.. _sec-contributing-guide: **************************** Contributing to Pyrokinetics **************************** .. note:: Large parts of this document came from the `Xarray Contributing Guide `_. Overview ======== Thank you for joining the pyrokinetics development team! There is always plenty of development to do and together we can make this an ever more powerful tool. All contributions, including bug reports, bug fixes, documentation improvements, enhancement suggestions, and other ideas are welcome. If you have any questions on the process or how to fix something feel free to ask us! The recommended place to ask a question is on `GitHub Discussions `_ There is also a slack channel that you are welcome to join here `Pyrokinetics slack Stack Overflow `_ which we monitor for questions. This project is a community effort, and everyone is welcome to contribute. Where to start? =============== If you are brand new to *pyrokinetics* or open-source development, we recommend going through the `GitHub "issues" tab `_ to find issues (both open and closed) that interest you. Once you've found an interesting issue, you can return here to get your development environment setup. The pyrokinetics project does not assign issues. Issues are "assigned" by opening a Pull Request(PR). .. _sec-contributing-guide.bug_reports: Bug reports and enhancement requests ==================================== Bug reports are an important part of making *pyrokinetics* more stable. Having a complete bug report will allow others to reproduce the bug and provide insight into fixing. Trying out the bug-producing code on the *unstable* branch is often a worthwhile exercise to confirm that the bug still exists. It is also worth searching existing bug reports and pull requests to see if the issue has already been reported and/or fixed. Submitting a bug report ----------------------- If you find a bug in the code or documentation, do not hesitate to submit a ticket to the `Issue Tracker `_. You are also welcome to post feature requests or pull requests. If you are reporting a bug, please use the provided template which includes the following: #. Include a short, self-contained Python snippet reproducing the problem. You can format the code nicely by using `GitHub Flavored Markdown `_:: ```python from pyrokinetics import Pyro pyro = Pyro(...) ... ``` #. Explain why the current behavior is wrong/not desired and what you expect instead. The issue will then show up to the *pyrokinetics* community and be open to comments/ideas from others. See this `stackoverflow article for tips on writing a good bug report `_ . .. _sec-contributing-guide.github: Now that you have an issue you want to fix, enhancement to add, or documentation to improve, you need to learn how to work with GitHub and the *pyrokinetics* code base. .. _sec-contributing-guide.version_control: Version control, Git, and GitHub ================================ The code is hosted on `GitHub `_. To contribute you will need to sign up for a `free GitHub account `_. We use `Git `_ for version control to allow many people to work together on the project. Some great resources for learning Git: * the `GitHub help pages `_. * the `NumPy's documentation `_. * Matthew Brett's `Pydagogue `_. Getting started with Git ------------------------ `GitHub has instructions for setting up Git `__ including installing git, setting up your SSH key, and configuring git. All these steps need to be completed before you can work seamlessly between your local repository and GitHub. .. note:: The following instructions assume you want to learn how to interact with github via the git command-line utility, but contributors who are new to git may find it easier to use other tools instead such as `Github Desktop `_. Development workflow ==================== To keep your work well organized, with readable history, and in turn make it easier for project maintainers to see what you've done, and why you did it, we recommend you to follow workflow: 1. `Create an account `_ on GitHub if you do not already have one. 2. You will need your own fork to work on the code. Go to the `pyrokinetics project page `_ and hit the ``Fork`` button near the top of the page. This creates a copy of the code under your account on the GitHub server. 3. Clone your fork to your machine:: git clone https://github.com/your-user-name/pyrokinetics.git cd pyrokinetics git remote add upstream https://github.com/pyro-kinetics/pyrokinetics.git This creates the directory `pyrokinetics` and connects your repository to the upstream (main project) *pyrokinetics* repository. Creating a development environment ---------------------------------- To test out code changes locally, you'll need to build *pyrokinetics* from source, which requires you to `create a local development environment `_. Update the ``unstable`` branch ------------------------------ Before starting a new set of changes, fetch all changes from ``upstream/unstable``, and start a new feature branch from that. From time to time you should fetch the upstream changes from GitHub: :: git fetch upstream/unstable git merge upstream/unstable