Add Docker and poetry dependency management

.gitignore

@@ -82,4 +82,7 @@ venv.bak/
 /site
 
 # mypy
-.mypy_cache/
+.mypy_cache/
+
+# Docker log
+docker_build.log

Dockerfile

@@ -0,0 +1,121 @@
+# The Linux distro install instructions from https://miktex.org/download are used here.
+# This Dockerfile creates a docker container that has all necessary packages installed to create the NN diagrams
+# Remember, if needed to rebuild, look at the README for cmd line instructions
+#
+# Authors: [Christopher Endres ([email protected])]
+# Date Created: 06/26/2023
+# Last Updated: 06/26/2023
+# Version: 1.0
+
+### Stage 1, use Ubuntu 20.04 as base image ###
+FROM ubuntu:20.04 AS base
+
+# Set home directory
+ENV HOME=/home/pnn
+WORKDIR $HOME
+
+# Set user to root
+USER root
+
+# Set env name
+ARG ENV_NAME=pnn
+
+# Update and install dependencies for python3.10 install
+RUN apt-get update -y && \
+	apt-get install software-properties-common -y && \
+	add-apt-repository ppa:deadsnakes/ppa
+
+# Install python3.10 and other dependencies
+RUN apt-get install python3.10 -y && \
+	apt-get install -y python3-distutils python3-pip python3-apt
+
+# Remove python3 virtualenv, install virtualenv
+RUN apt-get remove -y python3-virtualenv && \
+	pip install --user virtualenv --force-reinstall 
+
+# Add the 'tree' command for debugging
+RUN apt-get update && \
+	apt-get install -y tree
+
+
+### Stage 2, install miktex ###
+# All credits to this stage go to Christian Schenk, contents can be found at https://github.com/MiKTeX/docker-miktex/blob/master/Dockerfile
+FROM base AS miktex
+
+# Install dependencies for miktex
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+		apt-transport-https \
+		ca-certificates \
+		dirmngr \
+		ghostscript \
+		gnupg \
+		gosu \
+		make \
+		perl
+
+# Download mixtex from source
+RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys D6BC243565B2087BC3F897C9277A7293F59E4889
+RUN echo "deb http://miktex.org/download/ubuntu focal universe" | tee /etc/apt/sources.list.d/miktex.list
+
+# Install miktex
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        miktex
+
+# Setup miktex
+RUN miktexsetup finish && \
+    initexmf --admin --set-config-value=[MPM]AutoInstall=1 && \
+    mpm --admin \
+		--install amsfonts \
+		--install biber-linux-x86_64 && \
+    initexmf --admin --update-fndb
+
+### Stage 3, setup python venv and install poetry dependencies ###
+FROM miktex AS env_setup
+
+# Set Python/pip/Poetry ENV settings
+ENV YOUR_ENV=${ENV_NAME} \
+  	PYTHONFAULTHANDLER=1 \
+  	PYTHONUNBUFFERED=1 \
+  	PYTHONHASHSEED=random \
+  	PIP_NO_CACHE_DIR=off \
+  	PIP_DISABLE_PIP_VERSION_CHECK=on \
+  	PIP_DEFAULT_TIMEOUT=100 \
+  	PSUTILS_VERSION=5.9.4 \
+  	POETRY_VERSION=1.4.1 \
+	PIP_VERSION=22.3.1
+
+# Install Poetry ans psutil, upgrade requests
+RUN pip install --upgrade --user requests && \
+	pip install --user "psutil==$PSUTILS_VERSION" && \
+	pip install --user "poetry==$POETRY_VERSION" && \
+	pip install --user "pip==$PIP_VERSION"
+
+# Set project app workspace in linux distro
+ENV WORK_DIR=$HOME/app
+
+# Copy the poetry lock and pyproject toml file to the Dockerfile working dir (assuming the lock and toml files are in same dir as Dockerfile)
+WORKDIR $WORK_DIR
+# COPY poetry.lock $WORK_DIR/poetry.lock
+# COPY pyproject.toml $WORK_DIR/pyproject.toml
+
+# Copy the project files to the Dockerfile working dir (assuming the project files are in same dir as Dockerfile)
+COPY . $WORK_DIR
+
+# Set Poetry and Venv paths
+ENV POETRY_PATH=$HOME/.poetry/bin/poetry \
+  	VENV_PATH=$HOME/.local/bin/venv \
+	BIN_PATH=$HOME/.local/bin/
+
+# Add poetry, venv, and bin to path
+ENV PATH="$POETRY_PATH:$VENV_PATH:$BIN_PATH:$PATH"
+
+# Create virtual env
+RUN poetry config virtualenvs.create true && \
+	poetry config virtualenvs.options.system-site-packages true
+
+# Install Poetry dependencies from lock file via requirements.txt file rather than poetry install (sometimes poetry install breaks from depreciated pip install)
+RUN poetry export --without-hashes --with dev --format=requirements.txt > requirements.txt && \
+	pip install --user -r requirements.txt && \
+	rm requirements.txt

