carrliitos/data-project-template-python

This is a template for all of my data projects written in Python.

Project/Study Name

[Author name goes here]

Introduction

Sample project template with example connections to OCHIN-Epic Clarity.

Refer to this documentation to read more about structuring our projects.

Execution

Create and activate virtualenv:

# Create venv
virtualenv -p /usr/bin/python3 venv

# Active venv
source venv/bin/activate

# Deactivate
deactivate

To execute, navigate to the src folder and run the following command:

python main.py

Structure

This project contains the following general sturcture:

• data: Datasets produced for cleaning, analysis, or distribution after execution of scripts. These are ignored by Git to protect any PHI.
• data-raw: Incoming datasets that should be considered read-only. These are ignored by Git to protect any PHI.
• output: Any documents or datasets intended for distribution from
• project_logs: Project logs created during development. Handled by Python's logging module. this project. These are ignored by Git to protect any PHI.
• reports: Any rendered markdown/HTML documents that support the manipulation and analysis of datasets. These are ignored by Git to protect any PHI.
• sql: SQL scripts to extract datasets. Before adding SQL scripts here, ensure no PHI is added in any clauses.
• src: Main source codes of interest.