About

pyathena is a set of python scripts for reading and analyzing simulation data produced by the Athena-TIGRESS and TIGRIS codes.

Requirement

Python version 3.10 or higher

Installation

Below is an example of how you can set up pyathena. It assumes that you have already installed miniforge (recommended), miniconda, or anaconda on your system. Miniforge defaults to the conda-forge channel and avoids Anaconda Inc.'s commercial-use licensing on the defaults channel. Miniforge also ships mamba, a faster drop-in replacement for conda — swap conda for mamba in any command below.

git clone https://github.com/jeonggyukim/pyathena.git
cd pyathena

Then pick one of the options below. Use -e (editable) if you plan to edit the source — changes take effect without reinstalling; drop it for a non-editable install.

Option 1 — conda + pip

conda env create -f env.yml
conda activate pyathena
pip install -e . --no-deps    # conda already installed the dependencies

Option 2 — conda + uv

Same as Option 1, but uv resolves the editable install faster. uv uses the active conda environment (add --python "$(which python)" if it does not detect it).

conda env create -f env.yml
conda activate pyathena
uv pip install -e . --no-deps    # conda already installed the dependencies

Option 3 — uv only (no conda)

uv installs every dependency from PyPI, so conda is not required. The dependencies are declared in pyproject.toml.

uv venv --python 3.10
source .venv/bin/activate
uv pip install -e .

Sanity check any option with:

python -c "import pyathena; print(pyathena.__file__)"

If conda cannot install the environment because two packages need different versions of the same thing, install an older version of one of them, for example:

conda install -c conda-forge <package-name>=<version>

To update the existing pyathena environment with an updated env.yml file

conda activate pyathena
conda env update --file env.yml --prune

Uninstall

To remove only the pyathena package but keep the environment (matches Options 1 and 2):

conda activate pyathena
pip uninstall pyathena          # or: uv pip uninstall pyathena

To remove the whole conda environment (Options 1 and 2):

conda deactivate
conda env remove -n pyathena    # or: conda remove --name pyathena --all

To remove the uv-only environment (Option 3), delete its directory:

deactivate
rm -rf .venv

The editable install only links to this repository, so uninstalling never deletes the source.

Example Usage

See example notebooks and documentation.

Contributing

Fork the repo, follow one of the editable (Installation) options, then submit a pull request from a feature branch.

License

See LICENSE.md.