Merge pull request #20 from vncntprvst/SI-container

Spike Interface container

Author: alejoe91

.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto
+
+# Force batch scripts to always use CRLF line endings so that if a repo is accessed
+# in Windows via a file share from Linux, the scripts will work.
+*.{cmd,[cC][mM][dD]} text eol=crlf
+*.{bat,[bB][aA][tT]} text eol=crlf
+
+# Force bash scripts to always use LF line endings so that if a repo is accessed
+# in Unix via a file share from Windows, the scripts will work.
+*.sh text eol=lf

kilosort_with_license/matlab_for_kilosort/docker1/build.sh

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+FROM jupyter/datascience-notebook:hub-1.5.0
+
+LABEL maintainer="Vincent Prevosto <prevosto@mit.edu>"
+
+USER root
+# APT packages
+RUN apt update && \
+    apt install -y --no-install-recommends \
+    libgl1-mesa-glx \
+    datalad && \
+    apt clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# copy repo
+WORKDIR /srv
+RUN git clone https://github.com/SpikeInterface/spikeinterface.git
+
+RUN fix-permissions $CONDA_DIR && \
+fix-permissions /home/$NB_USER && \
+fix-permissions /srv/spikeinterface
+
+#Switch to user
+USER $NB_UID
+
+# update Anaconda and install pip 
+RUN conda update -y conda && \
+     conda install -y pip
+
+# Conda installs
+# RUN conda config --set channel_priority flexible && \
+RUN conda install -y -c conda-forge \
+    nb_conda_kernels \
+    jupyterlab-git \
+    pynwb && \
+    conda clean -tipy
+
+# Install jupyter_contrib_nbextensions with pip (conda install has major conflicts)
+RUN pip install https://github.com/ipython-contrib/jupyter_contrib_nbextensions/tarball/master
+
+# Create environment
+RUN ln -s /srv/spikeinterface /home/$NB_USER/
+WORKDIR /home/$NB_USER/spikeinterface/installation_tips/
+RUN conda env create -f full_spikeinterface_environment_mac.yml
+
+# Make kernels available
+SHELL ["conda","run","-n","si_env","/bin/bash","-c"]
+RUN conda install --quiet --yes ipykernel && \
+    conda install --quiet --yes -c conda-forge datalad && \
+    python -m ipykernel install --user --name si_env --display-name "spikeinterface"
+RUN pip install jupytext
+
+# Configure git (required by datalad)
+WORKDIR /home/$NB_USER/spikeinterface/
+RUN git config --global --add user.name "Jovyan" && \
+    git config --global --add user.email jovyan@example.net
+
+# Create "getting started" notebook in home directory
+WORKDIR /home/$NB_USER/spikeinterface/examples/getting_started/
+RUN jupytext --to notebook plot_getting_started.py && \
+    cp ~/spikeinterface/examples/getting_started/plot_getting_started.ipynb ~/getting_started.ipynb
+
+# Make sure to switch back to user (avoid running ui containers as root)
+USER $NB_UID
+WORKDIR /home/$NB_USER

