dev ms5

si_mountainsort5/Dockerfile

@@ -1,5 +1,17 @@
 FROM spikeinterface/mountainsort5-base:0.5.3
 
+# Copy files into the container
+WORKDIR /app
+COPY /common /app/common
+COPY si_mountainsort5/*.py /app/
+COPY si_mountainsort5/requirements.txt /app/requirements.txt
+RUN pip install -r requirements.txt
+
+# Give execution permission to /app/main.py
+RUN chmod +x /app/main.py
+
+# BELOW ARE TEMPORARY DEV INSTALLATIONS ---------------------
+
 # Install Dendro from source, for now
 WORKDIR /src
 RUN git clone https://github.com/flatironinstitute/dendro.git && \
@@ -12,32 +24,22 @@ RUN git clone https://github.com/SpikeInterface/spikeinterface_pipelines.git &&
     # git checkout dev && \
     pip install -e .
 
-# Install neuroconv from source, for now
-RUN git clone https://github.com/catalystneuro/neuroconv.git && \
-    cd neuroconv && \
-    pip install -e .
-
-# # Install spikeinterface from source, for now
-# RUN git clone https://github.com/SpikeInterface/spikeinterface.git && \
-#     cd spikeinterface && \
-#     # git checkout dev && \
-#     pip install -e .[full]
-
-# Install mountainsort from source, for now
-RUN git clone https://github.com/flatironinstitute/mountainsort5.git && \
-    cd mountainsort5 && \
-    git checkout cached-chunk-size && \
-    pip install -e .
-
-# Install spikeinterface
-RUN pip install spikeinterface[full]==0.100.2
-
-# Copy files into the container
-WORKDIR /app
-COPY /common /app/common
-COPY si_mountainsort5/*.py /app/
-COPY si_mountainsort5/requirements.txt /app/requirements.txt
-RUN pip install -r requirements.txt
-
-# Give execution permission to /app/main.py
-RUN chmod +x /app/main.py
+# # Install neuroconv from source, for now
+# RUN git clone https://github.com/catalystneuro/neuroconv.git && \
+#     cd neuroconv && \
+#     pip install -e .
+
+# Install spikeinterface from source, for now
+RUN git clone https://github.com/alejoe91/spikeinterface && \
+    cd spikeinterface && \
+    # git remote add alejoe91 https://github.com/alejoe91/spikeinterface && \
+    git checkout 0.100.5-ms5 && \
+    pip install -e .[full]
+
+# # Install mountainsort from source, for now
+# RUN git clone https://github.com/flatironinstitute/mountainsort5.git && \
+#     cd mountainsort5 && \
+#     git checkout cached-chunk-size && \
+#     pip install -e .
+
+# -----------------------------------------------------------

si_mountainsort5/requirements.txt

@@ -1,5 +1,7 @@
 pynwb
 pyvips==2.2.2
-# spikeinterface[full]==0.100.2
+spikeinterface[full]==0.100.5
+mountainsort5==0.5.6
+neuroconv
 # spikeinterface_pipelines
 # dendro

si_mountainsort5/sample_context_1.yaml

@@ -7,7 +7,7 @@ recording_context:
   electrical_series_path: /acquisition/ElectricalSeriesAp
   lazy_read_input: true
   stub_test: true
-  stub_test_duration_sec: 30
+  stub_test_duration_sec: 10
 run_preprocessing: true
 preprocessing_context:
   motion_correction:
@@ -31,4 +31,4 @@ postprocessing_context:
     nn_isolation: false
     nn_noise_overlap: false
 run_curation: true
-run_visualization: true
+run_visualization: false