search

openworm / tests

OpenWorm tests across various repos
MIT License
3 stars 3 forks source link

cannot build and Docker Container #7

Closed russelljjarvis closed 6 years ago

russelljjarvis commented 6 years ago

I have added these lines to a Dockerfile https://github.com/russelljjarvis/tests/blob/master/Dockerfile#L28-L37

FROM jupyter/scipy-notebook
RUN git clone https://github.com/openworm/ChannelWorm.git
WORKDIR ChannelWorm 
RUN pip install . 
WORKDIR $HOME
RUN pip install git+https://github.com/OpenSourceBrain/osb-model-validation
RUN pip install git+https://github.com/openworm/CElegansNeuroML.git
#RUN sudo chown -R jovyan $HOME
WORKDIR $HOME 
WORKDIR openworm
#RUN sudo chown -R jovyan $HOME
ENV OPENWORM_HOME pwd
# over looked
ENV OW_HOME pwd
# over looked
RUN pip install quantities sciunit
WORKDIR $HOME 
RUN git clone http://github.com/openworm/tests.git
WORKDIR tests 
RUN pip install -e . --process-dependency-links
russelljjarvis commented 6 years ago

Without docker and just raw BASH on Ubuntu I get:

Even after running:

 sudo pip install --upgrade idna

Also things are better on raw BASH an overlooked dependancy is _tkinter',

Error: ImportError: No named '_tkinter', please install the python3-tk package Workaround:

sudo apt-get install python3-tk
rgerkin commented 6 years ago

You must have old cruft in your Docker build. For example, you shouldn't be installing quantities manually anymore (the bug that motivated it was fixed months ago). I have no problem (at least through the first few steps with): 

docker run -it jupyter/scipy-notebook /bin/bash

and then inside the container

mkdir openworm
export OPENWORM_HOME=/home/jovyan/work/openworm
cd $OPENWORM_HOME
git clone http://github.com/openworm/tests; cd tests
pip install -e . --process-dependency-links

That at least gets you past the first part of installation. I'll check to see if the subprojects are installing correctly now.

russelljjarvis commented 6 years ago

If I git clone the lastest idna and then run sudo python3 setup.py install, in idna and then owtests.

I have not tried opening the MuscleModel.ipynb yet, as that would be the real test of if everything works. I prefer to run on Docker instead of the raw system. Docker builds just give me more confidence in the standardization of the environment.

russelljjarvis commented 6 years ago

I have extended the exercise you described above by inheriting jupyter/scipy-notebook.

This fresher Dockerfile builds:

FROM jupyter/scipy-notebook
RUN git clone https://github.com/openworm/ChannelWorm.git
WORKDIR ChannelWorm 
RUN pip install . 
WORKDIR $HOME
RUN pip install git+https://github.com/OpenSourceBrain/osb-model-validation
RUN pip install git+https://github.com/openworm/CElegansNeuroML.git
WORKDIR $HOME 
WORKDIR openworm
ENV OPENWORM_HOME pwd
ENV OW_HOME pwd
# over looked
RUN pip install quantities sciunit
WORKDIR $HOME 
RUN git clone http://github.com/openworm/tests.git
WORKDIR tests 
RUN pip install -e . --process-dependency-links

However I am finding two problems

russelljjarvis commented 6 years ago

Also things are better on raw BASH an overlooked dependancy is _tkinter',

Error: ImportError: No named '_tkinter', please install the python3-tk package Workaround:

sudo apt-get install python3-tk
rgerkin commented 6 years ago

I'm not sure where all of these errors are coming from, but if you move to the jupyter/scipy-notebook docker container they will all go away.