2.3 KiB
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
- Download the latest source code distribution (in
.tar.gz
format) of the TREXIO Python API - Unpack and
cd
in the output directory - Run
pip3 install -r requirements.txt
(this installs all python dependencies) - Run
pip3 install .
(this installtrexio
in your environment) - 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:
- Press the
Kernel
button in the navigation panel - In the output list of options select
Change kernel
- 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