[pull] main from mne-tools:main

doc/changes/dev/13497.bugfix.rst

@@ -0,0 +1 @@
+Fixed a bug where ``mne.io.read_raw_gdf`` failed with NumPy ≥1.24 due to the removal of ``np.fromstring`` binary mode. Replaced with ``np.frombuffer`` for compatibility, by :newcontrib:`Dev Parikh`.

doc/changes/names.inc

@@ -67,6 +67,7 @@
 .. _David Sabbagh: https://github.com/DavidSabbagh
 .. _Demetres Kostas: https://github.com/kostasde
 .. _Denis Engemann: https://denis-engemann.de
+.. _Dev Parikh: https://github.com/devparikh0506
 .. _Dinara Issagaliyeva: https://github.com/dissagaliyeva
 .. _Diptyajit Das: https://github.com/dasdiptyajit
 .. _Dirk Gütlin: https://github.com/DiGyt

doc/sphinxext/related_software.py

@@ -37,7 +37,7 @@
 
 # If it's not available on PyPI, add it to this dict:
 MANUAL_PACKAGES = {
-    # TODO: These packages are not pip-installable as of 2024/07/17, so we have to
+    # TODO: These packages are not pip-installable as of 2025/11/19, so we have to
     # manually populate them -- should open issues on their package repos.
     "best-python": {
         "Home-page": "https://github.com/multifunkim/best-python",
@@ -54,68 +54,34 @@
     # This package does not provide wheels, so don't force CircleCI to build it.
     # If it eventually provides binary wheels we could add it to
     # `tools/circleci_dependencies.sh` and remove from here.
+    # https://github.com/Eelbrain/Eelbrain/issues/130
     "eelbrain": {
         "Home-page": "https://eelbrain.readthedocs.io/en/stable/",
         "Summary": "Open-source Python toolkit for MEG and EEG data analysis.",
     },
-    # mne-kit-gui requires mayavi (ugh)
-    "mne-kit-gui": {
-        "Home-page": "https://github.com/mne-tools/mne-kit-gui",
-        "Summary": "A module for KIT MEG coregistration.",
-    },
-    # fsleyes requires wxpython, which needs to build
-    "fsleyes": {
-        "Home-page": "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes",
-        "Summary": "FSLeyes is the FSL image viewer.",
-    },
-    # dcm2niix must be built from source
-    "dcm2niix": {
-        "Home-page": "https://github.com/rordenlab/dcm2niix",
-        "Summary": "DICOM to NIfTI converter",
-    },
     # TODO: these do not set a valid homepage or documentation page on PyPI
     "python-picard": {  # https://github.com/mind-inria/picard/issues/60
         "Home-page": "https://github.com/mind-inria/picard",
         "Summary": "Preconditioned ICA for Real Data",
     },
-    "eeg_positions": {
-        "Home-page": "https://eeg-positions.readthedocs.io",
-        "Summary": "Compute and plot standard EEG electrode positions.",
-    },
-    "mne-faster": {
-        "Home-page": "https://github.com/wmvanvliet/mne-faster",
-        "Summary": "MNE-FASTER: automatic bad channel/epoch/component detection.",  # noqa: E501
-    },
     "mne-features": {
         "Home-page": "https://mne.tools/mne-features",
         "Summary": "MNE-Features software for extracting features from multivariate time series",  # noqa: E501
     },
-    "mne-rsa": {
-        "Home-page": "https://users.aalto.fi/~vanvlm1/mne-rsa",
-        "Summary": "Code for performing Representational Similarity Analysis on MNE-Python data structures.",  # noqa: E501
-    },
     "mffpy": {
         "Home-page": "https://github.com/BEL-Public/mffpy",
         "Summary": "Reader and Writer for Philips' MFF file format.",
     },
-    "emd": {
-        "Home-page": "https://emd.readthedocs.io/en/stable",
-        "Summary": "Empirical Mode Decomposition in Python.",
-    },
-    # Needs a release with homepage set properly
-    "meegkit": {
-        "Home-page": "https://nbara.github.io/python-meegkit",
-        "Summary": "Denoising tools for M/EEG processing.",
-    },
     # not on PyPI
     "conpy": {
         "Home-page": "https://github.com/aaltoimaginglanguage/conpy",
         "Summary": "Functions and classes for performing connectivity analysis on MEG data.",  # noqa: E501
     },
 }
 
