Merge branch 'main' into layout

.circleci/config.yml

@@ -22,58 +22,6 @@ _check_skip: &check_skip
     fi
 
 jobs:
-  pytest-macos-arm64:
-    parameters:
-      scheduled:
-        type: string
-        default: "false"
-    macos:
-      xcode: "14.2.0"
-    resource_class: macos.m1.medium.gen1
-    environment:
-      HOMEBREW_NO_AUTO_UPDATE: 1
-    steps:
-      - checkout
-      - run:
-          <<: *check_skip
-      - run:
-          name: Install Python and dependencies
-          command: |
-            set -eo pipefail
-            brew install [email protected]
-            which python
-            which pip
-            pip install --upgrade pip
-            pip install --upgrade --only-binary "numpy,scipy,dipy,statsmodels" -ve .[full,test_extra]
-            # 3D too slow on Apple's software renderer, and numba causes us problems
-            pip uninstall -y vtk pyvista pyvistaqt numba
-            mkdir -p test-results
-            echo "set -eo pipefail" >> $BASH_ENV
-      - run:
-          command: mne sys_info
-      - run:
-          command: ./tools/get_testing_version.sh && cat testing_version.txt
-      - restore_cache:
-          keys:
-            - data-cache-testing-{{ checksum "testing_version.txt" }}
-      - run:
-          command: python -c "import mne; mne.datasets.testing.data_path(verbose=True)"
-      - save_cache:
-          key: data-cache-testing-{{ checksum "testing_version.txt" }}
-          paths:
-            - ~/mne_data/MNE-testing-data  # (2.5 G)
-      - run:
-          command: pytest -m "not slowtest" --tb=short --cov=mne --cov-report xml -vv mne
-      - run:
-          name: Prepare test data upload
-          command: cp -av junit-results.xml test-results/junit.xml
-      - store_test_results:
-          path: ./test-results
-      # Codecov orb has bugs on macOS (gpg issues)
-      # - codecov/upload
-      - run:
-          command: bash <(curl -s https://codecov.io/bash)
-
   build_docs:
     parameters:
       scheduled:
@@ -454,6 +402,7 @@ jobs:
         default: "false"
     docker:
       - image: cimg/base:current-22.04
+    resource_class: large
     steps:
       - restore_cache:
           keys:
@@ -496,8 +445,8 @@ jobs:
 
 
   deploy:
-    machine:
-      image: ubuntu-2004:202111-01
+    docker:
+      - image: cimg/base:current-22.04
     steps:
       - attach_workspace:
           at: /tmp/build
@@ -591,20 +540,6 @@ workflows:
               only:
                 - main
 
-  weekly:
-    jobs:
-      - pytest-macos-arm64:
-          name: pytest_macos_arm64_weekly
-          scheduled: "true"
-    triggers:
-      - schedule:
-          # "At 6:00 AM GMT every Monday"
-          cron: "0 6 * * 1"
-          filters:
-            branches:
-              only:
-                - main
-
   monthly:
     jobs:
       - linkcheck:

.git-blame-ignore-revs

@@ -2,3 +2,6 @@ e81ec528a42ac687f3d961ed5cf8e25f236925b0  # black
 12395f9d9cf6ea3c72b225b62e052dd0d17d9889  # YAML indentation
 d6d2f8c6a2ed4a0b27357da9ddf8e0cd14931b59  # isort
 e7dd1588013179013a50d3f6b8e8f9ae0a185783  # ruff format
+e39995d9be6fc831c7a4a59f09b7a7c0a41ae315  # percent formatting
+940ac9553ce42c15b4c16ecd013824ca3ea7244a  # whitespace
+1c5b39ff1d99bbcb2fc0e0071a989b3f3845ff30  # ruff UP028

.git_archival.txt

@@ -1,4 +1,3 @@
 node: $Format:%H$
 node-date: $Format:%cI$
 describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
-ref-names: $Format:%D$

.github/CONTRIBUTING.md

@@ -10,4 +10,4 @@ This project and everyone participating in it is governed by the [MNE-Python's C
 
 ## How to contribute
 
-Before contributing make sure you are familiar with [our contributing guide](https://mne.tools/dev/install/contributing.html).
+Before contributing make sure you are familiar with [our contributing guide](https://mne.tools/dev/development/contributing.html).

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -29,8 +29,8 @@ body:
         Paste here a code snippet or minimal working example
         ([MWE](https://en.wikipedia.org/wiki/Minimal_Working_Example))
         to replicate your problem, using one of the
-        [datasets shipped with MNE-Python](https://mne.tools/dev/overview/datasets_index.html),
-        preferably the one called [sample](https://mne.tools/dev/overview/datasets_index.html#sample).
+        [datasets shipped with MNE-Python](https://mne.tools/stable/documentation/datasets.html#datasets),
+        preferably the one called [sample](https://mne.tools/stable/documentation/datasets.html#sample).
       render: Python
     validations:
       required: true

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,5 +1,5 @@
 Thanks for contributing a pull request! Please make sure you have read the
-[contribution guidelines](https://mne.tools/dev/install/contributing.html)
+[contribution guidelines](https://mne.tools/dev/development/contributing.html)
 before submitting.
 
