AMICI developer’s guide

This document contains information for AMICI developers, not too relevant to regular users.

When starting to work on some issue

When starting to work on some GitHub issue, please assign yourself to let other developers know that you are working on it to avoid duplicate work. If the respective issue is not completely clear, it is generally a good idea to ask for clarification before starting to work on it.

If you want to work on something new, please create a GitHub issue first.

Code contributions

When making code contributions, please follow our style guide and the process described below:

Check if you agree to release your contribution under AMICI’s license conditions. By opening a pull requests you confirm us that you do agree.
Start a new branch from main (on your fork, or at the main repository if you have access)
Implement your changes
Update CHANGELOG.md with a short description of your changes. This can be omitted for small changes that do not affect the functionality of AMICI, e.g. fixing typos or formatting issues, private refactoring, …
Submit a pull request to the main branch
Ensure all tests pass
When adding new functionality, please also provide test cases (see tests/cpp/, python/tests/, and documentation/CI.md)
Write meaningful commit messages
Run all tests to ensure nothing was broken (more details)
- Run scripts/buildAll.sh && scripts/run-cpp-tests.sh.
- If you made changes related to code generation or version number, run
```
python -c "from amici.testing.models import import_test_models; import_test_models()"
```
- If you made changes to the Python or C++ code, run make python-tests in build
When all tests are passing and you think your code is ready to merge, request a code review (see also our code review guideline)
Wait for feedback. If you do not receive feedback to your pull request within a week, please give us a friendly reminder.

Style/compatibility guide

General

All files and functions should come with file-level and function-level documentation.
All new functionality should be covered by unit or integration tests. Runtime of those tests should be kept as short as possible.

Python

In terms of Python compatibility, we follow numpy’s NEP 29.
For the Python code we want to follow PEP8. Although this is not the case for all existing code, any new contributions should do so. We use ruff for automated code formatting.

To run ruff as pre-commit hook, install the pre-commit package (e.g. pip install pre-commit), and enable AMICI-hooks by running pre-commit install from within the AMICI directory.
We use Python type hints for all functions and attributes. We do not include any other redundant type annotation in docstrings.
We use the sphinx docstring-style for new code.

C++

We use C++20
We want to maintain compatibility with g++, clang, and the Intel C++ compiler
For code formatting, we use clang-format and cmake-format. They can be invoked by make clang-format cmake-format from the CMake build directory.
For new code, we use Google’s C++ style guide as a reference.

Branches / releases

For AMICI, we mostly do trunk-based development. All new contributions are merged into main after passing the test suite and code review. Releases are usually created directly from main. New releases are created on GitHub and are automatically deployed to Zenodo for archiving and to obtain a digital object identifier (DOI) to make them citable. Furthermore, our CI pipeline will automatically create and deploy a new release on PyPI.

We try to keep a clean git history. Therefore, feature pull requests are squash-merged to main.

Release process

Releases are created by the maintainer team.

To create a new release, please follow these steps:

Ensure that all changes intended for the new release are merged into main.
Update CHANGELOG.md with a short description of the changes included in the new release. Focus on user-relevant changes.
Bump the version number in version.txt according to Semantic Versioning.

Regenerate the test models by running

  python -c "from amici.testing.models import import_test_models; import_test_models()"

This ensures that the models can be imported with the new version.

Create a new release on GitHub, using the new version number prefixed by “v” (e.g., “v0.12.0”). Copy the relevant parts of CHANGELOG.md into the release notes.
After creating the release, our GitHub Actions pipeline will automatically create and deploy the new release on Zenodo and PyPI. Verify that this was successful.
Bump the version number in version.txt back to a development version (e.g., after release “1.1.0”, set the version to “1.2.0-dev”) and commit this change to main. This ensures that documentation at https://amici.readthedocs.io/en/latest/ will show the correct development version and won’t be confused with the latest release, and that models imported with a development version will be marked as such.

In rare cases, it might be necessary to create a hotfix release for a critical bug in an existing release. In this case, create a new branch from the respective tag, apply the fix (usually a backport from main), and follow the same steps as above, starting from step 2. Merge the updated CHANGELOG and version bump back into main afterwards.