Merge pull request #728 from OpenSourceBrain/feature/jlab_req_updates

JupyterLab docker improvements
OpenSourceBrain · Apr 19, 2023 · 5ece70a · 5ece70a
2 parents 3919963 + c608622
commit 5ece70a
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diff --git a/applications/jupyterlab/Dockerfile b/applications/jupyterlab/Dockerfile
@@ -37,7 +37,13 @@ RUN jupyter labextension install plotlywidget
 USER root
 
 ### Some aliases
-RUN echo -e '\n\nalias cd..="cd .." \nalias h=history \nalias ll="ls -alt" \nalias jnml="java -classpath /opt/conda/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-*-jar-with-dependencies.jar  org.neuroml.JNeuroML"\n' >> ~/.bashrc
+RUN echo -e '\n\nalias cd..="cd .." \nalias h=history \nalias ll="ls -alt" \n' >> ~/.bashrc
+
+### Set up jnml, reusing pynml jar
+RUN echo -e '#!/bin/bash\n#Reusing the jNeuroML jar from the pip installed pyNeuroML for the jnml command\n\njava -classpath /opt/conda/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-*-jar-with-dependencies.jar  org.neuroml.JNeuroML $@' >> /opt/conda/bin/jnml
+RUN chmod +x /opt/conda/bin/jnml
+ENV JNML_HOME=/opt/conda/bin
+
 RUN cat ~/.bashrc
 
 

diff --git a/applications/jupyterlab/requirements.txt b/applications/jupyterlab/requirements.txt
@@ -45,12 +45,7 @@ seaborn
 torch==1.11.0+cpu
 
 # For MDF
-git+https://github.com/SheffieldML/GPy.git@devel
-dask==2.30.0
-distributed==2.30.1
-protobuf==3.17.0
-git+https://github.com/SheffieldML/GPy.git@devel
-#modeci_mdf==0.3.3 # big jump in size of image...
+modeci_mdf==0.4.5 # big jump in size of image...
 
 scikit-learn # Required for some Neuromatch Academy material
 fasttext # Required for some Neuromatch Academy material