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

Author: waldie11

.github/workflows/release.yml

@@ -19,6 +19,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          fetch-tags: true
       - uses: actions/setup-python@v5
         with:
           python-version: '3.12'
@@ -32,6 +35,7 @@ jobs:
         with:
           name: dist
           path: dist
+          include-hidden-files: true
 
   pypi-upload:
     needs: package

.github/workflows/unit_tests.yml

@@ -22,6 +22,9 @@ jobs:
         python-version: ["3.12"]
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        fetch-tags: true
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
@@ -65,6 +68,9 @@ jobs:
         python -m pip install build twine
 
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        fetch-tags: true
     - name: Build sdist
       run: python -m build --sdist
     - name: Check sdist
@@ -81,6 +87,9 @@ jobs:
       run: python -m pip uninstall -y mne-bids
 
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        fetch-tags: true
     - name: Build wheel
       run: python -m build --wheel
     - name: Check wheel
@@ -97,6 +106,9 @@ jobs:
       run: python -m pip uninstall -y mne-bids
 
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        fetch-tags: true
     - name: Test extras install
       run: |
         python -m pip install .[full]
@@ -161,6 +173,9 @@ jobs:
       FORCE_COLOR: true
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        fetch-tags: true
 
     - name: Set up Node.js
       uses: actions/setup-node@v4
@@ -275,7 +290,7 @@ jobs:
       run: make test
 
     - name: Upload coverage stats to codecov
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         files: ./coverage.xml
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -289,6 +304,9 @@ jobs:
         python-version: ["3.12"]
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        fetch-tags: true
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
@@ -310,3 +328,4 @@ jobs:
       with:
         name: documentation
         path: doc/_build/html
+        include-hidden-files: true

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.3
+    rev: v0.8.2
     hooks:
       - id: ruff
         name: ruff mne_bids/
@@ -33,7 +33,7 @@ repos:
       - id: check-docstring-first
 
   - repo: https://github.com/pappasam/toml-sort
-    rev: v0.23.1
+    rev: v0.24.2
     hooks:
       - id: toml-sort-fix
         files: pyproject.toml

CITATION.cff

@@ -198,6 +198,10 @@ authors:
       family-names: Turner
       affiliation: 'Wu Tsai Neurosciences Institute, Stanford University'
       orcid: 'https://orcid.org/0000-0001-8639-9769'
+    - given-names: Christian
+      family-names: O'Reilly
+      affiliation: 'Computer Science and Engineering, University of South Carolina'
+      orcid: 'https://orcid.org/0000-0002-3149-4934'
     - given-names: Alexandre
       family-names: Gramfort
       affiliation: 'Université Paris-Saclay, Inria, CEA, Palaiseau, France'

doc/authors.rst

@@ -51,3 +51,4 @@
 .. _Tom Donoghue: https://github.com/TomDonoghue
 .. _William Turner: https://bootstrapbill.github.io/
 .. _Yorguin Mantilla: https://github.com/yjmantilla
+.. _Christian O'Reilly: https://github.com/christian-oreilly

doc/whats_new.rst

@@ -7,74 +7,51 @@
 What's new?
 ===========
 
-.. _changes_0_16:
+.. _changes_0_17:
 
