BUG: Fix bug with parallel doc build (mne-tools#13140)

Author: larsoner

doc/sphinxext/mne_doc_utils.py

@@ -51,125 +51,46 @@ def reset_warnings(gallery_conf, fname):
     )
     # internal warnings
     warnings.filterwarnings("default", module="sphinx")
-    # allow these warnings, but don't show them
+    # don't error on joblib warning during parallel doc build otherwise we get a
+    # cryptic deadlock instead of a nice traceback
+    warnings.filterwarnings(
+        "always",
+        "A worker stopped while some jobs were given to the executor.*",
+        category=UserWarning,
+    )
+    # ignore (DeprecationWarning)
     for key in (
-        "invalid version and will not be supported",  # pyxdf
-        "distutils Version classes are deprecated",  # seaborn and neo
-        "is_categorical_dtype is deprecated",  # seaborn
-        "`np.object` is a deprecated alias for the builtin `object`",  # pyxdf
-        # nilearn, should be fixed in > 0.9.1
-        "In future, it will be an error for 'np.bool_' scalars to",
-        # sklearn hasn't updated to SciPy's sym_pos dep
-        "The 'sym_pos' keyword is deprecated",
-        # numba
-        "`np.MachAr` is deprecated",
-        # joblib hasn't updated to avoid distutils
-        "distutils package is deprecated",
-        # jupyter
-        "Jupyter is migrating its paths to use standard",
-        r"Widget\..* is deprecated\.",
-        # PyQt6
-        "Enum value .* is marked as deprecated",
-        # matplotlib PDF output
-        "The py23 module has been deprecated",
-        # pkg_resources
-        "Implementing implicit namespace packages",
-        "Deprecated call to `pkg_resources",
-        # nilearn
-        "pkg_resources is deprecated as an API",
-        r"The .* was deprecated in Matplotlib 3\.7",
-        # Matplotlib->tz
-        r"datetime\.datetime\.utcfromtimestamp",
-        # joblib
-        r"ast\.Num is deprecated",
-        r"Attribute n is deprecated and will be removed in Python 3\.14",
-        # numpydoc
-        r"ast\.NameConstant is deprecated and will be removed in Python 3\.14",
-        # pooch
-        r"Python 3\.14 will, by default, filter extracted tar archives.*",
-        # seaborn
-        r"DataFrameGroupBy\.apply operated on the grouping columns.*",
-        # pandas
-        r"\nPyarrow will become a required dependency of pandas.*",
-        # latexcodec
-        r"open_text is deprecated\. Use files.*",
-        # python-quantities, via neo
-        r"numpy\.core is deprecated and has been renamed to numpy\._core",
-        # matplotlib
-        "__array_wrap__ must accept context and return_scalar.*",
         # nibabel
         "__array__ implementation doesn't accept.*",
+        # pybtex (from sphinxcontrib-bibtex)
+        "pkg_resources is deprecated as an API.*",
+        "\nImplementing implicit namespace packages",
+        # latexcodec
+        r"open_text is deprecated\. Use files",
     ):
         warnings.filterwarnings(  # deal with other modules having bad imports
             "ignore", message=f".*{key}.*", category=DeprecationWarning
         )
-    warnings.filterwarnings(
-        "ignore",
-        message="Matplotlib is currently using agg, which is a non-GUI backend.*",
-    )
-    warnings.filterwarnings(
-        "ignore",
-        message=".*is non-interactive, and thus cannot.*",
-    )
-    # seaborn
-    warnings.filterwarnings(
-        "ignore",
-        message="The figure layout has changed to tight",
-        category=UserWarning,
-    )
-    # xarray/netcdf4
-    warnings.filterwarnings(
-        "ignore",
-        message=r"numpy\.ndarray size changed, may indicate.*",
-        category=RuntimeWarning,
-    )
-    # qdarkstyle
-    warnings.filterwarnings(
-        "ignore",
-        message=r".*Setting theme=.*6 in qdarkstyle.*",
-        category=RuntimeWarning,
-    )
-    # pandas, via seaborn (examples/time_frequency/time_frequency_erds.py)
+    # ignore (UserWarning)
     for message in (
-        "use_inf_as_na option is deprecated.*",
-        r"iteritems is deprecated.*Use \.items instead\.",
-        "is_categorical_dtype is deprecated.*",
-        "The default of observed=False.*",
-        "When grouping with a length-1 list-like.*",
+        # Matplotlib
+        ".*is non-interactive, and thus cannot.*",
     ):
         warnings.filterwarnings(
             "ignore",
             message=message,
-            category=FutureWarning,
+            category=UserWarning,
+        )
+    # ignore (RuntimeWarning)
+    for message in (
+        # mne-python config file "corruption" due to doc build parallelization
+        ".*The MNE-Python config file.*valid JSON.*",
+    ):
+        warnings.filterwarnings(
+            "ignore",
+            message=message,
+            category=RuntimeWarning,
         )
-    # pandas in 50_epochs_to_data_frame.py
-    warnings.filterwarnings(
-        "ignore", message=r"invalid value encountered in cast", category=RuntimeWarning
-    )
-    # xarray _SixMetaPathImporter (?)
-    warnings.filterwarnings(
-        "ignore", message=r"falling back to find_module", category=ImportWarning
-    )
-    # Sphinx deps
-    warnings.filterwarnings(
-        "ignore", message="The str interface for _CascadingStyleSheet.*"
-    )
-    # mne-qt-browser until > 0.5.2 released
-    warnings.filterwarnings(
-        "ignore",
-        r"mne\.io\.pick.channel_indices_by_type is deprecated.*",
-    )
-    # parallel building
-    warnings.filterwarnings(
-        "ignore",
-        "A worker stopped while some jobs were given to the executor.*",
-        category=UserWarning,
-    )
-    # neo
-    warnings.filterwarnings(
-        "ignore",
-        "The 'copy' argument in Quantity is deprecated.*",
-    )
 