This will combine your commits with the latest *pyrokinetics* git ``unstable``. If this leads to merge conflicts, you must resolve these before submitting your pull request. If you have uncommitted changes, you will need to ``git stash`` them prior to updating. This will effectively store your changes, which can be reapplied after updating. Create a new feature branch --------------------------- Create a branch to save your changes, even before you start making changes. You want your ``unstable branch`` to contain only production-ready code:: git checkout -b shiny-new-feature This changes your working directory to the ``shiny-new-feature`` branch. Keep any changes in this branch specific to one bug or feature so it is clear what the branch brings to *pyrokinetics*. You can have many "shiny-new-features" and switch in between them using the ``git checkout`` command. Generally, you will want to keep your feature branches on your public GitHub fork of pyrokinetics. To do this, you ``git push`` this new branch up to your GitHub repo. Generally (if you followed the instructions in these pages, and by default), git will have a link to your fork of the GitHub repo, called ``origin``. You push up to your own fork with: :: git push origin shiny-new-feature In git >= 1.7 you can ensure that the link is correctly set by using the ``--set-upstream`` option: :: git push --set-upstream origin shiny-new-feature From now on git will know that ``shiny-new-feature`` is related to the ``shiny-new-feature branch`` in the GitHub repo. The editing workflow -------------------- 1. Make some changes 2. See which files have changed with ``git status``. You'll see a listing like this one: :: # On branch shiny-new-feature # Changed but not updated: # (use "git add ..." to update what will be committed) # (use "git checkout -- ..." to discard changes in working directory) # # modified: README 3. Check what the actual changes are with ``git diff``. 4. Build the `documentation run `_ for the documentation changes. `Run the test suite `_ for code changes. Commit and push your changes ---------------------------- 1. To commit all modified files into the local copy of your repo, do ``git commit -am 'A commit message'``. 2. To push the changes up to your forked repo on GitHub, do a ``git push``. Open a pull request ------------------- When you're ready or need feedback on your code, open a Pull Request (PR) so that the pyrokinetics developers can give feedback and eventually include your suggested code into the ``unstable`` branch. `Pull requests (PRs) on GitHub `_ are the mechanism for contributing to pyrokinetics's code and documentation. Enter a title for the set of changes with some explanation of what you've done. Follow the PR template, which looks like this. :: [ ]Closes #xxxx [ ]Tests added [ ]User visible changes (including notable bug fixes) are documented in whats-new.rst [ ]New functions/methods are listed in api.rst Mention anything you'd like particular attention for - such as a complicated change or some code you are not happy with. If you don't think your request is ready to be merged, just say so in your pull request message and use the "Draft PR" feature of GitHub. This is a good way of getting some preliminary code review. .. _sec-contributing-guide.dev_env: Creating a development environment ================================== To test out code changes locally, you'll need to build *pyrokinetics* from source, which requires a Python environment. If you're making documentation changes, you can skip to :ref:`sec-contributing-guide.documentation` but you won't be able to build the documentation locally before pushing your changes. .. note:: For small changes, such as fixing a typo, you don't necessarily need to build and test pyrokinetics locally. If you make your changes then :ref:`commit and push them to a new branch `, pyrokinetics's automated :ref:`continuous integration tests ` will run and check your code in various ways. You can then try to fix these problems by committing and pushing more commits to the same branch. You can also avoid building the documentation locally by instead :ref:`viewing the updated documentation via the CI `. To speed up this feedback loop or for more complex development tasks you should build and test pyrokinetics locally. .. _sec-contributing-guide.dev_python: Creating a Python Environment ----------------------------- Before starting any development, you'll need to create an isolated pyrokinetics development environment: - Install either `Anaconda `_ or `miniconda `_ - Make sure your conda is up to date (``conda update conda``) - Make sure that you have cloned the latest repository - ``cd`` to the *pyrokinetics* source directory We'll now kick off a two-step process: 1. Install the build dependencies 2. Build and install pyrokinetics .. code-block:: sh # Build and install pyrokinetics pip install -e . At this point you should be able to import *pyrokinetics* from your locally built version: .. code-block:: sh $ python # start an interpreter >>> import pyrokinetics >>> pyrokinetics.