PYTHEOS

Overview

Pytheos provides a tool set for a wide range of tasks in high pressure science:

• calculate pressure from a number of built-in pressure scales
• convert pressure scales
• propagate uncertainties properly using the uncertainties package
• fit pressure-volume and pressure-volume-temperature data sets using the scipy and lmfit packages
• fit with a wide range of different equations and their combinations

Installation

This section describes how to download pytheos from GitHub and install it using conda. The procedure is suitable for macOS and Linux.

1. Clone the GitHub repository

Clone the repository and enter the source directory:

git clone https://github.com/SHDShim/pytheos.git
cd pytheos

2. Create a dedicated conda environment

Create a clean conda environment to avoid dependency conflicts:

conda create -n pytheos python=3.11 -y
conda activate pytheos

Python version 3.9 or newer is recommended.

3. Install core dependencies

Install numerical and scientific dependencies from conda-forge:

conda install -c conda-forge numpy scipy matplotlib sympy pandas jupyter -y

If you plan to run the example notebooks, also install Jupyter support:

conda install -c conda-forge ipykernel nbconvert -y
python -m ipykernel install --user --name pytheos

4. Install pytheos

From the repository root (where setup.py or pyproject.toml is located), install pytheos:

pip install .

Verify the installation:

python - <<EOF
import pytheos
print(pytheos.__version__)
EOF

5. Test the installation

Run a simple test to confirm that core functionality works:

python - <<EOF
from pytheos import bm3_p, vinet_p
print(bm3_p(10.0, 160.0, 4.0, 4.0))
print(vinet_p(10.0, 160.0, 4.0))
EOF

6. Updating pytheos

To update pytheos to the latest version from GitHub:

cd pytheos
git pull origin master
pip install .

7. Clean removal

To completely remove pytheos and its conda environment:

conda deactivate
conda remove -n pytheos --all

Contact

Please contact Dan Shim (shdshim@gmail.com) for bug reports, comments, and suggestions. I am happy to include new pressure scales or other pressure scales in pytheos as well.

Examples and Tutorials

The pytheos package includes examples in Jupyter Notebook (under the examples folder), which demonstrate a range of operations, calculations, and fittings you can do with pytheos. Pytheos is designed to support data analysis using Jupyter Notebook as well as python scripts.

Documentation is available at: https://shdshim.github.io/pytheos-docs/.

How to cite

S.-H. Shim (2017) Pytheos - a python tool set for equations of state. Zenodo. http://doi.org/10.5281/zenodo.802392