MAINT: Post-release deprecations, updates [circle deploy] (#11887)

README.rst

@@ -88,17 +88,17 @@ Dependencies
 The minimum required dependencies to run MNE-Python are:
 
 - Python >= 3.8
-- NumPy >= 1.20.2
-- SciPy >= 1.6.3
-- Matplotlib >= 3.4.0
+- NumPy >= 1.21.2
+- SciPy >= 1.7.1
+- Matplotlib >= 3.4.3
 - pooch >= 1.5
 - tqdm
 - Jinja2
 - decorator
 
 For full functionality, some functions require:
 
-- Scikit-learn >= 0.24.2
+- Scikit-learn >= 1.0
 - joblib >= 0.15 (for parallelization control)
 - mne-qt-browser >= 0.1 (for fast raw data visualization)
 - Qt5 >= 5.12 via one of the following bindings (for fast raw data visualization and interactive 3D visualization):
@@ -108,10 +108,10 @@ For full functionality, some functions require:
   - PyQt5 >= 5.12
   - PySide2 >= 5.12
 
-- Numba >= 0.53.1
+- Numba >= 0.54.0
 - NiBabel >= 3.2.1
 - OpenMEEG >= 2.5.6
-- Pandas >= 1.2.4
+- Pandas >= 1.3.2
 - Picard >= 0.3
 - CuPy >= 9.0.0 (for NVIDIA CUDA acceleration)
 - DIPY >= 1.4.0

doc/changes/latest.inc

@@ -0,0 +1,34 @@
+.. NOTE: we use cross-references to highlight new functions and classes.
+   Please follow the examples below like :func:`mne.stats.f_mway_rm`, so the
+   whats_new page will have a link to the function/class documentation.
+
+.. NOTE: there are 3 separate sections for changes, based on type:
+   - "Enhancements" for new features
+   - "Bugs" for bug fixes
+   - "API changes" for backward-incompatible changes
+
+.. NOTE: changes from first-time contributors should be added to the TOP of
+   the relevant section (Enhancements / Bugs / API changes), and should look
+   like this (where xxxx is the pull request number):
+
+       - description of enhancement/bugfix/API change (:gh:`xxxx` by
+         :newcontrib:`Firstname Lastname`)
+
+   Also add a corresponding entry for yourself in doc/changes/names.inc
+
+.. _current:
+
+Current (1.6.dev0)
+------------------
+
+Enhancements
+~~~~~~~~~~~~
+- None yet
+
+Bugs
+~~~~
+- None yet
+
+API changes
+~~~~~~~~~~~
+- None yet

doc/changes/latest.inc.template

@@ -18,7 +18,7 @@
 
 .. _current:
 
-Current (1.1.dev0)
+Current (X.Y.dev0)
 ------------------
 
 Enhancements

doc/install/installers.rst

@@ -17,7 +17,7 @@ Got any questions? Let us know on the `MNE Forum`_!
         :class-content: text-center
         :name: linux-installers
 
-        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.4.2/MNE-Python-1.4.2_0-Linux.sh
+        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.5.0/MNE-Python-1.5.0_0-Linux.sh
             :ref-type: ref
             :color: primary
             :shadow:
@@ -31,14 +31,14 @@ Got any questions? Let us know on the `MNE Forum`_!
 
         .. code-block:: console
 
-            $ sh ./MNE-Python-1.4.2_0-Linux.sh
+            $ sh ./MNE-Python-1.5.0_0-Linux.sh
 
 
     .. tab-item:: macOS (Intel)
         :class-content: text-center
         :name: macos-intel-installers
 
-        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.4.2/MNE-Python-1.4.2_0-macOS_Intel.pkg
+        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.5.0/MNE-Python-1.5.0_0-macOS_Intel.pkg
             :ref-type: ref
             :color: primary
             :shadow:
@@ -54,7 +54,7 @@ Got any questions? Let us know on the `MNE Forum`_!
         :class-content: text-center
         :name: macos-apple-installers
 
-        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.4.2/MNE-Python-1.4.2_0-macOS_M1.pkg
+        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.5.0/MNE-Python-1.5.0_0-macOS_M1.pkg
             :ref-type: ref
             :color: primary
             :shadow:
@@ -70,7 +70,7 @@ Got any questions? Let us know on the `MNE Forum`_!
         :class-content: text-center
         :name: windows-installers
 
-        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.4.2/MNE-Python-1.4.2_0-Windows.exe
+        .. button-link:: https://github.com/mne-tools/mne-installers/releases/download/v1.5.0/MNE-Python-1.5.0_0-Windows.exe
             :ref-type: ref
             :color: primary
             :shadow:
@@ -118,7 +118,7 @@ information, including a line that will read something like:
 
 .. code-block::
 
