-ci/action@7a166d7532b277f34e16238930461bf77f9d7ed8

.github/workflows/credit.yml

@@ -37,10 +37,10 @@ jobs:
           set -xeo pipefail
           git config --global user.email "[email protected]"
           git config --global user.name "mne[bot]"
-          BRANCH=credit/$GITHUB_RUN_ID
+          BRANCH=credit/$(date '+%Y%m%d')
           git checkout -b $BRANCH
           git commit -am "mne[bot]: Update code credit"
           git push origin $BRANCH
-          PR_NUM=$(gh pr create --base main --head $BRANCH --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to \`doc/changes/credit_tools.py\` or \`.mailmap\` etc. to get CircleCI to pass.*" --label "no-changelog-entry-needed")
+          PR_NUM=$(gh pr create --base main --head $BRANCH --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to \`doc/sphinxext/credit_tools.py\` or \`.mailmap\` etc. to get CircleCI to pass.*" --label "no-changelog-entry-needed")
           echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
         if: steps.status.outputs.dirty == 'true'

.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

@@ -37,24 +37,32 @@ jobs:
           fi
       - name: Setup Remote SSH Connection
         if: env.ENABLE_SSH == 'true'
-        uses: mxschmitt/action-tmate@v3
+        uses: Warpbuilds/action-[email protected]
         timeout-minutes: 10
         with:
           detached: true
-      - uses: actions/setup-python@v6
+      - uses: astral-sh/setup-uv@v7
         with:
-          python-version: '3.12'
-      - run: pip install packaging requests tomlkit
-      - run: python tools/dev/spec_zero_update_versions.py
-      - run: |
+          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: Create lockfile for old CI
+        # uv pip compile requires setting the python version explicitly in the command :(
+        run: |
+          uv pip compile pyproject.toml --python "3.10" --python-platform "x86_64-unknown-linux-gnu" --group test --group lockfile_extras --resolution lowest-direct --format pylock.toml --output-file tools/pylock.ci-old.toml
+          python tools/github_actions_check_old_lockfile.py
+      - name: check if files changed
+        run: |
           git diff && git status --porcelain
           if [[ $(git status --porcelain) ]]; then
             echo "dirty=true" >> $GITHUB_OUTPUT
           fi
         id: status
       - name: Run pre-commit hooks to update other files
         run: |
-          pip install pre-commit
+          uv pip install pre-commit
           pre-commit run --all || true
         if: steps.status.outputs.dirty == 'true'
       - name: Create PR

.github/workflows/tests.yml

@@ -107,7 +107,7 @@ jobs:
           fi
       - name: Setup Remote SSH Connection
         if: env.ENABLE_SSH == 'true'
-        uses: mxschmitt/action-tmate@v3
+        uses: Warpbuilds/action-[email protected]
         timeout-minutes: 80
         with:
           detached: true
@@ -143,18 +143,27 @@ 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
           log-level: ${{ runner.debug == '1' && 'debug' || 'info' }}
           create-args: >-
             python=${{ env.PYTHON_VERSION }}
             -v
-        if: ${{ !startswith(matrix.kind, 'pip') }}
+        if: matrix.kind == 'conda' || matrix.kind == 'mamba'
         timeout-minutes: 20
+      # Python (if old)
+      - uses: astral-sh/setup-uv@v7
+        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_dependencies.sh
-      - run: python ./tools/github_actions_check_old.py
+      - run: python ./tools/github_actions_check_old_env.py
         if: matrix.kind == 'old'
       # Minimal commands on Linux (macOS stalls)
       - run: bash ./tools/get_minimal_commands.sh
@@ -173,7 +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

