PySpark Template Project

People has asked me several times how to setup a good/clean/code organization for Python project with PySpark. I didn't find a fully feature project, so this is my attempt for one. Moreover, have a simple integration with Jupyter Notebook inside the project too.

Table of Contents

• PySpark Template Project
  • Usage
  • Inspiration
  • Development
    • Prerequisites
    • Add format, lint code tools
      • Autolint/Format code with Black in IDE:
      • Checked optional type with Mypy PEP 484
      • Isort
  • Fix
  • Usage Local
  • Use with poetry
  • Usage in distributed-mode depending on your cluster manager type

Usage

Inspiration

• https://mungingdata.com/pyspark/chaining-dataframe-transformations/
• https://medium.com/albert-franzi/the-spark-job-pattern-862bc518632a
• https://pawamoy.github.io/copier-poetry/
• https://drivendata.github.io/cookiecutter-data-science/#why-use-this-project-structure

Development

Prerequisites

All you need is the following configuration already installed:

• Git
• The project was tested with Python 3.10.9 managed by pyenv:
  • pyenv prerequisites for ubuntu. Check the prerequisites for your OS.

  sudo apt-get update; sudo apt-get install make build-essential libssl-dev zlib1g-dev \
  libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm \
  libncursesw5-dev xz-utils tk-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev
  

  • pyenv installed and available in path pyenv installation with Prerequisites
• JAVA_HOME environment variable configured with a Java JDK11
• SPARK_HOME environment variable configured with Spark version spark-3.3.1-bin-hadoop3 package
• PYSPARK_PYTHON environment variable configured with "python3.10"
• PYSPARK_DRIVER_PYTHON environment variable configured with "python3.10"
• Install Make to run Makefile file
• Why Python 3.10 because PySpark 3.3.1 doesn't work with Python 3.11 at the moment it seems (I haven't tried with Python 3.12)
• Install python 3.10 with pyenv on homebrew/linuxbrew

CONFIGURE_OPTS="--with-openssl=$(brew --prefix openssl)" pyenv install 3.10

Add format, lint code tools

Autolint/Format code with Black in IDE:

• Auto format via IDE https://github.com/psf/black#pycharmintellij-idea

• [Optional] You could setup a pre-commit to enforce Black format before commit https://github.com/psf/black#version-control-integration

• Or remember to type black . to apply the black rules formatting to all sources before commit

• Add integratin with Jenkins and it will complain and tests will fail if black format is not applied

• Add same mypy option for vscode in Preferences: Open User Settings

• Use the option to lint/format with black and flake8 on editor save in vscode

Checked optional type with Mypy PEP 484

Configure Mypy to help annotating/hinting type with Python Code. It's very useful for IDE and for catching errors/bugs early.

• Install mypy plugin for intellij
• Adjust the plugin with the following options:

  "--follow-imports=silent",
  "--show-column-numbers",
  "--ignore-missing-imports",
  "--disallow-untyped-defs",
  "--check-untyped-defs"
  

• Documentation: Type hints cheat sheet (Python 3)
• Add same mypy option for vscode in Preferences: Open User Settings

Isort

• isort is the default on pycharm
• isort with vscode
• Lint/format/sort import on save with vscode in Preferences: Open User Settings:

{
    "editor.formatOnSave": true,
    "python.formatting.provider": "black",
    "[python]": {
        "editor.codeActionsOnSave": {
            "source.organizeImports": true
        }
    }
}

• isort configuration for pycharm. See Set isort and black formatting code in pycharm
• You can use make lint command to check flake8/mypy rules & apply automatically format black and isort to the code with the previous configuration

isort .

Fix

• Show a way to treat json erroneous file like data/pubmed.json

Usage Local

• Create a poetry env with python 3.10

poetry env use 3.10

• Install dependencies in poetry env (virtualenv) make deps
• Lint & Test make build
• Lint,Test & Run make run
• Run dev make dev
• Build binary/python whell make dist

Use with poetry

poetry run drugs_gen --help

Usage: drugs_gen [OPTIONS]

Options:
  -d, --drugs TEXT             Path to drugs.csv
  -p, --pubmed TEXT            Path to pubmed.csv
  -c, --clinicals_trials TEXT  Path to clinical_trials.csv
  -o, --output TEXT            Output path to result.json (e.g
                               /path/to/result.json)
  --help                       Show this message and exit.

Usage in distributed-mode depending on your cluster manager type

• Use spark-submit with the Python Wheel file build by make-dist in the dist folder.