Contributing to the NMODL Framework

We would love for you to contribute to the NMODL Framework and help make it better than it is today. As a contributor, here are the guidelines we would like you to follow: - Question or Problem? <#question>__ - Issues and Bugs <#issue>__ - Feature Requests <#feature>__ - Submission Guidelines <#submit>__ - Development Conventions <#devconv>__

Got a Question?

Please do not hesitate to raise an issue on github project page <https://github.com/BlueBrain/nmodl>__.

Found a Bug?

If you find a bug in the source code, you can help us by submitting an issue <#submit-issue>__ to our GitHub Repository <https://github.com/BlueBrain/nmodl>. Even better, you can submit a Pull Request <#submit-pr> with a fix.

Missing a Feature?

You can request a new feature by submitting an issue <#submit-issue>__ to our GitHub Repository. If you would like to implement a new feature, please submit an issue with a proposal for your work first, to be sure that we can use it.

Please consider what kind of change it is:

  • For a Major Feature, first open an issue and outline your proposal so that it can be discussed. This will also allow us to better coordinate our efforts, prevent duplication of work, and help you to craft the change so that it is successfully accepted into the project.

  • Small Features can be crafted and directly submitted as a Pull Request <#submit-pr>__.

Submission Guidelines

Submitting an Issue


Before you submit an issue, please search the issue tracker, maybe an
issue for your problem already exists and the discussion might inform
you of workarounds readily available.

We want to fix all the issues as soon as possible, but before fixing a
bug we need to reproduce and confirm it. In order to reproduce bugs we
will need as much information as possible, and preferably a sample MOD
file or Python example.

 Submitting a Pull Request (PR)

When you wish to contribute to the code base, please consider the following guidelines:

  • Make a fork <https://guides.github.com/activities/forking/>__ of this repository.

  • Make your changes in your fork, in a new git branch:

    .. code:: shell

    git checkout -b my-fix-branch master

  • Create your patch, including appropriate test cases.

  • Enable NMODL_TEST_FORMATTING CMake variable to ensure that your change follows the coding conventions of this project when running the tests. The formatting utility can also be used directly:

    • to format CMake and C++ files: cmake/hpc-coding-conventions/bin/format

    • to format only the C++ files: cmake/hpc-coding-conventions/bin/format --lang c++

    • to format a subset of files or directories: cmake/hpc-coding-conventions/bin/format src/codegen/ src/main.cpp

    • to check the formatting of CMake files: cmake/hpc-coding-conventions/bin/format --dry-run --lang cmake

  • Run the full test suite, and ensure that all tests pass.

  • Commit your changes using a descriptive commit message.

    .. code:: shell

    git commit -a

  • Push your branch to GitHub:

    .. code:: shell

    git push origin my-fix-branch

  • In GitHub, send a Pull Request to the master branch of the upstream repository of the relevant component.

  • If we suggest changes then:

    • Make the required updates.

    • Re-run the test suites to ensure tests are still passing.

    • Rebase your branch and force push to your GitHub repository (this will update your Pull Request):

      .. code:: shell

      git rebase master -i
git push -f

That’s it! Thank you for your contribution!

After your pull request is merged ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

After your pull request is merged, you can safely delete your branch and pull the changes from the main (upstream) repository:

  • Delete the remote branch on GitHub either through the GitHub web UI or your local shell as follows:

    .. code:: shell

    git push origin –delete my-fix-branch

  • Check out the master branch:

    .. code:: shell

    git checkout master -f

  • Delete the local branch:

    .. code:: shell

    git branch -D my-fix-branch

  • Update your master with the latest upstream version:

    .. code:: shell

    git pull –ff upstream master

Development Conventions

New Lines


When generating/printing code it's important to use ``add_newline`` to
start a new line of code. When printing a string containing multiple lines,
i.e. one that contains a ``"\n"`` one must use ``add_multi_line``.

It's important that NMODL knows the line number it's currently on.

Formatting

Run the HPC coding conventions formatter to format all source files:

.. code:: bash

cmake/hpc-coding-conventions/bin/format

The HPC coding conventions formatter installs any dependencies into a Python virtual environment.

Updating Golden References


Run

.. code:: bash

   cmake --build <build-dir> --target generate_references

to regenerate the golden references. They are saved in a submodule
``tests/usecases/references``, which points to ``BlueBrain/nmodl-references``.

Create a PR for the changes to the references and update the SHA in the NMODL
repo. It might be useful to change to SSH authentication:

.. code:: bash

   git remote set-url origin ssh://git@github.com/BlueBrain/nmodl-references

(from inside ``tests/usecases/references``).

Remember the rules of submodules: They're checked out on a specific commit,
i.e. detached HEAD. If you want to modify the submodule, it's usual best to
checkout ``main`` from then on the submodule will behave much like a Git repo
that happens to be located inside a Git repo.


Validate the Python package

You may run the Python test-suites if your contribution has an impact on the Python API:

  1. setup a sandbox environment with either virtualenv, pyenv, or pipenv. For instance with virtualenv: python -m venv .venv && source .venv/bin/activate

  2. build the Python package with the command: python setup.py build

  3. install pytest Python package: pip install pytest

  4. execute the unit-tests: pytest

Memory Leaks and clang-tidy


If you want to test for memory leaks, do :

::

   valgrind --leak-check=full --track-origins=yes  ./bin/nmodl_lexer

Or using CTest as:

::

   ctest -T memcheck

If you want to enable ``clang-tidy`` checks with CMake, make sure to
have ``CMake >= 3.15`` and use following cmake option:

::

   cmake .. -DENABLE_CLANG_TIDY=ON

Blaming NMODL
~~~~~~~~~~~~~

While developing NMODL one may want to know which line of code in NMODL
produced a particular line of code in the generated file, e.g. when faced with
a compiler error such as

.. code-block::

   hodhux.cpp:105:26: error: ‘coreneuron’ has not been declared
     105 |         double* celsius{&coreneuron::celsius};
         |                          ^~~~~~~~~~

One can find the line by doing:

.. code-block::

   $ nmodl hodhux.mod ... blame --line 105

which will print a backtrace every time NMODL writes to line 105. While this is
useful for finding the line responsible for printing, i.e. convert AST to C++,
that line it doesn't immediately explain why the AST ended up that way.
Currently, we don't have a tool for the latter.