[ENH] Add support for AAHC clustering

docs/references.bib

@@ -94,6 +94,28 @@ @article{MICHEL2018577
  year = {2018}
 }
 
+@article{Murray2008,
+ author = {Murray, Micah M. and Brunet, Denis and Michel, Christoph M.},
+ doi = {10.1007/s10548-008-0054-5},
+ journal = {Brain Topography},
+ number = {4},
+ pages = {249--264},
+ title = {Topographic {ERP} {Analyses}: {A} {Step}-by-{Step} {Tutorial} {Review}},
+ volume = {20},
+ year = {2008}
+}
+
+@inproceedings{Roweis1997,
+ author = {Roweis, Sam},
+ booktitle = {Advances in Neural Information Processing Systems},
+ editor = {M. Jordan and M. Kearns and S. Solla},
+ publisher = {MIT Press},
+ title = {EM Algorithms for PCA and SPCA},
+ url = {https://proceedings.neurips.cc/paper/1997/file/d9731321ef4e063ebbee79298fa36f56-Paper.pdf},
+ volume = {10},
+ year = {1997}
+}
+
 @article{Silhouettes,
  author = {Peter J. Rousseeuw},
  doi = {10.1016/0377-0427(87)90125-7},

docs/source/api/cluster.rst

@@ -13,3 +13,4 @@ Cluster
    :toctree: generated/
 
    ModKMeans
+   AAHCluster

docs/source/dev/changes/latest.rst

@@ -25,6 +25,7 @@ Current 0.3.0.dev
 Enhancements
 ~~~~~~~~~~~~
 - Improve changelog. (:pr:`86` by `Victor Férat`_)
+- Support for AAHC clustering (:pr:`92` by `Reinmar Kobler`_)
 
 Bugs
 ~~~~

docs/source/dev/changes/names.inc

@@ -1,3 +1,5 @@
 .. _Victor Férat: https://github.com/vferat
 
 .. _Mathieu Scheltienne: https://github.com/mscheltienne
+
+.. _Reinmar Kobler: https://github.com/rkobler

pycrostates/cluster/__init__.py

@@ -14,6 +14,7 @@
 :class:`~pycrostates.segmentation.EpochsSegmentation` depending on the dataset
 to segment."""
 
+from .aahc import AAHCluster  # noqa: F401
 from .kmeans import ModKMeans  # noqa: F401
 
-__all__ = ("ModKMeans",)
+__all__ = ("ModKMeans", "AAHCluster")

pycrostates/cluster/_base.py

@@ -17,15 +17,15 @@
 from ..segmentation import EpochsSegmentation, RawSegmentation
 from ..utils import _corr_vectors
 from ..utils._checks import (
-    _check_n_jobs,
     _check_picks_uniqueness,
     _check_reject_by_annotation,
     _check_tmin_tmax,
     _check_type,
     _check_value,
 )
 from ..utils._docs import fill_doc
-from ..utils._logs import logger, verbose
+from ..utils._logs import _set_verbose, logger
+from ..utils._logs import verbose as verbose_decorator
 from ..utils.mixin import ChannelsMixin, ContainsMixin, MontageMixin
 from ..viz import plot_cluster_centers
 
@@ -192,7 +192,8 @@ def fit(
         tmin: Optional[Union[int, float]] = None,
         tmax: Optional[Union[int, float]] = None,
         reject_by_annotation: bool = True,
-        n_jobs: int = 1,
+        *,
+        verbose: Optional[str] = None,
     ) -> NDArray[float]:
         """Compute cluster centers.
 
@@ -213,12 +214,13 @@ def fit(
         %(tmin_raw)s
         %(tmax_raw)s
         %(reject_by_annotation_raw)s
-        %(n_jobs)s
+        %(verbose)s
         """
         from ..io import ChData, ChInfo
 
+        _set_verbose(verbose)
+
         self._check_unfitted()
-        n_jobs = _check_n_jobs(n_jobs)
         _check_type(inst, (BaseRaw, BaseEpochs, ChData), item_name="inst")
         if isinstance(inst, (BaseRaw, BaseEpochs)):
             tmin, tmax = _check_tmin_tmax(inst, tmin, tmax)
@@ -554,7 +556,7 @@ def save(self, fname: Union[str, Path]):
         self._check_fit()
         _check_type(fname, ("path-like",), "fname")
 
-    @verbose
+    @verbose_decorator
     def predict(
         self,
         inst: Union[BaseRaw, BaseEpochs],