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Development workflow

doc/source/dev/contributor/development_workflow.rst

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.. _development-workflow:

==================== Development workflow

Note: consider watching SciPy Development Workflow_ before or after reading to see an example of fixing a bug and submitting a pull request.

This guide assumes that you have created your own fork (copy) of the SciPy repository, cloned the repository on your own machine, and built SciPy from this source code. If you haven't, check the :ref:building-from-source pages appropriate to your system. Before getting started here, there are three other things you need to do just once before you start modifying SciPy.

#. In a terminal, introduce yourself to Git::

  git config --global user.email [email protected]
  git config --global user.name "Your Name"

This information credits you for your work, but note that it will become publicly available if you "push" your work to GitHub. See Setting your commit email address in Git_ for more information.

#. Navigate to the root directory of your local SciPy repository and enter::

  git remote add upstream https://github.com/scipy/scipy.git

This associates the name upstream with the official SciPy repository located at https://github.com/scipy/scipy.git <https://github.com/scipy/scipy.git>. Note that when you cloned your fork of the SciPy repository, Git already associated the name origin with your fork. The reason you need both of these "remotes" is that you will typically start with the latest version of SciPy from the official repository upstream, make changes, "push" your changes to your fork of the repository origin, and then submit a "pull request" asking SciPy to "pull" your changes from your fork into the official repository.

#. Initialize git submodules::

  git submodule update --init

This fetches and updates any submodules that SciPy needs (such as Boost).

Basic workflow ##############

In short:

  1. Start a new feature branch for each set of edits that you do. See :ref:below <making-a-new-feature-branch>.

  2. Hack away! See :ref:below <editing-workflow>.

  3. When finished:

    • Contributors: push your feature branch to your own Github repo, and :ref:create a pull request <asking-for-merging>.

    • Core developers If you want to push changes without further review, see the notes :ref:below <pushing-to-main>.

This way of working helps to keep work well organized and the history as clear as possible.

.. seealso::

There are many online tutorials to help you learn git. For discussions of specific git workflows, see these discussions on linux git workflow, and ipython git workflow_.

.. _making-a-new-feature-branch:

Making a new feature branch

First, navigate to the SciPy root directory in your terminal and fetch new commits from the upstream repository::

git fetch upstream

Then, create a new branch based on the main branch of the upstream repository::

git checkout -b my-new-feature upstream/main

Equivalently, you might want to keep the main branch of your own repository up to date and create a new branch based on that::

git checkout main git rebase upstream/main git checkout -b my-new-feature

In order, these commands

#. ensure that the main branch of your local repository is checked out,

#. apply all the latest changes from the upstream/main (main SciPy repository main branch) to your local main branch, and

#. create and check out a new branch (-b) based on your local main branch.

In any case, it's important that your feature branch include the latest changes from the upstream main to help avoid merge conflicts <https://help.github.com/en/articles/resolving-a-merge-conflict-using-the-command-line>_ when it's time to submit a pull request.

It's also a good idea to build this branch and run tests before continuing. Assuming you've followed one of the :ref:building-from-source pages to set up your development environment, you'll need to activate your development environment and then run tests (note that the spin test command will perform a build automatically if needed)::

conda activate scipy-dev spin test -v

.. _editing-workflow:

The editing workflow

Overview

::

hack hack

git status # Optional git diff # Optional git add modified_file git commit

push the branch to your own Github repo

git push origin my-new-feature

In more detail

#. Make some changes. When you feel that you've made a complete, working set of related changes, move on to the next steps.

#. Optional: Check which files have changed with git status (see git status_). You'll see a listing like this one::

 # On branch my-new-feature
 # Changed but not updated:
 #   (use "git add <file>..." to update what will be committed)
 #   (use "git checkout -- <file>..." to discard changes in working directory)
 #
 #	modified:   README
 #
 # Untracked files:
 #   (use "git add <file>..." to include in what will be committed)
 #
 #	INSTALL
 no changes added to commit (use "git add" and/or "git commit -a")

#. Optional: Compare the changes with the previous version using with git diff (git diff_). This brings up a simple text browser interface that highlights the difference between your files and the previous version.

#. Add any relevant modified or new files using git add modified_file (see git add_). This puts the files into a staging area, which is a queue of files that will be added to your next commit. Only add files that have related, complete changes. Leave files with unfinished changes for later commits.

#. To commit the staged files into the local copy of your repo, do git commit. At this point, a text editor will open up to allow you to write a commit message. Read the :ref:commit message section<writing-the-commit-message> to be sure that you are writing a properly formatted and sufficiently detailed commit message. After saving your message and closing the editor, your commit will be saved. For trivial commits, a short commit message can be passed in through the command line using the -m flag. For example, git commit -am "ENH: Some message".