 Please be aware that we are a loose team of volunteers so patience is

.github/actions/rename_towncrier/rename_towncrier.py

@@ -11,22 +11,22 @@
 from github import Github
 from tomllib import loads
 
-event_name = os.getenv('GITHUB_EVENT_NAME', 'pull_request')
-if not event_name.startswith('pull_request'):
-    print(f'No-op for {event_name}')
+event_name = os.getenv("GITHUB_EVENT_NAME", "pull_request")
+if not event_name.startswith("pull_request"):
+    print(f"No-op for {event_name}")
     sys.exit(0)
-if 'GITHUB_EVENT_PATH' in os.environ:
-    with open(os.environ['GITHUB_EVENT_PATH'], encoding='utf-8') as fin:
+if "GITHUB_EVENT_PATH" in os.environ:
+    with open(os.environ["GITHUB_EVENT_PATH"], encoding="utf-8") as fin:
         event = json.load(fin)
-    pr_num = event['number']
-    basereponame = event['pull_request']['base']['repo']['full_name']
+    pr_num = event["number"]
+    basereponame = event["pull_request"]["base"]["repo"]["full_name"]
     real = True
 else:  # local testing
     pr_num = 12318  # added some towncrier files
     basereponame = "mne-tools/mne-python"
     real = False
 
-g = Github(os.environ.get('GITHUB_TOKEN'))
+g = Github(os.environ.get("GITHUB_TOKEN"))
 baserepo = g.get_repo(basereponame)
 
 # Grab config from upstream's default branch
@@ -45,9 +45,7 @@
 assert directory.endswith("/"), directory
 
 file_re = re.compile(rf"^{directory}({type_pipe})\.rst$")
-found_stubs = [
-    f for f in modified_files if file_re.match(f)
-]
+found_stubs = [f for f in modified_files if file_re.match(f)]
 for stub in found_stubs:
     fro = stub
     to = file_re.sub(rf"{directory}{pr_num}.\1.rst", fro)

.github/workflows/autofix.yml

@@ -18,4 +18,4 @@ jobs:
           python-version: '3.12'
       - run: pip install --upgrade towncrier pygithub
       - run: python ./.github/actions/rename_towncrier/rename_towncrier.py
-      - uses: autofix-ci/action@ea32e3a12414e6d3183163c3424a7d7a8631ad84
+      - uses: autofix-ci/action@d3e591514b99d0fca6779455ff8338516663f7cc

.github/workflows/tests.yml

@@ -4,11 +4,9 @@ concurrency:
   cancel-in-progress: true
 on:  # yamllint disable-line rule:truthy
   push:
-    branches:
-      - '*'
+    branches: ["main", "maint/*"]
   pull_request:
-    branches:
-      - '*'
+    branches: ["main", "maint/*"]
 
 permissions:
   contents: read
@@ -22,15 +20,18 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
-      - uses: pre-commit/[email protected]
+          python-version: '3.12'
+      - uses: pre-commit/[email protected]
+      - run: pip install mypy numpy scipy vulture
+      - run: mypy
+      - run: vulture
 
   bandit:
     name: Bandit
     needs: style
     runs-on: ubuntu-latest
     steps:
-      - uses: davidslusser/[email protected].0
+      - uses: davidslusser/[email protected].1
         with:
           src: "mne"
           options: "-c pyproject.toml -ll -r"
@@ -56,13 +57,16 @@ jobs:
       matrix:
         include:
           - os: ubuntu-latest
-            python: '3.10'
-            kind: conda
-          - os: ubuntu-latest
-            python: '3.11'
+            python: '3.12'
             kind: pip-pre
-          - os: macos-latest
-            python: '3.9'
+          - os: ubuntu-latest
+            python: '3.12'
+            kind: conda
+          - os: macos-14  # arm64
+            python: '3.12'
+            kind: mamba
+          - os: macos-latest  # intel
+            python: '3.12'
             kind: mamba
           - os: windows-latest
             python: '3.10'
@@ -89,6 +93,12 @@ jobs:
           python-version: ${{ matrix.python }}
         if: startswith(matrix.kind, 'pip')
       # Python (if conda)
+      - name: Remove numba and dipy
+        run: |  # TODO: Remove when numba 0.59 and dipy 1.8 land on conda-forge
+          sed -i '/numba/d' environment.yml
+          sed -i '/dipy/d' environment.yml
+          sed -i 's/- mne$/- mne-base/' environment.yml
+        if: matrix.os == 'ubuntu-latest' && startswith(matrix.kind, 'conda') && matrix.python == '3.12'
       - uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ${{ env.CONDA_ENV }}
@@ -98,6 +108,9 @@ jobs:
             mamba
             fmt!=10.2.0
         if: ${{ !startswith(matrix.kind, 'pip') }}
+      # Make sure we have the right Python
+      - run: python -c "import platform; assert platform.machine() == 'arm64', platform.machine()"
+        if: matrix.os == 'macos-14'
       - run: ./tools/github_actions_dependencies.sh
       # Minimal commands on Linux (macOS stalls)
       - run: ./tools/get_minimal_commands.sh
@@ -110,11 +123,13 @@ jobs:
         run: MNE_SKIP_TESTING_DATASET_TESTS=true pytest -m "not (ultraslowtest or pgtest)" --tb=short --cov=mne --cov-report xml -vv -rfE mne/
         if: matrix.kind == 'minimal'
       - run: ./tools/get_testing_version.sh
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         with:
           key: ${{ env.TESTING_VERSION }}
           path: ~/mne_data
       - run: ./tools/github_actions_download.sh
       - run: ./tools/github_actions_test.sh
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
         if: success()

