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CONTRIBUTING.md

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How to contribute

We are happy about contributions to AMICI in any form (new functionality, documentation, bug reports, ...).

Making code changes

When making code changes:

  • Check if you agree to release your contribution under the conditions provided in LICENSE
  • Start a new branch from develop
  • Implement your changes
  • Submit a pull request to the develop branch
  • Make sure your code is documented appropriately
    • Run mtoc/makeDocumentation.m to check completeness of your documentation
  • Make sure your code is compatible with C++11, gcc and clang
  • when adding new functionality, please also provide test cases (see tests/cpputest/)
  • Write meaningful commit messages
  • Run all tests to ensure nothing was broken
    • Run tests/cpputest/wrapTestModels.m followed by CI tests scripts/buildAll.sh && scripts/run-cpputest.sh
    • Run tests/testModels.m
    • Run make python-tests in build
  • When all tests are passing and you think your code is ready to merge, request a code review

Adding/Updating tests

To add new tests add a new corresponding python script (see, e.g., tests/example_dirac.py) and add it to and run tests/generateTestConfigurationForExamples.sh To update test results replace tests/cpputest/expectedResults.h5 by tests/cpputest/writeResults.h5.bak [ONLY DO THIS AFTER TRIPLE CHECKING CORRECTNESS OF RESULTS] Before replacing the test results, confirm that only expected datasets have changed, e.g. using h5diff -v -r 1e-8 tests/cpputest/expectedResults.h5 tests/cpputest/writeResults.h5.bak | less