Merge branch 'main' into main

.circleci/config.yml

@@ -48,7 +48,13 @@ jobs:
             name: Build the documentation
             no_output_timeout: 30m
             command: |
-              make build-doc
+              make build-doc 2>&1 | tee sphinx_log.txt
+
+        - run:
+            name: Check sphinx log for warnings (which are treated as errors)
+            when: always
+            command: |
+              ! grep "^.*WARNING: .*$" sphinx_log.txt
 
         - persist_to_workspace:
             root: doc/_build

.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:
@@ -203,7 +204,7 @@ jobs:
     - name: Install MNE (previous stable)
       if: matrix.mne-version == 'mne-prev-stable'
       run: |
-        git clone --single-branch --branch maint/1.5 https://github.com/mne-tools/mne-python.git
+        git clone --single-branch --branch maint/1.6 https://github.com/mne-tools/mne-python.git
         python -m pip install -e ./mne-python
 
     - name: Install MNE (main)
@@ -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

@@ -1,10 +1,11 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.5
+    rev: v0.5.5
     hooks:
       - id: ruff
         name: ruff mne_bids/
         files: ^mne_bids/
+        args: ["--fix"]
       - id: ruff
         name: ruff examples/
         # D103: missing docstring in public function

CITATION.cff

@@ -179,6 +179,10 @@ authors:
       family-names: Wolter
       orcid: 'https://orcid.org/0000-0002-6785-9886'
       affiliation: 'Centre for Integrative Neuroscience, Tübingen, Germany'
+    - given-names: Julius
+      family-names: Welzel
+      affiliation: 'Department of Neurology, Kiel University, Germany'
+      orcid: 'https://orcid.org/0000-0003-4782-5360'
     - given-names: Alexandre
       family-names: Gramfort
       affiliation: 'Université Paris-Saclay, Inria, CEA, Palaiseau, France'

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2018-2023, mne-bids developers
+Copyright (c) 2017, The 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/authors.rst

@@ -41,8 +41,9 @@
 .. _Daniel McCloy: http://dan.mccloy.info
 .. _Moritz Gerster: http://moritz-gerster.com
 .. _Laetitia Fesselier: https://github.com/laemtl
-.. _Jonathan Vanhoecke: https://github.com/JonathanVHoecke
+.. _Jonathan Vanhoecke: https://sfb-retune.de/people/jonathan-vanhoecke/
 .. _Ford McDonald: https://github.com/fordmcdonald
 .. _Pierre Guetschel: https://github.com/PierreGtch
 .. _Mara Wolter: https://github.com/marakw
 .. _Amaia Benitez: https://github.com/AmaiaBA
+.. _Julius Welzel: https://github.com/JuliusWelzel

doc/conf.py

@@ -1,14 +1,16 @@
 """Configure details for documentation with sphinx."""
+
+# Authors: The MNE-BIDS developers
+# SPDX-License-Identifier: BSD-3-Clause
+
 import os
 import sys
 from datetime import date
 
-import sphinx_gallery  # noqa: F401
 from sphinx.config import is_serializable
 
 import mne_bids
 
-
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -92,10 +94,10 @@
 
 # General information about the project.
 project = "MNE-BIDS"
-td = date.today()
-copyright = "2017-%s, MNE Developers. Last updated on %s" % (td.year, td.isoformat())
+today = date.today().isoformat()
+copyright = f"2017, The MNE-BIDS developers. Last updated on {today}"  # noqa: A001
 
-author = "MNE Developers"
+author = "The MNE-BIDS developers"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/install.rst

@@ -12,7 +12,7 @@ Dependencies
 
 Required:
 