-   Using Python: /some/directory/mne-python_1.4.2_0/bin/python
+   Using Python: /some/directory/mne-python_1.5.0_0/bin/python
 
 This path is what you need to enter in VS Code when selecting the Python
 interpreter.

doc/whats_new.rst

@@ -7,6 +7,7 @@ What's new
 
 .. currentmodule:: mne
 
+.. include:: changes/latest.inc
 .. include:: changes/1.5.inc
 .. include:: changes/1.4.inc
 .. include:: changes/1.3.inc

mne/epochs.py

@@ -1287,7 +1287,7 @@ def plot(
         n_epochs=20,
         n_channels=20,
         title=None,
-        events=None,
+        events=False,
         event_color=None,
         order=None,
         show=True,

mne/io/eyelink/eyelink.py

@@ -60,22 +60,20 @@
 @fill_doc
 def read_raw_eyelink(
     fname,
-    preload=False,
-    verbose=None,
+    *,
     create_annotations=True,
     apply_offsets=False,
     find_overlaps=False,
     overlap_threshold=0.05,
-    gap_description=None,
+    preload=False,
+    verbose=None,
 ):
     """Reader for an Eyelink .asc file.
 
     Parameters
     ----------
     fname : path-like
         Path to the eyelink file (.asc).
-    %(preload)s
-    %(verbose)s
     create_annotations : bool | list (default True)
         Whether to create mne.Annotations from occular events
         (blinks, fixations, saccades) and experiment messages. If a list, must
@@ -100,16 +98,8 @@ def read_raw_eyelink(
         the left and right eyes are separated by less than 50 ms, and the blink stop
         times of the left and right eyes are separated by less than 50 ms, then the
         blink will be merged into a single :class:`mne.Annotations`.
-    gap_description : str (default 'BAD_ACQ_SKIP')
-        Label for annotations that span across the gap period between the
-        blocks. Uses ``'BAD_ACQ_SKIP'`` by default so that these time periods will
-        be considered bad by MNE and excluded from operations like epoching.
-
-        .. deprecated:: 1.5
-
-           This parameter is deprecated and will be removed in version 1.6. Use
-           :meth:`mne.Annotations.rename` if you want something other than
-           ``BAD_ACQ_SKIP`` as the annotation label.
+    %(preload)s
+    %(verbose)s
 
     Returns
     -------
@@ -132,13 +122,12 @@ def read_raw_eyelink(
 
     raw_eyelink = RawEyelink(
         fname,
-        preload=preload,
-        verbose=verbose,
         create_annotations=create_annotations,
         apply_offsets=apply_offsets,
         find_overlaps=find_overlaps,
         overlap_threshold=overlap_threshold,
-        gap_desc=gap_description,
+        preload=preload,
+        verbose=verbose,
     )
     return raw_eyelink
 
@@ -171,14 +160,6 @@ class RawEyelink(BaseRaw):
         the :class:`mne.Annotations` will be kept separate (i.e. "blink_L",
         "blink_R"). If the gap is smaller than the threshold, the
         :class:`mne.Annotations` will be merged (i.e. "blink_both").
-    gap_desc : str
-        If there are multiple recording blocks in the file, the description of
-        the annotation that will span across the gap period between the
-        blocks. Default is ``None``, which uses 'BAD_ACQ_SKIP' by default so that these
-        timeperiods will be considered bad by MNE and excluded from operations like
-        epoching. Note that this parameter is deprecated and will be removed in 1.6.
-        Use ``mne.annotations.rename`` instead.
-
 
     %(preload)s
     %(verbose)s
@@ -197,13 +178,13 @@ class RawEyelink(BaseRaw):
     def __init__(
         self,
         fname,
-        preload=False,
-        verbose=None,
+        *,
         create_annotations=True,
         apply_offsets=False,
         find_overlaps=False,
         overlap_threshold=0.05,
-        gap_desc=None,
+        preload=False,
+        verbose=None,
     ):
         logger.info("Loading {}".format(fname))
 
@@ -214,16 +195,6 @@ def __init__(
         self._meas_date = None
         self._rec_info = None
         self._ascii_sfreq = None
-        if gap_desc is None:
-            gap_desc = "BAD_ACQ_SKIP"
-        else:
-            warn(
-                "gap_description is deprecated in 1.5 and will be removed in 1.6, "
-                "use raw.annotations.rename to use a description other than "
-                "'BAD_ACQ_SKIP'",
-                FutureWarning,
-            )
-        self._gap_desc = gap_desc
         self.dataframes = {}
 