-Version 0.16 (2024-11-16)
+Version 0.17 (unreleased)
 -------------------------
 
 👩🏽‍💻 Authors
 ~~~~~~~~~~~~~~~
 
 The following authors contributed for the first time. Thank you so much! 🤩
 
-* `Aaron Earle-Richardson`_
-* `Amaia Benitez`_
-* `Kaare Mikkelsen`_
-* `Simon Kern`_
-* `Thomas Hartmann`_
-* `William Turner`_
+* `Christian O'Reilly`_
 
 The following authors had contributed before. Thank you for sticking around! 🤘
 
-* `Daniel McCloy`_
-* `Eric Larson`_
-* `Mathieu Scheltienne`_
-* `Richard Höchenberger`_
-* `Scott Huberty`_
 * `Stefan Appelhoff`_
+* `Daniel McCloy`_
 
 Detailed list of changes
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
 🚀 Enhancements
 ^^^^^^^^^^^^^^^
 
-- :meth:`mne_bids.BIDSPath.match()` and :func:`mne_bids.find_matching_paths` now have additional parameters ``ignore_json`` and ``ignore_nosub``, to give users more control over which type of files are matched, by `Kaare Mikkelsen`_ (:gh:`1281`)
-- :func:`mne_bids.write_raw_bids()` can now handle event metadata as a pandas DataFrame, by `Thomas Hartmann`_ (:gh:`1285`)
+- :func:`mne_bids.write_raw_bids()` can now handle mne `Raw` objects with `eyegaze` and `pupil` channels, by `Christian O'Reilly`_ (:gh:`1344`)
+
 
 🧐 API and behavior changes
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-- :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`)
-- :func:`mne_bids.mark_channels` will no longer create a ``status_description`` column filled with ``n/a`` in the ``channels.tsv`` file, by `Stefan Appelhoff`_ (:gh:`1293`)
-- :func:`mark_channels(..., ch_names=[]) <mne_bids.mark_channels>` now raises a deprecation warning, and in future its behavior will change from marking *all* channels to marking *no* channels; to avoid the warning use ``mark_channels(..., ch_names="all")``, by `Daniel McCloy`_ (:gh:`1307`)
-
+- Nothing yet
 
 🛠 Requirements
 ^^^^^^^^^^^^^^^
 
-- MNE-BIDS now requires Python 3.10 or higher.
-- MNE-BIDS now requires ``mne`` 1.7 or higher.
+- Nothing yet
 
 🪲 Bug fixes
 ^^^^^^^^^^^^
 
-- Writing MEGIN data with MNE channel types `chpi` will now map to BIDS type HLU by `Simon Kern`_ (:gh:`1325`)
-- 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`)
-- Dealing with alphanumeric ``sub`` entity labels is now fixed for :func:`~mne_bids.write_raw_bids`, by `Aaron Earle-Richardson`_ (:gh:`1291`)
-- When processing subject_info data that MNE Python imports as numpy arrays with only one item, MNE-BIDS now unpacks these, resulting in a correct participants.tsv, by `Thomas Hartmann`_ (:gh:`1310`)
-- Fixed broken links in examples 7 and 8, by `William Turner`_ (:gh:`1316`)
-- All valid extensions for ``README`` files are now accepted. This prevents an extra ``README`` file being created, when one with a ``.txt``, ``.md``, or ``.rst`` extension is already present. By `Thomas Hartmann`_ (:gh:`1318`)
-- A warning was given if no events were provided but the task was starting with 'rest' as recommended by `Simon Kern`_ (:gh:`1327`)
+- :func:`mne_bids.read_raw_bids` can optionally return an ``event_id`` dictionary suitable for use with :func:`mne.events_from_annotations`, and if a ``values`` column is present in ``events.tsv`` it will be used as the source of the integer event ID codes, by `Daniel McCloy`_ (:gh:`1349`)
 
 ⚕️ Code health
 ^^^^^^^^^^^^^^
 
-- 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`)
-- Updates to use ``intersphinx_registry`` and sorting TOML files, by `Mathieu Scheltienne`_ (:gh:`1314`)
-- Fix dropdown menu in website, by `Scott Huberty`_ (:gh:`1298`)
+- Tests that were adding or deleting files to/from a session-scoped dataset now properly clean up after themselves, by `Daniel McCloy`_ (:gh:`1347`)
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`
 

doc/whats_new_previous_releases.rst

@@ -7,6 +7,75 @@
 What was new in previous releases?
 ==================================
 
+.. _changes_0_16:
+
+Version 0.16 (2024-11-16)
+-------------------------
+
+👩🏽‍💻 Authors
+~~~~~~~~~~~~~~~
+
+The following authors contributed for the first time. Thank you so much! 🤩
+
+* `Aaron Earle-Richardson`_
+* `Amaia Benitez`_
+* `Kaare Mikkelsen`_
+* `Simon Kern`_
+* `Thomas Hartmann`_
+* `William Turner`_
+
+The following authors had contributed before. Thank you for sticking around! 🤘
+
+* `Daniel McCloy`_
+* `Eric Larson`_
+* `Mathieu Scheltienne`_
