Merge pull request #77 from SpikeInterface/update-ks4

Update to KS 4.0.12

Author: alejoe91

kilosort4/Dockerfile

@@ -35,4 +35,4 @@ RUN conda init bash
 RUN pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
 
 # install kilosort4
-RUN pip install kilosort==4.0.6
+RUN pip install kilosort==4.0.12

kilosort4/build.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-docker build -t spikeinterface/kilosort4-base:latest -t spikeinterface/kilosort4-base:4.0.6_cuda-12.0.0 .
+docker build -t spikeinterface/kilosort4-base:latest -t spikeinterface/kilosort4-base:4.0.12_cuda-12.0.0 .

requirements_test.txt

@@ -1,3 +1,4 @@
 spikeinterface[full] @ git+https://github.com/SpikeInterface/spikeinterface.git
 spython==0.2.1
+docker==7.1.0
 pytest==7.1.2

tests/test_containers_gpu.py

@@ -60,35 +60,35 @@ def run_kwargs(work_dir):
 def test_kilosort2(run_kwargs):
     if DOCKER_SINGULARITY == "singularity":
         clean_singularity_cache()
-    sorting = ss.run_sorter("kilosort2", output_folder="kilosort2", **run_kwargs)
+    sorting = ss.run_sorter("kilosort2", folder="kilosort2", **run_kwargs)
     print(sorting)
 
 
 def test_kilosort2_5(run_kwargs):
     if DOCKER_SINGULARITY == "singularity":
         clean_singularity_cache()
-    sorting = ss.run_sorter("kilosort2_5", output_folder="kilosort2_5", **run_kwargs)
+    sorting = ss.run_sorter("kilosort2_5", folder="kilosort2_5", **run_kwargs)
     print(sorting)
 
 
 def test_kilosort3(run_kwargs):
     if DOCKER_SINGULARITY == "singularity":
         clean_singularity_cache()
-    sorting = ss.run_sorter("kilosort3", output_folder="kilosort3", **run_kwargs)
+    sorting = ss.run_sorter("kilosort3", folder="kilosort3", **run_kwargs)
     print(sorting)
 
 
 def test_pykilosort(run_kwargs):
     if DOCKER_SINGULARITY == "singularity":
         clean_singularity_cache()
-    sorting = ss.run_sorter("pykilosort", output_folder="pykilosort", **run_kwargs)
+    sorting = ss.run_sorter("pykilosort", folder="pykilosort", **run_kwargs)
     print(sorting)
 
 @pytest.mark.skip(reason="Legcay sorter: requires Python=3.7")
 def test_yass(run_kwargs):
     if DOCKER_SINGULARITY == "singularity":
         clean_singularity_cache()
-    sorting = ss.run_sorter("yass", output_folder="yass", **run_kwargs)
+    sorting = ss.run_sorter("yass", folder="yass", **run_kwargs)
     print(sorting)
 
 if __name__ == "__main__":

tests/test_singularity_containers.py

@@ -60,49 +60,49 @@ def run_kwargs(work_dir):
 def test_spykingcircus(run_kwargs):
     if DOCKER_SINGULARITY == "singularity":
         clean_singularity_cache()
-    sorting = ss.run_sorter("spykingcircus", output_folder="spykingcircus", **run_kwargs)
+    sorting = ss.run_sorter("spykingcircus", folder="spykingcircus", **run_kwargs)
     print(sorting)
 
 
 def test_mountainsort4(run_kwargs):
     if DOCKER_SINGULARITY == "singularity":
         clean_singularity_cache()
-    sorting = ss.run_sorter("mountainsort4", output_folder="mountainsort4", **run_kwargs)
+    sorting = ss.run_sorter("mountainsort4", folder="mountainsort4", **run_kwargs)
     print(sorting)
 
 
 def test_tridesclous(run_kwargs):
     if DOCKER_SINGULARITY == "singularity":
         clean_singularity_cache()
-    sorting = ss.run_sorter("tridesclous", output_folder="tridesclous", **run_kwargs)
+    sorting = ss.run_sorter("tridesclous", folder="tridesclous", **run_kwargs)
     print(sorting)
 
 
 def test_ironclust(run_kwargs):
     if DOCKER_SINGULARITY == "singularity":
         clean_singularity_cache()
-    sorting = ss.run_sorter("ironclust", output_folder="ironclust", fGpu=False, **run_kwargs)
+    sorting = ss.run_sorter("ironclust", folder="ironclust", fGpu=False, **run_kwargs)
     print(sorting)
 
 
 def test_waveclus(run_kwargs):
     if DOCKER_SINGULARITY == "singularity":
         clean_singularity_cache()
-    sorting = ss.run_sorter("waveclus", output_folder="waveclus", **run_kwargs)
+    sorting = ss.run_sorter("waveclus", folder="waveclus", **run_kwargs)
     print(sorting)
 
 
 def test_hdsort(run_kwargs):
     if DOCKER_SINGULARITY == "singularity":
         clean_singularity_cache()
-    sorting = ss.run_sorter("hdsort", output_folder="hdsort", **run_kwargs)
+    sorting = ss.run_sorter("hdsort", folder="hdsort", **run_kwargs)
     print(sorting)
 
 
 def test_kilosort1(run_kwargs):
     if DOCKER_SINGULARITY == "singularity":
         clean_singularity_cache()
-    sorting = ss.run_sorter("kilosort", output_folder="kilosort", useGPU=False, **run_kwargs)
+    sorting = ss.run_sorter("kilosort", folder="kilosort", useGPU=False, **run_kwargs)
     print(sorting)
 
 def test_combinato(run_kwargs):
@@ -112,7 +112,7 @@ def test_combinato(run_kwargs):
     channels = rec.get_channel_ids()[0:1]
     rec_one_channel = rec.channel_slice(channels)
     run_kwargs['recording'] = rec_one_channel
-    sorting = ss.run_sorter("combinato", output_folder='combinato', **run_kwargs)
+    sorting = ss.run_sorter("combinato", folder='combinato', **run_kwargs)
     print(sorting)
 
 @pytest.mark.skip(reason="Legcay sorter: requires Python=3.7")
@@ -122,7 +122,7 @@ def test_klusta(run_kwargs):
     recording = run_kwargs["recording"]
     recording.extra_requirements.append("pandas")
     run_kwargs["recording"] = recording
-    sorting = ss.run_sorter("klusta", output_folder="klusta", **run_kwargs)
+    sorting = ss.run_sorter("klusta", folder="klusta", **run_kwargs)
     print(sorting)
 
 if __name__ == "__main__":