rxnDB 0.1.0a18

A Python Shiny app for reaction database management

rxnDB: a mineral reaction database

📚 See the documentation for details.

Prerequisite software

This project is written in python. For most users, I recommend installing the miniforge python distribution. This distributions includes a minimal installation of python and the package manager conda, which is required to build the necessary python environment for this software.

For macOS users, miniforge can be installed with homebrew:

brew install miniforge

For Window's users, miniforge can be installed from a binary .exe. Follow the instructions for miniconda, anaconda, or miniforge (recommended) here.

Installation Guide

To install with Conda (recommended):

# Create conda environment
conda create -n rxnDB python=3.13 pip

# Activate conda environment
conda activate rxnDB

# Install rxnDB
pip install rxnDB

If you want to install the development version for local testing in "editable" mode:

# Clone repo
git clone https://github.com/buchanankerswell/kerswell_et_al_rxnDB.git
cd kerswell_et_al_rxnDB

# Checkout develop branch
git checkout develop

# Create conda environment and install rxnDB locally in editable mode
# including optional development and documentation dependencies
make create_conda_env

Usage Guide

After installing rxnDB, you can launch the Shiny app directly from the command line:

# Activate conda environment
conda activate rxnDB

# Launch app
rxndb

For more advanced usage, you can use the following options:

# Activate conda environment
conda activate rxnDB

# rxndb --host 0.0.0.0   (Make accessible from other machines)
# rxndb --port 8080      (Run on a specific port)
# rxndb --launch-browser (Open browser automatically)
# rxndb --reload         (Auto-reload when files change)

# Default command
rxndb --host 127.0.0.1 --port 8000 --launch-browser --reload

Coauthors

• Simon Hunt (University of Manchester)
• John Wheeler (University of Liverpool)

Acknowledgement

This work was funded by the UKRI NERC Large Grant no. NE/V018477/1 awarded to John Wheeler at the University of Liverpool.