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Adding Docker config
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‎.env‎

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# Project
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COMPOSE_PROJECT_NAME=deep-root-gen
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APP_VERSION=0.1.0
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GITHUB_CONTAINER_REPO=ghcr.io/jbris/${COMPOSE_PROJECT_NAME}
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# Postgres
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DB_NAME=deeprootgen

‎.github/workflows/docker-build.yaml‎

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on:
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workflow_dispatch: {}
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release:
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types:
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- published
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permissions:
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actions: write
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packages: write

‎README.md‎

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![DeepRootGen](docs/logos/deep_root_gen.png)
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# DeepRootGen
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A simulation model for the digital reconstruction of 3D root system architectures. Integrated with a simulation-based inference generative deep learning model.
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[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
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[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
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[![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)
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[![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)
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[![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)
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*A simulation model for the digital reconstruction of 3D root system architectures. Integrated with a simulation-based inference generative deep learning model.*
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# Table of contents
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- [DeepRootGen](#deeprootgen)
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- [Table of contents](#table-of-contents)
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- [Introduction](#introduction)
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- [Data Schema](#data-schema)
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- [Contacts](#contacts)
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# Introduction
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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.
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# Data Schema
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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:
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| Column | Type | Description |
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| ------------ | ---------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| id | Discrete | A unique ID for each row. |
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| plant_id | Discrete | A unique ID for each plant. |
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| organ_id | Discrete | A unique ID for each root. |
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| 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. |
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| root_type | Discrete | The root type classification. Can be one of 1 = Structural Root or 2 = Fine Root. |
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| 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. |
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| 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. |
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| coordinates | Continuous | The combined 3D coordinates (x, y, and z) of each root segment. |
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| diameter | Continuous | The root segment diameter. |
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| length | Continuous | The root segment length. |
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| x | Continuous | The x coordinate of the root segment. |
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| y | Continuous | The y coordinate of the root segment. |
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| z | Continuous | The z coordinate of the root segment. |
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# Contacts
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- DeepRootGen Developer: James Bristow
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- DeepRootGen Project Supervisor: Junqi Zhu
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- Crop System Modeller: Xiumei Yang

