Merge pull request #54 from SpikeInterface/ibl-pykilosort

IBL pykilosort

Author: alejoe91

pykilosort/Dockerfile

@@ -29,15 +29,14 @@ RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> /root/.profile
 # make conda activate command available from /bin/bash --interactive shells
 RUN conda init bash
 
-# Install python port of pykilosort
-RUN git clone -b drift_test_stable https://github.com/kushbanga/pykilosort.git /src/pykilosort
+# Install IBL python port of pykilosort
+RUN git clone https://github.com/int-brain-lab/pykilosort.git /src/pykilosort
 WORKDIR /src/pykilosort
-# Switch to MouseLand/develop branch - may revert to kushbanga/drift_test_stable in the future
-RUN git remote add MouseLand https://github.com/MouseLand/pykilosort.git && \
-    git fetch MouseLand && git checkout MouseLand/develop && git checkout -b develop
 
 # modify env file so that env extends on base
 RUN sed -i "s/pyks2/base/" pyks2.yml
+RUN sed -i "s/- spikeinterface//" pyks2.yml
+RUN cat pyks2.yml
 
 # Create environment
 RUN conda env update --name base --file pyks2.yml --prune

pykilosort/build.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-docker build -t spikeinterface/pykilosort-base:latest -t spikeinterface/pykilosort-base:0.1.0 .
+docker build -t spikeinterface/pykilosort-base:latest -t spikeinterface/pykilosort-base:ibl-1.3 .

pykilosort/push.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-docker push --all-tags spikeinterface/pykilosort-base
+docker push --all-tags spikeinterface/pykilosort-base

tests/test_containers_gpu.py

@@ -8,6 +8,28 @@
 
 os.environ['SINGULARITY_DISABLE_CACHE'] = 'true'
 
+# test docker or singularity
+DOCKER_SINGULARITY = "singularity" # "docker"
+
+
+def generate_run_kwargs():
+    test_recording, _ = se.toy_example(
+        duration=30,
+        seed=0,
+        num_channels=64,
+        num_segments=1
+    )
+    test_recording = test_recording.save(name='toy')
+    test_recording.set_channel_gains(1)
+    test_recording.set_channel_offsets(1)
+    run_kwargs = dict(recording=test_recording, verbose=True)
+    if DOCKER_SINGULARITY == "singularity":
+        run_kwargs["singularity_image"] = True
+    elif DOCKER_SINGULARITY == "docker":
+        run_kwargs["docker_image"] = True
+    else:
+        raise Exception("DOCKER_SINGULARITY can be 'docker' or 'singularity'")
+    return run_kwargs
 
 @pytest.fixture(autouse=True)
 def work_dir(request, tmp_path):
@@ -27,14 +49,7 @@ def work_dir(request, tmp_path):
 
 @pytest.fixture
 def run_kwargs(work_dir):
-    test_recording, _ = se.toy_example(
-        duration=30,
-        seed=0,
-        num_channels=64,
-        num_segments=1
-    )
-    test_recording = test_recording.save(name='toy')
-    return dict(recording=test_recording, verbose=True, singularity_image=True)
+    return generate_run_kwargs()
 
 
 def test_kilosort2(run_kwargs):
@@ -60,3 +75,7 @@ def test_yass(run_kwargs):
 def test_pykilosort(run_kwargs):
     sorting = ss.run_pykilosort(output_folder="pykilosort", **run_kwargs)
     print(sorting)
+
+if __name__ == "__main__":
+    kwargs = generate_run_kwargs()
+    test_pykilosort(kwargs)

tests/test_singularity_containers.py

@@ -8,6 +8,29 @@
 
 os.environ['SINGULARITY_DISABLE_CACHE'] = 'true'
 
+# test docker or singularity
+DOCKER_SINGULARITY = "singularity" # "docker"
+
+
+def generate_run_kwargs():
+    test_recording, _ = se.toy_example(
+        duration=30,
+        seed=0,
+        num_channels=64,
+        num_segments=1
+    )
+    test_recording = test_recording.save(name='toy')
+    test_recording.set_channel_gains(1)
+    test_recording.set_channel_offsets(1)
+    run_kwargs = dict(recording=test_recording, verbose=True)
+    if DOCKER_SINGULARITY == "singularity":
+        run_kwargs["singularity_image"] = True
+    elif DOCKER_SINGULARITY == "docker":
+        run_kwargs["docker_image"] = True
+    else:
+        raise Exception("DOCKER_SINGULARITY can be 'docker' or 'singularity'")
+    return run_kwargs
+
 
 @pytest.fixture(autouse=True)
 def work_dir(request, tmp_path):
@@ -27,16 +50,7 @@ def work_dir(request, tmp_path):
 
 @pytest.fixture
 def run_kwargs(work_dir):
-    test_recording, _ = se.toy_example(
-        duration=30,
-        seed=0,
-        num_channels=64,
-        num_segments=1
-    )
-    test_recording.set_channel_gains(1)
-    test_recording.set_channel_offsets(1)
-    test_recording = test_recording.save(name='toy')
-    return dict(recording=test_recording, verbose=True, singularity_image=True)
+    return generate_run_kwargs()
 
 
 def test_spykingcircus(run_kwargs):
@@ -78,11 +92,14 @@ def test_kilosort1(run_kwargs):
     sorting = ss.run_kilosort(output_folder="kilosort", useGPU=False, **run_kwargs)
     print(sorting)
 
-
 def test_combinato(run_kwargs):
     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)
     print(sorting)
+
+if __name__ == "__main__":
+    kwargs = generate_run_kwargs()
+    test_ironclust(kwargs)