Working Prefect config

.env

@@ -12,6 +12,14 @@ DB_PORT=5432
 ADMINER_TAG=4.7.9-standalone
 ADMINER_PORT=8081
 
+# Prefect
+PREFECT_TAG=2.13.2-python3.10
+PREFECT_PORT=4200
+PREFECT_UI_URL=http://127.0.0.1:4200/api
+PREFECT_SERVER_API_URL=http://127.0.0.1:4200/api
+PREFECT_API_DATABASE_CONNECTION_URL=postgresql+asyncpg://${DB_USER}:${DB_PASSWORD}@postgres:5432/${DB_NAME}
+PREFECT_API_URL=http://prefect-server:4200/api
+
 # MLFlow
 MLFLOW_PORT=5000
 MLFLOW_BACKEND_STORE_URI=postgresql://${DB_USER}:${DB_PASSWORD}@postgres:5432/${DB_NAME}

README.md

@@ -1,10 +1,10 @@
 # Prefect Surrogate Models
 
-[![Validate Pipeline](https://github.com/JBris/prefect-surrogate-models/actions/workflows/validation.yml/badge.svg)](https://github.com/JBris/prefect-surrogate-models/actions/workflows/validation.yml) [![Generate Documentation](https://github.com/JBris/prefect-surrogate-models/actions/workflows/docs.yml/badge.svg)](https://github.com/JBris/prefect-surrogate-models/actions/workflows/docs.yml) [![pages-build-deployment](https://github.com/JBris/prefect-surrogate-models/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/JBris/prefect-surrogate-models/actions/workflows/pages/pages-build-deployment)
+[![Validate Pipeline](https://github.com/JBris/prefect-surrogate-models/actions/workflows/validation.yaml/badge.svg?branch=main)](https://github.com/JBris/prefect-surrogate-models/actions/workflows/validation.yaml) [![Generate Documentation](https://github.com/JBris/prefect-surrogate-models/actions/workflows/docs.yaml/badge.svg)](https://github.com/JBris/prefect-surrogate-models/actions/workflows/docs.yaml) [![pages-build-deployment](https://github.com/JBris/prefect-surrogate-models/actions/workflows/pages/pages-build-deployment/badge.svg?branch=gh-pages)](https://github.com/JBris/prefect-surrogate-models/actions/workflows/pages/pages-build-deployment)
 
 Website: [Prefect Surrogate Models](https://jbris.github.io/prefect-surrogate-models/)
 
-*Demonstrating the use of Prefect to orchestrate the creation of machine learning surrogate models applied to mechanistic crop models.*
+*Demonstrating the use of Prefect to orchestrate the creation of machine learning surrogate models as applied to mechanistic crop models.*
 
 # Table of contents
 

docker-compose.yml

@@ -2,24 +2,66 @@ version: "3.9"
 
 services:
 
