clean up directory

vncntprvst · vncntprvst · commit 049265779613 · 2022-06-07T17:49:35.000-04:00
diff --git a/spikeinterface/Dockerfile b/spikeinterface/Dockerfile
@@ -27,12 +27,15 @@ RUN conda update -y conda && \
      conda install -y pip
 
 # Conda installs
-RUN conda config --set channel_priority flexible && \
-    conda install -y -c conda-forge nb_conda_kernels \
-    jupyter_contrib_nbextensions \
+# RUN conda config --set channel_priority flexible && \
+RUN conda install -y -c conda-forge \
+    nb_conda_kernels \
     jupyterlab-git \
     pynwb && \
-    conda clean -tipsy
+    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/
diff --git a/spikeinterface/README.md b/spikeinterface/README.md
@@ -1,9 +1,9 @@
 
 ### How to run the spikeinterface container
-**Method 1: drag and drop**  (Windows only)  
-Drag and drop the data folder on either `.bat` file.  For convenience, create a shortcut and put it on your desktop.
+**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](DragAndDropDemo.gif)
+![Drag and Drop](images/DragAndDropDemo.gif)
 
 Which launch script should you pick?   
   `SpikeInterface_OneOff.bat` will start a on-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.  
@@ -18,13 +18,13 @@ Files can be downloaded with right-click > download.
 2. Start the container  
 *On Linux/MacOS*  
 `export JUPYTER_TOKEN='mytoken'`
-`docker run -d --rm --name spikeinterface -v "${PWD}":/home/jovyan/data -p 8888:8888 -e JUPYTER_TOKEN wanglabneuro/spikeinterface:0.2`  
+`docker run -d --rm --name spikeinterface -v "${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 wanglabneuro/spikeinterface:0.2`  
+`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 `wanglabneuro` or replace it with your docker handle. 
+  * 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.   
 
@@ -35,7 +35,7 @@ The `--rm` flag means the container is a on-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/wanglabneuro/spikeinterface/). Providing you have Docker installed, it will automatically download when starting the container. 
+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:   
diff --git a/spikeinterface/build.sh b/spikeinterface/build.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-docker build -t wanglabneuro/spikeinterface:0.1 .
+docker build -t spikeinterface/spikeinterface:0.2 .
diff --git a/spikeinterface/images/DragAndDropDemo.gif b/spikeinterface/images/DragAndDropDemo.gif
diff --git a/spikeinterface/launch_scripts/SpikeInterface_OneOff.bat b/spikeinterface/launch_scripts/SpikeInterface_OneOff.bat
@@ -3,7 +3,7 @@ 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 wanglabneuro/spikeinterface:0.2
+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
diff --git a/spikeinterface/launch_scripts/SpikeInterface_Persist.bat b/spikeinterface/launch_scripts/SpikeInterface_Persist.bat
@@ -3,7 +3,7 @@ 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 wanglabneuro/spikeinterface:0.2
+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
diff --git a/spikeinterface/push.sh b/spikeinterface/push.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker push spikeinterface/spikeinterface:0.2 .

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,3 @@`
`1`	`1`	`#!/bin/bash`
`2`	`2`
`3`		`-docker build -t wanglabneuro/spikeinterface:0.1 .`
	`3`	`+docker build -t spikeinterface/spikeinterface:0.2 .`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+#!/bin/bash`
	`2`	`+`
	`3`	`+docker push spikeinterface/spikeinterface:0.2 .`