+* `Richard Höchenberger`_
+* `Scott Huberty`_
+* `Stefan Appelhoff`_
+
+Detailed list of changes
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+🚀 Enhancements
+^^^^^^^^^^^^^^^
+
+- :meth:`mne_bids.BIDSPath.match()` and :func:`mne_bids.find_matching_paths` now have additional parameters ``ignore_json`` and ``ignore_nosub``, to give users more control over which type of files are matched, by `Kaare Mikkelsen`_ (:gh:`1281`)
+- :func:`mne_bids.write_raw_bids()` can now handle event metadata as a pandas DataFrame, by `Thomas Hartmann`_ (:gh:`1285`)
+
+🧐 API and behavior changes
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+- :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`)
+- :func:`mne_bids.mark_channels` will no longer create a ``status_description`` column filled with ``n/a`` in the ``channels.tsv`` file, by `Stefan Appelhoff`_ (:gh:`1293`)
+- :func:`mark_channels(..., ch_names=[]) <mne_bids.mark_channels>` now raises a deprecation warning, and in future its behavior will change from marking *all* channels to marking *no* channels; to avoid the warning use ``mark_channels(..., ch_names="all")``, by `Daniel McCloy`_ (:gh:`1307`)
+
+
+🛠 Requirements
+^^^^^^^^^^^^^^^
+
+- MNE-BIDS now requires Python 3.10 or higher.
+- MNE-BIDS now requires ``mne`` 1.7 or higher.
+
+🪲 Bug fixes
+^^^^^^^^^^^^
+
+- Writing MEGIN data with MNE channel types `chpi` will now map to BIDS type HLU by `Simon Kern`_ (:gh:`1325`)
+- 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`)
+- Dealing with alphanumeric ``sub`` entity labels is now fixed for :func:`~mne_bids.write_raw_bids`, by `Aaron Earle-Richardson`_ (:gh:`1291`)
+- When processing subject_info data that MNE Python imports as numpy arrays with only one item, MNE-BIDS now unpacks these, resulting in a correct participants.tsv, by `Thomas Hartmann`_ (:gh:`1310`)
+- Fixed broken links in examples 7 and 8, by `William Turner`_ (:gh:`1316`)
+- All valid extensions for ``README`` files are now accepted. This prevents an extra ``README`` file being created, when one with a ``.txt``, ``.md``, or ``.rst`` extension is already present. By `Thomas Hartmann`_ (:gh:`1318`)
+- A warning was given if no events were provided but the task was starting with 'rest' as recommended by `Simon Kern`_ (:gh:`1327`)
+
+⚕️ Code health
+^^^^^^^^^^^^^^
+
+- 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`)
+- Updates to use ``intersphinx_registry`` and sorting TOML files, by `Mathieu Scheltienne`_ (:gh:`1314`)
+- Fix dropdown menu in website, by `Scott Huberty`_ (:gh:`1298`)
+
 .. _changes_0_15:
 
 Version 0.15 (2024-06-04)
@@ -1179,5 +1248,4 @@ People who contributed to this release (in alphabetical order):
 * `Stefan Appelhoff`_
 * `Teon Brooks`_
 
-
 .. include:: authors.rst

examples/anonymize_dataset.py

@@ -194,7 +194,7 @@
 # To ensure results are reproducible across runs, you can pass the
 # ``random_state`` parameter, causing the random number generator to produce
 # the same results every time you execute the function. This may come in handy
-# e.g. in situations where you discover a problem with the data while working
+# in situations where you discover a problem with the data while working
 # with the anonymized dataset, fix the issue in the original dataset, and
 # run anonymization again.
 #
@@ -203,6 +203,15 @@
 # in a dataset with multiple subjects will the effects of randomly-picked IDs
 # become apparent.)
 #
+# A good random seed is truly random. Avoid using random seeds from popular
+# culture, like "42", or "1337". To obtain a truly random seed, you can paste
+# the following into your console:
+# ``python -c "import secrets; print(secrets.randbits(31))"``
+# Here, 31 bits correspond to the maximum seed "size" that the the legacy
+# ``RandomState`` by NumPy, which many scientific libraries still rely on,
+# can accept. For more information, see also this blog post on
+# `NumPy RNG best practices <https://blog.scientific-python.org/numpy/numpy-rng/>`_.
+#
 # .. note::
 #    Passing ``random_state`` merely guarantees that subject IDs and time shift
 #    remain the same across anonymization runs if the original dataset
@@ -218,6 +227,6 @@
         bids_root_in=bids_root,
         bids_root_out=bids_root_anon,
         datatypes="meg",
-        random_state=42,
+        random_state=293201004,
     )
     print_dir_tree(bids_root_anon)