Add archived sorters and change rt-sort to rtsort

doc/modules/sorters.rst

@@ -472,24 +472,29 @@ Here is the list of external sorters accessible using the run_sorter wrapper:
 * **Kilosort2.5** :code:`run_sorter(sorter_name='kilosort2_5')`
 * **Kilosort3** :code:`run_sorter(sorter_name='kilosort3')`
 * **PyKilosort** :code:`run_sorter(sorter_name='pykilosort')`
-* **Klusta** :code:`run_sorter(sorter_name='klusta')`
 * **Mountainsort4** :code:`run_sorter(sorter_name='mountainsort4')`
 * **Mountainsort5** :code:`run_sorter(sorter_name='mountainsort5')`
-* **RT-Sort** :code:`run_sorter(sorter_name='rt-sort')`
+* **RTSort** :code:`run_sorter(sorter_name='rtsort')`
 * **SpyKING Circus** :code:`run_sorter(sorter_name='spykingcircus')`
 * **Tridesclous** :code:`run_sorter(sorter_name='tridesclous')`
 * **Wave clus** :code:`run_sorter(sorter_name='waveclus')`
 * **Combinato** :code:`run_sorter(sorter_name='combinato')`
 * **HDSort** :code:`run_sorter(sorter_name='hdsort')`
-* **YASS** :code:`run_sorter(sorter_name='yass')`
-
 
-Here a list of internal sorter based on `spikeinterface.sortingcomponents`; they are totally
+Here is a list of internal sorter based on `spikeinterface.sortingcomponents`; they are totally
 experimental for now:
 
 * **Spyking Circus2** :code:`run_sorter(sorter_name='spykingcircus2')`
 * **Tridesclous2** :code:`run_sorter(sorter_name='tridesclous2')`
 
+
+Here is the list of legacy sorters that are no longer supported, but can still be run
+with an older version of SpikeInterface:
+
+* **Klusta** :code:`run_sorter(sorter_name='klusta')`
+* **YASS** :code:`run_sorter(sorter_name='yass')`
+
+
 In 2024, we expect to add many more sorters to this list.
 
 

doc/references.rst

@@ -43,7 +43,7 @@ please include the appropriate citation for the :code:`sorter_name` parameter yo
 - :code:`herdingspikes` [Muthmann]_ [Hilgen]_
 - :code:`kilosort`  [Pachitariu]_
 - :code:`mountainsort` [Chung]_
-- :code:`rt-sort` [van_der_Molen]_
+- :code:`rtsort` [van_der_Molen]_
 - :code:`spykingcircus` [Yger]_
 - :code:`wavclus` [Chaure]_
 - :code:`yass` [Lee]_

src/spikeinterface/sorters/container_tools.py

@@ -263,7 +263,6 @@ def install_package_in_container(
         if extra is not None:
             cmd += f"{extra}"
         res_output = container_client.run_command(cmd)
-
     else:
         raise ValueError(f"install_package_incontainer, wrong installation_mode={installation_mode}")
 

src/spikeinterface/sorters/external/rt_sort.py

@@ -10,7 +10,7 @@
 class RTSortSorter(BaseSorter):
     """RTSort sorter object"""
 
-    sorter_name = "rt-sort"
+    sorter_name = "rtsort"
 
     _default_params = {
         "detection_model": "neuropixels",

src/spikeinterface/sorters/runsorter.py

@@ -18,8 +18,8 @@
 
 from spikeinterface.core import BaseRecording, NumpySorting, load
 from spikeinterface.core.core_tools import check_json, is_editable_mode
-from .sorterlist import sorter_dict
-from .utils import (
+from spikeinterface.sorters.sorterlist import sorter_dict, archived_sorters
+from spikeinterface.sorters.utils import (
     SpikeSortingError,
     has_nvidia,
     has_docker,
@@ -28,7 +28,7 @@
     has_spython,
     has_docker_nvidia_installed,
 )
-from .container_tools import (
+from spikeinterface.sorters.container_tools import (
     find_recording_folders,
     path_to_unix,
     windows_extractor_dict_to_unix,
@@ -43,14 +43,14 @@
     combinato="combinato",
     herdingspikes="herdingspikes",
     kilosort4="kilosort4",
-    klusta="klusta",
     mountainsort4="mountainsort4",
     mountainsort5="mountainsort5",
     pykilosort="pykilosort",
+    rtsort="rtsort",
     spykingcircus="spyking-circus",
     spykingcircus2="spyking-circus2",
     tridesclous="tridesclous",
-    yass="yass",
+    tridesclous2="tridesclous2",
     # Matlab compiled sorters:
     hdsort="hdsort-compiled",
     ironclust="ironclust-compiled",
@@ -60,6 +60,9 @@
     kilosort3="kilosort3-compiled",
     waveclus="waveclus-compiled",
     waveclus_snippets="waveclus-compiled",
+    # archived
+    # klusta="klusta",
+    # yass="yass",
 )
 
 SORTER_DOCKER_MAP = {k: f"{REGISTRY}/{v}-base" for k, v in SORTER_DOCKER_MAP.items()}
@@ -127,6 +130,11 @@ def run_sorter(
     --------
     >>> sorting = run_sorter("tridesclous", recording)
     """
+    if sorter_name in archived_sorters():
+        raise ValueError(
+            f"The sorter {sorter_name} is archived and no longer supported. "
+            "Please use a different sorter or an older version of SpikeInterface."
+        )
 
     common_kwargs = dict(
         sorter_name=sorter_name,
@@ -547,7 +555,7 @@ def run_sorter_container(
             res_output += str(container_client.run_command(cmd))
         need_si_install = "ModuleNotFoundError" in res_output
 
-    if need_si_install:
+    if need_si_install or installation_mode == "dev":
         # update pip in container
         cmd = f"pip install --user --upgrade pip"
         res_output = container_client.run_command(cmd)

src/spikeinterface/sorters/sorterlist.py

@@ -37,7 +37,6 @@
     Kilosort3Sorter,
     Kilosort4Sorter,
     PyKilosortSorter,
-    KlustaSorter,
     Mountainsort4Sorter,
     Mountainsort5Sorter,
     RTSortSorter,
@@ -52,6 +51,8 @@
     SimpleSorter,
 ]
 
+# archived
+archived_sorter_list = [KlustaSorter, YassSorter]
 
 try:
     # if the spikeinterface_kilosort_components source are installed on the machine
@@ -71,6 +72,12 @@ def available_sorters():
     return sorted(list(sorter_dict.keys()))
 
 
+def archived_sorters():
+    """Lists archived sorters."""
+
+    return sorted([s.sorter_name for s in archived_sorter_list])
+
+
 def installed_sorters():
     """Lists installed sorters."""