use the custom NUMPY_INCLUDEDIR environment variable derived from a call to numpy.get_include |
||
---|---|---|
.. | ||
pytrexio | ||
test | ||
.gitignore | ||
install_pytrexio.sh | ||
MANIFEST.in | ||
pyproject.toml | ||
README_SETUP.txt | ||
README.md | ||
requirements.txt | ||
set_NUMPY_INCLUDEDIR.sh | ||
setup.cfg | ||
setup.py |
TREXIO Python API
TREXIO provides a Python API, which enables interactive calls to the library. It facilitates the development of interfaces between different codes and can be used to convert data from one input/output file format into another.
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. For more details, see the corresponding part of the Python documentation.
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 installstrexio
in your environment) - Run
cd test && python3 test_api.py
(this executes several tests that verify the installation)
You are ready to go!
Examples
An interactive Jupyter notebook called
tutorial_benzene.ipynb
is provided in the
examples
directory. It demonstrates some basic use cases of
the TREXIO library in general and of the Python API in particular.
Jupyter can be installed using pip install jupyter
. If
you are not familiar with it, feel free to consult the Jupyter
documentation.
Running the notebook
The example notebook can be launched using the following command:
jupyter notebook tutorial_benzene.ipynb
Additional steps needed to run a custom virtual environment in Jupyter notebooks
If you have installed trexio
in a virtual environemnt
called, e.g. myvenv
, but would like to use your system-wide
Jupyter installation, this is also possible. This requires
ipykernel
python package to be installed, which usually
comes together with the Jupyter installation. If this is not the case,
run pip install ipykernel
. You can install
myvenv
as a kernel by executing the following command:
python3 -m ipykernel install --user --name=myvenv
Now you can launch a Jupyter notebook. Once it is open, make sure that your virtual environment is selected as the current kernel. If this is not the case, try this:
- 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 custom virtual environment called
myvenv
in your notebook.
To uninstall the kernel named myvenv
, execute the
following command:
jupyter kernelspec uninstall myvenv