Merge remote-tracking branch 'upstream/main' into dev-aifpaif

pycrostates/cluster/_base.py

@@ -2,7 +2,7 @@
 from copy import copy, deepcopy
 from itertools import groupby
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import Any, Optional, Union
 
 import numpy as np
 from matplotlib.axes import Axes
@@ -277,11 +277,11 @@ def fit(
 
     def rename_clusters(
         self,
-        mapping: Optional[Dict[str, str]] = None,
+        mapping: Optional[dict[str, str]] = None,
         new_names: Optional[
             Union[
-                List[str],
-                Tuple[str, ...],
+                list[str],
+                tuple[str, ...],
             ]
         ] = None,
     ) -> None:
@@ -341,11 +341,11 @@ def rename_clusters(
 
     def reorder_clusters(
         self,
-        mapping: Optional[Dict[int, int]] = None,
+        mapping: Optional[dict[int, int]] = None,
         order: Optional[
             Union[
-                List[int],
-                Tuple[int, ...],
+                list[int],
+                tuple[int, ...],
                 NDArray[int],
             ]
         ] = None,
@@ -458,8 +458,8 @@ def invert_polarity(
         self,
         invert: Union[
             bool,
-            List[bool],
-            Tuple[bool, ...],
+            list[bool],
+            tuple[bool, ...],
             NDArray[bool],
         ],
     ) -> None:
@@ -518,7 +518,7 @@ def plot(
         self,
         axes: Optional[Union[Axes, NDArray[Axes]]] = None,
         show_gradient: Optional[bool] = False,
-        gradient_kwargs: Dict[str, Any] = {
+        gradient_kwargs: dict[str, Any] = {
             "color": "black",
             "linestyle": "-",
             "marker": "P",
@@ -1180,7 +1180,7 @@ def labels_(self) -> NDArray[int]:
         return self._labels_.copy()
 
     @property
-    def cluster_names(self) -> List[str]:
+    def cluster_names(self) -> list[str]:
         """Name of the clusters.
 
         :type: `list`

pycrostates/cluster/aahc.py

@@ -1,7 +1,7 @@
 """Atomize and Agglomerate Hierarchical Clustering (AAHC)."""
 
 from pathlib import Path
-from typing import Any, Optional, Tuple, Union
+from typing import Any, Optional, Union
 
 import numpy as np
 from mne import BaseEpochs
@@ -183,7 +183,7 @@ def _aahc(
         n_clusters: int,
         ignore_polarity: bool,
         normalize_input: bool,
-    ) -> Tuple[float, NDArray[float], NDArray[int]]:
+    ) -> tuple[float, NDArray[float], NDArray[int]]:
         """Run the AAHC algorithm."""
         gfp_sum_sq = np.sum(data**2)
         maps, segmentation = AAHCluster._compute_maps(
@@ -200,7 +200,7 @@ def _compute_maps(
         n_clusters: int,
         ignore_polarity: bool,
         normalize_input: bool,
-    ) -> Tuple[NDArray[float], NDArray[int]]:
+    ) -> tuple[NDArray[float], NDArray[int]]:
         """Compute microstates maps."""
         n_chan, n_frame = data.shape
 

pycrostates/cluster/kmeans.py

@@ -1,7 +1,7 @@
 """Class and functions to use modified Kmeans."""
 
 from pathlib import Path
-from typing import Any, Optional, Tuple, Union
+from typing import Any, Optional, Union
 
 import numpy as np
 from mne import BaseEpochs
@@ -263,7 +263,7 @@ def _kmeans(
         max_iter: int,
         random_state: Union[RandomState, Generator],
         tol: Union[int, float],
-    ) -> Tuple[float, NDArray[float], NDArray[int], bool]:
+    ) -> tuple[float, NDArray[float], NDArray[int], bool]:
         """Run the k-means algorithm."""
         gfp_sum_sq = np.sum(data**2)
         maps, converged = ModKMeans._compute_maps(
@@ -282,7 +282,7 @@ def _compute_maps(
         max_iter: int,
         random_state: Union[RandomState, Generator],
         tol: Union[int, float],
-    ) -> Tuple[NDArray[float], bool]:
+    ) -> tuple[NDArray[float], bool]:
         """Compute microstates maps.
 