     # In case we use np.set_printoptions in any tutorials, we only
     # want it to affect those:

mne/event.py

@@ -767,6 +767,7 @@ def find_events(
     picks = pick_channels(raw.info["ch_names"], include=stim_channel)
     if len(picks) == 0:
         raise ValueError("No stim channel found to extract event triggers.")
+    logger.info(f"Finding events on: {', '.join(raw.ch_names[pick] for pick in picks)}")
     data, _ = raw[picks, :]
 
     events_list = []

mne/io/eyelink/_utils.py

@@ -440,7 +440,10 @@ def _set_missing_values(df, columns):
     missing_vals = (".", "MISSING_DATA")
     for col in columns:
         # we explicitly use numpy instead of pd.replace because it is faster
-        df[col] = np.where(df[col].isin(missing_vals), np.nan, df[col])
+        # if a stim channel (DIN) we should use zero so it can cast to int properly
+        # in find_events
+        replacement = 0 if col == "DIN" else np.nan
+        df[col] = np.where(df[col].isin(missing_vals), replacement, df[col])
 
 
 def _sort_by_time(df, col="time"):
@@ -517,9 +520,13 @@ def _adjust_times(
     new_times = pd.DataFrame(
         np.arange(first, last + step / 2, step), columns=[time_col]
     )
-    return pd.merge_asof(
+    df = pd.merge_asof(
         new_times, df, on=time_col, direction="nearest", tolerance=step / 2
     )
+    # fix DIN NaN values
+    if "DIN" in df.columns:
+        df["DIN"] = df["DIN"].fillna(0)
+    return df
 
 
 def _find_overlaps(df, max_time=0.05):

mne/io/eyelink/tests/test_eyelink.py

@@ -8,6 +8,7 @@
 import pytest
 from numpy.testing import assert_allclose
 
+from mne import find_events
 from mne._fiff.constants import FIFF
 from mne._fiff.pick import _DATA_CH_TYPES_SPLIT
 from mne.datasets.testing import data_path, requires_testing_data
@@ -285,6 +286,9 @@ def test_multi_block_misc_channels(fname, tmp_path):
     assert not np.isnan(data[0, np.where(times < 1)[0]]).any()
     assert np.isnan(data[0, np.logical_and(times > 1, times <= 1.1)]).all()
 
+    # smoke test for reading events with missing samples (should not emit a warning)
+    find_events(raw, verbose=True)
+
 
 @requires_testing_data
 @pytest.mark.parametrize("this_fname", (fname, fname_href))

tutorials/preprocessing/90_eyetracking_data.py

@@ -9,11 +9,11 @@
 a pupillary light reflex task. We will combine the eye-tracking and EEG data, and plot
 the ERP and pupil response to the light flashes (i.e. the pupillary light reflex).
 
-"""  # noqa: E501
+"""
+
 # Authors: Scott Huberty <[email protected]>
 #          Dominik Welke <[email protected]>
 #
-#
 # License: BSD-3-Clause
 # Copyright the MNE-Python contributors.