Merge branch 'main' into main

.github/workflows/release.yml

@@ -0,0 +1,51 @@
+# Upload a Python Package using Twine when a release is created
+
+name: build
+on:  # yamllint disable-line rule:truthy
+  release:
+    types: [published]
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+permissions:
+  contents: read
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+      - run: python -m build --sdist --wheel
+      - run: twine check --strict dist/*
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+  pypi-upload:
+    needs: package
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+    permissions:
+      id-token: write  # for trusted publishing
+    environment:
+      name: pypi
+      url: https://pypi.org/p/mne
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        if: github.event_name == 'release'

.github/workflows/unit_tests.yml

@@ -7,6 +7,7 @@ concurrency:
 on:
   push:
     branches: ['**']
+    tags: ['**']
   pull_request:
     branches: ['**']
   schedule:
@@ -289,3 +290,33 @@ jobs:
       uses: codecov/codecov-action@v4
       with:
         files: ./coverage.xml
+
+  build_docs:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - uses: actions/cache@v4
+      with:
+        path: ${{ env.pythonLocation }}
+        key: build_docs-0-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        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
+      run: |
+        make build-doc
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: documentation
+        path: doc/_build/html

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.5
+    rev: v0.4.8
     hooks:
       - id: ruff
         name: ruff mne_bids/

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2018-2023, mne-bids developers
+Copyright (c) 2018, mne-bids developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

doc/_static/versions.json

@@ -1,12 +1,17 @@
 [
     {
-        "name": "0.15 (devel)",
+        "name": "0.16 (devel)",
         "version": "dev",
         "url": "https://mne.tools/mne-bids/dev/"
     },
     {
-        "name": "0.14 (stable)",
+        "name": "0.15 (stable)",
         "version": "stable",
+        "url": "https://mne.tools/mne-bids/v0.15/"
+    },
+    {
+        "name": "0.14",
+        "version": "0.14",
         "url": "https://mne.tools/mne-bids/v0.14/"
     },
     {

doc/whats_new.rst

@@ -7,26 +7,20 @@
 What's new?
 ===========
 
-.. _changes_0_15:
+.. _changes_0_16:
 
