Merge remote-tracking branch 'upstream/main' into main

Author: chyumin

combinato/Dockerfile

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+FROM python:3.8
+
+LABEL maintainer="Vincent Prevosto <[email protected]>"
+
+# Ubuntu package installs
+RUN apt update && \
+    apt install -y --no-install-recommends \
+    git \
+    nano && \
+    apt clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install dependencies
+RUN pip install \
+    numpy \
+    scipy \
+    matplotlib \
+    PyWavelets \
+    tables \
+    pyqt5 \
+    ipython
+
+# Clone Combinato
+WORKDIR /src
+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
+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
+
+# Install Combinato
+WORKDIR /src/combinato
+RUN python3 setup_options.py
+
+

combinato/README.md

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+### Build this image
+Build default image: 
+docker build -t combinato:latest .
+
+### Run container in bash
+docker run --rm -it -v <host-data-folder>:<docker-data-folder> spikeinterface/combinato-base /bin/sh
+flags:
+--rm: removes container once it's stopped
+-it: for interactive session
+-v: mounted volumes (directories)
+
+### Test
+docker run --rm -it spikeinterface/combinato-base /bin/sh
+python3 tools/test_installation.py

combinato/build.sh

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+#!/bin/bash
+
+docker build -t spikeinterface/combinato-base:latest -t spikeinterface/combinato-base:0.1.0 .

combinato/push.sh

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+#!/bin/bash
+
+docker push --all-tags spikeinterface/combinato-base