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

Author: drammock

.github/workflows/unit_tests.yml

@@ -212,7 +212,7 @@ jobs:
       uses: actions/cache@v4
       with:
         path: ${{ env.pythonLocation }}
-        key: test-2-${{ env.pythonLocation }}-${{ env.os }}-${{ hashFiles('pyproject.toml') }}
+        key: test-2-${{ env.pythonLocation }}-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.mne-version }}-${{ 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
@@ -311,7 +311,7 @@ jobs:
 
     - uses: actions/cache@v4
       with:
-        key: testing_data-1-${{ env.TESTING_VERSION }}
+        key: testing_data-1-${{ env.TESTING_VERSION }}-${{ matrix.mne-version }}
         path: ~/mne_data
       name: 'Cache testing data'
 

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.2
+    rev: v0.14.3
     hooks:
       - id: ruff
         name: ruff mne_bids/
@@ -37,3 +37,10 @@ repos:
     hooks:
       - id: toml-sort-fix
         files: pyproject.toml
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: file-contents-sorter
+        files: ^doc/authors.rst|^.mailmap
+        args: ["--ignore-case"]

CITATION.cff

@@ -225,6 +225,10 @@ authors:
       family-names: Aristimunha
       affiliation: 'Université Paris-Saclay, LISN, Inria TAU/INRIA Nerv, France'
       orcid: 'https://orcid.org/0000-0001-5258-2995'
+    - given-names: Kalle
+      family-names: Mäkelä
+      affiliation: 'University of Helsinki, Helsinki, Finland'
+      orcid: 'https://orcid.org/0009-0005-5706-0842'
     - given-names: Alexandre
       family-names: Gramfort
       affiliation: 'Université Paris-Saclay, Inria, CEA, Palaiseau, France'

doc/Makefile

@@ -18,11 +18,22 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(O)
+
+# Build without executing the example gallery (faster)
+html-noplot:
+	@$(SPHINXBUILD) $(SPHINXOPTS) -D plot_gallery=0 $(SOURCEDIR) $(BUILDDIR)
 
 # View the built documentation
+# If we build the example gallery, the index file is at _build/html/index.html
+# If we don't (e.g. html-noplot), then it is at _build/index.html
 view:
-	@python -c "import webbrowser; webbrowser.open_new_tab('file://$(PWD)/_build/html/index.html')"
+	@if [ -f "$(BUILDDIR)/html/index.html" ]; then \
+		python -c "import webbrowser; webbrowser.open_new_tab('file://$(PWD)/$(BUILDDIR)/html/index.html')"; \
+	elif [ -f "$(BUILDDIR)/index.html" ]; then \
+		python -c "import webbrowser; webbrowser.open_new_tab('file://$(PWD)/$(BUILDDIR)/index.html')"; \
+	else echo "No index.html file found to open. Did you build the docs?"; \
+	fi
 
 clean:
 	-rm -rf _build auto_examples generated

doc/authors.rst

@@ -32,6 +32,7 @@
 .. _Julia Guiomar Niso Galán: https://github.com/guiomar
 .. _Julius Welzel: https://github.com/JuliusWelzel
 .. _Kaare Mikkelsen: https://github.com/kaare-mikkelsen
+.. _Kalle Mäkelä: https://github.com/Kallemakela
 .. _Kambiz Tavabi: https://github.com/ktavabi
 .. _Laetitia Fesselier: https://github.com/laemtl
 .. _Mainak Jas: https://jasmainak.github.io/
@@ -60,4 +61,3 @@
 .. _waldie11: https://github.com/waldie11
 .. _William Turner: https://bootstrapbill.github.io/
 .. _Yorguin Mantilla: https://github.com/yjmantilla
-.. _Julius Welzel: https://github.com/JuliusWelzel

doc/install.rst

@@ -26,6 +26,7 @@ Optional:
 * ``pandas`` (>=1.3.2, for generating event statistics)
 * ``edfio`` (>=0.4.10, for writing EDF data)
 * ``defusedxml`` (for writing reading EGI MFF data and BrainVision montages)
+* ``filelock`` (for atomic file writing, and parallel processing support)
 
 We recommend installing ``mne-bids`` into an isolated Python environment,
 for example created via ``conda``

doc/whats_new.rst

@@ -22,6 +22,7 @@ The following authors contributed for the first time. Thank you so much! 🤩
 * `Julius Welzel`_
 * `Alex Lopez Marquez`_
 * `Bruno Aristimunha`_
+* `Kalle Mäkelä`_
 
 The following authors had contributed before. Thank you for sticking around! 🤘
 
@@ -37,15 +38,18 @@ Detailed list of changes
 - :func:`mne_bids.write_raw_bids()` has a new parameter `electrodes_tsv_task` which allows adding the `task` entity to the `electrodes.tsv` filepath, by `Alex Lopez Marquez`_ (:gh:`1424`)
 - Extended the configuration to recognise `motion` as a valid BIDS datatype by `Julius Welzel`_ (:gh:`1430`)
 - Better control of verbosity in several functions, by `Bruno Aristimunha`_ (:gh:`1449`)
+- Added parallel reading and writing in all the `open` operations using `_open_lock` mechanism from mne, creating a small wrapper to manage the locks by `Bruno Aristimunha`_ (:gh:`1451`)
 - :meth:`mne_bids.BIDSPath.match()` now short-circuits root directory scans when ``subject``, ``session``, or ``datatype`` entities are known, reducing lookup time on large datasets, by `Bruno Aristimunha`_ and `Maximilien Chaumon`_ (:gh:`1450`)
 
 🧐 API and behavior changes
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 -  `tracksys` accepted as argument in :class:`mne_bids.BIDSPath()` by `Julius Welzel`_ (:gh:`1430`)
+- :func:`mne_bids.read_raw_bids()` has a new parameter ``on_ch_mismatch`` that controls behaviour when there is a mismatch between channel names in ``channels.tsv`` and the raw data; accepted values are ``'raise'`` (default), ``'reorder'``, and ``'rename'``, by `Kalle Mäkelä`_.
 
 🛠 Requirements
 ^^^^^^^^^^^^^^^
+- Including ``filelock`` as a dependency to handle atomic file writing and parallel processing support by `Bruno Aristimunha`_ (:gh:`1451`)
 
 - None yet
 
@@ -54,6 +58,8 @@ Detailed list of changes
 
 - Fixed a bug that modified the name and help message of some of the available commands, by `Alex Lopez Marquez`_ (:gh:`1441`)
 - Updated MEG/iEEG writers to satisfy the stricter checks in the latest BIDS validator releases: BTi/4D run folders now retain their ``.pdf`` suffix (falling back to the legacy naming when an older validator is detected), KIT marker files encode the run via the ``acq`` entity instead of ``run``, datasets lacking iEEG montages receive placeholder ``electrodes.tsv``/``coordsystem.json`` files, and the ``AssociatedEmptyRoom`` entry stores dataset-relative paths  by `Bruno Aristimunha`_ (:gh:`1449`)
+- Made the lock helpers skip reference counting when the optional ``filelock`` dependency is missing, preventing spurious ``AttributeError`` crashes during reads, by `Bruno Aristimunha`_ (:gh:`1469`)
+- Fixed a bug in :func:`mne_bids.read_raw_bids` that caused it to fail when reading BIDS datasets where the acquisition time was specified in local time rather than UTC only in Windows, by `Bruno Aristimunha`_ (:gh:`1452`)
 
 ⚕️ Code health
 ^^^^^^^^^^^^^^