From c1e3fed5bcb0da4ae145887f71ec3c20b900ca64 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Mon, 21 Jul 2025 17:38:17 +0200
Subject: [PATCH 1/2] update docker images

---
 {klusta => archived/klusta}/Dockerfile        |  0
 {klusta => archived/klusta}/build.sh          |  0
 {klusta => archived/klusta}/push.sh           |  0
 {yass => archived/yass}/Dockerfile            |  0
 {yass => archived/yass}/build.sh              |  0
 {yass => archived/yass}/push.sh               |  0
 combinato/Dockerfile                          |  6 ++-
 combinato/build.sh                            |  2 +-
 hdsort-compiled/Dockerfile                    | 10 +++--
 hdsort-compiled/build.sh                      |  2 +-
 hdsort-compiled/compile.sh                    |  3 +-
 ironclust-compiled/Dockerfile                 |  8 ++--
 ironclust-compiled/build.sh                   |  2 +-
 ironclust-compiled/compile.sh                 |  1 +
 kilosort-compiled/compile_and_build_all_ks.sh |  2 +
 kilosort4/Dockerfile                          | 10 ++---
 mountainsort4/Dockerfile                      |  7 +---
 mountainsort5/Dockerfile                      |  6 +--
 rtsort/Dockerfile                             | 39 +++++++++++++++++++
 rtsort/build.sh                               |  3 ++
 rtsort/push.sh                                |  3 ++
 waveclus-compiled/Dockerfile                  | 11 ++++--
 waveclus-compiled/build.sh                    |  2 +-
 waveclus-compiled/compile.sh                  |  5 ++-
 24 files changed, 88 insertions(+), 34 deletions(-)
 rename {klusta => archived/klusta}/Dockerfile (100%)
 rename {klusta => archived/klusta}/build.sh (100%)
 rename {klusta => archived/klusta}/push.sh (100%)
 rename {yass => archived/yass}/Dockerfile (100%)
 rename {yass => archived/yass}/build.sh (100%)
 rename {yass => archived/yass}/push.sh (100%)
 create mode 100644 rtsort/Dockerfile
 create mode 100755 rtsort/build.sh
 create mode 100644 rtsort/push.sh

diff --git a/klusta/Dockerfile b/archived/klusta/Dockerfile
similarity index 100%
rename from klusta/Dockerfile
rename to archived/klusta/Dockerfile
diff --git a/klusta/build.sh b/archived/klusta/build.sh
similarity index 100%
rename from klusta/build.sh
rename to archived/klusta/build.sh
diff --git a/klusta/push.sh b/archived/klusta/push.sh
similarity index 100%
rename from klusta/push.sh
rename to archived/klusta/push.sh
diff --git a/yass/Dockerfile b/archived/yass/Dockerfile
similarity index 100%
rename from yass/Dockerfile
rename to archived/yass/Dockerfile
diff --git a/yass/build.sh b/archived/yass/build.sh
similarity index 100%
rename from yass/build.sh
rename to archived/yass/build.sh
diff --git a/yass/push.sh b/archived/yass/push.sh
similarity index 100%
rename from yass/push.sh
rename to archived/yass/push.sh
diff --git a/combinato/Dockerfile b/combinato/Dockerfile
index 501576d..4fe4215 100644
--- a/combinato/Dockerfile
+++ b/combinato/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.8
+FROM python:3.12
 
 LABEL maintainer="Vincent Prevosto <prevosto@mit.edu>"
 
@@ -27,12 +27,14 @@ RUN git clone https://github.com/jniediek/combinato.git
 # Add Combinato repository to paths
 ENV COMBINATO_PATH=/src/combinato
 ENV PATH=$PATH:$COMBINATO_PATH
-ENV PYTHONPATH=$PYTHONPATH:/usr/local/bin/python3:$COMBINATO_PATH
+ENV PYTHONPATH=/usr/local/bin/python3:$COMBINATO_PATH
 RUN echo '\n\
 export PATH=$PATH:/src/combinato\n\
 export PYTHONPATH=$PYTHONPATH:/usr/local/bin/python3:/src/combinato\n\
 export COMBINATO_PATH=/src/combinato' >> /root/.bashrc
 
