AMICI developer’s guide

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

Branches / releases

AMICI roughly follows the GitFlow. All new contributions are merged into develop. These changes are regularly merged into master as new releases. For release versioning we are trying to follow semantic versioning. 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 develop. Merging of release branches to master is done via merge commits.

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 the conditions provided in LICENSE. By opening a pull requests you confirm us that you do agree.
Start a new branch from develop (on your fork, or at the main repository if you have access)
Implement your changes
Submit a pull request to the develop 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 to the Matlab or C++ code and have a Matlab license, please also run tests/cpp/wrapTestModels.m and tests/testModels.m
- 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 black for code formatting.

To run black 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 (but not for class attributes, since they are not supported by the current Python doxygen filter). In Python code, type hints should be used instead of doxygen @type.

For function docstrings, follow this format:

"""One-line description.

Possible a more detailed description

Arguments:
    Argument1: This needs to start on the same line, otherwise the current
        doxygen filter will fail.

    Returns:
        Return value

    Raises:
        SomeError in case of some error.
"""

C++

We use C++17
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.

Matlab

To be defined