spikeinterface/Dockerfile

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+
+### How to run the spikeinterface container
+**Method 1: drag and drop**  (Windows only for now)  
+Drag and drop the data folder on either `.bat` file (see `launch_scripts` folder).  For convenience, create a shortcut and put it on your desktop.
+
+![Drag and Drop](images/DragAndDropDemo.gif)
+
+_Which launch script should you pick?_   
+  
+  `SpikeInterface_OneOff.bat` will start a one-off sesssion. The container will self-destroy upon shutdown (not just closing the tab though). If the tab is closed, go back to your session at this address: http://localhost:8888/lab?token=mytoken.  
+   
+  `SpikeInterface_Persist.bat` will start a persistent container that can be reused. The drawback is that data folder will stay the same until the container is stopped and remove (which can be done following instructions below).  
+In the `.bat`, please replace "mytoken" by some other word of your choice.  
+
+To add files and notebooks to your session, drag and drop them on the left side mneu.  
+Files can be downloaded with right-click > download.   
+  
+**Method 2: manual start**  
+1. Open a terminal and navigate to the data directory. Then follow these instructions.  
+2. Start the container  
+*On Linux/MacOS*  
+`export JUPYTER_TOKEN='mytoken'`
+`docker run -d --rm --name spikeinterface -v "${PWD}":/home/jovyan/data -p 8888:8888 -e JUPYTER_TOKEN spikeinterface/spikeinterface:0.2`  
+*On Windows*  
+`set JUPYTER_TOKEN=mytoken`
+`docker run -d --rm --name spikeinterface -v "%CD%":/home/jovyan/data -p 8888:8888 -e JUPYTER_TOKEN spikeinterface/spikeinterface:0.2`  
+  
+  * Replace "mytoken" by some other word. 
+  * If you built the image (see below), remove `spikeinterface/` or replace it with your docker handle. 
+  
+3. Then open http://localhost:8888/lab?token=mytoken in a browser.   
+
+
+
+**Important Note**  
+The `--rm` flag means the container is a one-off (will self-destroy upon closure). 
+To make the container persitant, remove the `--rm flag` from the docker call. In which case, the container will persist. To start a stopped container, run `docker start spikeinterface` in a terminal, or use the Docker Desktop interface to start it.  
+
+### How to build this image
+The container image is [available on DockerHub](https://hub.docker.com/repository/docker/spikeinterface/spikeinterface/). Providing you have Docker installed, it will automatically download when starting the container. 
+
+If you want to build it, follow the instructions below.
+Open a terminal, navigate to the spikeinterface directory, then run:   
+`docker build -t spikeinterface:0.2 .`  
+On Linux systems, you can also use the build script (after making it executable `chmod +x build.sh`):    
+`./build.sh`  
+
+
+  
+
+
+
+
+

spikeinterface/README.md

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+#!/bin/bash
+
+docker build -t spikeinterface/spikeinterface:0.2 .

spikeinterface/build.sh

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+@echo off
+Title Drag and drop a data folder
+Mode con cols=60 lines=3
+IF [%1] EQU [] Goto:Error
+set JUPYTER_TOKEN=mytoken
+docker run -d --rm --name spikeinterface -v "%~1":/home/jovyan/data -p 8888:8888 -e JUPYTER_TOKEN spikeinterface/spikeinterface:0.2
+TIMEOUT /T 2
+START /W "" http://localhost:8888/lab?token=mytoken
+ECHO Spike Interface started
+TIMEOUT /T 2
+Exit /b
+
+::**********************************************************
+:Error
+Color 0C & echo(
+ECHO    You must drag and drop a folder on this batch program 
+Timeout /T 5 /NoBreak >nul
+Exit /b
+::**********************************************************

spikeinterface/images/DragAndDropDemo.gif

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+@echo off
+Title Drag and drop a data folder
+Mode con cols=60 lines=3
+IF [%1] EQU [] Goto:Error
+set JUPYTER_TOKEN=mytoken
+docker run -d --rm --name spikeinterface -v "%~1":/home/jovyan/data -p 8888:8888 -e JUPYTER_TOKEN spikeinterface/spikeinterface:0.2
+TIMEOUT /T 2
+START /W "" http://localhost:8888/lab?token=mytoken
+ECHO Spike Interface started
+TIMEOUT /T 2
+Exit /b
+
+::**********************************************************
+:Error
+Color 0C & echo(
+ECHO    You must drag and drop a folder on this batch program 
+Timeout /T 5 /NoBreak >nul
+Exit /b
+::**********************************************************

spikeinterface/launch_scripts/SpikeInterface_OneOff.bat

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+#!/bin/bash
+
+docker push spikeinterface/spikeinterface:0.2 .