Merge branch 'main' into fix/channel-mismatch

Author: Kallemakela

.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'
 

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/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

@@ -39,6 +39,7 @@ 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
@@ -48,6 +49,7 @@ Detailed list of changes
 
 🛠 Requirements
 ^^^^^^^^^^^^^^^
+- Including ``filelock`` as a dependency to handle atomic file writing and parallel processing support by `Bruno Aristimunha`_ (:gh:`1451`)
 
 - None yet
 
@@ -56,6 +58,7 @@ 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`)
+- 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
 ^^^^^^^^^^^^^^