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.github/release.yaml

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changelog:
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exclude:
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authors:
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- dependabot[bot]
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- pre-commit-ci[bot]
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- github-actions[bot]

.github/workflows/cffconvert.yml

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runs-on: ubuntu-latest
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steps:
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- name: Check out a copy of the repository
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uses: actions/checkout@v4
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uses: actions/checkout@v5
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- name: Check whether the citation metadata from CITATION.cff is valid
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uses: citation-file-format/[email protected]

.github/workflows/release.yml

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package:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v5
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with:
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fetch-depth: 0
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fetch-tags: true
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- uses: actions/setup-python@v5
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- uses: actions/setup-python@v6
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with:
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python-version: '3.13'
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- name: Install dependencies
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name: pypi
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url: https://pypi.org/p/mne-bids
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- uses: actions/download-artifact@v4
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.github/workflows/unit_tests.yml

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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v6
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python-version: ${{ matrix.python-version }}
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- uses: actions/cache@v4
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python-version: ["3.10", "3.13"] # Oldest and newest supported versions
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steps:
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v6
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python-version: ${{ matrix.python-version }}
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pip check
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- name: Remove sdist install
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run: python -m pip uninstall -y mne-bids
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fetch-depth: 0
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- name: Remove wheel install
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run: python -m pip uninstall -y mne-bids
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- uses: actions/checkout@v5
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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- uses: actions/cache@v4

.pre-commit-config.yaml

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repos:
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.11.8
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rev: v0.12.12
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hooks:
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- id: ruff
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name: ruff mne_bids/
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files: ^examples/
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v6.0.0
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- id: end-of-file-fixer

CITATION.cff

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family-names: Dold
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affiliation: 'Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands'
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orcid: 'https://orcid.org/0009-0003-1477-4912'
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- given-names: Harrison
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family-names: Ritz
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affiliation: 'Princeton Neuroscience Institute, Princeton University, Princeton, USA'
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orcid: 'https://orcid.org/0009-0003-1477-4912'
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- given-names: Nathan
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family-names: Azrak
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orcid: 'https://orcid.org/0000-0001-7695-4634'
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- given-names: Alexandre
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family-names: Gramfort
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affiliation: 'Université Paris-Saclay, Inria, CEA, Palaiseau, France'

doc/_static/versions.json

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[
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{
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"name": "0.17 (devel)",
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"name": "0.18 (devel)",
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"version": "dev",
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"url": "https://mne.tools/mne-bids/dev/"
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},
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{
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"name": "0.16 (stable)",
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"name": "0.17 (stable)",
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"version": "stable",
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"url": "https://mne.tools/mne-bids/v0.17/"
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},
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{
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"name": "0.16",
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"version": "0.16",
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},
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{

doc/authors.rst

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.. _Ford McDonald: https://github.com/fordmcdonald
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.. _Franziska von Albedyll: https://www.researchgate.net/profile/Franziska-Von-Albedyll
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.. _Fu-Te Wong: https://github.com/zuxfoucault
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.. _Harrison Ritz: https://github.com/harrisonritz
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.. _Jean-Rémi King: https://kingjr.github.io
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.. _Jonathan Vanhoecke: https://sfb-retune.de/people/jonathan-vanhoecke/
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.. _Julia Guiomar Niso Galán: https://github.com/guiomar
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.. _Matthias Dold: https://www.linkedin.com/in/matthiasdold/
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.. _Maximilien Chaumon: https://github.com/dnacombo
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.. _Moritz Gerster: http://moritz-gerster.com
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.. _Nathan Azrak: https://github.com/nathan-az
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.. _Pierre Guetschel: https://github.com/PierreGtch
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.. _Richard Höchenberger: https://github.com/hoechenberger
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.. _Richard Köhler: https://github.com/richardkoehler
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.. _Teon Brooks: https://teonbrooks.com
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.. _Thomas Hartmann: https://github.com/thht
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.. _Tom Donoghue: https://github.com/TomDonoghue
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.. _waldie11: https://github.com/waldie11
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.. _William Turner: https://bootstrapbill.github.io/
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.. _Yorguin Mantilla: https://github.com/yjmantilla