-Version 0.15 (unreleased)
+Version 0.16 (unreleased)
 -------------------------
 
 👩🏽‍💻 Authors
 ~~~~~~~~~~~~~~~
 
 The following authors contributed for the first time. Thank you so much! 🤩
 
-* `Daniel McCloy`_
-* `Mara Wolter`_
-* `Julius Welzel`_
+* nobody yet
 
 The following authors had contributed before. Thank you for sticking around! 🤘
 
-* `Alex Rockhill`_
-* `Eric Larson`_
-* `Laetitia Fesselier`_
-* `Richard Höchenberger`_
 * `Stefan Appelhoff`_
 
 Detailed list of changes
@@ -35,52 +29,27 @@ Detailed list of changes
 🚀 Enhancements
 ^^^^^^^^^^^^^^^
 
-- Including a description for ``onset`` and  ``duration`` in the ``events.json`` file, by `Julius Welzel`_ (:gh:`1255`)
+- nothing yet
 
 🧐 API and behavior changes
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-- The experimental support for running MNE-BIDS examples from your browser using Binder has
-  been removed, by `Stefan Appelhoff`_ (:gh:`1202`)
-- MNE-BIDS will no longer zero-pad ("zfill") entity indices passed to :class:`~mne_bids.BIDSPath`.
-  For example, If ``run=1`` is passed to MNE-BIDS, it will no longer be silently auto-converted to ``run-01``, by `Alex Rockhill`_ (:gh:`1215`)
-- MNE-BIDS will no longer warn about missing leading punctuation marks for extensions passed :class:`~mne_bids.BIDSPath`.
-  For example, MNE-BIDS will now silently auto-convert ``edf`` to ```.edf``, by `Alex Rockhill`_ (:gh:`1215`)
+- nothing yet
 
 🛠 Requirements
 ^^^^^^^^^^^^^^^
 
-- MNE-BIDS now requires Python 3.9 or higher.
-- MNE-BIDS now requires MNE-Python 1.5.0 or higher.
-- ``edfio`` replaces ``EDFlib-Python`` for export to EDF with MNE-Python >= 1.7.0.
-- Installing ``mne-bids[full]`` will now also install ``defusedxml`` on all platforms.
-- Version requirements for optional dependency packages have been bumped up, see installation instructions.
+- nothing yet
 
 🪲 Bug fixes
 ^^^^^^^^^^^^
 
-- The datatype in the dataframe returned by :func:`mne_bids.stats.count_events` is now
-  ``pandas.Int64Dtype`` instead of ``float64``, by `Eric Larson`_ (:gh:`1227`)
-- The :func:`mne_bids.copyfiles.copyfile_ctf` now accounts for files with ``.{integer}_meg4`` extension, instead of only .meg4,
-  when renaming the files of a .ds folder, by `Mara Wolter`_ (:gh:`1230`)
-- We fixed handling of time zones when reading ``*_scans.tsv`` files; specifically, non-UTC timestamps are now processed correctly,
-  by `Stefan Appelhoff`_ and `Richard Höchenberger`_  (:gh:`1240`)
+- nothing yet
 
 ⚕️ Code health
 ^^^^^^^^^^^^^^
 
-- The configuration of MNE-BIDS has been consolidated from several files (e.g., ``setup.cfg``,
-  ``setup.py``, ``requirements.txt``) and is now specified in a standard ``pyproject.toml``
-  file, by `Stefan Appelhoff`_ (:gh:`1202`)
-- Linting and code formatting is now done entirely using ``ruff``. Previously used tools
-  (e.g., ``flake8``, ``black``) have been fully replaced, by `Stefan Appelhoff`_ (:gh:`1203`)
-- The package build backend has been switched from ``setuptools`` to ``hatchling``. This
-  only affects users who build and install MNE-BIDS from source, and should not lead to
-  changed runtime behavior, by `Richard Höchenberger`_ (:gh:`1204`)
-- Display of the version number on the website is now truncated for over-long version strings,
-  by `Daniel McCloy`_ (:gh:`1206`)
-- The long deprecated ``events_data`` parameter has been fully removed from
-  :func:`~mne_bids.write_raw_bids` in favor of ``events``, by `Stefan Appelhoff`_ (:gh:`1229`)
+- nothing yet
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`
 

doc/whats_new_previous_releases.rst

@@ -7,6 +7,84 @@
 What was new in previous releases?
 ==================================
 
+.. _changes_0_15:
+
+Version 0.15 (2024-06-04)
+-------------------------
+
+👩🏽‍💻 Authors
+~~~~~~~~~~~~~~~
+
+The following authors contributed for the first time. Thank you so much! 🤩
+
+* `Mara Wolter`_
+* `Julius Welzel`_
+
+The following authors had contributed before. Thank you for sticking around! 🤘
+
+* `Alex Rockhill`_
+* `Daniel McCloy`_
+* `Eric Larson`_
+* `Laetitia Fesselier`_
+* `Mathieu Scheltienne`_
+* `Richard Höchenberger`_
+* `Stefan Appelhoff`_
+
+Detailed list of changes
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+🚀 Enhancements
+^^^^^^^^^^^^^^^