+RUN pip install "numpy<2"  # Ensure compatibility with Combinato
+
 # Install Combinato
 WORKDIR /src/combinato
 RUN python3 setup_options.py
diff --git a/combinato/build.sh b/combinato/build.sh
index 01e9aea..a071805 100755
--- a/combinato/build.sh
+++ b/combinato/build.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-docker build -t spikeinterface/combinato-base:latest -t spikeinterface/combinato-base:0.1.0 .
+docker build -t spikeinterface/combinato-base:latest -t spikeinterface/combinato-base:0.2.0 .
diff --git a/hdsort-compiled/Dockerfile b/hdsort-compiled/Dockerfile
index bd77067..3a32192 100644
--- a/hdsort-compiled/Dockerfile
+++ b/hdsort-compiled/Dockerfile
@@ -1,5 +1,6 @@
 FROM hdsort-matlab-base
 
+USER root
 RUN chmod 755 /usr/bin/mlrtapp/hdsort_compiled
 ENV PATH="/usr/bin/mlrtapp:${PATH}"
 
@@ -11,10 +12,11 @@ RUN apt-get update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-ENV MINICONDA_VERSION 4.8.2
-ENV CONDA_DIR /home/miniconda3
-ENV LATEST_CONDA_SCRIPT "Miniconda3-py38_$MINICONDA_VERSION-Linux-x86_64.sh"
-
+ENV MINICONDA_VERSION=25.5.1-0
+ENV PYTHON_VERSION=py312
+ENV CONDA_DIR=/home/miniconda3
+ENV LATEST_CONDA_SCRIPT="Miniconda3-${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 && \
     rm ~/miniconda.sh
diff --git a/hdsort-compiled/build.sh b/hdsort-compiled/build.sh
index cb25fa2..5632000 100755
--- a/hdsort-compiled/build.sh
+++ b/hdsort-compiled/build.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 
-docker build -t spikeinterface/hdsort-compiled-base:latest -t spikeinterface/hdsort-compiled-base:0.1.0 .
+docker build -t spikeinterface/hdsort-compiled-base:latest -t spikeinterface/hdsort-compiled-base:0.2.0 .
 
diff --git a/hdsort-compiled/compile.sh b/hdsort-compiled/compile.sh
index b6ceb78..e0f1a57 100755
--- a/hdsort-compiled/compile.sh
+++ b/hdsort-compiled/compile.sh
@@ -29,7 +29,8 @@ mkdir -p $TMP_DIR
 
 echo "Compiling hdsort..."
 cd $TMP_DIR
-matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/hdsort/hdsort_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${HDSORT_PATH} -o ${HDSORT_COMPILED_NAME}"
+EXTERNAL_SORTERS_FOLDER=${SI_PATH}/src/spikeinterface/sorters/external/
+matlab -batch "mcc -m ${EXTERNAL_SORTERS_FOLDER}/hdsort_master.m -a ${SI_PATH}/src/spikeinterface/sorters/utils -a ${HDSORT_PATH} -o ${HDSORT_COMPILED_NAME}"
 
 echo "Creating base docker image..."
 matlab -batch "compiler.package.docker('${HDSORT_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'hdsort-matlab-base')"
diff --git a/ironclust-compiled/Dockerfile b/ironclust-compiled/Dockerfile
index 2085e33..a779433 100644
--- a/ironclust-compiled/Dockerfile
+++ b/ironclust-compiled/Dockerfile
@@ -1,5 +1,6 @@
 FROM ironclust-matlab-base
 
+USER root
 RUN chmod 755 /usr/bin/mlrtapp/p_ironclust
 ENV PATH="/usr/bin/mlrtapp:${PATH}"
 
