Misc maintenance (#1299)

* sort authors list

* misc

.github/workflows/unit_tests.yml

@@ -193,6 +193,7 @@ jobs:
     - name: Install MNE (previous stable)
       if: matrix.mne-version == 'mne-prev-stable'
       # Have to install NumPy<2.1 here because of a change in positional arg handling + MNE 1.7
+      # XXX: drop when mne < 1.8 is no longer supported
       run: |
         git clone --single-branch --branch maint/1.7 https://github.com/mne-tools/mne-python.git
         python -m pip install -e ./mne-python "numpy<2.1"

CONTRIBUTING.md

@@ -181,6 +181,12 @@ The latter command will result in a faster build but produce no plots in the exa
 More information on our documentation setup can be found in our
 [mne-bids WIKI](https://github.com/mne-tools/mne-bids/wiki).
 
+## A note on MNE-Python compatibility
+
+We aim to make `mne-bids` compatible with the current stable release of `mne`,  as well as the previous stable release.
+Both of these versions are tested in our continuous integration infrastructure.
+Additional versions of `mne` may be compatible, but this is not guaranteed.
+
 ## Instructions for first-time contributors
 
 When you are making your first contribution to `mne-bids`, we kindly request you to:

README.md

@@ -18,7 +18,8 @@ MNE-BIDS is a Python package that allows you to read and write
 Why?
 ----
 
-MNE-BIDS links BIDS and MNE-Python with the goal to make your analyses faster to code, more robust, and facilitate data and code sharing with co-workers and collaborators.
+MNE-BIDS links BIDS and MNE-Python with the goal to make your analyses faster to code and more robust,
+and to facilitate data and code sharing with co-workers and collaborators.
 
 How?
 ----
@@ -32,9 +33,8 @@ Getting Help
 ------------
 [<img alt="MNE Forum" src="https://user-images.githubusercontent.com/1681963/52239617-e2683480-289c-11e9-922b-5da55472e5b4.png" height=60/>](https://mne.discourse.group)
 
-For any usage questions, please post to the
-[MNE Forum](https://mne.discourse.group). Be sure to add the `mne-bids` tag to
-your question.
+For any usage questions, please post to the [MNE Forum](https://mne.discourse.group).
+Be sure to add the `mne-bids` tag to your question.
 