+
+- Including a description for ``onset`` and  ``duration`` in the ``events.json`` file, by `Julius Welzel`_ (:gh:`1255`)
+
+🧐 API and behavior changes
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+- The experimental support for running MNE-BIDS examples from your browser using Binder has
+  been removed, by `Stefan Appelhoff`_ (:gh:`1202`)
+- MNE-BIDS will no longer zero-pad ("zfill") entity indices passed to :class:`~mne_bids.BIDSPath`.
+  For example, If ``run=1`` is passed to MNE-BIDS, it will no longer be silently auto-converted to ``run-01``, by `Alex Rockhill`_ (:gh:`1215`)
+- MNE-BIDS will no longer warn about missing leading punctuation marks for extensions passed :class:`~mne_bids.BIDSPath`.
+  For example, MNE-BIDS will now silently auto-convert ``edf`` to ```.edf``, by `Alex Rockhill`_ (:gh:`1215`)
+- MNE-BIDS will no longer error during `~mne_bids.write_raw_bids` if there are ``BAD_ACQ_SKIP`` annotations in the raw file and no corresponding key in ``event_id``.
+  Instead, it will automatically add the necessary key and assign an unused integer event code to it. By `Daniel McCloy`_ (:gh:`1258`)
+
+🛠 Requirements
+^^^^^^^^^^^^^^^
+
+- MNE-BIDS now requires Python 3.9 or higher.
+- MNE-BIDS now requires MNE-Python 1.5.0 or higher.
+- ``edfio`` replaces ``EDFlib-Python`` for export to EDF with MNE-Python >= 1.7.0.
+- Installing ``mne-bids[full]`` will now also install ``defusedxml`` on all platforms.
+- Version requirements for optional dependency packages have been bumped up, see installation instructions.
+
+🪲 Bug fixes
+^^^^^^^^^^^^
+
+- The datatype in the dataframe returned by :func:`mne_bids.stats.count_events` is now
+  ``pandas.Int64Dtype`` instead of ``float64``, by `Eric Larson`_ (:gh:`1227`)
+- The :func:`mne_bids.copyfiles.copyfile_ctf` now accounts for files with ``.{integer}_meg4`` extension, instead of only .meg4,
+  when renaming the files of a .ds folder, by `Mara Wolter`_ (:gh:`1230`)
+- We fixed handling of time zones when reading ``*_scans.tsv`` files; specifically, non-UTC timestamps are now processed correctly,
+  by `Stefan Appelhoff`_ and `Richard Höchenberger`_  (:gh:`1240`)
+
+⚕️ Code health
+^^^^^^^^^^^^^^
+
+- The configuration of MNE-BIDS has been consolidated from several files (e.g., ``setup.cfg``,
+  ``setup.py``, ``requirements.txt``) and is now specified in a standard ``pyproject.toml``
+  file, by `Stefan Appelhoff`_ (:gh:`1202`)
+- Linting and code formatting is now done entirely using ``ruff``. Previously used tools
+  (e.g., ``flake8``, ``black``) have been fully replaced, by `Stefan Appelhoff`_ (:gh:`1203`)
+- The package build backend has been switched from ``setuptools`` to ``hatchling``. This
+  only affects users who build and install MNE-BIDS from source, and should not lead to
+  changed runtime behavior, by `Richard Höchenberger`_ (:gh:`1204`)
+- Display of the version number on the website is now truncated for over-long version strings,
+  by `Daniel McCloy`_ (:gh:`1206`)
+- The long deprecated ``events_data`` parameter has been fully removed from
+  :func:`~mne_bids.write_raw_bids` in favor of ``events``, by `Stefan Appelhoff`_ (:gh:`1229`)
+
 .. _changes_0_14:
 
 Version 0.14 (2023-11-16)

mne_bids/read.py

@@ -151,9 +151,18 @@ def _read_events(events, event_id, raw, bids_path=None):
                 'To specify custom event codes, please pass "event_id".'
             )
         else:
+            special_annots = {"BAD_ACQ_SKIP"}
             desc_without_id = sorted(
                 set(raw.annotations.description) - set(event_id.keys())
             )
+            # auto-add entries to `event_id` for "special" annotation values
+            # (but only if they're needed)
+            if set(desc_without_id) & special_annots:
+                for annot in special_annots:
+                    # use a value guaranteed to not be in use
+                    event_id = {annot: max(event_id.values()) + 90000} | event_id
+                # remove the "special" annots from the list of problematic annots
+                desc_without_id = sorted(set(desc_without_id) - special_annots)
             if desc_without_id:
                 raise ValueError(
                     f"The provided raw data contains annotations, but "