@@ -20,6 +20,7 @@ Andrew Dykstra <[email protected]>
 Andrew Quinn <[email protected]> AJQuinn <[email protected]>
 Andy Gilbert <[email protected]> Andrew Gilbert <[email protected]>
 Andy Gilbert <[email protected]> Andrew Gilbert <[email protected]>
+Aniket Singh Yadav <[email protected]> Aniket <[email protected]>
 Anna Padee <[email protected]> apadee <[email protected]>
 Anne-Sophie Dubarry <[email protected]> annesodub <[email protected]>
 Archit Singhal <[email protected]> archit singhal <[email protected]>
@@ -246,6 +247,7 @@ Matti Hämäläinen <[email protected]> Matti Hämäläinen <[email protected]
 Matti Hämäläinen <[email protected]> mshamalainen <[email protected]>
 Matti Toivonen <[email protected]> mattitoi <[email protected]>
 Maureen Shader <[email protected]> mshader <[email protected]>
+Melih Yayli <[email protected]>
 Michiru Kaneda <[email protected]> rcmdnk <[email protected]>
 Mikołaj Magnuski <[email protected]> Mikolaj Magnuski <[email protected]>
 Mikołaj Magnuski <[email protected]> mmagnuski <[email protected]>
@@ -256,6 +258,7 @@ Motofumi Fushimi <[email protected]> motofumi-f
 Natalie Klein <[email protected]> natalieklein <[email protected]>
 Nathalie Gayraud <[email protected]> Nathalie <[email protected]>
 Nathalie Gayraud <[email protected]> Nathalie <[email protected]>
+Natneal B <[email protected]>
 Naveen Srinivasan <[email protected]> Naveen <[email protected]>
 Nicolas Barascud <[email protected]> nbara <[email protected]>
 Nicolas Barascud <[email protected]> Nicolas Barascud <[email protected]>
@@ -288,6 +291,8 @@ Pierre-Antoine Bannier <[email protected]> Pierre-Antoine Bannier
 Pierre-Antoine Bannier <[email protected]> Pierre-Antoine Bannier <[email protected]>
 Pierre-Antoine Bannier <[email protected]> Pierre-Antoine Bannier <[email protected]>
 Ping-Keng Jao <[email protected]> nafraw <[email protected]>
+Pragnya Khandelwal <[email protected]> Pragnya <[email protected]>
+Pragnya Khandelwal <[email protected]> PragnyaKhandelwal <[email protected]>
 Praveen Sripad <[email protected]> prav <prav@prav-dell.(none)>
 Praveen Sripad <[email protected]> prav <[email protected]>
 Proloy Das <[email protected]> pdas6 <[email protected]>
@@ -359,6 +364,7 @@ Tziona NessAiver <[email protected]> TzionaN <[email protected]>
 user27182 <[email protected]>
 Valerii Chirkov <[email protected]> Valerii <[email protected]>
 Valerii Chirkov <[email protected]> Valerii <[email protected]>
+varshaa-1616 <[email protected]>
 Velu Prabhakar Kumaravel <[email protected]> Velu Prabhakar Kumaravel <[email protected]>
 Victoria Peterson <[email protected]> vpeterson <[email protected]>
 Wei Xu <[email protected]> Wei <[email protected]>

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.14
+    rev: v0.15.9
     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:
@@ -58,7 +58,7 @@ repos:
         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
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.22.0
+    rev: v1.23.1
     hooks:
       - id: zizmor
         args: [--fix]

azure-pipelines.yml

@@ -114,7 +114,7 @@ stages:
           - bash: |
               set -e
               python -m pip install --progress-bar off --upgrade pip
-              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git" "git+https://github.com/python-quantities/python-quantities" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1,!=6.9.1" pandas neo pymatreader antio defusedxml curryreader pymef
+              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1,!=6.9.1" pandas neo pymatreader antio defusedxml curryreader pymef
               python -m pip uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e . --group=test
             displayName: 'Install dependencies with pip'
@@ -173,7 +173,7 @@ 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"
-              python -m pip install --progress-bar off --upgrade -ve .[full] --group=test_extra "git+https://github.com/python-quantities/python-quantities"
+              python -m pip install --progress-bar off --upgrade -ve .[full] --group=test_extra
             displayName: 'Install dependencies with pip'
           - bash: |
               set -e

doc/_includes/bem_model.rst

@@ -17,7 +17,7 @@ Using the watershed algorithm
 
 The watershed algorithm [Segonne *et al.*,
 2004] is part of the FreeSurfer software.
-The name of the program is ``mri_watershed``.
+The name of the program is mri_watershed_.
 Its use in the MNE environment is facilitated by the script
 :ref:`mne watershed_bem`.