 Citing
 ------

doc/authors.rst

@@ -1,52 +1,52 @@
 .. _Aaron Earle-Richardson: https://github.com/Aaronearlerichardson
-.. _Mainak Jas: https://jasmainak.github.io/
-.. _Teon Brooks: https://teonbrooks.com
-.. _Chris Holdgraf: https://bids.berkeley.edu/people/chris-holdgraf
-.. _Matt Sanderson: https://github.com/monkeyman192
-.. _Stefan Appelhoff: https://stefanappelhoff.com/
-.. _Romain Quentin: https://github.com/romquentin
-.. _Dominik Welke: https://github.com/dominikwelke
-.. _Maximilien Chaumon: https://github.com/dnacombo
-.. _Ezequiel Mikulan: https://github.com/ezemikulan
-.. _Marijn van Vliet: https://github.com/wmvanvliet
-.. _Alex Rockhill: https://github.com/alexrockhill
-.. _Sophie Herbst: https://github.com/SophieHerbst
 .. _Adam Li: https://github.com/adam2392
-.. _Fu-Te Wong: https://github.com/zuxfoucault
-.. _Richard Höchenberger: https://github.com/hoechenberger
+.. _Alex Rockhill: https://github.com/alexrockhill
 .. _Alexandre Gramfort: http://alexandre.gramfort.net
+.. _Amaia Benitez: https://github.com/AmaiaBA
+.. _Anand Saini: https://github.com/anandsaini024
 .. _Ariel Rokem: https://github.com/arokem
-.. _Evgenii Kalenkovich: https://github.com/kalenkovich
 .. _Austin Hurst: https://github.com/a-hurst
-.. _Robert Luke: https://github.com/rob-luke
-.. _Ethan Knights: https://github.com/ethanknights
+.. _Bruno Hebling Vieira: https://github.com/bhvieira
+.. _Chris Holdgraf: https://bids.berkeley.edu/people/chris-holdgraf
+.. _Clemens Brunner: https://github.com/cbrnr
+.. _Daniel McCloy: http://dan.mccloy.info
+.. _Denis Engemann: https://github.com/dengemann
 .. _Diego Lozano-Soldevilla: https://github.com/dieloz
+.. _Dominik Welke: https://github.com/dominikwelke
 .. _Eduard Ort: https://github.com/eort
-.. _Tom Donoghue: https://github.com/TomDonoghue
-.. _Richard Köhler: https://github.com/richardkoehler
-.. _Sin Kim: https://ohbm.github.io/osr2020/volunteers/sin_kim.html
+.. _Eric Larson: https://github.com/larsoner
+.. _Ethan Knights: https://github.com/ethanknights
+.. _Evgenii Kalenkovich: https://github.com/kalenkovich
+.. _Ezequiel Mikulan: https://github.com/ezemikulan
+.. _Ford McDonald: https://github.com/fordmcdonald
+.. _Franziska von Albedyll: https://www.researchgate.net/profile/Franziska-Von-Albedyll
+.. _Fu-Te Wong: https://github.com/zuxfoucault
 .. _Jean-Rémi King: https://kingjr.github.io
+.. _Jonathan Vanhoecke: https://sfb-retune.de/people/jonathan-vanhoecke/
 .. _Julia Guiomar Niso Galán: https://github.com/guiomar
-.. _Eric Larson: https://github.com/larsoner
-.. _Clemens Brunner: https://github.com/cbrnr
+.. _Julius Welzel: https://github.com/JuliusWelzel
+.. _Kaare Mikkelsen: https://github.com/kaare-mikkelsen
 .. _Kambiz Tavabi: https://github.com/ktavabi
-.. _Franziska von Albedyll: https://www.researchgate.net/profile/Franziska-Von-Albedyll
-.. _Simon Kern: https://github.com/skjerns
-.. _Yorguin Mantilla: https://github.com/yjmantilla
-.. _Swastika Gupta: https://swastyy.github.io
-.. _Scott Huberty: https://github.com/scott-huberty
-.. _Anand Saini: https://github.com/anandsaini024
+.. _Laetitia Fesselier: https://github.com/laemtl
+.. _Mainak Jas: https://jasmainak.github.io/
+.. _Mara Wolter: https://github.com/marakw
+.. _Marijn van Vliet: https://github.com/wmvanvliet
 .. _Mathieu Scheltienne: https://github.com/mscheltienne
-.. _Denis Engemann: https://github.com/dengemann
-.. _Bruno Hebling Vieira: https://github.com/bhvieira
-.. _Daniel McCloy: http://dan.mccloy.info
+.. _Matt Sanderson: https://github.com/monkeyman192
+.. _Maximilien Chaumon: https://github.com/dnacombo
 .. _Moritz Gerster: http://moritz-gerster.com
-.. _Laetitia Fesselier: https://github.com/laemtl
-.. _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
-.. _Julius Welzel: https://github.com/JuliusWelzel
-.. _Kaare Mikkelsen: https://github.com/kaare-mikkelsen
-.. _Amaia Benitez: https://github.com/AmaiaBA
+.. _Richard Höchenberger: https://github.com/hoechenberger
+.. _Richard Köhler: https://github.com/richardkoehler
+.. _Robert Luke: https://github.com/rob-luke
+.. _Romain Quentin: https://github.com/romquentin
+.. _Scott Huberty: https://github.com/scott-huberty
+.. _Simon Kern: https://github.com/skjerns
+.. _Sin Kim: https://ohbm.github.io/osr2020/volunteers/sin_kim.html
+.. _Sophie Herbst: https://github.com/SophieHerbst
+.. _Stefan Appelhoff: https://stefanappelhoff.com/
+.. _Swastika Gupta: https://swastyy.github.io
+.. _Teon Brooks: https://teonbrooks.com
 .. _Thomas Hartmann: https://github.com/thht
+.. _Tom Donoghue: https://github.com/TomDonoghue
+.. _Yorguin Mantilla: https://github.com/yjmantilla

doc/index.rst

@@ -15,14 +15,14 @@ MNE-BIDS is a Python package that allows you to read and write
 
 Why?
 ----
-MNE-BIDS links BIDS and MNE-Python with the goal to make your analyses faster
-to code, more robust, and facilitate data and code sharing with co-workers
-and collaborators.
+MNE-BIDS links BIDS and MNE-Python with the goal to make your analyses faster to code and more robust,
+and to facilitate data and code sharing with co-workers and collaborators.
 
 What is this BIDS thing, anyway?
 --------------------------------
-BIDS, the Brain Imaging Data Structure, is a standard that describes how to
-organize neuroimaging and electrophysiological data. In particular, it defines:
+BIDS, the Brain Imaging Data Structure,
+is a standard that describes how to organize neuroimaging and electrophysiological data.
+In particular, it defines:
 
 - which file formats to use
 - how to name your files
@@ -36,9 +36,9 @@ Supported file formats
 ----------------------
 
 Currently, we support all file formats that are in the BIDS specification for MEG, EEG, fNIRS, and iEEG data.
-We also support a range of additional manufacturer formats to facilitate converting them to their BIDS-recommended
-formats. For example, if you have a Nihon Kohden file, you can read that file using MNE-Python, and
-then use MNE-BIDS convert it to the BrainVision format and store it according to BIDS.
+We also support a range of additional manufacturer formats to facilitate converting them to their BIDS-recommended formats.
+For example, if you have a Nihon Kohden file, you can read that file using MNE-Python,
+and then use MNE-BIDS convert it to the BrainVision format and store it according to BIDS.
 
