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trexio/python/README.md
2021-09-09 17:29:17 +02:00

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## 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](https://docs.python.org/3/library/venv.html#creating-virtual-environments).
### 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. Export custom environment variables needed for the installation. Steps 1 and 2 can be skipped if HDF5 is properly configured for `pkg-config` (i.e. if executing `pkg-config --libs hdf5` returns a list of options).
1. `export H5_CFLAGS=-I/path/to/hdf5/include`
2. `export H5_LDFLAGS=-L/path/to/hdf5/lib`
3. `source tools/set_NUMPY_INCLUDEDIR.sh`
5. Run `pip3 install .` (this installs `trexio` in your environment)
6. 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](https://jupyter-notebook.readthedocs.io/en/stable/notebook.html).
#### 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
In some cases, it may happen that the Jupyter kernels in the activated virtual environment (e.g. `myvenv`) still point to the system-wide python binaries and not to the environment ones.
This will result in `ImportError` when importing `trexio` in the notebook cell. In order to avoid this, the `myvenv` has to be installed as an additional kernel.
This requires `ipykernel` python package, 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:
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 custom virtual environment called `myvenv` in your notebook.
To uninstall the kernel named `myvenv`, execute the following command:
`jupyter kernelspec uninstall myvenv`