-REQUIRE_METADATA = os.getenv("MNE_REQUIRE_RELATED_SOFTWARE_INSTALLED", "false").lower()
-REQUIRE_METADATA = REQUIRE_METADATA in ("true", "1")
+REQUIRE_INSTALLED = os.getenv("MNE_REQUIRE_RELATED_SOFTWARE_INSTALLED", "false").lower()
+REQUIRE_INSTALLED = REQUIRE_INSTALLED in ("true", "1")
+REQUIRE_METADATA = REQUIRE_INSTALLED
 
 # These packages pip-install with a different name than the package name
 RENAMES = {
@@ -201,7 +167,7 @@ def _get_packages() -> dict[str, str]:
             if "Home-page" in md:
                 url = md["Home-page"]
             else:
-                for prefix in ("homepage", "documentation"):
+                for prefix in ("homepage", "documentation", "user documentation"):
                     for key, val in md.items():
                         if key == "Project-URL" and val.lower().startswith(
                             f"{prefix}, "
@@ -217,6 +183,12 @@ def _get_packages() -> dict[str, str]:
                     continue
             out[package]["url"] = url
             out[package]["description"] = md["Summary"].replace("\n", "")
+    if not REQUIRE_INSTALLED:
+        reasons = [
+            reason
+            for reason in reasons
+            if "not found, needs to be installed" not in reason
+        ]
     reason_str = "\n".join(reasons)
     if reason_str and REQUIRE_METADATA:
         raise ExtensionError(
@@ -263,6 +235,9 @@ def setup(app):
 
 
 if __name__ == "__main__":  # pragma: no cover
+    # running `python doc/sphinxext/related_software.py` for testing
+    # require metadata for any installed packages (for debugging)
+    REQUIRE_METADATA = True
     items = list(RelatedSoftwareDirective.run(None)[0].children)
     print(f"Got {len(items)} related software packages:")
     for item in items:

doc/sphinxext/related_software.txt

@@ -5,6 +5,7 @@ autoreject
 bycycle
 conpy
 curryreader
+dcm2niix
 eeg_positions
 emd
 fooof

doc/sphinxext/related_software_nodeps.txt

@@ -0,0 +1,4 @@
+# deps with onerous requirements (tensorflow, wxPython, mayavi)
+cross-domain-saliency-maps
+fsleyes
+mne-kit-gui

mne/io/edf/edf.py

@@ -1734,9 +1734,9 @@ def _read_gdf_header(fname, exclude, include=None):
                 edf_info["data_offset"] + edf_info["n_records"] * edf_info["bytes_tot"]
             )
             fid.seek(etp)  # skip data to go to event table
-            etmode = fid.read(1).decode()
-            if etmode != "":
-                etmode = np.fromstring(etmode, UINT8).tolist()[0]
+            etmode = fid.read(1)
+            if isinstance(etmode, (bytes, bytearray)) and len(etmode) == 1:
+                etmode = np.frombuffer(etmode, dtype=UINT8).tolist()[0]
 
                 if edf_info["number"] < 1.94:
                     sr = read_from_file_or_buffer(fid, UINT8, 3)

mne/io/edf/tests/test_gdf.py

@@ -199,3 +199,13 @@ def test_gdf_read_from_file_like():
 
     with pytest.raises(Exception, match="Bad GDF file provided."):
         read_raw_gdf(BytesIO(), preload=True)
+
+
+@testing.requires_testing_data
+@pytest.mark.filterwarnings("ignore:Highpass cutoff frequency")
+def test_gh_13414():
+    """Test handling bytes objects when reading GDF events."""
+    fpath = data_path / "GDF" / "test_gdf_1.99.gdf"
+    raw = read_raw_gdf(fpath)
+    # Should be 1 event in this GDF file.
+    assert len(raw.annotations) == 1

tools/circleci_dependencies.sh

@@ -11,4 +11,5 @@ python -m pip install --upgrade --progress-bar off \
     "git+https://github.com/mne-tools/mne-qt-browser.git" \
     "git+https://github.com/pyvista/pyvista.git" \
     "git+https://github.com/sphinx-gallery/sphinx-gallery.git"
-python -m pip install --upgrade --progress-bar off --no-deps cross-domain-saliency-maps
+python -m pip install --upgrade --progress-bar off --no-deps \
+    -r doc/sphinxext/related_software_nodeps.txt