.mailmap

@@ -114,11 +114,13 @@ Giorgio Marinato <[email protected]> neurogima <76406896+neurogima@users
 Guillaume Dumas <[email protected]> deep-introspection <[email protected]>
 Guillaume Dumas <[email protected]> Guillaume Dumas <[email protected]>
 Hamid Maymandi <[email protected]> Hamid <[email protected]>
+Hasrat Ali Arzoo <[email protected]> hasrat17 <[email protected]>
 Hongjiang Ye <[email protected]> YE Hongjiang <[email protected]>
 Hubert Banville <[email protected]> hubertjb <[email protected]>
 Hüseyin Orkun Elmas <[email protected]> Hüseyin <[email protected]>
 Hyonyoung Shin <[email protected]> mcvain <[email protected]>
 Ingoo Lee <[email protected]> dlsrnsi <[email protected]>
+Ivo de Jong <[email protected]> ivopascal <[email protected]>
 Jaakko Leppakangas <[email protected]> Jaakko Leppakangas <[email protected]>
 Jaakko Leppakangas <[email protected]> jaeilepp <[email protected]>
 Jaakko Leppakangas <[email protected]> jaeilepp <[email protected]>
@@ -220,6 +222,7 @@ Mikołaj Magnuski <[email protected]> Mikolaj Magnuski <[email protected]
 Mikołaj Magnuski <[email protected]> mmagnuski <[email protected]>
 Mohamed Sherif <[email protected]> mohdsherif <[email protected]>
 Mohammad Daneshzand <[email protected]> mdaneshzand <[email protected]>
+Motofumi Fushimi <[email protected]> motofumi-fushimi <[email protected]>
 Natalie Klein <[email protected]> natalieklein <[email protected]>
 Nathalie Gayraud <[email protected]> Nathalie <[email protected]>
 Nathalie Gayraud <[email protected]> Nathalie <[email protected]>

.pre-commit-config.yaml

@@ -1,33 +1,28 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.9
+    rev: v0.4.5
     hooks:
       - id: ruff
         name: ruff lint mne
         args: ["--fix"]
         files: ^mne/
-      - id: ruff-format
-        name: ruff format mne
+      - id: ruff
+        name: ruff lint mne preview
+        args: ["--fix", "--preview", "--select=NPY201"]
         files: ^mne/
-
-  # Ruff tutorials and examples
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.9
-    hooks:
       - id: ruff
-        name: ruff lint tutorials and examples
+        name: ruff lint doc, tutorials, and examples
         # D103: missing docstring in public function
         # D400: docstring first line must end with period
         args: ["--ignore=D103,D400", "--fix"]
-        files: ^tutorials/|^examples/
+        files: ^doc/|^tutorials/|^examples/
       - id: ruff-format
-        name: ruff format tutorials and examples
-        files: ^tutorials/|^examples/
+        files: ^mne/|^doc/|^tutorials/|^examples/
 
   # Codespell
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         additional_dependencies:
@@ -37,7 +32,7 @@ repos:
 
   # yamllint
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.33.0
+    rev: v1.35.1
     hooks:
       - id: yamllint
         args: [--strict, -c, .yamllint.yml]
@@ -51,11 +46,14 @@ repos:
           - tomli
         files: ^doc/.*\.(rst|inc)$
 
-  # mypy
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
-    hooks:
-      - id: mypy
-        # Avoid the conflict between mne/__init__.py and mne/__init__.pyi by ignoring the former
-        exclude: ^mne/(beamformer|channels|commands|datasets|decoding|export|forward|gui|html_templates|inverse_sparse|io|minimum_norm|preprocessing|report|simulation|source_space|stats|time_frequency|utils|viz)?/?__init__\.py$
-        additional_dependencies: ["numpy==1.26.2"]
+# 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
+#     rev: v1.9.0
+#     hooks:
+#       - id: mypy
+#
+#   - repo: https://github.com/jendrikseipp/vulture
+#     rev: 'v2.11'  # or any later Vulture version
+#     hooks:
+#       - id: vulture