Adding Docker config

.env

@@ -1,7 +1,6 @@
 # Project 
 COMPOSE_PROJECT_NAME=deep-root-gen
 APP_VERSION=0.1.0
-GITHUB_CONTAINER_REPO=ghcr.io/jbris/${COMPOSE_PROJECT_NAME}
 
 # Postgres
 DB_NAME=deeprootgen

.github/workflows/docker-build.yaml

@@ -2,7 +2,10 @@ name: Docker Build
 
 on: 
   workflow_dispatch: {}
-
+  release:
+    types:
+      - published 
+
 permissions:
   actions: write
   packages: write

README.md

@@ -1,3 +1,49 @@
+![DeepRootGen](docs/logos/deep_root_gen.png)
+
 # DeepRootGen
 
-A simulation model for the digital reconstruction of 3D root system architectures. Integrated with a simulation-based inference generative deep learning model.
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Tests](https://github.com/JBris/deep-root-gen/actions/workflows/tests.yaml/badge.svg?branch=main)](https://github.com/JBris/deep-root-gen/actions/workflows/tests.yaml)
+[![Documentation](https://github.com/JBris/deep-root-gen/actions/workflows/docs.yaml/badge.svg?branch=main)](https://github.com/JBris/deep-root-gen/actions/workflows/docs.yaml)
+[![Build](https://github.com/JBris/deep-root-gen/actions/workflows/docker-build.yaml/badge.svg?branch=main)](https://github.com/JBris/deep-root-gen/actions/workflows/docker-build.yaml)
+
+*A simulation model for the digital reconstruction of 3D root system architectures. Integrated with a simulation-based inference generative deep learning model.*
+
+# Table of contents
+
+- [DeepRootGen](#deeprootgen)
+- [Table of contents](#table-of-contents)
+- [Introduction](#introduction)
+- [Data Schema](#data-schema)
+- [Contacts](#contacts)
+
+# Introduction
+
+This repository contains an implementation of a simulation model for generating the root system architecture, for the estimation of root parameters as informed by observational data collected from the field.
+
+# Data Schema
+
+The primary purpose of DeepRootGen is to output a synthetic root system into a tabular data format. The tabular data are composed of several columns:
+
+| Column       | Type       | Description                                                                                                                                                                     |
+| ------------ | ---------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| id           | Discrete   | A unique ID for each row.                                                                                                                                                       |
+| plant_id     | Discrete   | A unique ID for each plant.                                                                                                                                                     |
+| organ_id     | Discrete   | A unique ID for each root.                                                                                                                                                      |
+| order        | Discrete   | The plant order. A first order root grows from the plant base,  second order roots emerge from first order roots, third order  roots emerge from second order roots, and so on. |
+| root_type    | Discrete   | The root type classification. Can be one of 1 = Structural Root or 2 = Fine Root.                                                                                               |
+| segment_rank | Discrete   | The rank number for each root segment. A small rank refers to  segments that are close to the root base, while a large rank  refers to roots that are near the root apex.       |
+| parent       | Discrete   | The parent organ of the root segment. The parent node of the organ within the GroIMP graph. Used by the XEG reader to  recursively import the synthetic root data.              |
+| coordinates  | Continuous | The combined 3D coordinates (x, y, and z) of each root segment.                                                                                                                 |
+| diameter     | Continuous | The root segment diameter.                                                                                                                                                      |
+| length       | Continuous | The root segment length.                                                                                                                                                        |
+| x            | Continuous | The x coordinate of the root segment.                                                                                                                                           |
+| y            | Continuous | The y coordinate of the root segment.                                                                                                                                           |
+| z            | Continuous | The z coordinate of the root segment.                                                                                                                                           |
+
+# Contacts
+
+- DeepRootGen Developer: James Bristow 
+- DeepRootGen Project Supervisor: Junqi Zhu
+- Crop System Modeller: Xiumei Yang 

apptainer/python/Apptainer.0.1.0

@@ -0,0 +1,17 @@
+Bootstrap: docker
+From: ghcr.io/jbris/deep-root-gen:0.1.0
+
+%labels
+    Maintainer [email protected]
+    Version 0.1.0
+
+%post
+    prefect config set PREFECT_API_ENABLE_HTTP2=false
+    prefect config set PREFECT_API_TLS_INSECURE_SKIP_VERIFY=true
+    prefect config set PREFECT_EXPERIMENTAL_ENABLE_TASK_SCHEDULING=true
+
+%help
+    This is a container to run the DeepRootGen model.
+
+%runscript
+  exec "$@"