-  # mlflow:
-  #   image: $GITHUB_CONTAINER_REPO
-  #   container_name: ${PROJECT_NAME}-mlflow
-  #   hostname: mlflow
-  #   restart: unless-stopped
-  #   stop_grace_period: 10s
-  #   env_file: .env
-  #   environment:
-  #     MLFLOW_BACKEND_STORE_URI: $MLFLOW_BACKEND_STORE_URI
-  #     MLFLOW_S3_ENDPOINT_URL: $MLFLOW_S3_ENDPOINT_URL
-  #     AWS_ACCESS_KEY_ID: $AWS_ACCESS_KEY_ID
-  #     AWS_SECRET_ACCESS_KEY: $AWS_SECRET_ACCESS_KEY
-  #   ports:
-  #     - ${MLFLOW_PORT}:5000
-  #   command: >
-  #     mlflow server --serve-artifacts --host 0.0.0.0 --port 5000 
-  #     --backend-store-uri "${MLFLOW_BACKEND_STORE_URI}" --default-artifact-root s3://mlflow/
+  prefect-cli:
+    image: $GITHUB_CONTAINER_REPO
+    container_name: ${PROJECT_NAME}-prefect-cli
+    env_file: .env
+    working_dir: /flows
+    environment:
+      PREFECT_API_URL: $PREFECT_API_URL
+    volumes:
+      - ./flows:/flows
+    entrypoint: "python"
+
+  mlflow:
+    image: $GITHUB_CONTAINER_REPO
+    container_name: ${PROJECT_NAME}-mlflow
+    hostname: mlflow
+    restart: unless-stopped
+    stop_grace_period: 10s
+    env_file: .env
+    environment:
+      MLFLOW_BACKEND_STORE_URI: $MLFLOW_BACKEND_STORE_URI
+      MLFLOW_S3_ENDPOINT_URL: $MLFLOW_S3_ENDPOINT_URL
+      AWS_ACCESS_KEY_ID: $AWS_ACCESS_KEY_ID
+      AWS_SECRET_ACCESS_KEY: $AWS_SECRET_ACCESS_KEY
+    ports:
+      - ${MLFLOW_PORT}:5000
+    command: >
+      mlflow server --serve-artifacts --host 0.0.0.0 --port 5000 
+      --backend-store-uri "${MLFLOW_BACKEND_STORE_URI}" --default-artifact-root s3://mlflow/
+
+  prefect-server:
+    image: prefecthq/prefect:${PREFECT_TAG}
+    container_name: ${PROJECT_NAME}-prefect-server
+    hostname: prefect-server
+    restart: unless-stopped
+    stop_grace_period: 10s
+    env_file: .env
+    environment:
+      PREFECT_UI_URL: $PREFECT_UI_URL
+      PREFECT_API_URL: $PREFECT_SERVER_API_URL
+      PREFECT_SERVER_API_HOST: 0.0.0.0
+      PREFECT_API_DATABASE_CONNECTION_URL: $PREFECT_API_DATABASE_CONNECTION_URL 
+    depends_on:
+      - postgres
+    ports:
+      - ${PREFECT_PORT}:4200
+    volumes:
+      - prefect-data:/root/.prefect
+    entrypoint: ["/opt/prefect/entrypoint.sh", "prefect", "server", "start"]
 
+  prefect-agent:
+    image: prefecthq/prefect:${PREFECT_TAG}
+    container_name: ${PROJECT_NAME}-prefect-agent
+    hostname: prefect-agent
+    restart: unless-stopped
+    stop_grace_period: 10s
+    env_file: .env
+    environment:
+      PREFECT_API_URL: $PREFECT_API_URL
+    entrypoint: ["/opt/prefect/entrypoint.sh", "prefect", "agent", "start", "-q", "queue"]
+
   minio:
     image: minio/minio:${MINIO_TAG}
     container_name: ${PROJECT_NAME}-minio
@@ -56,6 +98,7 @@ services:
       /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/prefect-flows;  /usr/bin/mc policy download s3/prefect-flows;  
       [[ ! -z "`/usr/bin/mc ls s3 | grep challenge`" ]] || /usr/bin/mc mb s3/data;  /usr/bin/mc policy download s3/data; exit 0; '
 
   postgres:
@@ -104,6 +147,7 @@ networks:
     driver: bridge
 
 volumes:
+  prefect-data: {}
   postgres-data: {}
   minio-data: {}
   portainer-data: {}

docs/source/flows/index.rst

@@ -0,0 +1,6 @@
+Prefect Surrogate Models Flows
+=================================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:

docs/source/index.rst

@@ -10,7 +10,7 @@ Welcome to Prefect Surrogate Models's documentation!
    :maxdepth: 2
    :caption: Contents:
 
-
+   flows/index.rst
 
 Indices and tables
 ==================

flows/.prefectignore

@@ -0,0 +1,161 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+*.db

flows/test.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python
+
+from prefect import flow, task
+
+@task
+def hello_world(name):
+    print(f"hello world: {name}")
+
+@task
+def bye_world(name):
+    print(f"bye world: {name}")
+
+@flow(name="test flow")
+def test_flow(names=["john", "smith"]):
+    for name in names:
+        hello_world(name)
+        bye_world(name)
+
+if __name__ == "__main__":
+    test_flow()

scripts/prefect.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+. .env
+
+docker compose run --rm prefect-cli "$@"