README.md

@@ -1,4 +1,5 @@
 # PlotNeuralNet
+
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2526396.svg)](https://doi.org/10.5281/zenodo.2526396)
 
 Latex code for drawing neural networks for reports and presentation. Have a look into examples to see how they are made. Additionally, lets consolidate any improvements that you make and fix any bugs to help more people with this code.
@@ -10,39 +11,62 @@ Following are some network representations:
 <p align="center"><img  src="https://user-images.githubusercontent.com/17570785/50308846-c2231880-049c-11e9-8763-3daa1024de78.png" width="85%" height="85%"></p>
 <h6 align="center">FCN-8 (<a href="https://www.overleaf.com/read/kkqntfxnvbsk">view on Overleaf</a>)</h6>
 
-
 <p align="center"><img  src="https://user-images.githubusercontent.com/17570785/50308873-e2eb6e00-049c-11e9-9587-9da6bdec011b.png" width="85%" height="85%"></p>
 <h6 align="center">FCN-32 (<a href="https://www.overleaf.com/read/wsxpmkqvjnbs">view on Overleaf</a>)</h6>
 
-
 <p align="center"><img  src="https://user-images.githubusercontent.com/17570785/50308911-03b3c380-049d-11e9-92d9-ce15669017ad.png" width="85%" height="85%"></p>
 <h6 align="center">Holistically-Nested Edge Detection (<a href="https://www.overleaf.com/read/jxhnkcnwhfxp">view on Overleaf</a>)</h6>
 
 ## Getting Started
+
 1. Install the following packages on Ubuntu.
-    * Ubuntu 16.04
-        ```
-        sudo apt-get install texlive-latex-extra
-        ```
 
-    * Ubuntu 18.04.2
+* Ubuntu 16.04
+
+```sh
+sudo apt-get install texlive-latex-extra
+
+```
+
+* Ubuntu 18.04.2
 Base on this [website](https://gist.github.com/rain1024/98dd5e2c6c8c28f9ea9d), please install the following packages.
-        ```
-        sudo apt-get install texlive-latex-base
-        sudo apt-get install texlive-fonts-recommended
-        sudo apt-get install texlive-fonts-extra
-        sudo apt-get install texlive-latex-extra
-        ```
 
-    * Windows
-    1. Download and install [MikTeX](https://miktex.org/download).
-    2. Download and install bash runner on Windows, recommends [Git bash](https://git-scm.com/download/win) or Cygwin(https://www.cygwin.com/)
+```sh
+sudo apt-get install texlive-latex-base
+sudo apt-get install texlive-fonts-recommended
+sudo apt-get install texlive-fonts-extra
+sudo apt-get install texlive-latex-extra
+
+```
+
+* Windows
+
+1. Download and install [MikTeX](https://miktex.org/download).
+2. Download and install bash runner on Windows, recommends [Git bash](https://git-scm.com/download/win) or Cygwin(https://www.cygwin.com/)
 
