Merge pull request #63 from SpikeInterface/update-tests

Clean singularity cache before each run

Author: alejoe91

tests/test_containers_gpu.py

@@ -12,6 +12,11 @@
 DOCKER_SINGULARITY = "singularity" # "docker"
 
 
+def clean_singularity_cache():
+    print("Cleaning singularity cache")
+    os.system("singularity cache clean --force")
+
+
 def generate_run_kwargs():
     test_recording, _ = se.toy_example(
         duration=30,
@@ -53,27 +58,37 @@ def run_kwargs(work_dir):
 
 
 def test_kilosort2(run_kwargs):
-    sorting = ss.run_kilosort2(output_folder="kilosort2", **run_kwargs)
+    if DOCKER_SINGULARITY == "singularity":
+        clean_singularity_cache()
+    sorting = ss.run_sorter("kilosort2", output_folder="kilosort2", **run_kwargs)
     print(sorting)
 
 
 def test_kilosort2_5(run_kwargs):
-    sorting = ss.run_kilosort2_5(output_folder="kilosort2_5", **run_kwargs)
+    if DOCKER_SINGULARITY == "singularity":
+        clean_singularity_cache()
+    sorting = ss.run_sorter("kilosort2_5", output_folder="kilosort2_5", **run_kwargs)
     print(sorting)
 
 
 def test_kilosort3(run_kwargs):
-    sorting = ss.run_kilosort3(output_folder="kilosort3", **run_kwargs)
+    if DOCKER_SINGULARITY == "singularity":
+        clean_singularity_cache()
+    sorting = ss.run_sorter("kilosort3", output_folder="kilosort3", **run_kwargs)
     print(sorting)
 
 
-def test_yass(run_kwargs):
-    sorting = ss.run_yass(output_folder="yass", **run_kwargs)
+def test_pykilosort(run_kwargs):
+    if DOCKER_SINGULARITY == "singularity":
+        clean_singularity_cache()
+    sorting = ss.run_sorter("pykilosort", output_folder="pykilosort", **run_kwargs)
     print(sorting)
 
-
-def test_pykilosort(run_kwargs):
-    sorting = ss.run_pykilosort(output_folder="pykilosort", **run_kwargs)
+@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)
     print(sorting)
 
 if __name__ == "__main__":

tests/test_singularity_containers.py

@@ -11,6 +11,10 @@
 # test docker or singularity
 DOCKER_SINGULARITY = "singularity" # "docker"
 
+def clean_singularity_cache():
+    print("Cleaning singularity cache")
+    os.system("singularity cache clean --force")
+
 
 def generate_run_kwargs():
     test_recording, _ = se.toy_example(
@@ -54,50 +58,71 @@ def run_kwargs(work_dir):
 
 
 def test_spykingcircus(run_kwargs):
-    sorting = ss.run_spykingcircus(output_folder="spykingcircus", **run_kwargs)
+    if DOCKER_SINGULARITY == "singularity":
+        clean_singularity_cache()
+    sorting = ss.run_sorter("spykingcircus", output_folder="spykingcircus", **run_kwargs)
     print(sorting)
 
 
 def test_mountainsort4(run_kwargs):
-    sorting = ss.run_mountainsort4(output_folder="mountainsort4", **run_kwargs)
+    if DOCKER_SINGULARITY == "singularity":
+        clean_singularity_cache()
+    sorting = ss.run_sorter("mountainsort4", output_folder="mountainsort4", **run_kwargs)
     print(sorting)
 
 
 def test_tridesclous(run_kwargs):
-    sorting = ss.run_tridesclous(output_folder="tridesclous", **run_kwargs)
-    print(sorting)
-
-
-def test_klusta(run_kwargs):
-    sorting = ss.run_klusta(output_folder="klusta", **run_kwargs)
+    if DOCKER_SINGULARITY == "singularity":
+        clean_singularity_cache()
+    sorting = ss.run_sorter("tridesclous", output_folder="tridesclous", **run_kwargs)
     print(sorting)
 
 
 def test_ironclust(run_kwargs):
-    sorting = ss.run_ironclust(output_folder="ironclust", fGpu=False, **run_kwargs)
+    if DOCKER_SINGULARITY == "singularity":
+        clean_singularity_cache()
+    sorting = ss.run_sorter("ironclust", output_folder="ironclust", fGpu=False, **run_kwargs)
     print(sorting)
 
 
 def test_waveclus(run_kwargs):
-    sorting = ss.run_waveclus(output_folder="waveclus", **run_kwargs)
+    if DOCKER_SINGULARITY == "singularity":
+        clean_singularity_cache()
+    sorting = ss.run_sorter("waveclus", output_folder="waveclus", **run_kwargs)
     print(sorting)
 
 
 def test_hdsort(run_kwargs):
-    sorting = ss.run_hdsort(output_folder="hdsort", **run_kwargs)
+    if DOCKER_SINGULARITY == "singularity":
+        clean_singularity_cache()
+    sorting = ss.run_sorter("hdsort", output_folder="hdsort", **run_kwargs)
     print(sorting)
 
 
 def test_kilosort1(run_kwargs):
-    sorting = ss.run_kilosort(output_folder="kilosort", useGPU=False, **run_kwargs)
+    if DOCKER_SINGULARITY == "singularity":
+        clean_singularity_cache()
+    sorting = ss.run_sorter("kilosort", output_folder="kilosort", useGPU=False, **run_kwargs)
     print(sorting)
 
 def test_combinato(run_kwargs):
+    if DOCKER_SINGULARITY == "singularity":
+        clean_singularity_cache()
     rec = run_kwargs['recording']
     channels = rec.get_channel_ids()[0:1]
     rec_one_channel = rec.channel_slice(channels)
     run_kwargs['recording'] = rec_one_channel
-    sorting = ss.run_combinato(output_folder='combinato', **run_kwargs)
+    sorting = ss.run_sorter("combinato", output_folder='combinato', **run_kwargs)
+    print(sorting)
+
+@pytest.mark.skip(reason="Legcay sorter: requires Python=3.7")
+def test_klusta(run_kwargs):
+    if DOCKER_SINGULARITY == "singularity":
+        clean_singularity_cache()
+    recording = run_kwargs["recording"]
+    recording.extra_requirements.append("pandas")
+    run_kwargs["recording"] = recording
+    sorting = ss.run_sorter("klusta", output_folder="klusta", **run_kwargs)
     print(sorting)
 
 if __name__ == "__main__":