@@ -11,9 +12,10 @@ RUN apt-get update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-ENV MINICONDA_VERSION 4.8.2
-ENV CONDA_DIR /home/miniconda3
-ENV LATEST_CONDA_SCRIPT "Miniconda3-py38_$MINICONDA_VERSION-Linux-x86_64.sh"
+ENV MINICONDA_VERSION=25.5.1-0
+ENV PYTHON_VERSION=py312
+ENV CONDA_DIR=/home/miniconda3
+ENV LATEST_CONDA_SCRIPT="Miniconda3-${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 && \
diff --git a/ironclust-compiled/build.sh b/ironclust-compiled/build.sh
index b307a48..f381652 100755
--- a/ironclust-compiled/build.sh
+++ b/ironclust-compiled/build.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 
-docker build -t spikeinterface/ironclust-compiled-base:latest -t spikeinterface/ironclust-compiled-base:5.9.8 .
+docker build -t spikeinterface/ironclust-compiled-base:latest -t spikeinterface/ironclust-compiled-base:5.9.8_cuda-12.0.0 .
 
diff --git a/ironclust-compiled/compile.sh b/ironclust-compiled/compile.sh
index 38952ef..02e0376 100755
--- a/ironclust-compiled/compile.sh
+++ b/ironclust-compiled/compile.sh
@@ -39,6 +39,7 @@ for fname in $(eval "ls ${IC_PATH} -I \"*.pdf\" -p | grep -v /"); do
 done
 ADD_FILES="${ADD_FILES} -a ${IC_PATH}/prb"
 ADD_FILES="${ADD_FILES} -a ${IC_PATH}/prb_json"
+ADD_FILES="${ADD_FILES} -a ${IC_PATH}/jsonlab-1.5"
 
 matlab -batch "mcc -m ${IC_PATH}/p_ironclust.m ${ADD_FILES} -o ${IC_COMPILED_NAME}"
 
diff --git a/kilosort-compiled/compile_and_build_all_ks.sh b/kilosort-compiled/compile_and_build_all_ks.sh
index 152ad35..cd55ead 100644
--- a/kilosort-compiled/compile_and_build_all_ks.sh
+++ b/kilosort-compiled/compile_and_build_all_ks.sh
@@ -23,6 +23,8 @@ KILOSORT2_PATH=${3%/}
 KILOSORT25_PATH=${4%/}
 KILOSORT3_PATH=${5%/}
 
+export MW_NVCC_PATH=/usr/bin/
+export MW_ALLOW_ANY_CUDA=1
 
 cd kilosort-compiled
 bash compile.sh $KILOSORT_PATH $SPIKEINTERFACE_PATH
diff --git a/kilosort4/Dockerfile b/kilosort4/Dockerfile
index 80121cb..48060e7 100644
--- a/kilosort4/Dockerfile
+++ b/kilosort4/Dockerfile
@@ -16,11 +16,11 @@ RUN apt update && \
     rm -rf /var/lib/apt/lists/*
 
 # install miniconda
-ENV MINICONDA_VERSION 24.1.2-0
-ENV PY_VERSION py311
-ENV CONDA_DIR /home/miniconda3
-ENV LATEST_CONDA_SCRIPT "Miniconda3-${PY_VERSION}_${MINICONDA_VERSION}-Linux-x86_64.sh"
-
+ENV MINICONDA_VERSION=25.5.1-0
+ENV PYTHON_VERSION=py312
+ENV CONDA_DIR=/home/miniconda3
+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 && \
     rm ~/miniconda.sh
diff --git a/mountainsort4/Dockerfile b/mountainsort4/Dockerfile
index 1e9bd07..2dd9483 100644
--- a/mountainsort4/Dockerfile
+++ b/mountainsort4/Dockerfile
@@ -1,9 +1,6 @@
-FROM python:3.8
+FROM python:3.10
 