doc/whats_new.rst

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.. currentmodule:: mne_bids
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.. include:: authors.rst
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What's new?
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===========
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.. _changes_0_17:
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.. _changes_0_18:
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Version 0.17 (unreleased)
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Version 0.18 (unreleased)
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-------------------------
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👩🏽‍💻 Authors
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~~~~~~~~~~~~~~~
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The following authors contributed for the first time. Thank you so much! 🤩
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* `Christian O'Reilly`_
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* `Berk Gerçek`_
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* `Arne Gottwald`_
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* `Matthias Dold`_
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* TBD
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The following authors had contributed before. Thank you for sticking around! 🤘
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* `Stefan Appelhoff`_
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* `Daniel McCloy`_
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* `Scott Huberty`_
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* `Pierre Guetschel`_
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* TBD
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Detailed list of changes
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~~~~~~~~~~~~~~~~~~~~~~~~
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🚀 Enhancements
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^^^^^^^^^^^^^^^
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- :func:`mne_bids.write_raw_bids()` can now handle mne `Raw` objects with `eyegaze` and `pupil` channels, by `Christian O'Reilly`_ (:gh:`1344`)
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- :func:`mne_bids.get_entity_vals()` has a new parameter ``ignore_suffixes`` to easily ignore sidecar files, by `Daniel McCloy`_ (:gh:`1362`)
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- Empty-room matching now preferentially finds recordings in the subject directory tagged as `task-noise` before looking in the `sub-emptyroom` directories. This adds support for a part of the BIDS specification for ER recordings, by `Berk Gerçek`_ (:gh:`1364`)
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- Path matching is now implemenented in a more efficient manner within :meth:`mne_bids.BIDSPath.match()` and :func:`mne_bids.find_matching_paths()`, by `Arne Gottwald` (:gh:`1355`)
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- :func:`mne_bids.get_entity_vals()` has a new parameter ``include_match`` to prefilter item matching and ignore non-matched items from begin of directory scan, by `Arne Gottwald` (:gh:`1355`)
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- Data from ``events.tsv`` can now be read into an OrderedDict using :func:`mne_bids.events_file_to_annotation_kwargs()`, by `Matthias Dold` (:gh:`1389`)
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- None yet
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🧐 API and behavior changes
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^^^^^^^^^^^^^^^^^^^^^^^^^^^
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- :func:`mne_bids.make_dataset_description` will now auto-generate basic ``GeneratedBy`` fields if ``generated_by=None``. To suppress the auto-generated fields, pass an empty list. By `Daniel McCloy`_ (:gh:`1384`)
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- None yet
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🛠 Requirements
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^^^^^^^^^^^^^^^
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- MNE-BIDS now requires ``mne`` 1.8 or higher.
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- None yet
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🪲 Bug fixes
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^^^^^^^^^^^^
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- :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`)
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- BIDS dictates that the recording entity should be displayed as "_recording-" in the filename. This PR makes :class:`mne_bids.BIDSPath` correctly display "_recording-" (instead of "_rec-") in BIDSPath.fpath. By `Scott Huberty`_ (:gh:`1348`)
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- :func:`mne_bids.make_dataset_description` now correctly encodes the dataset description as UTF-8 on disk, by `Scott Huberty`_ (:gh:`1357`)
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- Corrects extension when filtering filenames in :meth:`mne_bids.BIDSPath.match()` and :func:`mne_bids.find_matching_paths()`, by `Arne Gottwald` (:gh:`1355`)
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- Fix :class:`mne_bids.BIDSPath` partially matching a value, by `Pierre Guetschel` (:gh:`1388`)
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- None yet
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⚕️ Code health
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^^^^^^^^^^^^^^
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- Tests that were adding or deleting files to/from a session-scoped dataset now properly clean up after themselves, by `Daniel McCloy`_ (:gh:`1347`)
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- None yet
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:doc:`Find out what was new in previous releases <whats_new_previous_releases>`
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.. include:: authors.rst

