py4vasp-core 0.9.0

Tool for assisting with the analysis and setup of VASP calculations.

py4vasp

Please note that this document is intended mostly for developers that want to use the version of py4vasp provided on Github. If you just want to install py4vasp to use it, please follow the official documentation.

Installation

We use the poetry dependency manager which takes care of all dependencies and maintains a virtual environment to check the code. If you want to test something in the virtual environment, just use e.g. poetry run jupyter-notebook.

We recommend installing py4vasp in a conda environment to resolve issues related to installing mdtraj with pip. To do this please use the following steps. The last step will test whether everything worked

conda create --name py4vasp-env python=3.8
git clone [e-mail]:vasp-dev/py4vasp.git
pip install poetry
poetry install
conda install -c conda-forge mdtraj
poetry run pytest

Note that this will install py4vasp into the conda environment. This isolates the code from all packages you have installed in other conda environments. Using poetry makes sure that when you modify the code all the relevant dependencies are tracked.

py4vasp core

If you want to use py4vasp to develop your own scripts, you may want to limit the amount of external dependencies. To this end, we provide alternative configuration files that only install numpy, h5py, and the development dependencies. To install this core package replace the configurations files in the root folder with the ones in the core folder

cp core/* .

Then you can install py4vasp with the same steps as above. Alternatively, since py4vasp-core does not use mdtraj, you can also install everything in a virtual environment mangaged by poetry

pip install poetry
poetry install
poetry run pytest

Note that some tests will be skipped because they require the external packages to run. If you want to exclude even the development dependencies, you can run

poetry install --without dev

for the minimal installation.

Code style

Code style is enforced, but is not something the developer should spend time on, so we decided on using black and isort. Please run

black src tests
isort src tests

before committing the code. This will autoformat your code and sort the import statements in a consistent order. If you would like this code formatting to be done along with each commit, you can run

pre-commit install

Contributing to py4vasp

We welcome contributions to py4vasp. To improve the code please follow this workflow

• Create an issue for the bugfix or feature you plan to work on, this gives the option to provide some input before work is invested.
• Implement your work in a fork of the repository and create a pull request for it. Please make sure to test your code thoroughly and commit the tests in the pull request in the tests directory.
• In the message to your merge request mention the issue the code attempts to solve.
• We will try to include your merge request rapidly when all the tests pass and your code is covered by tests.

Please limit the size of a pull request to approximately 200 lines of code otherwise reviewing the changes gets unwieldy. Prefer splitting the work into multiple smaller chunks if necessary.