__version__ '0.1.dev1779+g269d073' This will create the new environment, and not touch any of your existing environments, nor any existing Python installation. To view your environments:: conda info -e To return to your root environment:: conda deactivate See the full `conda docs here `__. Install pre-commit hooks ------------------------ We highly recommend that you setup `pre-commit `_ hooks to automatically run all the above tools every time you make a git commit. To install the hooks:: python -m pip install pre-commit pre-commit install This can be done by running: :: pre-commit run from the root of the pyrokinetics repository. You can skip the pre-commit checks with ``git commit --no-verify``. .. _sec-contributing-guide.documentation: Contributing to the documentation ================================= If you're not the developer type, contributing to the documentation is still of huge value. You don't even have to be an expert on *pyrokinetics* to do so! In fact, there are sections of the docs that are worse off after being written by experts. If something in the docs doesn't make sense to you, updating the relevant section after you figure it out is a great way to ensure it will help the next person. .. contents:: Documentation: :local: About the *pyrokinetics* documentation -------------------------------------- The documentation is written in **reStructuredText**, which is almost like writing in plain English, and built using `Sphinx `__. The Sphinx Documentation has an excellent `introduction to reST `__. Review the Sphinx docs to perform more complex changes to the documentation as well. Some other important things to know about the docs: - The *pyrokinetics* documentation consists of two parts: the docstrings in the code itself and the docs in this folder ``pyrokinetics/doc/``. The docstrings are meant to provide a clear explanation of the usage of the individual functions, while the documentation in this folder consists of tutorial-like overviews per topic together with some other information (what's new, installation, etc). - The docstrings follow the **NumPy Docstring Standard**, which is used widely in the Scientific Python community. This standard specifies the format of the different sections of the docstring. Refer to the `documentation for the Numpy docstring format `_ for a detailed explanation, or look at some of the existing functions to extend it in a similar manner. - The tutorials make heavy use of the `ipython directive `_ sphinx extension. This directive lets you put code in the documentation which will be run during the doc build. For example: .. code:: rst .. ipython:: python x = 2 x**3 will be rendered as:: In [1]: x = 2 In [2]: x**3 Out[2]: 8 Almost all code examples in the docs are run (and the output saved) during the doc build. This approach means that code examples will always be up to date, but it does make building the docs a bit more complex. - Our API documentation in ``doc/api.rst`` houses the auto-generated documentation from the docstrings. For classes, there are a few subtleties around controlling which methods and attributes have pages auto-generated. Every method should be included in a ``toctree`` in ``api.rst``, else Sphinx will emit a warning. How to build the *pyrokinetics* documentation --------------------------------------------- Information on writing documentation for pyrokinetics can be found here `writing_docs` Contributing to the code base ============================= .. contents:: Code Base: :local: Code standards -------------- Writing good code is not just about what you write. It is also about *how* you write it. During :ref:`Continuous Integration ` testing, several tools will be run to check your code for stylistic errors. Generating any warnings will cause the test to fail. Thus, good style is a requirement for submitting code to *pyrokinetics*. In addition, because a lot of people use our library, it is important that we do not make sudden changes to the code that could have the potential to break a lot of user code as a result, that is, we need it to be as *backwards compatible* as possible to avoid mass breakages. Code Formatting ~~~~~~~~~~~~~~~ pyrokinetics uses several tools to ensure a consistent code format throughout the project: - `Black `_ for standardized code formatting, - `blackdoc `_ for standardized code formatting in documentation, - `Flake8 `_ for style enforncement We highly recommend that you setup `pre-commit hooks `_ to automatically run all the above tools every time you make a git commit. This can be done by running:: pre-commit install from the root of the pyrokinetics repository. You can skip the pre-commit checks with ``git commit --no-verify``. Backwards Compatibility ~~~~~~~~~~~~~~~~~~~~~~~ Please try to maintain backwards compatibility. *pyrokinetics* has a growing number of users with lots of existing code, so don't break it if at all possible. If you think breakage is required, clearly state why as part of the pull request. Be especially careful when changing function and method signatures, because any change may require a deprecation warning. For example, if your pull request means that the argument ``old_arg`` to ``func`` is no longer valid, instead of simply raising an error if a user passes ``old_arg``, we would instead catch it: .. code-block:: python def func(new_arg, old_arg=None): if old_arg is not None: from warnings import warn warn( "`old_arg` has been deprecated, and in the future will raise an error." "Please use `new_arg` from now on.", DeprecationWarning, ) # Still do what the user intended here This temporary check would then be removed in a subsequent version of pyrokinetics. This process of first warning users before actually breaking their code is known as a "deprecation cycle", and makes changes significantly easier to handle both for users of pyrokinetics, and for developers of other libraries that depend on pyrokinetics. .. _sec-contributing-guide.ci: Testing With Continuous Integration ----------------------------------- The *pyrokinetics* test suite runs automatically via the `GitHub Actions `__, continuous integration service, once your pull request is submitted. A pull-request will be considered for merging when you have an all 'green' build. If any tests are failing, then you will get a red 'X', where you can click through to see the individual failed tests. .. note:: Each time you push to your PR branch, a new run of the tests will be triggered on the CI. If they haven't already finished, tests for any older commits on the same branch will be automatically cancelled. .. _sec-contributing-guide.tdd: Test-driven development/code writing ------------------------------------ *pyrokinetics* is serious about testing and strongly encourages contributors to embrace `test-driven development (TDD) `_. This development process "relies on the repetition of a very short development cycle: first the developer writes an (initially failing) automated test case that defines a desired improvement or new function, then produces the minimum amount of code to pass that test." So, before actually writing any code, you should write your tests. Often the test can be taken from the original GitHub issue. However, it is always worth considering additional use cases and writing corresponding tests. Adding tests is one of the most common requests after code is pushed to *pyrokinetics*. Therefore, it is worth getting in the habit of writing tests ahead of time so that this is never an issue. Like many packages, *pyrokinetics* uses `pytest `_ and the convenient extensions in `numpy.testing `_. Writing tests ~~~~~~~~~~~~~ All tests should go into the ``tests`` subdirectory of the specific package. This folder contains many current examples of tests, and we suggest looking to these for inspiration. *pyrokinetics* existing test structure uses a *functional* style using the `pytest `__ framework, which offers a richer testing framework that will facilitate testing and developing. Thus, writing test functions will look like this: .. code-block:: python def test_really_cool_feature(): ... Using ``pytest`` ~~~~~~~~~~~~~~~~ Here is an example of a self-contained set of tests that illustrate multiple features that we like to use. - functional style: tests are like ``test_*`` and *only* take arguments that are either fixtures or parameters - ``pytest.mark`` can be used to set metadata on test functions, e.g. ``skip`` or ``xfail``. - using ``parametrize``: allow testing of multiple cases - to set a mark on a parameter, ``pytest.param(..., marks=...)`` syntax should be used - ``fixture``, code for object construction, on a per-test basis - using bare ``assert`` for scalars and truth-testing We would name this file ``test_cool_feature.py`` and put in an appropriate place in the ``pyrokinetics/tests/`` structure. .. code-block:: python import pytest import numpy as np from pyrokinetics import Pyro from pyrokinetics import Numerics from pyrokinetics.templates import gk_templates, template_dir from pyrokinetics.local_species import LocalSpecies from pyrokinetics.local_geometry import LocalGeometryMiller from pyrokinetics.gk_code import GKInput def test_keys(): numerics = Numerics() # use defaults # Test you can set an existing key numerics["ntheta"] = 42 assert numerics.ntheta == 42 # Test you can't set a key that doesn't exist with pytest.raises(KeyError): numerics["n_theta"] = 42 def test_attrs(): numerics = Numerics() # use defaults # Test you can set an existing attr numerics.ntheta = 42 assert numerics.ntheta == 42 # Test you can't set a key that doesn't exist with pytest.raises(AttributeError): numerics.n_theta = 42 @pytest.mark.parametrize("gk_code", ["GS2", "CGYRO", "GENE"]) def test_pyro_read_gk_file(gk_code): pyro = Pyro() pyro.read_gk_file(gk_templates[gk_code]) # Ensure the correct file data now exists assert pyro.gk_file == gk_templates[gk_code] assert pyro.file_name == gk_templates[gk_code].name assert pyro.run_directory == template_dir assert pyro.gk_code == gk_code # Ensure that the correct geometry/species/numerics are set assert isinstance(pyro.gk_input, GKInput._factory[gk_code]) assert isinstance(pyro.local_species, LocalSpecies) assert isinstance(pyro.local_geometry, LocalGeometryMiller) assert isinstance(pyro.numerics, Numerics) A test run