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