doc/whats_new_previous_releases.rst

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What was new in previous releases?
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==================================
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.. _changes_0_17:
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Version 0.17 (2025-09-10)
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-------------------------
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👩🏽‍💻 Authors
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~~~~~~~~~~~~~~~
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The following authors contributed for the first time. Thank you so much! 🤩
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22+
* `Nathan Azrak`_
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* `Matthias Dold`_
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* `Berk Gerçek`_
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* `Arne Gottwald`_
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* `Christian O'Reilly`_
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* `Harrison Ritz`_
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* `waldie11`_
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The following authors had contributed before. Thank you for sticking around! 🤘
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* `Stefan Appelhoff`_
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* `Teon Brooks`_
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* `Pierre Guetschel`_
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* `Richard Höchenberger`_
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* `Scott Huberty`_
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* `Eric Larson`_
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* `Daniel McCloy`_
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40+
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Detailed list of changes
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~~~~~~~~~~~~~~~~~~~~~~~~
43+
44+
🚀 Enhancements
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^^^^^^^^^^^^^^^
46+
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- :func:`mne_bids.write_raw_bids()` can now handle mne `Raw` objects with `eyegaze` and `pupil` channels, by `Christian O'Reilly`_ (:gh:`1344`)
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- :func:`mne_bids.get_entity_vals()` has a new parameter ``ignore_suffixes`` to easily ignore sidecar files, by `Daniel McCloy`_ (:gh:`1362`)
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- Empty-room matching now preferentially finds recordings in the subject directory tagged as `task-noise` before looking in the `sub-emptyroom` directories. This adds support for a part of the BIDS specification for ER recordings, by `Berk Gerçek`_ (:gh:`1364`)
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- Path matching is now implemenented in a more efficient manner within :meth:`mne_bids.BIDSPath.match()` and :func:`mne_bids.find_matching_paths()`, by `Arne Gottwald` (:gh:`1355`)
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- :func:`mne_bids.get_entity_vals()` has a new parameter ``include_match`` to prefilter item matching and ignore non-matched items from begin of directory scan, by `Arne Gottwald` (:gh:`1355`)
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- Data from ``events.tsv`` can now be read into an OrderedDict using :func:`mne_bids.events_file_to_annotation_kwargs()`, by `Matthias Dold` (:gh:`1389`)
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- Read the optionally present extra columns from ``events.tsv`` and pass them to :class:`mne.Annotations`, by `Pierre Guetschel` (:gh:`1401`)
54+
- ``_filter_fnames()`` now correctly checks the default extension, correcting suffix filtering, by `Nathan Azrak` (:gh:`1427`)
55+
56+
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🧐 API and behavior changes
58+
^^^^^^^^^^^^^^^^^^^^^^^^^^^
59+
60+
- :func:`mne_bids.make_dataset_description` will now auto-generate basic ``GeneratedBy`` fields if ``generated_by=None``. To suppress the auto-generated fields, pass an empty list. By `Daniel McCloy`_ (:gh:`1384`)
61+
- Add requirements that ``root``, ``subject``, ``task`` attributes must be set when using :func:`mne_bids.read_raw_bids` to avoid implicit behavior and file ambiguity, by `Teon Brooks`_ (:gh:`1414`)
62+
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🛠 Requirements
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^^^^^^^^^^^^^^^
65+
66+
- MNE-BIDS now requires ``mne`` 1.8 or higher.
67+
68+
🪲 Bug fixes
69+
^^^^^^^^^^^^
70+
71+
- :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`)
72+
- BIDS dictates that the recording entity should be displayed as "_recording-" in the filename. This PR makes :class:`mne_bids.BIDSPath` correctly display "_recording-" (instead of "_rec-") in BIDSPath.fpath. By `Scott Huberty`_ (:gh:`1348`)
73+
- :func:`mne_bids.make_dataset_description` now correctly encodes the dataset description as UTF-8 on disk, by `Scott Huberty`_ (:gh:`1357`)
74+
- Corrects extension when filtering filenames in :meth:`mne_bids.BIDSPath.match()` and :func:`mne_bids.find_matching_paths()`, by `Arne Gottwald` (:gh:`1355`)
75+
- Fix :class:`mne_bids.BIDSPath` partially matching a value, by `Pierre Guetschel` (:gh:`1388`)
76+
- Ensures that ``check`` parameter in :meth:`mne_bids.BIDSPath.update()` is passed to :class:`mne_bids.BIDSPath`, by `Teon Brooks`_ (:gh:`1411`)
77+
- minor: added `T2w` to the suffix allowlist, by `Harrison Ritz`_ (:gh:`1420`)
78+
79+
⚕️ Code health
80+
^^^^^^^^^^^^^^
81+
82+
- Tests that were adding or deleting files to/from a session-scoped dataset now properly clean up after themselves, by `Daniel McCloy`_ (:gh:`1347`)
83+
84+
:doc:`Find out what was new in previous releases <whats_new_previous_releases>`
85+
86+
.. include:: authors.rst
87+
88+
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.. _changes_0_16:
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Version 0.16 (2024-11-16)

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