Docker + Pipenv + multi-stage builds

Dockerfile

FROM alpine:3.9 AS build
WORKDIR /opt/app

# Install Python and external dependencies, including headers and GCC
RUN apk add --no-cache python3 python3-dev py3-pip libffi libffi-dev musl-dev gcc

# Install Pipenv
RUN pip3 install pipenv

# Create a virtual environment and activate it
RUN python3 -m venv /opt/venv
ENV PATH="/opt/venv/bin:$PATH" VIRTUAL_ENV="/opt/venv"

# Install dependencies into the virtual environment with Pipenv
COPY Pipfile Pipfile.lock /opt/app/
RUN pipenv install --deploy

FROM alpine:3.9
WORKDIR /opt/app

# Install Python and external runtime dependencies only
RUN apk add --no-cache python3 libffi

# Copy the virtual environment from the previous image
COPY --from=build /opt/venv /opt/venv

# Activate the virtual environment
ENV PATH="/opt/venv/bin:$PATH" VIRTUAL_ENV="/opt/venv"

# Copy your application
COPY . /opt/app/

This makes sense. I guess if your "app" was a click application then app.py might just be a shell script invoking your CLI?