Merge remote-tracking branch 'upstream/main' into add_emg_support

Author: drammock

.github/release.yaml

@@ -0,0 +1,6 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot[bot]
+      - pre-commit-ci[bot]
+      - github-actions[bot]

.github/workflows/cffconvert.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out a copy of the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/[email protected]

.github/workflows/release.yml

@@ -18,17 +18,18 @@ jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
           fetch-tags: true
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
-          python-version: '3.12'
+          python-version: '3.13'
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install build twine
+          pip check
+          python -m pip install build twine
       - run: python -m build --sdist --wheel
       - run: twine check --strict dist/*
       - uses: actions/upload-artifact@v4
@@ -47,7 +48,7 @@ jobs:
       name: pypi
       url: https://pypi.org/p/mne-bids
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v5
         with:
           name: dist
           path: dist

.github/workflows/unit_tests.yml

@@ -19,23 +19,24 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
         fetch-tags: true
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - uses: actions/cache@v4
       with:
         path: ${{ env.pythonLocation }}
-        key: style-0-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+        key: style-2-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        pip check
         python -m pip install ruff
     - name: Display versions and environment information
       run: |
@@ -50,24 +51,25 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.10", "3.12"]  # Oldest and newest supported versions
+        python-version: ["3.10", "3.13"]  # Oldest and newest supported versions
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
     - uses: actions/cache@v4
       with:
         path: ${{ env.pythonLocation }}
-        key: build-1-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+        key: build-3-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        pip check
         python -m pip install build twine
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
         fetch-tags: true
@@ -86,7 +88,7 @@ jobs:
     - name: Remove sdist install
       run: python -m pip uninstall -y mne-bids
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
         fetch-tags: true
@@ -105,7 +107,7 @@ jobs:
     - name: Remove wheel install
       run: python -m pip uninstall -y mne-bids
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
         fetch-tags: true
@@ -126,22 +128,23 @@ jobs:
     # For GitHub "required" CI checks, add in branch protection:
     #
     # 8 checks:
-    # for each machine type (ubuntu, macos, macos-13, windows):
-    # (NOTE: macos-13=x86_64, macos>13=arm64)
+    # for each machine type (ubuntu, macos, windows):
     # 3.10 / mne-stable / full / validator-stable
-    # 3.12 / mne-stable / full / validator-stable
+    # 3.13 / mne-stable / full / validator-stable
     #
-    # 3 additional checks with alternative MNE-Python and BIDS validator versions:
-    # ubuntu / 3.12 / mne-main / full / validator-main
-    # ubuntu / 3.10 / mne-prev / full / validator-stable
-    # ubuntu / 3.12 / mne-stable / minimal / validator-stable
+    # 4 additional checks with alternative MNE-Python and BIDS validator versions:
+    # ubuntu / 3.13 / mne-main / full / validator-main -->  to test cutting edge of everything
+    # ubuntu / 3.10 / mne-prev / full / validator-stable --> to test last supported of everything
+    # ubuntu / 3.13 / mne-stable / minimal / validator-stable --> to test a minimal installation
+    # ubuntu / 3.12 / mne-stable / full / validator-main-schema --> to test next-gen BIDS validator
+    # macos-15-intel / 3.13 / mne-stable / full / validator-stable --> to test macos x86_64
     timeout-minutes: 60
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, macos-13, windows-latest]
-        python-version: ["3.10", "3.12"]  # Oldest and newest supported versions
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.13"]  # Oldest and newest supported versions
         mne-version: [mne-stable]
         mne-bids-install: [full]
         bids-validator-version: [validator-stable]
@@ -150,7 +153,7 @@ jobs:
           # special test runs running only on single CI systems to save resources
           # Test development versions
           - os: ubuntu-latest
-            python-version: "3.12"
+            python-version: "3.13"
             mne-version: mne-main
             mne-bids-install: full
             bids-validator-version: validator-main
@@ -162,41 +165,60 @@ jobs:
             bids-validator-version: validator-stable
           # Test minimal mne-bids install
           - os: ubuntu-latest
-            python-version: "3.12"
+            python-version: "3.13"
             mne-version: mne-stable
             mne-bids-install: minimal
             bids-validator-version: validator-stable
-
+          # Test next gen BIDS schema validator
+          - os: ubuntu-latest
+            python-version: "3.12"
+            mne-version: mne-stable
+            mne-bids-install: full
+            bids-validator-version: validator-main-schema
+          # Test macos on x86_64 architecture
+          - os: macos-15-intel
+            python-version: "3.13"
+            mne-version: mne-stable
+            mne-bids-install: full
+            bids-validator-version: validator-stable
 
     env:
       TZ: Europe/Berlin
       FORCE_COLOR: true
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
         fetch-tags: true
 
-    - name: Set up Node.js
-      uses: actions/setup-node@v4
+    - name: Set up Node.js (validator-stable and validator-main)
+      if: matrix.bids-validator-version == 'validator-stable' || matrix.bids-validator-version == 'validator-main'
+      uses: actions/setup-node@v6
       with:
         node-version: 20
 
+    - name: Set up deno (validator-main-schema)
+      if: matrix.bids-validator-version == 'validator-main-schema'
+      uses: denoland/setup-deno@v2
+      with:
+        deno-version: v1.x
+
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Restore cache
       uses: actions/cache@v4
       with:
         path: ${{ env.pythonLocation }}
-        key: test-0-${{ env.pythonLocation }}-${{ env.os }}-${{ hashFiles('pyproject.toml') }}
+        key: test-2-${{ env.pythonLocation }}-${{ env.os }}-${{ hashFiles('pyproject.toml') }}
 
