PINTS-Py

Python wrapper for PINTS (Pipelines for Non-Target Screening). This package provides Python APIs and a command-line interface (CLI) to manage and query PINTS databases based on the pints-core-sql schema.

Features

• Initialize and seed a DuckDB with the PINTS Core schema
• Add samples, runs, and features programmatically
• Export tables to CSV for downstream analysis
• Query using either the Python API or the CLI (pints ...)
• Reuses the universal SQL definitions from pints-core-sql

Installation

Clone and install in editable mode:

git clone https://github.com/odea-project/pints-py.git
cd pints-py
python -m venv .venv                # For virtual environment
.venv/Scripts/Activate.ps1          # For virtual environment on Windows PowerShell
pip install -e .

This will also fetch the pints-core-sql submodule.

Update Submodules

To update the pints-core-sql submodule to the latest commit on its main branch:

cd extern/pints-plugins
git fetch origin
git checkout main        # oder dein Branchname
git pull origin main
cd ../..

Then commit the updated submodule reference in the main repo.

Quick Start

Using Python CLI

Initialize a new PINTS feature list:

pints init --db myFeatures.duckdb

Seed the feature list with the core schema:

pints seed --db myFeatures.duckdb

Add a sample:

pints add-sample --db myFeatures.duckdb --id S001 --type Sample --desc "River water"

Add a run linked to the sample:

pints add-run --db myFeatures.duckdb --id R001 --sample S001 --time "2025-09-12 09:00:00" --instrument QTOF-XYZ --method POS_5min --batch B01

Add a feature linked to the run:

pints add-feature --db myFeatures.duckdb --id R001_F0001 --run R001 --sample S001 --mz 301.123456 --rt 312.4 --area 154321.2

Export the features table to CSV:

pints export features --db myFeatures.duckdb --out features.csv

Check schema and vocabulary versions:

pints show-version --db myFeatures.duckdb

List all tables in the database:

pints list-tables --db myFeatures.duckdb

Using Plugins

The CLI supports plugins for extended functionality from pints-plugins (e.g., intra_run_components). To use plugins, install them in the same environment:

pints plugin install --db myFeatures.duckdb --name intra_run_components

Add data using plugin commands:

pints plugin insert --db myFeatures.duckdb --name intra_run_components --rows "R001,R001_F0001,C001" "R001,R001_F0002,C001" --materialize

Export plugin tables:

pints plugin export --db my.duckdb --name intra_run_components --out intra.csv

Development

This repo depends on pints-core-sql as a Git submodule. After cloning, make sure to initialize submodules:

git submodule update --init --recursive

The SQL files from pints-core-sql/sql are synced into pints/sql before packaging.

License

This project is licensed under the MIT License. See the LICENSE file for details.