FIX: Replace np.fromstring with np.frombuffer in GDF reader for NumPy…

[devparikh0506]

… ≥1.24

Note that .encode() was added because np.frombuffer requires bytes.

Reference issue (if any)

Fixes #13414.

What does this implement/fix?

• np.fromstring in binary mode was removed in NumPy ≥1.24.
• Replaced with np.frombuffer(etmode.encode(), dtype=UINT8) in _read_gdf_header.
• This preserves the original behavior and restores compatibility.

How was this tested?

• Ran pytest mne/io/edf/tests successfully (all relevant tests passed).
• Verified on BCI Competition IV Dataset 2b .gdf files using Python 3.11.7 + NumPy 2.3.3.
• read_raw_gdf("B0101T.gdf", preload=True) now works without errors.

Additional information

• No API changes.
• Minor internal fix for compatibility with modern NumPy.

[welcome]

Hello! 👋 Thanks for opening your first pull request here! ❤️ We will try to get back to you soon. 🚴

[larsoner]

We decode it just to encode it? Maybe we could do instead

etmode = fid.read(1) if len(etmode): etmode = np.frombuffer(etmode, dtype=UINT8)[0] 

[larsoner]

Also needs a changelog entry in doc/changes/devel/13415.bugfix.rst with :newcontrib: and a name+link in doc/changes/names.inc. Thanks for working on this @devparikh0506 !

[drammock]

would be great if the test coverage gap @scott-huberty mentioned in #13414 (comment) could also be closed here. @devparikh0506 let us know if you want help with that part.

[devparikh0506]

Hi @larsoner, thanks for pointing out the improvement! I’ve updated the PR with the suggested change.

Also @drammock, I’d be happy to add test coverage for this. Could you please provide a brief outline of the steps or the best place in the test suite to add it? That would help me make sure I implement it correctly.

[scott-huberty]

Could you please provide a brief outline of the steps or the best place in the test suite to add it?

@devparikh0506 we are trying to figure that part out. Stand by!

[scott-huberty]

Needs mne-tools/mne-testing-data#124

@devparikh0506 I submitted a PR to add a test file to mne-testing-data . Once it is merged and @larsoner cuts a new release, You will need to update this PR to point to the newly released testing dataset, by following the directions here:

mne-python/mne/datasets/config.py

Lines 85 to 94 in a8e2fe8

	# To update the `testing` or `misc` datasets, push or merge commits to their
	# respective repos, and make a new release of the dataset on GitHub. Then
	# update the checksum in the MNE_DATASETS dict below, and change version
	# here: ↓↓↓↓↓↓↓↓
	RELEASES = dict(
	testing="0.161",
	misc="0.27",
	phantom_kit="0.2",
	ucl_opm_auditory="0.2",
	)

mne-python/mne/datasets/config.py

Lines 115 to 122 in a8e2fe8

	# Testing and misc are at the top as they're updated most often
	MNE_DATASETS["testing"] = dict(
	archive_name=f"{TESTING_VERSIONED}.tar.gz",
	hash="md5:a32cfb9e098dec39a5f3ed6c0833580d",
	url=(
	"https://codeload.github.com/mne-tools/mne-testing-data/"
	f"tar.gz/{RELEASES['testing']}"
	),

Once this is updated, you can run:

import mne testing_fpath = mne.datasets.testing.data_path(force_update=True) # FYI The new test file will be located at: testing_fpath / "GDF" / "test_gdf_1.99.gdf"

Which should download the updated testing dataset. At this point you can add a unit test to mne/io/edf/tests/test_gdf.py, that reads 'test_gdf_1.99.gdf' . This should confirm that your patch works and address our coverage gap!

Let us know if you have any questions along the way or need any help.

[scott-huberty]

https://github.com/mne-tools/mne-testing-data/releases/tag/0.165

release: 0.165
md5: 5b791cb91e0f62732aa5827d9aba706d

[scott-huberty]

Hey @devparikh0506 Let us know if you don't have time to work on this and need us to push it over the line! (i.e. close this PR and open a superceding PR that builds off the work done here).

[devparikh0506]

Hey @devparikh0506 Let us know if you don't have time to work on this and need us to push it over the line! (i.e. close this PR and open a superceding PR that builds off the work done here).

Hi @scott-huberty, Thank you for checking in. I am currently traveling and will not be able to write the tests or complete this work. I apologize for the delay, and I would appreciate it if you could take it forward.