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76 lines
2.8 KiB
Markdown
76 lines
2.8 KiB
Markdown
## TREXIO Python API
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TREXIO provides a Python API, which enables interactive calls to the library.
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It facilitates the development of interfaces between different codes and
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can be used to convert data from one input/output file format into another.
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### Requirements
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- python3 (>= 3.6)
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- numpy
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- C compiler (gcc/icc)
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### Installation from PyPI
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Run `pip3 install trexio`
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**Note: we highly recommend to use virtual environments to avoid compatibility issues.**
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For more details, see the corresponding part of the [Python documentation](https://docs.python.org/3/library/venv.html#creating-virtual-environments).
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### Additional requirements (for installation from source)
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- HDF5 library (>= 1.8)
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- pkgconfig (TODO: CHECK THIS by installing wheels)
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### Installation from source
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1. Download the latest source code distribution (in `.tar.gz` format) of the TREXIO Python API
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2. Unpack and `cd` in the output directory
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3. Run `pip3 install -r requirements.txt` (this installs all python dependencies)
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4. Run `pip3 install .` (this installs `trexio` in your environment)
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5. Run `cd test && python3 test_api.py` (this executes several tests that verify the installation)
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You are ready to go!
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### Examples
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An interactive Jupyter notebook called `tutorial_benzene.ipynb` is provided in the `examples` directory.
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It demonstrates some basic use cases of the TREXIO library in general and of the Python API in particular.
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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).
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#### Running the notebook
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The example notebook can be launched using the following command:
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`jupyter notebook tutorial_benzene.ipynb`
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#### Additional steps needed to run a custom virtual environment in Jupyter notebooks
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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.
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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`.
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You can install `myvenv` as a kernel by executing the following command:
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`python3 -m ipykernel install --user --name=myvenv`
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Now you can launch a Jupyter notebook. Once it is open, make sure that your virtual environment is selected as the current kernel.
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If this is not the case, try this:
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1. Press the `Kernel` button in the navigation panel
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2. In the output list of options select `Change kernel`
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3. Find the name of your virtual environment (e.g. `myvenv`) in the list and select it
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That's it, you have activated the custom virtual environment called `myvenv` in your notebook.
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To uninstall the kernel named `myvenv`, execute the following command:
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`jupyter kernelspec uninstall myvenv`
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