         Based on mne_microstates by Marijn van Vliet <[email protected]>

pycrostates/io/fiff.py

@@ -5,7 +5,7 @@
 from functools import reduce
 from numbers import Integral
 from pathlib import Path
-from typing import List, Union
+from typing import Union
 
 import numpy as np
 from mne import Info, Transform
@@ -98,7 +98,7 @@ def _write_cluster(
     cluster_centers_: NDArray[float],
     chinfo: Union[CHInfo, Info],
     algorithm: str,
-    cluster_names: List[str],
+    cluster_names: list[str],
     fitted_data: NDArray[float],
     labels_: NDArray[int],
     **kwargs,
@@ -398,7 +398,7 @@ def _check_fit_parameters_and_variables(
 def _create_ModKMeans(
     cluster_centers_: NDArray[float],
     info: CHInfo,
-    cluster_names: List[str],
+    cluster_names: list[str],
     fitted_data: NDArray[float],
     labels_: NDArray[int],
     n_init: int,
@@ -423,7 +423,7 @@ def _create_ModKMeans(
 def _create_AAHCluster(
     cluster_centers_: NDArray[float],
     info: CHInfo,
-    cluster_names: List[str],
+    cluster_names: list[str],
     fitted_data: NDArray[float],
     labels_: NDArray[int],
     ignore_polarity: bool,  # pylint: disable=unused-argument

pycrostates/io/meas_info.py

@@ -2,7 +2,7 @@
 
 from copy import deepcopy
 from numbers import Number
-from typing import List, Optional, Tuple, Union
+from typing import Optional, Union
 
 import numpy as np
 from mne import Info, Projection, Transform
@@ -155,11 +155,11 @@ def __init__(
         ch_names: Optional[
             Union[
                 int,
-                List[str],
-                Tuple[str, ...],
+                list[str],
+                tuple[str, ...],
             ]
         ] = None,
-        ch_types: Optional[Union[str, List[str], Tuple[str, ...]]] = None,
+        ch_types: Optional[Union[str, list[str], tuple[str, ...]]] = None,
     ):
         if all(arg is None for arg in (info, ch_names, ch_types)):
             raise RuntimeError(
@@ -195,8 +195,8 @@ def _init_from_info(self, info: Info):
 
     def _init_from_channels(
         self,
-        ch_names: Union[int, List[str], Tuple[str, ...]],
-        ch_types: Union[str, List[str], Tuple[str, ...]],
+        ch_names: Union[int, list[str], tuple[str, ...]],
+        ch_types: Union[str, list[str], tuple[str, ...]],
     ):
         """Init instance from channel names and types."""
         self._unlocked = True

pycrostates/preprocessing/resample.py

@@ -1,6 +1,6 @@
 """Preprocessing functions to create resamples from raw or epochs instances."""
 
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import numpy as np
 from mne import BaseEpochs, pick_info
@@ -37,7 +37,7 @@ def resample(
     replace: bool = True,
     random_state: RANDomState = None,
     verbose=None,
-) -> List[CHData]:
+) -> list[CHData]:
     """Resample a recording into epochs of random samples.
 
     Resample :class:`~mne.io.Raw`. :class:`~mne.Epochs` or

pycrostates/segmentation/_base.py

@@ -2,12 +2,13 @@
 
 import itertools
 from abc import abstractmethod
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import numpy as np
 from matplotlib.axes import Axes
 from mne import BaseEpochs
 from mne.io import BaseRaw
+from mne.utils import check_version
 from numpy.typing import NDArray
 
 from .._typing import Segmentation
@@ -41,7 +42,7 @@ def __init__(
         labels: NDArray[int],
         inst: Union[BaseRaw, BaseEpochs],
         cluster_centers_: NDArray[float],
-        cluster_names: Optional[List[str]] = None,
+        cluster_names: Optional[list[str]] = None,
         predict_parameters: Optional[dict] = None,
     ):
         # check input
@@ -142,7 +143,8 @@ def compute_parameters(self, norm_gfp: bool = True, return_dist: bool = False):
             assert data.ndim == 2
             assert labels.size == data.shape[1]
         elif isinstance(self._inst, BaseEpochs):
-            data = self._inst.get_data()
+            kwargs_epochs = dict(copy=False) if check_version("mne", "1.6") else dict()
+            data = self._inst.get_data(**kwargs_epochs)
             # sanity-checks
             assert labels.ndim == 2
             assert data.ndim == 3
@@ -324,7 +326,8 @@ def plot_cluster_centers(
     # --------------------------------------------------------------------
     @staticmethod
     def _check_cluster_names(
-        cluster_names: List[str], cluster_centers_: NDArray[float]
+        cluster_names: list[str],
+        cluster_centers_: NDArray[float],
     ):
         """Check that the argument 'cluster_names' is valid."""
         _check_type(cluster_names, (list, None), "cluster_names")
@@ -399,7 +402,7 @@ def cluster_centers_(self) -> NDArray[float]:
         return self._cluster_centers_.copy()
 