-* ``mne`` (>=1.5)
+* ``mne`` (>=1.6)
 * ``numpy`` (>=1.21.2)
 * ``scipy`` (>=1.7.0)
 

doc/sphinxext/gen_cli.py

@@ -3,11 +3,10 @@
 Inspired by MNE-Python's `gen_commands.py`
 see: github.com/mne-tools/mne-python/blob/main/doc/sphinxext/gen_commands.py
 """
-# Authors: Eric Larson <[email protected]>
-#          Alexandre Gramfort <[email protected]>
-#          Stefan Appelhoff <[email protected]>
-#
-# License: BSD-3-Clause
+
+# Authors: The MNE-BIDS developers
+# SPDX-License-Identifier: BSD-3-Clause
+
 import glob
 import os
 import shutil
@@ -44,14 +43,14 @@ def setup(app):
 
 command_rst = """
 
-.. _gen_%s:
+.. _gen_{0}:
 
-%s
-%s
+{1}
+{2}
 
 .. rst-class:: callout
 
-%s
+{3}
 
 """
 
@@ -92,7 +91,7 @@ def generate_cli_rst(app=None):
             # Add code styling for the "Usage: " line
             for li, line in enumerate(output):
                 if line.startswith("Usage: mne_bids "):
-                    output[li] = "Usage: ``%s``" % line[7:]
+                    output[li] = f"Usage: ``{line[7:]}``"
                     break
 
             # Turn "Options:" into field list
@@ -105,8 +104,7 @@ def generate_cli_rst(app=None):
                 output.insert(ii + 4, "")
             output = "\n".join(output)
             f.write(
-                command_rst
-                % (
+                command_rst.format(
                     cmd_name,
                     cmd_name.replace("mne_bids_", "mne_bids "),
                     "=" * len(cmd_name),

doc/sphinxext/gh_substitutions.py

@@ -6,6 +6,10 @@
 https://doughellmann.com/blog/2010/05/09/defining-custom-roles-in-sphinx/
 
 """
+
+# Authors: The MNE-BIDS developers
+# SPDX-License-Identifier: BSD-3-Clause
+
 from docutils.nodes import reference
 from docutils.parsers.rst.roles import set_classes
 

doc/whats_new.rst

@@ -7,26 +7,25 @@
 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! 🤩
 
+* `Amaia Benitez`_
 * `Daniel McCloy`_
 * `Mara Wolter`_
-* `Amaia Benitez`_
+
 
 The following authors had contributed before. Thank you for sticking around! 🤘
 
-* `Alex Rockhill`_
+* `Daniel McCloy`_
 * `Eric Larson`_
-* `Laetitia Fesselier`_
-* `Richard Höchenberger`_
 * `Stefan Appelhoff`_
 
 Detailed list of changes
@@ -40,21 +39,13 @@ Detailed list of changes
 🧐 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`)
+- :func:`mne_bids.read_raw_bids` no longer warns about unit changes in channels upon reading, as that information is taken from ``channels.tsv`` and judged authorative, by `Stefan Appelhoff`_ (:gh:`1282`)
+- MEG OPM channels are now experimentally included, by `Amaia Benitez`_ (:gh:`1222`)
 
 🛠 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.
+- MNE-BIDS now requires MNE-Python 1.6.0 or higher.
 
 🪲 Bug fixes
 ^^^^^^^^^^^^
@@ -65,23 +56,13 @@ Detailed list of changes
   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`)
-- Fixed KeyError in ``write_raw_bids()`` for OPM data by including additional OPM channels in ``get_coil_types()`` by `Amaia Benitez`_ (:gh:`1222`)
+- When anonymizing the date of a recording, MNE-BIDS will no longer error during `~mne_bids.write_raw_bids` if passing a `~mne.io.Raw` instance to ``empty_room``, by `Daniel McCloy`_ (:gh:`1270`)
 
 ⚕️ 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`)
+- Keep MNE-BIDS up to date with recent changes on participant birthday date handling in MNE-Python, by `Eric Larson`_ (gh:1278:)
+- Make rules for linting more strict, make quality assessment exceptions less permissive, by `Stefan Appelhoff`_ (gh:1283:)
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`