pyiron_module_template

Overview

This repository is a template for new pyiron modules similar to the existing modules of the pyiron framework, e.g. pyiron_workflow, pyiron_ontology, etc.

Within this repository, the new module is called pyiron_module_template which should be renamed to pyiron_IntendedModuleName. This can be easily achieved by modifying and running bash ./update_module_name.sh script.

The licence is free to choose, but as a default the BSD3 licence packed here.

Continuous Integration

We collect all files relevant for the continuous integration (CI) pipelines in .ci_support, while the actual CI workflows are handled by GitHub and stored in .github. If you are cloning this template inside the pyiron GitHub organization, the full CI should work out-of-the-box by calling reusable workflows from pyiron/actions and inheriting organization-wide secrets. Otherwise, you will either need to modify the CI workflow files, or give your repository the following secrets:

• DEPENDABOT_WORKFLOW_TOKEN (GitHub token for an account that has permissions to your repository -- needs to differ from the default github_token already available though! In pyiron we have a special @pyiron_runner account for this purpose.)
• PYPI_PASSWORD (Token generated on PyPi to give access to your account there)
• CODACY_PROJECT_TOKEN (Token generated on Codacy to give access to your account there)

Make sure to go to Codacy and Coverall to register your repository.

The default CI setup from pyiron/actions makes some assumptions about your directory structure. The most important one is that your environment should be specified in .ci_support/environment.yml. There is a base environment there already, giving dependence on pyiron_base. The CI will automatically keep environment files read by readthedocs (which will look at .readthedocs.yml) and MyBinder (which looks in .binder) up-to-date based on this environment file.

In case you need extra environment files for some setups, you can modify the workflows in .github/workflows, which accept input variables for the docs, tests, and notebooks environments. For example, it's typically good to not make your project depend on the lammps package, since this is not available for windows. However, you might want to give some demo notebooks that run on MyBinder (a linux environment) and use LAMMPS calculations. In this case, you could add a new file .ci_support/environment-notebooks.yml, and then edit .github/workflows/push-pull.yml so that instead of reading

jobs:
  pyiron:
    uses: pyiron/actions/.github/workflows/[email protected]
    secrets: inherit
    # All the environment files variables point to .ci_support/environment.yml by default

It instead reads

jobs:
  pyiron:
    uses: pyiron/actions/.github/workflows/[email protected]
    secrets: inherit
    with:
      notebooks-env-files: .ci_support/environment.yml .ci_support/environment-notebooks.yml

Where .ci_support/environment-notebooks.yml looks like:

channels:
  - conda-forge
dependencies:
  - lammps

Dependencies

The CI for making new releases expects all the pyproject.toml dependencies to be fully specified with == and the conda dependencies to have their versions specified by =, i.e. precisely specifying the version the code here is intended to run on. At release time, these dependencies can be relaxed so that new users installing your code may have access to a wider variety of environment possibilities. For exact details on this relaxation, check documentation in the centralized CI.

Label-based CI

Some CI triggers when labels get applied to a PR. In a new repository, you will need to define these labels:

• format_black: Runs black analyis and creates a bot-generated commit to fix any format violations
• run_CodeQL: Runs the external CodeQL analysis (expensive, only do at the end)
• run_coverage: Run all the tests in tests and use coveralls to generate a coverage report (also expensive, only run near the end of your PR)

Documentation

You should modify this README to reflect the purpose of your new package. You can look at the other pyiron modules to get a hint for what sort of information to include, and how to link badges at the head of your README file.

At a minimum, we suggest creating a meaningful example notebook in the notebooks/ directory and creating a MyBinder badge so that people can quickly and easily explore your work.

You can also edit the docs for your package by modifying docs/index.rst. By default, this README is used as the landing page, and a simple API section is automatically generated.

Tests

There is space for "benchmark", "integration", and "unit" tests in the tests/ directory, with dummy tests for each. These are run by the default CI, so modify them to suit your needs.

Additionally, the standard CI will attempt to execute all notebooks in the notebooks/ directory. See pyiron/actions and the reusable workflows there to learn about modifying the environment for the CI, e.g. to use a different env for notebook runs than for the tests in tests/.

Finally, tests/integration/test_readme.py shows how example code in the documentation gets tested against its claimed output. E.g. if you change this:

>>> print(2 + 2)
4

To read 5 instead, those tests should fail.

Publishing your package

If you are inside the pyiron organization or have your own PYPI_PASSWORD secret configured, your package will be published on PyPI automatically when you make a new "release" on GitHub -- as long as that tag matches the pattern specified in setup.cfg; by default any tag that pyiron_module_template-, where pyiron_module_template is replaced with the name of your module. We recommend using semantic versioning so that your first release looks like pyiron_module_template-0.0.1.

Releasing your package on Conda-Forge is slightly more involved, but not too hard (at least for pure python packages). See conda-forge/staged-recipes for how to publish it there.