docker-compose.yaml

@@ -0,0 +1,132 @@
+services:
+
+  mlflow:
+    image: ghcr.io/jbris/deep-root-gen:${APP_VERSION}
+    build:
+      context: .
+      dockerfile: ./dockerfiles/python/Dockerfile.${APP_VERSION}  
+      args:
+        BUILD_DATE: date -u +'%Y-%m-%dT%H:%M:%SZ'
+    restart: always
+    stop_grace_period: 10s
+    environment:
+      MLFLOW_BACKEND_STORE_URI: $MLFLOW_BACKEND_STORE_URI
+      MLFLOW_S3_ENDPOINT_URL: http://minio:9000
+      AWS_ACCESS_KEY_ID: $AWS_ACCESS_KEY_ID
+      AWS_SECRET_ACCESS_KEY: $AWS_SECRET_ACCESS_KEY
+    ports:
+      - 5000:5000
+    command: >
+      mlflow server --serve-artifacts --host 0.0.0.0 --port 5000 
+      --backend-store-uri "${MLFLOW_BACKEND_STORE_URI}" --default-artifact-root s3://mlflow/
+      --expose-prometheus /prometheus
+      
+  prefect-server:
+    image: ghcr.io/jbris/deep-root-gen:${APP_VERSION}
+    build:
+      context: .
+      dockerfile: ./dockerfiles/python/Dockerfile.${APP_VERSION}  
+      args:
+        BUILD_DATE: date -u +'%Y-%m-%dT%H:%M:%SZ'
+    restart: always
+    stop_grace_period: 10s
+    environment:
+      PREFECT_UI_URL: http://127.0.0.1:4200/api
+      PREFECT_API_URL: http://127.0.0.1:4200/api
+      PREFECT_SERVER_API_HOST: 0.0.0.0
+      PREFECT_API_DATABASE_CONNECTION_URL: $PREFECT_API_DATABASE_CONNECTION_URL
+    ports:
+      - 4200:4200
+    entrypoint: >
+      prefect server start
+
+  postgres:
+    image: ${COMPOSE_PROJECT_NAME}-postgres:${APP_VERSION}
+    build:
+      context: .
+      dockerfile: ./dockerfiles/postgres/Dockerfile.${APP_VERSION}  
+      args:
+        BUILD_DATE: date -u +'%Y-%m-%dT%H:%M:%SZ'
+    restart: always
+    stop_grace_period: 10s
+    environment:
+      POSTGRES_PASSWORD: $DB_PASSWORD
+      POSTGRES_DB: $DB_NAME
+      POSTGRES_USER: $DB_USER
+    ports:
+      - 5432:5432
+    volumes:
+      - postgres-data:/var/lib/postgresql/data
+
+  minio:
+    image: minio/minio:RELEASE.2023-05-27T05-56-19Z
+    restart: always
+    stop_grace_period: 10s
+    working_dir: /data
+    volumes:
+      - minio-data:/data
+    ports:
+      - 9000:9000
+      - 9001:9001
+    environment:
+      MINIO_ACCESS_KEY: $MINIO_ACCESS_KEY
+      MINIO_SECRET_KEY: $MINIO_SECRET_KEY
+      MINIO_ROOT_USER: $MINIO_ROOT_USER
+      MINIO_ROOT_PASSWORD: $MINIO_ROOT_PASSWORD
+      MINIO_STORAGE_USE_HTTPS: False
+      MINIO_PROMETHEUS_AUTH_TYPE: public
+    command: server --console-address :9001 --address :9000 /data
+
+  mc:
+    image: minio/mc:RELEASE.2023-05-30T22-41-38Z
+    environment:
+      MINIO_PORT: 9000
+      MINIO_ACCESS_KEY: $MINIO_ACCESS_KEY
+      MINIO_SECRET_KEY: $MINIO_SECRET_KEY
+    depends_on:
+      - minio
+    entrypoint: >
+      /bin/sh -c ' sleep 5; 
+      /usr/bin/mc config host add s3 http://minio:9000 ${MINIO_ACCESS_KEY} ${MINIO_SECRET_KEY} --api S3v4;  
+      [[ ! -z "`/usr/bin/mc ls s3 | grep challenge`" ]] || /usr/bin/mc mb s3/mlflow;  /usr/bin/mc policy download s3/mlflow;  
+      [[ ! -z "`/usr/bin/mc ls s3 | grep challenge`" ]] || /usr/bin/mc mb s3/data;  /usr/bin/mc policy download s3/data; exit 0; '
+
+  cloudbeaver:
+    image: dbeaver/cloudbeaver:23.3.1
+    restart: always
+    stop_grace_period: 10s
+    ports:
+      - 8978:8978
+    volumes:
+      - cloudbeaver-data:/opt/cloudbeaver/workspace
+
+  metabase:
+    image: metabase/metabase:v0.48.0
+    restart: unless-stopped
+    stop_grace_period: 10s
+    environment:
+      MB_DB_TYPE: postgres
+      MB_DB_HOST: postgres
+      MB_DB_PORT: 5432
+      MB_DB_PASS: $DB_PASSWORD
+      MB_DB_DBNAME: $DB_NAME
+      MB_DB_USER: $DB_USER
+      MB_DB_FILE: /metabase-data/metabase.db
+      MB_PROMETHEUS_SERVER_PORT: 3001
+    ports:
+      - 3000:3000
+      - 3001:3001
+    volumes:
+      - metabase-data:/metabase-data
+
+networks:
+  default:
+    name: $COMPOSE_PROJECT_NAME
+    driver: bridge
+
+volumes:
+  minio-data: {}
+  postgres-data: {}
+  cloudbeaver-data: {}
+  metabase-data: {}
+

