[MAINT] Upgrade from Python 3.9 to 3.10 (mne-tools#228)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/linux_conda.yml

@@ -14,7 +14,7 @@ jobs:
   # Linux
   job:
     timeout-minutes: 90
-    name: 'py3.9'
+    name: 'py3.10'
     runs-on: ubuntu-20.04
     defaults:
       run:
@@ -23,7 +23,7 @@ jobs:
       MNE_LOGGING_LEVEL: 'warning'
       MKL_NUM_THREADS: '1'
       PYTHONUNBUFFERED: '1'
-      PYTHON_VERSION: '3.9'
+      PYTHON_VERSION: '3.10'
     steps:
       - uses: actions/checkout@v4
       - uses: pyvista/setup-headless-display-action@main

.github/workflows/unit_tests.yml

@@ -22,7 +22,7 @@ jobs:
       matrix:
         include:
           - os: ubuntu-latest
-            python-version: "3.9"
+            python-version: "3.10"
             mne-version: mne-main
           - os: ubuntu-latest
             python-version: "3.12"

doc/install.rst

@@ -15,7 +15,7 @@ Dependencies
 * ``netCDF4`` (>=1.6.5)
 * ``matplotlib`` (optional, for using the interactive data inspector)
 
-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-connectivity`` `via pip <#Installation via pip>`_,
 or conda.
 
@@ -27,7 +27,7 @@ simply run the following at the root of the repository:
 
 .. code-block:: bash
 
-   # with python>=3.9 at least
+   # with python>=3.10 at least
    conda create -n mne
    conda activate mne
    conda install -c conda-forge mne-connectivity

environment.yml

@@ -2,7 +2,7 @@ name: mne-connectivity
 channels:
   - conda-forge
 dependencies:
-  - python>=3.8
+  - python>=3.10
   - pip
   - numpy
   - scipy
@@ -20,6 +20,6 @@ dependencies:
   - pyvista>=0.32,!=0.35.2,!=0.38.0,!=0.38.1,!=0.38.2,!=0.38.3,!=0.38.4,!=0.38.5
   - pyvistaqt>=0.4
   - qtpy
-  - mne-base>=1.3
+  - mne-base>=1.6
   - h5netcdf
   - pyside6

mne_connectivity/decoding/decomposition.py

@@ -4,7 +4,6 @@
 #
 # License: BSD (3-clause)
 
-from typing import Optional, Union
 
 import numpy as np
 from mne import Info
@@ -81,12 +80,12 @@ class CoherencyDecomposition(BaseEstimator, TransformerMixin):
     .. footbibliography::
     """
 
-    filters_: Optional[tuple] = None
-    patterns_: Optional[tuple] = None
+    filters_: tuple | None = None
+    patterns_: tuple | None = None
 
-    _conn_estimator: Optional[Union[_CaCohEst, _MICEst]] = None
-    _indices: Optional[tuple] = None
-    _rank: Optional[tuple] = None
+    _conn_estimator: _CaCohEst | _MICEst | None = None
+    _indices: tuple | None = None
+    _rank: tuple | None = None
 
     @property
     def indices(self):
@@ -199,7 +198,7 @@ def __init__(
                 "`cwt_n_cycles`",
                 "int, float, or array-like",
             )
-            if isinstance(cwt_n_cycles, (tuple, list, np.ndarray)) and len(
+            if isinstance(cwt_n_cycles, tuple | list | np.ndarray) and len(
                 cwt_n_cycles
             ) != len(cwt_freqs):
                 raise ValueError(

mne_connectivity/spectral/epochs.py

@@ -589,7 +589,7 @@ def _get_n_epochs(epochs, n):
     """Generate lists with at most n epochs."""
     epochs_out = list()
     for epoch in epochs:
-        if not isinstance(epoch, (list, tuple)):
+        if not isinstance(epoch, list | tuple):
             epoch = (epoch,)
         epochs_out.append(epoch)
         if len(epochs_out) >= n:
@@ -620,7 +620,7 @@ def _get_and_verify_data_sizes(
     data, sfreq, n_signals=None, n_times=None, times=None, warn_times=True
 ):
     """Get and/or verify the data sizes and time scales."""
-    if not isinstance(data, (list, tuple)):
+    if not isinstance(data, list | tuple):
         raise ValueError("data has to be a list or tuple")
     n_signals_tot = 0
     # Sometimes data can be (ndarray, SourceEstimate) groups so in the case
@@ -1076,7 +1076,7 @@ def spectral_connectivity_epochs(
     n_bands = len(fmin)
 