-# downgrade pip version to avoid dependency issues during installations
-RUN pip install --no-input pip==21.2.4
-
-RUN pip install numpy
+RUN pip install "numpy<2"
 
 RUN pip install requests
 # Install MountainSort4
diff --git a/mountainsort5/Dockerfile b/mountainsort5/Dockerfile
index 000e504..383c907 100644
--- a/mountainsort5/Dockerfile
+++ b/mountainsort5/Dockerfile
@@ -1,8 +1,6 @@
-FROM python:3.10
+FROM python:3.12
 
 # downgrade pip version to avoid dependency issues during installations
 RUN pip install --upgrade pip
-
-RUN pip install numpy
-
+RUN pip install "numpy<2"
 RUN pip install mountainsort5==0.5.6
diff --git a/rtsort/Dockerfile b/rtsort/Dockerfile
new file mode 100644
index 0000000..f0d9b67
--- /dev/null
+++ b/rtsort/Dockerfile
@@ -0,0 +1,39 @@
+FROM nvidia/cuda:12.0.0-base-ubuntu20.04
+
+LABEL maintainer="Alessio Buccino <alessiop.buccino@gmail.com>"
+
+# USER root
+# Ubuntu package installs
+RUN apt update && \
+    apt install -y --no-install-recommends \
+    libfftw3-dev \
+    git \
+    wget && \
+    apt clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# install miniconda
+ENV MINICONDA_VERSION=25.5.1-0
+ENV PYTHON_VERSION=py312
+ENV CONDA_DIR=/home/miniconda3
+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 $CONDA_DIR && \
+    rm ~/miniconda.sh
+ENV PATH=$CONDA_DIR/bin:$PATH
+RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main && \
+    conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r && \
+    conda update conda && \
+    conda install conda-build
+
+# make conda activate command available from /bin/bash --login shells
+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 torch
+RUN pip install torch torch-tensorrt tensorrt
+
+# install rt-sort
+RUN pip install git+https://github.com/braingeneers/braindance#egg=braindance[rt-sort]
diff --git a/rtsort/build.sh b/rtsort/build.sh
new file mode 100755
index 0000000..655b064
--- /dev/null
+++ b/rtsort/build.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker build -t spikeinterface/rtsort-base:latest -t spikeinterface/rtsort-base:0.1.0_cuda-12.0.0 .
diff --git a/rtsort/push.sh b/rtsort/push.sh
new file mode 100644
index 0000000..6f1025f
--- /dev/null
+++ b/rtsort/push.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker push --all-tags spikeinterface/rtsort-base
diff --git a/waveclus-compiled/Dockerfile b/waveclus-compiled/Dockerfile
index 85c9f6c..38580c0 100644
--- a/waveclus-compiled/Dockerfile
+++ b/waveclus-compiled/Dockerfile
@@ -1,5 +1,7 @@
 FROM waveclus-matlab-base
 
+USER root
+
 COPY --from=waveclus-snippets-matlab-base /usr/bin/mlrtapp/waveclus_snippets_compiled /usr/bin/mlrtapp/waveclus_snippets_compiled
 RUN chmod 755 /usr/bin/mlrtapp/waveclus_compiled
 RUN chmod 755 /usr/bin/mlrtapp/waveclus_snippets_compiled
@@ -13,10 +15,11 @@ RUN apt-get update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-ENV MINICONDA_VERSION 4.8.2
-ENV CONDA_DIR /home/miniconda3
-ENV LATEST_CONDA_SCRIPT "Miniconda3-py38_$MINICONDA_VERSION-Linux-x86_64.sh"
-
+ENV MINICONDA_VERSION=25.5.1-0
+ENV PYTHON_VERSION=py312
+ENV CONDA_DIR=/home/miniconda3
+ENV LATEST_CONDA_SCRIPT="Miniconda3-${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 && \
     rm ~/miniconda.sh
diff --git a/waveclus-compiled/build.sh b/waveclus-compiled/build.sh
index bae75ca..fda973a 100755
--- a/waveclus-compiled/build.sh
+++ b/waveclus-compiled/build.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 
-docker build -t spikeinterface/waveclus-compiled-base:latest -t spikeinterface/waveclus-compiled-base:0.1.0 .
+docker build -t spikeinterface/waveclus-compiled-base:latest -t spikeinterface/waveclus-compiled-base:0.2.0 .
 