     @property
-    def cluster_names(self) -> List[str]:
+    def cluster_names(self) -> list[str]:
         """Name of the cluster centers.
 
         :type: `list`

pycrostates/utils/_docs.py

@@ -5,15 +5,15 @@
 Inspired from mne.utils.docs.py by Eric Larson <[email protected]>
 """
 import sys
-from typing import Callable, Dict, List, Tuple
+from typing import Callable
 
 from mne.utils.docs import docdict as docdict_mne
 
 # ------------------------- Documentation dictionary -------------------------
-docdict: Dict[str, str] = {}
+docdict: dict[str, str] = {}
 
 # ---- Documentation to inc. from MNE ----
-keys: Tuple[str, ...] = (
+keys: tuple[str, ...] = (
     "n_jobs",
     "picks_all",
     "random_state",
@@ -196,7 +196,7 @@
     axes."""
 
 # ------------------------- Documentation functions --------------------------
-docdict_indented: Dict[int, Dict[str, str]] = {}
+docdict_indented: dict[int, dict[str, str]] = {}
 
 
 def fill_doc(f: Callable) -> Callable:
@@ -242,7 +242,7 @@ def fill_doc(f: Callable) -> Callable:
     return f
 
 
-def _indentcount_lines(lines: List[str]) -> int:
+def _indentcount_lines(lines: list[str]) -> int:
     """Minimum indent for all lines in line list.
 
     >>> lines = [' one', '  two', '   three']

pycrostates/utils/sys_info.py

@@ -2,7 +2,7 @@
 import sys
 from functools import partial
 from importlib.metadata import requires, version
-from typing import IO, Callable, List, Optional
+from typing import IO, Callable, Optional
 
 import psutil
 from packaging.requirements import Requirement
@@ -71,14 +71,14 @@ def sys_info(fid: Optional[IO] = None, developer: bool = False):
 
 
 def _list_dependencies_info(
-    out: Callable, ljust: int, package: str, dependencies: List[Requirement]
+    out: Callable, ljust: int, package: str, dependencies: list[Requirement]
 ):
     """List dependencies names and versions."""
     unicode = sys.stdout.encoding.lower().startswith("utf")
     if unicode:
         ljust += 1
 
-    not_found: List[Requirement] = list()
+    not_found: list[Requirement] = list()
     for dep in dependencies:
         if dep.name == package:
             continue

pycrostates/viz/cluster_centers.py

@@ -1,6 +1,6 @@
 """Visualization module for plotting cluster centers."""
 
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, Optional, Union
 
 import numpy as np
 from matplotlib import pyplot as plt
@@ -15,7 +15,7 @@
 from ..utils._docs import fill_doc
 from ..utils._logs import logger, verbose
 
-_GRADIENT_KWARGS_DEFAULTS: Dict[str, str] = {
+_GRADIENT_KWARGS_DEFAULTS: dict[str, str] = {
     "color": "black",
     "linestyle": "-",
     "marker": "P",
@@ -27,10 +27,10 @@
 def plot_cluster_centers(
     cluster_centers: NDArray[float],
     info: Union[Info, CHInfo],
-    cluster_names: List[str] = None,
+    cluster_names: list[str] = None,
     axes: Optional[Union[Axes, NDArray[Axes]]] = None,
     show_gradient: Optional[bool] = False,
-    gradient_kwargs: Dict[str, Any] = _GRADIENT_KWARGS_DEFAULTS,
+    gradient_kwargs: dict[str, Any] = _GRADIENT_KWARGS_DEFAULTS,
     *,
     block: bool = False,
     verbose: Optional[str] = None,