     - name: Install Python dependencies using pip
       # This would be nicer once this feature is implemented: https://github.com/pypa/pip/issues/11440
       run: |
         python -m pip install --upgrade pip
+        pip check
         python -m pip install -e .[test]
 
     - name: Install MNE (stable)
@@ -222,6 +244,18 @@ jobs:
       run: |
         npm install -g bids-validator
 
+    - name: Install BIDS validator (main-schema)
+      if: matrix.bids-validator-version == 'validator-main-schema'
+      # Follow documentation here:
+      #  - https://github.com/bids-standard/bids-validator/tree/master/bids-validator/src
+      #  - https://github.com/bids-standard/bids-examples/blob/7c18d6840982518a0251cfeb59fe5c4610099ea1/.github/workflows/validate_datasets.yml#L69-L75
+      #
+      # Note: in the future, we may want to make it easy to use:
+      #  - a different version of the validator (stable, main)
+      #  - a different version of the schema (stable, main)
+      run: |
+        deno install -Agf https://github.com/bids-standard/bids-validator/raw/deno-build/bids-validator.js
+
     - name: Download BIDS validator (main)
       if: matrix.bids-validator-version == 'validator-main'
       run: |
@@ -244,14 +278,16 @@ jobs:
         popd
 
     - name: Display versions and environment information
+      shell: bash
       run: |
         echo $TZ
         date
-        echo "npm"; npm --version
+        echo "(npm version)"; npm --version
         echo "node"; node --version
-        echo "bids-validator"; bids-validator --version
-        echo "python"; python --version
-        which python
+        echo "(deno version)"; deno --version || echo ""
+        echo "(bids-validator version)"; bids-validator --version
+        echo "(python version)"; python --version
+        echo "(which python)"; which python
         mne sys_info
 
     - name: Install MNE-BIDS (minimal)
@@ -265,7 +301,7 @@ jobs:
     # Only run on a limited set of jobs
     - name: Run pytest without testing data
       run: make test
-      if: ${{ matrix.python-version == '3.12' && matrix.os == 'ubuntu-latest' && matrix.mne-version == 'mne-main' }}
+      if: ${{ matrix.python-version == '3.13' && matrix.os == 'ubuntu-latest' && matrix.mne-version == 'mne-main' }}
 
     # Get testing data
     - run: ./tools/get_testing_version.sh
@@ -275,7 +311,7 @@ jobs:
 
     - uses: actions/cache@v4
       with:
-        key: ${{ env.TESTING_VERSION }}
+        key: testing_data-1-${{ env.TESTING_VERSION }}
         path: ~/mne_data
       name: 'Cache testing data'
 
@@ -299,23 +335,24 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
         fetch-tags: true
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - uses: actions/cache@v4
       with:
         path: ${{ env.pythonLocation }}
-        key: build_docs-1-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+        key: build_docs-3-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        pip check
         python -m pip install --upgrade https://github.com/mne-tools/mne-python/archive/refs/heads/main.zip
         python -m pip install -e .[test,doc]
     - name: Build the documentation

.mailmap

@@ -5,6 +5,7 @@ Alex Rockhill <[email protected]> <[email protected]>
 Alexandre Gramfort <[email protected]>
 Alexandre Gramfort <[email protected]> <[email protected]>
 Ariel Rokem <[email protected]>
+Bruno Aristimunha <[email protected]>
 Chris Holdgraf <[email protected]>
 Chris Holdgraf <[email protected]> <[email protected]>
 Clemens Brunner <[email protected]>

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.0
+    rev: v0.14.1
     hooks:
       - id: ruff
         name: ruff mne_bids/
@@ -21,7 +21,7 @@ repos:
         files: ^examples/
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -33,7 +33,7 @@ repos:
       - id: check-docstring-first
 
   - repo: https://github.com/pappasam/toml-sort
-    rev: v0.24.2
+    rev: v0.24.3
     hooks:
       - id: toml-sort-fix
         files: pyproject.toml

CITATION.cff

@@ -206,6 +206,25 @@ authors:
       family-names: Gerçek
       affiliation: 'University of Geneva, Department of Fundamental Neuroscience'
       orcid: 'https://orcid.org/0000-0003-1063-6769'
+    - given-names: Matthias
+      family-names: Dold
+      affiliation: 'Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands'
+      orcid: 'https://orcid.org/0009-0003-1477-4912'
+    - given-names: Harrison
+      family-names: Ritz
+      affiliation: 'Princeton Neuroscience Institute, Princeton University, Princeton, USA'
+      orcid: 'https://orcid.org/0009-0003-1477-4912'
+    - given-names: Alex
+      family-names: Lopez Marquez
+      affiliation: 'Institut Guttmann, Barcelona, Spain'
+      orcid: 'https://orcid.org/0000-0002-3353-280X'
+    - given-names: Nathan
+      family-names: Azrak
+      orcid: 'https://orcid.org/0000-0001-7695-4634'
+    - given-names: Bruno
+      family-names: Aristimunha
+      affiliation: 'Université Paris-Saclay, LISN, Inria TAU/INRIA Nerv, France'
+      orcid: 'https://orcid.org/0000-0001-5258-2995'
     - given-names: Alexandre
       family-names: Gramfort
       affiliation: 'Université Paris-Saclay, Inria, CEA, Palaiseau, France'

README.md

@@ -58,3 +58,4 @@ Please also cite one of the following papers to credit BIDS, depending on which
 - [EEG-BIDS](https://doi.org/10.1038/s41597-019-0104-8)
 - [iEEG-BIDS](https://doi.org/10.1038/s41597-019-0105-7)
 - [NIRS-BIDS](https://doi.org/10.31219/osf.io/7nmcp)
+- [Motion-BIDS](https://doi.org/10.1038/s41597-024-03559-8)