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Clean singularity cache before each run #63

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Aug 1, 2023
Merged

Clean singularity cache before each run #63

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2983d2f
Clean singularity cache before each run
alejoe91 Jul 3, 2023
e899860
merge
alejoe91 Jul 11, 2023
28df0ac
Update run_* functions and skip klusta and YASS
alejoe91 Jul 11, 2023
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31 changes: 23 additions & 8 deletions tests/test_containers_gpu.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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__":
Expand Down
51 changes: 38 additions & 13 deletions tests/test_singularity_containers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down Expand Up @@ -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__":
Expand Down