Continuous integration

The continuous integration has multiple components,

• format: apply black, isort, etc.. Includes notebooks.

• lint: check flake8, and check whether black and isort are happy with the code. No formatting.

• test: Run the unittests with different backends, and run some doctests

• example: sync and execute the example notebooks. Bundles a bunch of bigger optional dependencies (scipy, diffrax, matplotlib, …), so it is kept separate from the rest of the dependencies.

• doc: build the sphinx docs.

which appear in different parts of the specification

• Groups of optional dependencies: pip install diffeqzoo[lint,test,example]. Formatting dependencies are a subset of the linting dependencies.

• In the makefile: make format; make lint; make test; make example; make doc

• In the workflows

One exception are the doc-requirements, which are not part of the setup.cfg, but are isolated in a separate requirements file in the docs/ directory. (Reason: readthedocs config.)

There are also the numpy and the jax optional dependencies. Combine any of the execution-based workflows (test, example) with either one, e.g.,

pip install diffeqzoo[jax]
pip install diffeqzoo[example,numpy]
pip install diffeqzoo[test,jax,numpy]

The makefile

To apply all {linting, formatting, testing, …} operations, use the makefile. In the root, run

make format
make lint
make test

To remove automatically generated files (caches, etc.), run make clean.

To check conformity with the pre-commit file, run make pre-commit. This command also updates the versions in the pre-commit.