 2. Execute the example as followed.
-    ```
-    cd pyexamples/
-    bash ../tikzmake.sh test_simple
-    ```
+
+```sh
+cd pyexamples/
+bash ../tikzmake.sh test_simple
+```
+
+* Docker
+
+1. Install [Docker](https://www.docker.com/). If using Windows, you can install Docker Desktop for Windows, or use WSL to install Docker CE for Ubuntu.
+    - The MikTex docker image is used as the base stage for the docker build, which is based on Ubuntu 20.04 LTS
+
+2. Run the `docker_build.sh` file using the following command to build the docker image (from the root directory of this repo). You need bash to run this script. If using Windows, you can install Git bash or Cygwin; WSL and Linux have bash built-in.
+
+```sh
+bash build_pnn_docker.sh
+```
+
+3. Run the container in docker (from a WSL or Linux terminal) with the following command (from the root directory of this repo). Ensure the command is being run as admin of the machine.
+
+```sh
+bash start_pnn_docker.sh
+```
 
 ## TODO
 
@@ -91,6 +115,7 @@ def main():
 
 if __name__ == '__main__':
     main()
+
 ```
 
 Now, run the program as follows:

build_pnn_docker.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+# Script to build the docker container
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+cd $SCRIPT_DIR
+
+# Try to stop docker if it is running.
+echo "Stopping docker..."
+sudo killall -9 dockerd || :
+
+# If the docker.pid file exists, then delete it
+rm -rf /var/run/docker.pid || :
+
+# Start docker in the background.
+echo "Starting docker..."
+sudo dockerd &
+sleep 5
+
+# Enable buildkit
+export DOCKER_BUILDKIT=1
+
+# Remove all builds not built in the last 24 hours and not associated with a container
+yes y 2>/dev/null | docker image prune -a --filter "until=24h" 
+
+# This will build the full docker image. Use buildkit inline cache.
+docker build -t pnn-docker:latest \
+        -f Dockerfile \
+        --progress=plain \
+        --cache-from pnn-docker:latest \
+        --build-arg BUILDKIT_INLINE_CACHE=1 \
+        . 2>&1 | tee ./docker_build.log
+
+# --no-cache \

pyproject.toml

@@ -0,0 +1,16 @@
+[tool.poetry]
+name = "plotneuralnet"
+license = "MIT License"
+version = "0.1.0"
+description = "PlotNeuralNet creates model architectures in easy-to-digest diagrams created via LaTeX engine"
+authors = ["Your Name <[email protected]>"]
+readme = "README.md"
+packages = [{include = "plotneuralnet"}]
+
+[tool.poetry.dependencies]
+python = ">=3.8,<3.11"
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

start_pnn_docker.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+# Shell script to run in a WSL/Linux terminal to start the container.
+
+# Set the name of the container.
+CONTAINER_NAME=pnn
+
+# Set the name of the image, from docker_build.sh.
+IMAGE_NAME=pnn-docker
+IMAGE_TAG=latest
+
+# Get the directory of this script
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+
+# Set the directory for the codebase.
+CODEBASE=$SCRIPT_DIR/
+
+# Try to stop docker if it is running.
+echo "Stopping docker..."
+sudo killall -9 dockerd || :
+
+# If the docker.pid file exists, then delete it
+rm -rf /var/run/docker.pid || :
+
+# Start docker in the background.
+echo "Starting docker..."
+sudo dockerd &
+sleep 5
+
+# Run the docker image.
+echo "Running docker image..."
+sudo docker run --gpus all --rm -it \
+    -v $CODEBASE:/app \
+    --name $CONTAINER_NAME \
+    --network host \
+    $IMAGE_NAME:$IMAGE_TAG
+