of this yields .. code-block:: shell ==================================================================== test session starts ===================================================================== platform linux -- Python 3.9.13, pytest-7.2.0, pluggy-1.0.0 -- /usr/local/depot/Python-3.9/bin/python3 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase('/home/bpatel2/pyrokinetics_testing/.hypothesis/examples') rootdir: /home/bpatel2/pyrokinetics_testing plugins: anyio-3.6.2, hypothesis-6.61.0, arraydiff-0.5.0, astropy-0.10.0, astropy-header-0.2.2, cov-4.0.0, doctestplus-0.12.1, filter-subpackage-0.1.2, mock-3.10.0, openfiles-0.5.0, remotedata-0.4.0 collected 5 items test_docs.py::test_keys PASSED [ 20%] test_docs.py::test_attrs PASSED [ 40%] test_docs.py::test_pyro_read_gk_file[GS2] PASSED [ 60%] test_docs.py::test_pyro_read_gk_file[CGYRO] PASSED [ 80%] test_docs.py::test_pyro_read_gk_file[GENE] PASSED [100%] ===================================================================== 5 passed in 3.71s ====================================================================== Tests that we have ``parametrized`` are now accessible via the test name, for example we could run these with ``-k test_pyro_read_gk_file`` to sub-select *only* those tests. .. code-block:: shell bash-3.2$ pytest test_cool_feature.py -v -k test_pyro_read_gk_file ==================================================================== test session starts ===================================================================== platform linux -- Python 3.9.13, pytest-7.2.0, pluggy-1.0.0 -- /usr/local/depot/Python-3.9/bin/python3 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase('/home/bpatel2/pyrokinetics_testing/.hypothesis/examples') rootdir: /home/bpatel2/pyrokinetics_testing plugins: anyio-3.6.2, hypothesis-6.61.0, arraydiff-0.5.0, astropy-0.10.0, astropy-header-0.2.2, cov-4.0.0, doctestplus-0.12.1, filter-subpackage-0.1.2, mock-3.10.0, openfiles-0.5.0, remotedata-0.4.0 collected 5 items / 2 deselected / 3 selected test_docs.py::test_pyro_read_gk_file[GS2] PASSED [ 33%] test_docs.py::test_pyro_read_gk_file[CGYRO] PASSED [ 66%] test_docs.py::test_pyro_read_gk_file[GENE] PASSED [100%] ============================================================== 3 passed, 2 deselected in 4.57s =============================================================== Running the test suite ---------------------- The tests can then be run directly inside your Git clone (without having to install *pyrokinetics*) by typing:: pytest pyrokinetics The tests suite is exhaustive and takes a few minutes. Often it is worth running only a subset of tests first around your changes before running the entire suite. The easiest way to do this is with:: pytest pyrokinetics/path/to/test.py -k regex_matching_test_name Using `pytest-xdist `_, one can speed up local testing on multicore machines, by running pytest with the optional -n argument:: pytest pyrok -n 4 This can significantly reduce the time it takes to locally run tests before submitting a pull request. For more, see the `pytest `_ documentation. Documenting your code --------------------- Changes should be reflected in the release notes located in ``doc/whats-new.rst``. This file contains an ongoing change log for each release. Add an entry to this file to document your fix, enhancement or (unavoidable) breaking change. Make sure to include the GitHub issue number when adding your entry (using ``:issue:`1234```, where ``1234`` is the issue/pull request number). If your code is an enhancement, it is most likely necessary to add usage examples to the existing documentation. This can be done by following the :ref:`guidelines for contributing to the documentation `. .. _sec-contributing-guide.changes: Contributing your changes to *pyrokinetics* =========================================== .. _sec-contributing-guide.committing: Committing your code -------------------- Keep style fixes to a separate commit to make your pull request more readable. Once you've made changes, you can see them by typing:: git status If you have created a new file, it is not being tracked by git. Add it by typing:: git add path/to/file-to-be-added.py Doing 'git status' again should give something like:: # On branch shiny-new-feature # # modified: /relative/path/to/file-you-added.py # The following defines how a commit message should ideally be structured: * A subject line with less than 72 chars. * One blank line. * Optionally, a commit message body. Please reference the relevant GitHub issues in your commit message using ``GH1234`` or ``#1234``. Either style is fine, but the former is generally preferred. Now you can commit your changes in your local repository:: git commit -m .. _sec-contributing-guide.pushing: Pushing your changes -------------------- When you want your changes to appear publicly on your GitHub page, push your forked feature branch's commits:: git push origin shiny-new-feature Here ``origin`` is the default name given to your remote repository on GitHub. You can see the remote repositories:: git remote -v If you added the upstream repository as described above you will see something