dockerfiles/postgres/Dockerfile.0.1.0

@@ -0,0 +1,9 @@
+FROM postgres:15.3-bullseye
+
+ARG BUILD_DATE
+
+LABEL [email protected] 
+
+LABEL org.label-schema.build-date=$BUILD_DATE
+
+COPY sql/init.sql /docker-entrypoint-initdb.d/init.sql

dockerfiles/python/Dockerfile.0.1.0

@@ -0,0 +1,43 @@
+FROM python:3.10.14-bullseye as base
+
+ARG BUILD_DATE
+
+LABEL [email protected] 
+
+LABEL org.label-schema.build-date=$BUILD_DATE
+
+WORKDIR /app
+
+COPY README.md README.md
+
+COPY deeprootgen deeprootgen
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends build-essential libpq-dev graphviz \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && rm -rf /tmp/downloaded_packages
+
+FROM base as builder
+
+ENV POETRY_NO_INTERACTION=1 \
+    POETRY_VIRTUALENVS_IN_PROJECT=1 \
+    POETRY_VIRTUALENVS_CREATE=1 \
+    POETRY_CACHE_DIR=/tmp/poetry_cache \
+    PATH="/root/.local/bin:$PATH"
+
+COPY pyproject.toml poetry.lock ./
+
+RUN curl -sSL https://install.python-poetry.org | python3 -\
+    && poetry install --without dev \
+    && rm -rf $POETRY_CACHE_DIR \
+    && curl -sSL https://install.python-poetry.org | python3 - --uninstall
+
+FROM base as runtime
+
+ENV VIRTUAL_ENV=/app/.venv \
+    PATH="/app/.venv/bin:$PATH"
+
+COPY --from=builder ${VIRTUAL_ENV} ${VIRTUAL_ENV}
+
+RUN chmod -R 755 /app

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/api_reference/index.rst

@@ -0,0 +1,5 @@
+API Reference
+=============
+
+..  toctree::
+    :maxdepth: 1

docs/source/changelogs/changelog.rst

@@ -0,0 +1,7 @@
+Changelog
+=========
+
+0.1.0 - 2024/08/17
+------------------
+
+* Stub

docs/source/conf.py

@@ -0,0 +1,41 @@
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../.."))
+
+project = "DeepRootGen"
+copyright = "2024, James Bristow"
+author = "James Bristow"
+release = "0.1.0"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+    "sphinxarg.ext",
+]
+
+numpydoc_show_class_members = False
+
+templates_path = ["_templates"]
+
+source_suffix = ".rst"
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+
+html_static_path = ["_static"]
+
+# The master toctree document.
+master_doc = "index"
+
+# Datetime
+
+today_fmt = "%d/%m/%y"