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README.md

TREXIO Python API

TREXIO provides a Python API for interactive calls to the library. It allows to simplify interfacing between different codes and can be used to convert between different input/output file formats.

Requirements

  • python3 (>= 3.6)
  • numpy
  • C compiler (gcc/icc)

Installation from PyPI

Run pip3 install trexio

Note: we highly recommend to use virtual environments to avoid compatibility issues.

Additional requirements (for installation from source)

  • HDF5 library (>= 1.8)
  • pkgconfig (TODO: CHECK THIS by installing wheels)

Installation from source

  1. Download the latest source code distribution (in .tar.gz format) of the TREXIO Python API
  2. Unpack and cd in the output directory
  3. Run pip3 install -r requirements.txt (this installs all python dependencies)
  4. Run pip3 install . (this install trexio in your environment)
  5. Run cd test && python3 test_api.py (this executes several tests that check the installation)

You are ready to go!

Examples

An interactive Jupyter notebook called tutorial_benzene.ipynb can be found in the examples directory or on Binder (TODO: link). It is provided to demonstrate some basic use cases of the TREXIO library in general and the Python API in particular.

Additional requirements to run Jupyter notebooks with TREXIO

Jupyter can be installed using pip install jupyter.

If you have installed trexio in the virtual environemnt called, e.g. myvenv, make sure to also install it as a kernel for (this requires ipykernel python package to be installed) by executing the following:

python3 -m ipykernel install --user --name=myvenv

Running the notebook

The example notebook can be launched using the following command

jupyter-notebook tutorial_benzene.ipynb

Once the notebook is open, make sure that your virtual environment is selected as the current kernel. If this is not the case, try the following:

  1. Press the Kernel button in the navigation panel
  2. In the output list of options select Change kernel
  3. Find the name of your virtual environment (e.g. myvenv) in the list and select it

That’s it, you have activated the virtual environment and can now run the cells of the tutorial_benzene.ipynb notebook.

To uninstall the kernel named myvenv from Jupyter, execute the following:

`jupyter kernelspec uninstall myvenv