In some cases, you will see this form of the commit command: git commit -a. The extra -a flag automatically commits all modified files and removes all deleted files. This can save you some typing of numerous git add commands; however, it can add unwanted changes to a commit if you're not careful. For more information, see why the -a flag?_ - and the helpful use-case description in the tangled working copy problem_.

#. Push the changes to your forked repo on github_::

  git push origin my-new-feature

For more information, see git push_.

.. note::

Assuming you have followed the instructions in these pages, git will create a default link to your github_ repo called origin. In git >= 1.7, you can ensure that the link to origin is permanently set by using the --set-upstream option::

  git push --set-upstream origin my-new-feature

From now on, git_ will know that my-new-feature is related to the my-new-feature branch in your own github_ repo. Subsequent push calls are then simplified to the following::

  git push

You have to use --set-upstream for each new branch that you create.

It may be the case that while you were working on your edits, new commits have been added to upstream that affect your work. In this case, follow the :ref:rebasing-on-main instructions to apply those changes to your branch.

.. _writing-the-commit-message:

Writing the commit message

Commit messages should be clear and follow a few basic rules.

Example::

MAINT/TST: fft: remove xp backend skips, test fftfreq device

The first line of the commit message starts with a capitalized acronym (or multiple, options listed below) indicating what type of commit this is. Then a blank line, then more text if needed. References to code names should be enclosed in backticks. If changes are limited to certain submodules or functions, they should be included after the acronym(s) - backticks are not needed here.

Example::

BUG:sparse.linalg.gmres: add early exit when x0 already solves problem

Lines shouldn't be longer than 72 characters. If the commit is related to an issue, indicate that with "See gh-3456", "Closes gh-3456", or similar, in the extended description. However, if you are pushing many commits to a PR, you should avoid including this in every commit message as it will clutter the linked issue.

Describing the motivation for a change, the nature of a bug for bug fixes or some details on what an enhancement does are also good to include in a commit message. Messages should be understandable without looking at the code changes. A commit message like MAINT: fixed another one is an example of what not to do; the reader has to go look for context elsewhere.

Standard acronyms to start the commit message with are::

API: an (incompatible) API change BENCH: changes to the benchmark suite BLD: change related to building SciPy BUG: bug fix DEP: deprecate something, or remove a deprecated object DEV: development tool or utility DOC: documentation ENH: enhancement MAINT: maintenance commit (refactoring, typos, etc.) REV: revert an earlier commit STY: style fix (whitespace, PEP8) TST: addition or modification of tests REL: related to releasing SciPy

.. note:: You can add some markers to skip part of the continuous integration. See :ref:continuous-integration.

.. _asking-for-merging:

Asking for your changes to be merged with the main repo

When you feel your work is finished, you can create a pull request (PR). Github has a nice help page that outlines the process for filing pull requests_.

If your changes involve modifications to the API or addition/modification of a function, you should initiate a code review. This involves sending an email to the SciPy forum_ with a link to your PR along with a description of and a motivation for your changes.

.. _pr-checklist:

Checklist before submitting a PR

  • Did you check that the code can be distributed under a BSD license? See :ref:license-considerations.
  • Have you checked SciPy's AI policy? See :ref:ai_policy.
  • Are there unit tests with good code coverage? See NumPy/SciPy Testing Guidelines_.
  • Do all unit tests pass locally? See :ref:the-spin-interface.
  • Do all public function have docstrings including examples? See the numpydoc docstring guide_.
  • Does the documentation render correctly? See :ref:rendering-documentation.
  • Is the code style correct? See :ref:pep8-scipy.
  • Are there benchmarks? See :ref:benchmarking-with-asv.
  • Is the commit message formatted correctly? See :ref:writing-the-commit-message.
  • Is the docstring of the new functionality tagged with .. versionadded:: X.Y.Z (where X.Y.Z is the version number of the next release? See the updating, workers, and constraints documentation of |differential_evolution|_, for example.
  • In case of larger additions, is there a tutorial or more extensive module-level description? Tutorial files are in doc/source/tutorial.
  • If new files are added, are they integrated correctly via meson.build? See :ref:compiled-code for more information.

.. include:: ../gitwash/git_links.inc

.. _Scipy Development Workflow: https://youtu.be/HgU01gJbzMY

.. _Setting your commit email address in Git: https://help.github.com/en/articles/setting-your-commit-email-address-in-git

.. _"remotes": https://help.github.com/en/categories/managing-remotes

.. _NumPy/SciPy Testing Guidelines: https://docs.scipy.org/doc/numpy/reference/testing.html

.. _numpydoc docstring guide: https://numpydoc.readthedocs.io/en/latest/format.html

.. _the wiki: https://github.com/scipy/scipy/wiki

.. |differential_evolution| replace:: differential_evolution .. _differential_evolution: https://github.com/scipy/scipy/blob/main/scipy/optimize/_differentialevolution.py