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better README for python

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q-posev 2021-09-08 19:53:45 +02:00
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@ -11,9 +11,6 @@ be used to convert between different input/output file formats.
- numpy - numpy
- C compiler (gcc/icc) - C compiler (gcc/icc)
- HDF5 library (when compiling from source)
- pkgconfig (when compiling from source ----------> TODO: CHECK THIS by installing wheels)
### Installation from PyPI ### Installation from PyPI
@ -22,6 +19,12 @@ Run `pip3 install trexio`
**Note:** we highly recommend to use virtual environments to avoid compatibility issues. **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 ### Installation from source
1. Download the latest source code distribution (in `.tar.gz` format) of the TREXIO Python API 1. Download the latest source code distribution (in `.tar.gz` format) of the TREXIO Python API
@ -35,15 +38,15 @@ You are ready to go!
### Examples ### Examples
An interactive `Jupyter` notebook called `tutorial_benzene.ipynb` can be found in the `examples` directory or on Binder (TODO: link). An interactive Jupyter notebook called `tutorial_benzene.ipynb` can be found in the `examples` directory or on Binder (TODO: link).
It's goal is to demonstrate some basic use cases of the `trexio` Python API. 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 #### Additional requirements to run Jupyter notebooks with TREXIO
`Jupyter` can be installed using `pip install jupyter`. 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 `ipython` (requires `ipykernel` to be installed) by executing the following: 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` `python3 -m ipykernel install --user --name=myvenv`
@ -55,7 +58,7 @@ The example notebook can be launched using the following command
`jupyter-notebook tutorial_benzene.ipynb` `jupyter-notebook tutorial_benzene.ipynb`
Once the notebook is open, make sure that your virtual environment is selected as the current kernel. Once the notebook is open, make sure that your virtual environment is selected as the current kernel.
If this is not the case: If this is not the case, try the following:
1. Press the `Kernel` button in the navigation panel 1. Press the `Kernel` button in the navigation panel
2. In the output list of options select `Change kernel` 2. In the output list of options select `Change kernel`
@ -63,3 +66,7 @@ If this is not the case:
That's it, you have activated the virtual environment and can now run the cells of the `tutorial_benzene.ipynb` notebook. 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