This document provides notes for contributing to or modifying the Carrot Transform tool.

If you only need to use carrot-transform - not develop it - check out the official documentation.

Development Notes

Using `uv`

We use uv for managing dependencies and running Python scripts.

What is `uv`?

uv is a small command line program that invokes other python tools. There’s also uvx, a companion to uv, which works like npx or pipx to run packages without installing them to a project.

Installing `uv`

Follow the installation guide. It’s surprisingly fast to set up.

Running Tests

We use pytest for testing. You can run all tests with:

uv run pytest

Running from Source

You can run the CLI directly like this:

uv run -m carrottransform.cli.subcommands.run mapstream \
    --input-dir carrottransform/examples/test/inputs \
    --person-file carrottransform/examples/test/inputs/Demographics.csv \
    --rules-file carrottransform/examples/test/rules/rules_14June2021.json \
    --output-dir build \
    --omop-ddl-file carrottransform/config/OMOPCDM_postgresql_5.3_ddl.sql \
    --omop-config-file carrottransform/config/omop.json

⚠️ On Windows, you would need to replace / with ^ for line continuation in the terminal.

Or just paste it into a text editor and hit END END BACKSPACE DELETE until you’ve reformatted it into one line, then, paste that into the command prompt

💡 Eventually we’d like to auto-detect --person-file:
See GitHub PR #53

Deploying to PyPI and CI / GitHub Actions

The CI file uses GitHub actions to test the project and (when appropriate) deploy to PyPI. When the CI job runs, it tests and assembles the project. If the commit being examined is against the main branch, then, the project will be deployed to PyPI Test. If the commit has been tagged with a tag starting with v... then the project will be deployed to PyPI Main.

Quickstart Expected Output