Consolidated dev and run environments

Dockerfile

@@ -1,29 +1,35 @@
+# Use the official Python image from the Docker Hub
 FROM python:3.10
 
-# Add Tini
-ENV TINI_VERSION v0.19.0
+# Add Tini, a minimal init system for containers
+ENV TINI_VERSION=v0.19.0
 ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
 RUN chmod +x /tini
 
-# The WORKDIR instruction sets the working directory for any RUN, CMD, ENTRYPOINT,
-# COPY and ADD instructions that follow it in the Dockerfile.
-# If the WORKDIR doesn’t exist, it will be created even if it’s not used
-# in any subsequent Dockerfile instruction.
+# Set the working directory inside the container
 WORKDIR /root/env
 
-# Prevent running interactive config
-ENV DEBIAN_FRONTEND noninteractive
+# Prevent running interactive config during package installation
+ENV DEBIAN_FRONTEND=noninteractive
 
+# Install system dependencies and remove the package list
+RUN apt-get update && \
+    apt-get install -y \
+    libgeos-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy the requirements file into the container
 COPY requirements.txt ./
 
+# Install Python dependencies
 RUN pip install --no-cache-dir --upgrade pip && \
     pip install --no-cache-dir -r requirements.txt
 
-RUN pip install jupyter
-RUN pip install networkx
-RUN pip install pandas
-RUN pip install seaborn
-RUN pip install basemap-data-hires
-RUN pip install basemap
+# Create a mount point for external volumes
+VOLUME /root/env
+
+# Set the entrypoint to Tini
+ENTRYPOINT ["/tini", "-g", "--"]
 
-ENTRYPOINT ["/tini", "-g", "--"]
+# Default command to run when the container starts
+CMD ["/bin/bash"]

requirements.txt

@@ -2,4 +2,16 @@ geopy
 networkx
 numpy
 pandas
-matplotlib
+matplotlib
+build
+twine
+pytest
+pytest-cov
+pytest-benchmark
+pytest-mock
+pylint
+black
+jupyter
+seaborn
+basemap-data-hires
+basemap

run.sh

@@ -2,15 +2,21 @@
 
 set -e
 
-IMAGE_TAG=ngraph
+DEFAULT_IMAGE_TAG=ngraph
+IMAGE_TAG=${2:-$DEFAULT_IMAGE_TAG}
+DEFAULT_CONTAINER_NAME=ngraph_jupyter
+CONTAINER_NAME=${3:-$DEFAULT_CONTAINER_NAME}
 IMAGE_ID=$(docker images --format "{{.ID}}" $IMAGE_TAG)
 
-USAGE="Usage: $0 COMMAND IMAGE_TAG\n"
-USAGE+="    COMMAND is what you expect script to do:\n"
+USAGE="Usage: $0 COMMAND [IMAGE_TAG] [CONTAINER_NAME]\n"
+USAGE+="    COMMAND is what you expect the script to do:\n"
 USAGE+="        build - Builds an image from a Dockerfile.\n"
-USAGE+="        run - Runs a container.\n"
-USAGE+="        killall - Stops and removes all running containers.\n"
-USAGE+="        forcecleanall - Clean-up Docker.\n"
+USAGE+="        run - Runs a container and starts Jupyter.\n"
+USAGE+="        shell - Attaches to the shell of a running container.\n"
+USAGE+="        killall - Stops and removes all running containers based on the image tag.\n"
+USAGE+="        forcecleanall - WARNING: Stops and removes all containers and images. This action cannot be undone.\n"
+USAGE+="    IMAGE_TAG is the optional Docker image tag (default: $DEFAULT_IMAGE_TAG).\n"
+USAGE+="    CONTAINER_NAME is the optional Docker container name (default: $DEFAULT_CONTAINER_NAME).\n"
 
 if [[ $# -lt 1 ]]; then
     echo>&2 "ERROR: Must specify the command"
@@ -21,7 +27,7 @@ fi
 [[ $(uname) -eq "Darwin" ]] && MODHACK="-v /lib/modules:/lib/modules:ro" || MODHACK=""
 
 function build {
-    echo "Building docker container"
+    echo "Building docker container with tag $IMAGE_TAG"
     docker build . -t $IMAGE_TAG
 
     IMAGE_ID=$(docker images --format "{{.ID}}" $IMAGE_TAG)
@@ -30,18 +36,24 @@ function build {
 }
 
 function run {
-    name=ngraph_jupyter
-    echo "Starting a container with the name $name using $IMAGE_TAG image..."
-    CONTAINER_ID=$(docker create --rm -it --name $name -v "$PWD":/root/env -p 8787:8787 --entrypoint=/bin/bash --privileged $MODHACK --cap-add ALL $IMAGE_TAG)
+    echo "Starting a container with the name $CONTAINER_NAME using $IMAGE_TAG image..."
+    CONTAINER_ID=$(docker create --rm -it --name $CONTAINER_NAME -v "$PWD":/root/env -p 8787:8787 --entrypoint=/bin/bash --privileged $MODHACK --cap-add ALL $IMAGE_TAG)
     docker start $CONTAINER_ID
-    echo "Started $CONTAINER_ID with the name $name"
+    echo "Started $CONTAINER_ID with the name $CONTAINER_NAME"
     docker exec -it $CONTAINER_ID pip install -e .
     echo "Starting Jupyter in a container. Open http://127.0.0.1:8787/ in your browser."
     docker exec -it $CONTAINER_ID jupyter notebook --port=8787 --no-browser --ip=0.0.0.0 --allow-root --NotebookApp.token='' /root/env
     return 0
 }
 
+function shell {
+    echo "Attaching to the shell of the running container $CONTAINER_NAME..."
+    docker exec -it $CONTAINER_NAME /bin/bash
+    return 0
+}
+
 function killall {
+    echo "Stopping and removing all running containers based on the image tag $IMAGE_TAG..."
     for container_id in $(docker ps -q --filter "ancestor=$IMAGE_TAG"); do
         echo "$(docker kill $container_id) - stopped and removed"
     done
@@ -50,6 +62,13 @@ function killall {
 }
 
 function forcecleanall {
+    echo "WARNING: This will stop and remove all containers and images. This action cannot be undone."
+    read -p "Are you sure you want to proceed? (Y/N): " confirm
+    if [[ $confirm != [Yy] ]]; then
+        echo "Aborting forcecleanall."
+        return 1
+    fi
+
     for container in $(docker container ls --format "{{.ID}}"); do docker container kill $container; done
     for container in $(docker container ls -a --format "{{.ID}}"); do docker container rm $container; done
     for image in $(docker images --format "{{.ID}}"); do docker image rm --force $image; done
@@ -68,6 +87,11 @@ case $1 in
         run "$@"
         ;;
 
+    shell)
+        echo "Executing SHELL command..."
+        shell "$@"
+        ;;
+
     killall)
         echo "Executing KILLALL command..."
         killall "$@"
@@ -83,4 +107,4 @@ case $1 in
         printf "$USAGE" >&2
         exit 2
         ;;
-esac
+esac