fresh build of Docker yields "ModuleNotFoundError: No module named 'pydicom'

[howardpchen]

Although the Dockerfile does in fact run "pip install pydicom" after the Docker image is built "docker run pydicom/deid" using a command like inspect will fail with a package not found error.

It is possible this is related to miniconda3 using Python 3.7 but "matplotlib=2.1.2" forces a downgrade to Python 3.6.6, which occurs after the "pip install pydicom" command in the Dockerfile.

I switched the order of the conda install for matplotlib and pip install pydicom in Dockerfile and the problem went away, like this:

RUN apt-get update && apt-get install -y wget git pkg-config libfreetype6-dev
RUN /opt/conda/bin/conda install matplotlib==2.1.2
RUN pip install pydicom
RUN mkdir /code
ADD . /code
WORKDIR /code
RUN python /code/setup.py install

Could this be investigated and incorporated into the code base, if it makes sense? Thank you!

[vsoch]

Could you please give me the command to reproduce the error?

[vsoch]

Ah I reproduced, let me see if I can test if this is what is happening (with respect to install order).

[vsoch]

Thanks for reporting the issue @howardpchen. Would you care to test the PR? I've build a container with your suggested change 👉 #82

[howardpchen]

Ok @vsoch I will try now.

[howardpchen]

Yes! Works well now. Thanks @vsoch

[vsoch]

Sure thing! I'll merge, and that should build / push the new container (and I'll deploy the updated pypi in a few minutes). Thanks for the catch and please report any other issues that you find! I think deid is less commonly used with the Docker container (a lot of users aren't familiar with containers) so it will be good to have a more thorough testing.

[vsoch]

Closing issue, thanks again!