aiida_eos 0.0.1

AiiDA plugin to calculate the equation of state of a material.

aiida_eos

A demonstration of creating a Python package for AiiDA plugins. The goal is to create a plugin package for the Equation of State workflow demonstrated in: https://aiida-qe-demo.readthedocs.io/en/latest/6_write_your_own_workflow.html.

Each commit in this repository corresponds to a step in the tutorial.

Note, https://github.com/aiidateam/aiida-plugin-cutter can be used to automate most of these steps, but here we shall do it manually explain each aspect of the package.

Initial creation

The first step is to create a new repository on GitHub. We will call it aiida_eos. The repository should be created with a README.md and a .gitignore file.

Interacting with the repository

We shall use Visual Studio Code to interact with the repository. This is a free, open-source, cross-platform IDE, with nice integration with GitHub, and many useful extensions.

Creating the package metadata

The first step is to create the package metadata. This is done by creating a pyproject.toml file in the root of the repository. This can be used by pip to install the package, and by other tools to build the package: https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml/

We shall use flit to build the package. This is a simple tool that is designed to build Python packages from a pyproject.toml file.

We can initialise the pyproject.toml file by running:

flit init

This also generates a license file, which is crucial for allowing others to use your package.

Create the package and install it

We create the initial package with a single file: src/aiida_eos/__init__.py. This file should have a docstring that describes the package, and a __version__ variable.

We now want to install the package in editable mode. This means that we can make changes to the package, and they will be immediately available to Python.

First we create a virtual environment, and activate it:

python -m venv .venv
source .venv/bin/activate

Virtual environments are a way of isolating Python environments.

We can now install the package in editable mode:

python -m pip install --upgrade pip
pip install -e .

We can now import the package in Python:

>>> import aiida_eos
>>> aiida_eos.__version__
'0.0.1'

Adding formatting and linting with pre-commit

We shall use pre-commit to automatically format and lint the code. This will ensure that the code is formatted consistently, and that it conforms to the style guide.

We can initialise a pre-commit configuration file with:

pre-commit sample-config > .pre-commit-config.yaml
pre-commit autoupdate
pre-commit install

We shall add a few additional hooks to the configuration file:

• black: a Python code formatter
• flake8: a Python linter
• isort: a tool to sort the Python imports

Adding testing

We shall use pytest to run tests on our package. To install pytest, we shall add it to an optional-dependencies section in the pyproject.toml file. This is because we only need pytest to run the tests, and not to use the package.

We can now install the package, with the optional dependencies:

pip install -e ".[test]"

We can now add a test to the package. We shall add a test that checks that the package can be imported. This is done by adding a tests directory, and a test_import.py file in it.

Now we can run the tests:

pytest

To check the coverage of the tests, we can run:

pytest --cov=aiida_eos

Using tox

The tox CLI tool is an optional way to automate both setting up the virtual environment, then running the tests within it. See the pyproject.toml section for the configuration. You can then simply run tox to run the tests, or tox -e py39 to run with a certain python version. See tox-conda for an example of how to use tox with conda.

Adding GitHub Actions

We can use GitHub Actions to automatically run the tests on each commit. This is done by adding a .github/workflows/test.yml file.

Adding the rescale calcfunction

We shall add a rescale calcfunction to the package. This is a simple function that takes a structure, and rescales it by a given factor.

Note that up until now, we have not added any AiiDA specific code. Now that we want to add an AiiDA specific calcfunction, we need to add the aiida-core dependency to the pyproject.toml file, and also ase for the structure manipulation.

If using tox, we can regenerate our virtual environment with:

tox -r

Type annotations

We will also notice that we added type annotations to the function. This is a good practice, to provide static type inference, and also allows us to use tools like mypy to check the type annotations.

Testing the calcfunction

We can now add a test for the rescale calcfunction. In fact, if we were to use test-driven development, we would first write the test, and then write the code to make the test pass!

Since the calcfunction needs to store data to an AiiDa profile, we need to create a profile for the tests. We can do this by utilising the pgtest package to create a temporary, local PostgreSQL database cluster, which allows us to create a temporary AiiDA profile, which we add to the pyproject.toml test dependencies.

For this we will first need an PostgreSQL server running, with which to connect. There are numerous ways to do this, such as using the Docker image, or installing via Homebrew on macOS, or via the PostgreSQL apt repository on Ubuntu.

To create the profile for the tests, we can add a conftest.py file to the tests directory. Then we register the AiiDA pytest fixtures in it. You can see all the available fixtures by running pytest --fixtures (or tox -- --fixtures). The initial one we need is the aiida_profile_clean fixture, which creates a temporary profile, and tears it down at the end of the test.

We can now add a passing test for the rescale calcfunction.

Setting up PostgreSQL on GitHub Actions

We also need to start a PostgreSQL server for our GitHub Actions, by specifying a service in the test.yml file. This actually uses the PostgreSQL Docker image, which is started before the tests are run.

Adding the EquationOfState workchain

We shall now add the workflow itself.

We add an project.entry-points."aiida.workflows" section to the pyproject.toml file, to register the EquationOfState workchain as an entry point, for AiiDA to access. After re-installing the package (pip install --no-deps -e ".[test]"), we can now use the verdi plugin list aiida.workflows eos.base command and see the registered workflow.

For the testing we need to set up some more resources, before running the workflow. We can do this by adding pytest fixtures to the conftest.py file.

We also need to run against the actual pw.x executable. One way to do this is to use conda, to install the quantum-espresso package, which will install the pw.x executable in the bin directory of the conda environment. Another way we are developing is aiida-testing.

Publishing the package

Once you have a working package, it is good to create a version tag, and a CHANGELOG.md to keep track of the changes.

We can now publish the package to PyPI. First create an account on PyPI, and then create an API token.

You can either use locally flit publish to publish the package, or use the GitHub Actions: Add the token to the PYPI_KEY secret in the GitHub repository settings. Then we add a publishing workflow that runs on a new release.

Once released to PyPI (or before) you can make a PR to the AiiDA plugin registry for others to find your plugin.