Update Kilosort compile and build scripts and remove kilosort with licence fodler'

Author: alejoe91

kilosort_no_license/README.md kilosort-compiled/README.mdkilosort_no_license/README.md renamed to kilosort-compiled/README.md

@@ -1,5 +1,7 @@
 FROM ks-matlab-base
 
+USER root
+
 RUN chmod 755 /usr/bin/mlrtapp/ks_compiled
 ENV PATH="/usr/bin/mlrtapp:${PATH}"
 
@@ -11,9 +13,10 @@ RUN apt-get update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-ENV MINICONDA_VERSION 4.8.2
+ENV MINICONDA_VERSION 23.1.0-1
+ENV PYTHON_VERSION py39
 ENV CONDA_DIR /home/miniconda3
-ENV LATEST_CONDA_SCRIPT "Miniconda3-py38_$MINICONDA_VERSION-Linux-x86_64.sh"
+ENV LATEST_CONDA_SCRIPT "Miniconda3-${PYTHON_VERSION}_${MINICONDA_VERSION}-Linux-x86_64.sh"
 
 RUN wget --quiet https://repo.anaconda.com/miniconda/$LATEST_CONDA_SCRIPT -O ~/miniconda.sh && \
     bash ~/miniconda.sh -b -p $CONDA_DIR && \

…_no_license/kilosort-compiled/Dockerfile …rt-compiled/kilosort-compiled/Dockerfilekilosort_no_license/kilosort-compiled/Dockerfile renamed to kilosort-compiled/kilosort-compiled/Dockerfile kilosort_no_license/kilosort-compiled/Dockerfile renamed to kilosort-compiled/kilosort-compiled/Dockerfile

@@ -1,4 +1,4 @@
 #!/bin/bash
 
-docker build -t spikeinterface/kilosort-compiled-base:latest -t spikeinterface/kilosort-compiled-base:0.1.0 .
+docker build -t spikeinterface/kilosort-compiled-base:latest -t spikeinterface/kilosort-compiled-base:0.2.0 .
 

…t_no_license/kilosort-compiled/README.md …ort-compiled/kilosort-compiled/README.mdkilosort_no_license/kilosort-compiled/README.md renamed to kilosort-compiled/kilosort-compiled/README.md kilosort_no_license/kilosort-compiled/README.md renamed to kilosort-compiled/kilosort-compiled/README.md

@@ -1,5 +1,7 @@
 FROM ks2-matlab-base
 
+USER root
+
 RUN chmod 755 /usr/bin/mlrtapp/ks2_compiled
 ENV PATH="/usr/bin/mlrtapp:${PATH}"
 
@@ -11,9 +13,10 @@ RUN apt-get update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-ENV MINICONDA_VERSION 4.8.2
+ENV MINICONDA_VERSION 23.1.0-1
+ENV PYTHON_VERSION py39
 ENV CONDA_DIR /home/miniconda3
-ENV LATEST_CONDA_SCRIPT "Miniconda3-py38_$MINICONDA_VERSION-Linux-x86_64.sh"
+ENV LATEST_CONDA_SCRIPT "Miniconda3-${PYTHON_VERSION}_${MINICONDA_VERSION}-Linux-x86_64.sh"
 
 RUN wget --quiet https://repo.anaconda.com/miniconda/$LATEST_CONDA_SCRIPT -O ~/miniconda.sh && \
     bash ~/miniconda.sh -b -p $CONDA_DIR && \

…rt_no_license/kilosort-compiled/build.sh …sort-compiled/kilosort-compiled/build.shkilosort_no_license/kilosort-compiled/build.sh renamed to kilosort-compiled/kilosort-compiled/build.sh kilosort_no_license/kilosort-compiled/build.sh renamed to kilosort-compiled/kilosort-compiled/build.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 
-docker build -t spikeinterface/kilosort2-compiled-base:latest -t spikeinterface/kilosort2-compiled-base:0.1.0 .
+docker build -t spikeinterface/kilosort2-compiled-base:latest -t spikeinterface/kilosort2-compiled-base:0.2.0 .
 

…_no_license/kilosort-compiled/compile.sh …rt-compiled/kilosort-compiled/compile.shkilosort_no_license/kilosort-compiled/compile.sh renamed to kilosort-compiled/kilosort-compiled/compile.sh kilosort_no_license/kilosort-compiled/compile.sh renamed to kilosort-compiled/kilosort-compiled/compile.sh

@@ -33,7 +33,7 @@ mkdir -p $TMP_DIR
 
 echo "Compiling kilosort_master..."
 cd $TMP_DIR
-matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/kilosort2/kilosort2_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${KS_PATH} -o ${KS2_COMPILED_NAME}"
+matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/external/kilosort2_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${KS_PATH} -o ${KS2_COMPILED_NAME}"
 
 echo "Creating base docker image..."
 matlab -batch "compiler.package.docker('${KS2_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'ks2-matlab-base')"