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sappelhoff committed Aug 24, 2024
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1 change: 1 addition & 0 deletions .github/workflows/unit_tests.yml
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Expand Up @@ -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"
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6 changes: 6 additions & 0 deletions CONTRIBUTING.md
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Expand Up @@ -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:
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8 changes: 4 additions & 4 deletions README.md
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Expand Up @@ -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?
----
Expand All @@ -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
------
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16 changes: 8 additions & 8 deletions doc/index.rst
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Expand Up @@ -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
Expand All @@ -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
---------------
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2 changes: 1 addition & 1 deletion doc/install.rst
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Expand Up @@ -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>`_.
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1 change: 0 additions & 1 deletion doc/whats_new.rst
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Expand Up @@ -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
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9 changes: 2 additions & 7 deletions mne_bids/tests/test_write.py
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Expand Up @@ -7,7 +7,6 @@
# SPDX-License-Identifier: BSD-3-Clause

import codecs
import inspect
import json
import os
import os.path as op
Expand Down Expand Up @@ -622,13 +621,9 @@ def test_fif(_bids_validate, tmp_path):
raw2, events2, event_id=event_id, tmin=-0.2, tmax=0.5, preload=True
)
assert_array_almost_equal(raw.get_data(), raw2.get_data())
kwargs = dict()
# XXX: remove logic once support for mne<1.6 is dropped
if "copy" in inspect.getfullargspec(epochs.get_data).kwonlyargs:
kwargs["copy"] = False
assert_array_almost_equal(
epochs.get_data(**kwargs),
epochs2.get_data(**kwargs),
epochs.get_data(),
epochs2.get_data(),
decimal=4,
)
_bids_validate(bids_root)
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2 changes: 1 addition & 1 deletion mne_bids/write.py
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Expand Up @@ -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):
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3 changes: 1 addition & 2 deletions pyproject.toml
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Expand Up @@ -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",
Expand All @@ -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
]
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