         # ======================== Parse ASCII File =========================
@@ -244,7 +215,7 @@ def __init__(
         if n_blocks > 1:
             logger.info(
                 f"There are {n_blocks} recording blocks in this file. Times between"
-                f"  blocks will be annotated with {self._gap_desc}."
+                f"  blocks will be annotated with BAD_ACQ_SKIP."
             )
             self.dataframes["samples"] = _adjust_times(
                 self.dataframes["samples"], self._ascii_sfreq
@@ -651,11 +622,10 @@ def _create_info(self, ch_names, sfreq):
     def _make_gap_annots(self, key="recording_blocks"):
         """Create Annotations for gap periods between recording blocks."""
         df = self.dataframes[key]
-        gap_desc = self._gap_desc
         onsets = df["end_time"].iloc[:-1]
         diffs = df["time"].shift(-1) - df["end_time"]
         durations = diffs.iloc[:-1]
-        descriptions = [gap_desc] * len(onsets)
+        descriptions = ["BAD_ACQ_SKIP"] * len(onsets)
         return Annotations(onset=onsets, duration=durations, description=descriptions)
 
     def _make_eyelink_annots(self, df_dict, create_annots, apply_offsets):

mne/utils/__init__.py

@@ -67,7 +67,6 @@
     _import_nibabel,
     _import_pymatreader_funcs,
     _check_head_radius,
-    has_nibabel,
 )
 from .config import (
     set_config,
@@ -129,24 +128,16 @@
 from .progressbar import ProgressBar
 from ._testing import (
     run_command_if_main,
-    requires_sklearn,
-    requires_version,
     requires_mne,
     requires_good_network,
-    requires_pandas,
-    requires_h5py,
     ArgvSetter,
     SilenceStdout,
     has_freesurfer,
     has_mne_c,
     _TempDir,
     buggy_mkl_svd,
-    requires_numpydoc,
     requires_freesurfer,
-    requires_nitime,
     requires_mne_mark,
-    requires_neuromag2ft,
-    requires_pylsl,
     assert_object_equal,
     assert_and_remove_boundary_annot,
     _raw_annot,
@@ -156,7 +147,6 @@
     assert_stcs_equal,
     _click_ch_name,
     requires_openmeeg_mark,
-    requires_mne_qt_browser,
 )
 from .numerics import (
     hashfunc,

mne/utils/_testing.py

@@ -125,51 +125,6 @@ def requires_freesurfer(arg):
 )
 
 
-# %%
-# Deprecated
-def requires_version(library, min_version="0.0"):
-    """Check for a library version."""
-    warn(
-        f"requires_version({repr(library)}, min_version={repr(min_version)}) "
-        "is deprecated and will be removed in 1.6, use pytest.importorskip("
-        f"{repr(library)}, minversion={repr(min_version)}) instead",
-        FutureWarning,
-    )
-    import pytest
-
-    reason = f"Requires {library}"
-    if min_version != "0.0":
-        reason += f" version >= {min_version}"
-    return pytest.mark.skipif(not check_version(library, min_version), reason=reason)
-
-
-def requires_module(function, name, call=None):
-    """Skip a test if package is not available (decorator)."""
-    msg = f"@requires_module({repr(name)}) is deprecated and will be removed " f"in 1.6"
-    if call is None:
-        msg += f" use pytest.importorskip({repr(name)}) instead"
-    else:
-        msg += f" use pytest.mark.skipif instead with the condition:\n\n{call}\n"
-    warn(msg, FutureWarning)
-    return _requires_module(function, name, call=call)
-
-
-_n2ft_call = """
-if 'NEUROMAG2FT_ROOT' not in os.environ:
-    raise ImportError
-"""
-requires_pandas = partial(requires_module, name="pandas")
-requires_pylsl = partial(requires_module, name="pylsl")
-requires_sklearn = partial(requires_module, name="sklearn")
-requires_mne_qt_browser = partial(requires_module, name="mne_qt_browser")
-requires_neuromag2ft = partial(requires_module, name="neuromag2ft", call=_n2ft_call)
-requires_nitime = partial(requires_module, name="nitime")
-requires_h5py = partial(requires_module, name="h5py")
-requires_numpydoc = partial(requires_version, "numpydoc", "1.0")
-
-# %% End deprecated
-
-
 def run_command_if_main():
     """Run a given command if it's __main__."""
     local_vars = inspect.currentframe().f_back.f_locals

mne/utils/check.py

@@ -16,7 +16,6 @@
 import numpy as np
 
 from ..fixes import _median_complex, _compare_version
-from .docs import deprecated
 from ._logging import warn, logger, verbose, _record_warnings, _verbose_safe_false
 
 
@@ -1203,12 +1202,6 @@ def _to_rgb(*args, name="color", alpha=False):
         ) from None
 
 
-@deprecated("has_nibabel is deprecated and will be removed in 1.5")
-def has_nibabel():
-    """Check if nibabel is installed."""
-    return check_version("nibabel")  # pragma: no cover
-
-
 def _import_nibabel(why="use MRI files"):
     try:
         import nibabel as nib