[FIXED] Cannot install modules inside Docker container with Jupiter notebook image

Issue

I have got the following Docker file

FROM jupyter/scipy-notebook

COPY . ./work

RUN pip install -r ./work/requirements.txt

COPY setup.py /work

RUN pip install --upgrade pip && pip install -e .



COPY src /work/src

WORKDIR /work

and the following project structure:

almond_analysis:
    notebooks:
        data_exploration.ipynb
    src:
       __init__.py
       plots.py
    .gitignore
    docker-compose.yml
    Dockerfile
    README.md
    requirements.txt
    setup.py

Inside the data_exploration.ipynb notebook, I would like to import the module src with the command import src as test. However, despite me having typed RUN pip install -e . in the Dockerfile, I get the error ModuleNotFoundError: No module named 'src'. When I do to my container though, inside the work directory, and run pip install -e . the error goes away. I tried adding CMD pip install -e . at the end of the Dockerfile without success. I read also what was suggested in this post (more specifically to add the lines RUN apt-get update and RUN apt-get install -y --no-install-recommends but without success.

My setup.py file looks like this:

from setuptools import find_packages, setup
import sys
import os

sys.path.insert(0, os.path.abspath( os.path.dirname(__file__)))


requirements_path="requirements.txt"
with open(requirements_path) as requirements_file:
    requirements = requirements_file.read().splitlines()

setup(
    name="almond_analysis",
    version="0.0.1",
    description = "Almond analysis",
    long_description="Analysing yield with Python."
    author= "George N",
    packages=find_packages(),
    install_requires=requirements,
    classifiers=[
        "Programming Language :: Python :: 3"
    ],
    python_requires =">= 3.0.*",
)

Does someone have an idea on how to make the ModuleNotFoundError go away?

Solution

Mount your code under the work folder, then you don't need to install anything, or really need a Dockerfile unless you have other dependencies.

On host, create folder for notebooks...

notebooks/src/plots.py

def foobar():
    print('Hello from plots')

In compose, mount it under the working directory /home/jovyan/work

notebook:
    image: jupyter/scipy-notebook
    ...
    volumes:
      - ./notebooks:/home/jovyan/work

Load up the Jupyter environment, and create a notebook in the work folder, and then import the module.

from src import plots
plots.foobar()  # Hello from plots

This is the same workflow you'd do on your host if you weren't using Docker or Jupyter, so neither of those are really the problem.

Answered By - OneCricketeer