like:: origin git@github.com:yourname/pyrokinetics.git (fetch) origin git@github.com:yourname/pyrokinetcs.git (push) upstream git://github.com/py-pyrokinetics/pyrokinetics.git (fetch) upstream git://github.com/pyro-kinetics/pyrokinetics.git (push) Now your code is on GitHub, but it is not yet a part of the *pyrokinetics* project. For that to happen, a pull request needs to be submitted on GitHub. .. _sec-contributing-guide.review: Review your code ---------------- When you're ready to ask for a code review, file a pull request. Before you do, once again make sure that you have followed all the guidelines outlined in this document regarding code style, tests, performance tests, and documentation. You should also double check your branch changes against the branch it was based on: #. Navigate to your repository on GitHub -- https://github.com/your-user-name/pyrokinetics #. Click on ``Branches`` #. Click on the ``Compare`` button for your feature branch #. Select the ``base`` and ``compare`` branches, if necessary. This will be ``main`` and ``shiny-new-feature``, respectively. .. _sec-contributing-guide.pr: Finally, make the pull request ------------------------------ If everything looks good, you are ready to make a pull request. A pull request is how code from a local repository becomes available to the GitHub community and can be looked at and eventually merged into the ``main`` version. This pull request and its associated changes will eventually be committed to the ``main`` branch and available in the next release. To submit a pull request: #. Navigate to your repository on GitHub #. Click on the ``Pull Request`` button #. You can then click on ``Commits`` and ``Files Changed`` to make sure everything looks okay one last time #. Write a description of your changes in the ``Preview Discussion`` tab #. Click ``Send Pull Request``. This request then goes to the repository maintainers, and they will review the code. If you have made updates to the documentation, you can now see a preview of the updated docs by clicking on "Details" under the ``docs/readthedocs.org`` check near the bottom of the list of checks that run automatically when submitting a PR, then clicking on the "View Docs" button on the right (not the big green button, the small black one further down). If you need to make more changes, you can make them in your branch, add them to a new commit, push them to GitHub, and the pull request will automatically be updated. Pushing them to GitHub again is done by:: git push origin shiny-new-feature This will automatically update your pull request with the latest code and restart the :ref:`Continuous Integration ` tests. .. _sec-contributing-guide.delete: Delete your merged branch (optional) ------------------------------------ Once your feature branch is accepted into upstream, you'll probably want to get rid of the branch. First, update your ``main`` branch to check that the merge was successful:: git fetch upstream git checkout main git merge upstream/main Then you can do:: git branch -D shiny-new-feature You need to use a upper-case ``-D`` because the branch was squashed into a single commit before merging. Be careful with this because ``git`` won't warn you if you accidentally delete an unmerged branch. If you didn't delete your branch using GitHub's interface, then it will still exist on GitHub. To delete it there do:: git push origin --delete shiny-new-feature .. _sec-contributing-guide.checklist: PR checklist ------------ - **Properly comment and document your code.** See `"Documenting your code" <.html#documenting-your-code>`_. - **Test that the documentation builds correctly** by typing ``make html`` in the ``doc`` directory. This is not strictly necessary, but this may be easier than waiting for CI to catch a mistake. See `"Contributing to the documentation" `_. - **Test your code**. - Write new tests if needed. See `"Test-driven development/code writing" `_. - Test the code using `Pytest `_. Running all tests (type ``pytest`` in the root directory) takes a while, so feel free to only run the tests you think are needed based on your PR (example: ``pytest pyrokinetics/tests/test_my_feature.py``). CI will catch any failing tests. - By default, the upstream dev CI is disabled on pull request and push events. You can override this behavior per commit by adding a ``[test-upstream]`` tag to the first line of the commit message. For documentation-only commits, you can skip the CI per commit by adding a ``[skip-ci]`` tag to the first line of the commit message. - **Properly format your code** and verify that it passes the formatting guidelines set by `Black `_ and `Flake8 `_. See `"Code formatting" `_. You can use `pre-commit `_ to run these automatically on each commit. - Run ``pre-commit run --all-files`` in the root directory. This may modify some files. Confirm and commit any formatting changes. - **Push your code** and `create a PR on GitHub `_. - **Use a helpful title for your pull request** by summarizing the main contributions rather than using the latest commit message. If the PR addresses an `issue `_, please `reference it `_.