diff --git a/waveclus-compiled/compile.sh b/waveclus-compiled/compile.sh
index 0f36a47..485cb00 100755
--- a/waveclus-compiled/compile.sh
+++ b/waveclus-compiled/compile.sh
@@ -30,13 +30,14 @@ mkdir -p $TMP_DIR
 
 echo "Compiling waveclus..."
 cd $TMP_DIR
-matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/waveclus/waveclus_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${WC_PATH} -o ${WC_COMPILED_NAME}"
+EXTERNAL_SORTERS_FOLDER=${SI_PATH}/src/spikeinterface/sorters/external/
+matlab -batch "mcc -m ${EXTERNAL_SORTERS_FOLDER}/waveclus_master.m -a ${SI_PATH}/src/spikeinterface/sorters/utils -a ${WC_PATH} -o ${WC_COMPILED_NAME}"
 
 echo "Creating base docker image..."
 matlab -batch "compiler.package.docker('${WC_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'waveclus-matlab-base')"
 
 echo "Compiling waveclus_snippets..."
-matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/waveclus/waveclus_snippets_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${WC_PATH} -o ${WC_SNIPPETS_COMPILED_NAME}"
+matlab -batch "mcc -m ${EXTERNAL_SORTERS_FOLDER}/waveclus_snippets_master.m -a ${SI_PATH}/src/spikeinterface/sorters/utils -a ${WC_PATH} -o ${WC_SNIPPETS_COMPILED_NAME}"
 
 echo "Creating base docker image..."
 matlab -batch "compiler.package.docker('${WC_SNIPPETS_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'waveclus-snippets-matlab-base')"

From f672e0f4f99da7b108e1761c45ea1d12ea7f9196 Mon Sep 17 00:00:00 2001
From: Alessio Buccino <alejoe9187@gmail.com>
Date: Wed, 23 Jul 2025 17:38:40 +0200
Subject: [PATCH 2/2] update Tridesclous

---
 tridesclous/Dockerfile | 12 +++---------
 tridesclous/build.sh   |  2 +-
 2 files changed, 4 insertions(+), 10 deletions(-)

diff --git a/tridesclous/Dockerfile b/tridesclous/Dockerfile
index 7267923..c8f917c 100644
--- a/tridesclous/Dockerfile
+++ b/tridesclous/Dockerfile
@@ -1,22 +1,16 @@
-FROM python:3.8
-
-# downgrade pip version to avoid dependency issues during installations
-RUN pip install --no-input pip==21.2.4
-
-
+FROM python:3.12
 
 # Install prerequisites
 RUN apt-get update && apt-get install -y libgl1-mesa-glx
 
 # need to force some version
-RUN pip install numpy==1.21
+RUN pip install numpy
 RUN pip install numba
 RUN pip install hdbscan
 
-
 RUN pip install Cython
 RUN pip install scipy pandas scikit-learn matplotlib seaborn tqdm openpyxl quantities neo
 RUN pip install h5py
 RUN pip install loky packaging
 
-RUN pip install tridesclous==1.6.5
+RUN pip install tridesclous==1.6.9
diff --git a/tridesclous/build.sh b/tridesclous/build.sh
index 4829441..8cdf7e9 100644
--- a/tridesclous/build.sh
+++ b/tridesclous/build.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-docker build -t spikeinterface/tridesclous-base:latest -t spikeinterface/tridesclous-base:1.6.5 .
+docker build -t spikeinterface/tridesclous-base:latest -t spikeinterface/tridesclous-base:1.6.9 .