‎apptainer/python/Apptainer.0.1.0‎

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

‎docker-compose.yaml‎

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services:
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mlflow:
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image: ghcr.io/jbris/deep-root-gen:${APP_VERSION}
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build:
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context: .
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dockerfile: ./dockerfiles/python/Dockerfile.${APP_VERSION}
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args:
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BUILD_DATE: date -u +'%Y-%m-%dT%H:%M:%SZ'
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restart: always
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stop_grace_period: 10s
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environment:
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MLFLOW_BACKEND_STORE_URI: $MLFLOW_BACKEND_STORE_URI
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MLFLOW_S3_ENDPOINT_URL: http://minio:9000
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AWS_ACCESS_KEY_ID: $AWS_ACCESS_KEY_ID
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AWS_SECRET_ACCESS_KEY: $AWS_SECRET_ACCESS_KEY
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ports:
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- 5000:5000
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command: >
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mlflow server --serve-artifacts --host 0.0.0.0 --port 5000
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--backend-store-uri "${MLFLOW_BACKEND_STORE_URI}" --default-artifact-root s3://mlflow/
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--expose-prometheus /prometheus
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prefect-server:
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image: ghcr.io/jbris/deep-root-gen:${APP_VERSION}
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build:
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context: .
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dockerfile: ./dockerfiles/python/Dockerfile.${APP_VERSION}
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args:
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BUILD_DATE: date -u +'%Y-%m-%dT%H:%M:%SZ'
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restart: always
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stop_grace_period: 10s
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environment:
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PREFECT_UI_URL: http://127.0.0.1:4200/api
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PREFECT_API_URL: http://127.0.0.1:4200/api
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PREFECT_SERVER_API_HOST: 0.0.0.0
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PREFECT_API_DATABASE_CONNECTION_URL: $PREFECT_API_DATABASE_CONNECTION_URL
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ports:
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- 4200:4200
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entrypoint: >
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prefect server start
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postgres:
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image: ${COMPOSE_PROJECT_NAME}-postgres:${APP_VERSION}
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build:
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context: .
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dockerfile: ./dockerfiles/postgres/Dockerfile.${APP_VERSION}
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args:
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BUILD_DATE: date -u +'%Y-%m-%dT%H:%M:%SZ'
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restart: always
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stop_grace_period: 10s
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environment:
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POSTGRES_PASSWORD: $DB_PASSWORD
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POSTGRES_DB: $DB_NAME
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POSTGRES_USER: $DB_USER
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ports:
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- 5432:5432
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volumes:
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- postgres-data:/var/lib/postgresql/data
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minio:
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image: minio/minio:RELEASE.2023-05-27T05-56-19Z
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restart: always
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stop_grace_period: 10s
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working_dir: /data
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volumes:
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- minio-data:/data
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ports:
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- 9000:9000
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- 9001:9001
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environment:
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MINIO_ACCESS_KEY: $MINIO_ACCESS_KEY
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MINIO_SECRET_KEY: $MINIO_SECRET_KEY
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MINIO_ROOT_USER: $MINIO_ROOT_USER
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MINIO_ROOT_PASSWORD: $MINIO_ROOT_PASSWORD
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MINIO_STORAGE_USE_HTTPS: False
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MINIO_PROMETHEUS_AUTH_TYPE: public
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command: server --console-address :9001 --address :9000 /data
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mc:
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image: minio/mc:RELEASE.2023-05-30T22-41-38Z
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environment:
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MINIO_PORT: 9000
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MINIO_ACCESS_KEY: $MINIO_ACCESS_KEY
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MINIO_SECRET_KEY: $MINIO_SECRET_KEY
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depends_on:
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- minio
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entrypoint: >
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/bin/sh -c ' sleep 5;
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/usr/bin/mc config host add s3 http://minio:9000 ${MINIO_ACCESS_KEY} ${MINIO_SECRET_KEY} --api S3v4;
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[[ ! -z "`/usr/bin/mc ls s3 | grep challenge`" ]] || /usr/bin/mc mb s3/mlflow; /usr/bin/mc policy download s3/mlflow;
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[[ ! -z "`/usr/bin/mc ls s3 | grep challenge`" ]] || /usr/bin/mc mb s3/data; /usr/bin/mc policy download s3/data; exit 0; '
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cloudbeaver:
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image: dbeaver/cloudbeaver:23.3.1
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restart: always
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stop_grace_period: 10s
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ports:
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- 8978:8978
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volumes:
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- cloudbeaver-data:/opt/cloudbeaver/workspace
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metabase:
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image: metabase/metabase:v0.48.0
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restart: unless-stopped
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stop_grace_period: 10s
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environment:
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MB_DB_TYPE: postgres
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MB_DB_HOST: postgres
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MB_DB_PORT: 5432
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MB_DB_PASS: $DB_PASSWORD
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MB_DB_DBNAME: $DB_NAME
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MB_DB_USER: $DB_USER
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MB_DB_FILE: /metabase-data/metabase.db
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MB_PROMETHEUS_SERVER_PORT: 3001
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ports:
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- 3000:3000
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- 3001:3001
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volumes:
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- metabase-data:/metabase-data
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networks:
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default:
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name: $COMPOSE_PROJECT_NAME
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driver: bridge
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volumes:
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minio-data: {}
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postgres-data: {}
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cloudbeaver-data: {}
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metabase-data: {}
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‎dockerfiles/postgres/Dockerfile.0.1.0‎

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

‎dockerfiles/python/Dockerfile.0.1.0‎

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

‎docs/Makefile‎

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

‎docs/logos/deep_root_gen.png‎

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‎docs/make.bat‎

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

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