     # assign names to connectivity methods
-    if not isinstance(method, (list, tuple)):
+    if not isinstance(method, list | tuple):
         method = [method]  # make it a list so we can iterate over it
 
     if n_bands != 1 and any(this_method in _gc_methods for this_method in method):
@@ -1105,7 +1105,7 @@ def spectral_connectivity_epochs(
     weights = None
     metadata = None
     spectrum_computed = False
-    if isinstance(data, (BaseEpochs, EpochsSpectrum, EpochsSpectrumArray)):
+    if isinstance(data, BaseEpochs | EpochsSpectrum | EpochsSpectrumArray):
         names = data.ch_names
         sfreq = data.info["sfreq"]
 
@@ -1126,7 +1126,7 @@ def spectral_connectivity_epochs(
             data.add_annotations_to_metadata(overwrite=True)
         metadata = data.metadata
 
-        if isinstance(data, (EpochsSpectrum, EpochsSpectrumArray)):
+        if isinstance(data, EpochsSpectrum | EpochsSpectrumArray):
             # XXX: Will need to be updated if new Spectrum methods are added
             if not np.iscomplexobj(data.get_data()):
                 raise TypeError(

mne_connectivity/spectral/epochs_multivariate.py

@@ -11,7 +11,6 @@
 
 import copy
 import inspect
-from typing import Optional
 
 import numpy as np
 from mne.epochs import BaseEpochs
@@ -33,7 +32,7 @@ def _check_rank_input(rank, data, indices):
             if "copy" in inspect.getfullargspec(data.get_data).kwonlyargs:
                 kwargs["copy"] = False
             data_arr = data.get_data(**kwargs)
-        elif isinstance(data, (EpochsSpectrum, EpochsSpectrumArray)):
+        elif isinstance(data, EpochsSpectrum | EpochsSpectrumArray):
             # Spectrum objs will drop bad channels, so specify picking all channels
             data_arr = data.get_data(picks=np.arange(data.info["nchan"]))
             # Convert to power (and aggregate over tapers) before computing rank
@@ -241,7 +240,7 @@ class _MultivariateCohEstBase(_EpochMeanMultivariateConEstBase):
     (2019). NeuroImage. DOI: 10.1016/j.neuroimage.2019.116009
     """
 
-    name: Optional[str] = None
+    name: str | None = None
     accumulate_psd = False
 
     def __init__(

mne_connectivity/spectral/time.py

@@ -442,11 +442,11 @@ def spectral_connectivity_time(
         multivariate_con = False
 
     # convert kernel width in time to samples
-    if isinstance(sm_times, (int, float)):
+    if isinstance(sm_times, int | float):
         sm_times = int(np.round(sm_times * sfreq))
 
     # convert frequency smoothing from hz to samples
-    if isinstance(sm_freqs, (int, float)):
+    if isinstance(sm_freqs, int | float):
         sm_freqs = int(np.round(max(sm_freqs, 1)))
 
     # temporal decimation
@@ -529,7 +529,7 @@ def spectral_connectivity_time(
         gc_n_lags = None
 
     # check freqs
-    if isinstance(freqs, (int, float)):
+    if isinstance(freqs, int | float):
         freqs = [freqs]
     # array conversion
     freqs = np.asarray(freqs)
@@ -812,7 +812,7 @@ def _spectral_connectivity(
             n_jobs=n_jobs,
             **kw_mt,
         )
-        if isinstance(n_cycles, (int, float)):
+        if isinstance(n_cycles, int | float):
             n_cycles = [n_cycles] * len(freqs)
         mt_bandwidth = mt_bandwidth if mt_bandwidth else 4
         n_tapers = int(np.floor(mt_bandwidth - 1))

mne_connectivity/utils/utils.py

@@ -77,7 +77,7 @@ def check_indices(indices):
         )
 
     if any(
-        isinstance(inds, (np.ndarray, list, tuple))
+        isinstance(inds, np.ndarray | list | tuple)
         for inds in [*indices[0], *indices[1]]
     ):
         raise TypeError("Channel indices must be integers, not array-likes")
@@ -158,7 +158,7 @@ def _check_multivariate_indices(indices, n_chans):
     max_n_chans = 0
     for group_idx, group in enumerate(indices):
         for con_idx, con in enumerate(group):
-            if not isinstance(con, (np.ndarray, list, tuple)):
+            if not isinstance(con, np.ndarray | list | tuple):
                 raise TypeError(
                     "multivariate indices must contain array-likes of channel indices "
                     "for each seed and target"

pyproject.toml

@@ -15,7 +15,6 @@ classifiers = [
   'Programming Language :: Python :: 3.10',
   'Programming Language :: Python :: 3.11',
   'Programming Language :: Python :: 3.12',
-  'Programming Language :: Python :: 3.9',
   'Topic :: Scientific/Engineering',
   'Topic :: Software Development',
 ]
@@ -43,7 +42,7 @@ maintainers = [
 ]
 name = 'mne-connectivity'
 readme = {content-type = "text/x-rst", file = 'README.rst'}
-requires-python = '>=3.9'
+requires-python = '>=3.10'
 
 [project.optional-dependencies]
 all = [