 Citing MNE-BIDS
 ---------------

doc/install.rst

@@ -31,7 +31,7 @@ Optional:
 We recommend installing ``mne-bids`` into an isolated Python environment,
 for example created via ``conda``
 (may be obtained through `miniconda <https://docs.conda.io/en/latest/miniconda.html>`_).
-We require that you **use Python 3.9 or higher**.
+We require that you **use Python 3.10 or higher**.
 You may choose to install ``mne-bids`` into your isolated Python environment
 `via pip <#installation-via-pip>`_ or
 `via conda <#installation-via-conda>`_.

doc/whats_new.rst

@@ -47,7 +47,6 @@ Detailed list of changes
 🛠 Requirements
 ^^^^^^^^^^^^^^^
 
-- MNE-BIDS now requires MNE-Python 1.6.0 or higher.
 - MNE-BIDS now requires Python 3.10 or higher.
 
 🪲 Bug fixes
@@ -59,8 +58,8 @@ Detailed list of changes
 ⚕️ 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:)
+- 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>`
 

doc/whats_new_previous_releases.rst

@@ -511,7 +511,7 @@ Enhancements
 
 - Modify iEEG tutorial to use MNE ``raw`` object, by `Alex Rockhill`_ (:gh:`859`)
 
-- Add :func:`mne_bids.search_folder_for_text` to find specific metadata entries (e.g. all ``"n/a"`` sidecar data fields, or to check that "60 Hz" was written properly as the power line frequency), by `Alex Rockhill`_ (:gh: `870`)
+- Add :func:`mne_bids.search_folder_for_text` to find specific metadata entries (e.g. all ``"n/a"`` sidecar data fields, or to check that "60 Hz" was written properly as the power line frequency), by `Alex Rockhill`_ (:gh:`870`)
 
 - Add :func:`mne_bids.get_bids_path_from_fname` to return a :class:`mne_bids.BIDSPath` from a file path, by `Adam Li`_ (:gh:`883`)
 
@@ -566,7 +566,7 @@ Bug fixes
 
 - :func:`mne_bids.write_raw_bids` now raises an exception if the provided :class:`mne_bids.BIDSPath` doesn't contain ``subject`` and ``task`` entities, which are required for neurophysiological data, by `Richard Höchenberger`_ (:gh:`903`)
 
-- :func:`mne_bids.read_raw_bids` now handles datasets with multiple electrophysiological data types correctly, by `Richard Höchenberger`_ (:gh:`910`, :gh`916`)
+- :func:`mne_bids.read_raw_bids` now handles datasets with multiple electrophysiological data types correctly, by `Richard Höchenberger`_ (:gh:`910`, :gh:`916`)
 
 - More robust handling of situations where :func:`mne_bids.read_raw_bids` tries to read a file that does not exist, by `Richard Höchenberger`_ (:gh:`904`)
 

mne_bids/tests/test_write.py

@@ -623,7 +623,7 @@ def test_fif(_bids_validate, tmp_path):
     )
     assert_array_almost_equal(raw.get_data(), raw2.get_data())
     kwargs = dict()
-    # XXX: remove logic once support for mne<1.6 is dropped
+    # XXX: remove logic once support for mne<1.8 is dropped
     if "copy" in inspect.getfullargspec(epochs.get_data).kwonlyargs:
         kwargs["copy"] = False
     assert_array_almost_equal(

mne_bids/write.py

@@ -479,7 +479,7 @@ def _participants_tsv(raw, subject_id, fname, overwrite=False):
 
         # determine the age of the participant
         age = subject_info.get("birthday", None)
-        if isinstance(age, tuple):  # can be removed once MNE >= 1.8 is required
+        if isinstance(age, tuple):  # XXX: can be removed once MNE >= 1.8 is required
             age = date(*age)
         meas_date = raw.info.get("meas_date", None)
         if isinstance(meas_date, tuple | list | np.ndarray):

pyproject.toml

@@ -33,7 +33,6 @@ classifiers = [
     "Operating System :: POSIX :: Linux",
     "Operating System :: MacOS",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -53,7 +52,7 @@ full = [
     "pymatreader >= 0.0.30",
     "matplotlib >= 3.5.0",
     "pandas >= 1.3.2",
-    "EDFlib-Python >= 1.0.6", # drop once mne <1.7 is no longer supported
+    "EDFlib-Python >= 1.0.6", # XXX: drop once mne <1.7 is no longer supported
     "edfio >= 0.2.1",
     "defusedxml",             # For reading EGI MFF data and BrainVision montages
 ]