numpy/doc/source/dev/development_workflow.rst

.. _development-workflow:

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

You already have your own forked copy of the NumPy repository, have configured
Git, and have linked the upstream repository as explained in
:ref:`development-process-summary`. What is described below is a recommended
workflow with Git.

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.

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

Making a new feature branch
===========================

First, 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


.. _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``. 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``. 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``.
   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.

#. Push the changes to your fork on GitHub::

      git push origin my-new-feature

.. note::

   Assuming you have followed the instructions in these pages, git will create
   a default link to your GitHub repo called ``origin``.  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` section of this document 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::

   ENH: add functionality X to numpy.<submodule>.

   The first line of the commit message starts with a capitalized acronym
   (options listed below) indicating what type of commit this is.  Then a blank
   line, then more text if needed.  Lines shouldn't be longer than 72
   characters.  If the commit is related to a ticket, indicate that with
   "See #3456", "See ticket 3456", "Closes #3456" or similar.

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 numpy
   BUG: bug fix
   CI: continuous integration
   DEP: deprecate something, or remove a deprecated object
   DEV: development tool or utility
   DOC: documentation
   ENH: enhancement
   MAINT: maintenance commit (refactoring, typos, etc.)
   MNT: alias for MAINT
   NEP: NumPy enhancement proposals
   REL: related to releasing numpy
   REV: revert an earlier commit
   STY: style fix (whitespace, PEP8)
   TST: addition or modification of tests
   TYP: static typing
   WIP: work in progress, do not merge

Commands to skip continuous integration
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

By default a lot of continuous integration (CI) jobs are run for every PR,
from running the test suite on different operating systems and hardware
platforms to building the docs. In some cases you already know that CI isn't
needed (or not all of it), for example if you work on CI config files, text in
the README, or other files that aren't involved in regular build, test or docs
sequences. In such cases you may explicitly skip CI by including one or more of
these fragments in each commit message of a PR:

* ``[skip ci]``: skip all CI

  Only recommended if you are still not ready for the checks to run on your PR
  (for example, if this is only a draft.)

* ``[skip actions]``: skip GitHub Actions jobs

  `GitHub Actions <https://docs.github.com/actions>`__ is where most of the CI
  checks are run, including the linter, benchmarking, running basic tests for
  most architectures and OSs, and several compiler and CPU optimization
  settings.
  `See the configuration files for these checks. <https://github.com/numpy/numpy/tree/main/.github/workflows>`__

* ``[skip circle]``: skip CircleCI jobs

  `CircleCI <https://circleci.com/>`__ is where we build the documentation and
  store the generated artifact for preview in each PR. This check will also run
  all the docstrings examples and verify their results. If you don't make
  documentation changes, but you make changes to a function's API, for example,
  you may need to run these tests to verify that the doctests are still valid.
  `See the configuration file for these checks. <https://github.com/numpy/numpy/blob/main/.circleci/config.yml>`__

Test building wheels
~~~~~~~~~~~~~~~~~~~~

NumPy currently uses `cibuildwheel <https://cibuildwheel.readthedocs.io/en/stable/>`_
in order to build wheels through continuous integration services. To save resources, the
cibuildwheel wheel builders are not run by default on every single PR or commit to main.

If you would like to test that your pull request do not break the wheel builders,
you can do so by appending ``[wheel build]`` to the first line of the commit
message of the newest commit in your PR. Please only do so for build-related
PRs, because running all wheel builds is slow and expensive.

The wheels built via github actions (including 64-bit Linux, x86-64 macOS, and
32/64-bit Windows) will be uploaded as artifacts in zip files. You can access
them from the Summary page of the "Wheel builder" action. The aarch64 Linux and
arm64 macOS wheels built via Cirrus CI are not available as artifacts.
Additionally, the wheels will be uploaded to
https://anaconda.org/scientific-python-nightly-wheels/ on the following conditions:

- by a weekly cron job or
- if the GitHub Actions or Cirrus build has been manually triggered, which
  requires appropriate permissions

The wheels will be uploaded to https://anaconda.org/multibuild-wheels-staging/
if the build was triggered by a tag to the repo that begins with ``v``


.. _workflow_mailing_list:

Get the mailing list's opinion
==============================

If you plan a new feature or API change, it's wisest to first email the
NumPy `mailing list <https://mail.python.org/mailman/listinfo/numpy-discussion>`_
asking for comment. If you haven't heard back in a week, it's
OK to ping the list again.


.. _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).
If your changes involve modifications to the API or addition/modification of a
function, add a release note to the ``doc/release/upcoming_changes/``
directory, following the instructions and format in the
``doc/release/upcoming_changes/README.rst`` file.

Use the same prefix convention for your pull request title as for commit
messages (e.g., ``BUG:``, ``ENH:``, ``DOC:``). This enables automated labeling
of your PR.


.. _pull-request-limit:

Open pull request limit
=======================

To keep the review queue manageable, GitHub is configured to allow only two
open non-draft pull requests per non-maintainer at a time. Draft pull requests
do not count towards the limit. The maintainer team can, at its discretion,
add contributors to the list of accounts allowed to open more pull requests
at once. We liberally add contributors who attend the community and triage
meetings, which alternate weekly on Wednesdays -- see the `community calendar
<https://scientific-python.org/calendars/>`__ for times.


.. _workflow_PR_timeline:

Getting your PR reviewed
========================

We review pull requests as soon as we can, typically within a week. If you get
no review comments within two weeks, feel free to ask for feedback by
adding a comment on your PR (this will notify maintainers).

If your PR is large or complicated, asking for input on the numpy-discussion
mailing list may also be useful.

Pull requests that go stale or do not meet our quality standards may be
labeled by a triager and closed automatically by a bot.


.. _rebasing-on-main:

Rebasing on main
================

This updates your feature branch with changes from the upstream NumPy
GitHub repo. If you do not absolutely need to do this, try to avoid doing
it, except perhaps when you are finished. The first step will be to update
the remote repository with new commits from upstream::

   git fetch upstream

Next, you need to update the feature branch::

   # go to the feature branch
   git checkout my-new-feature
   # make a backup in case you mess up
   git branch tmp my-new-feature
   # rebase on upstream main branch
   git rebase upstream/main

If you have made changes to files that have changed also upstream,
this may generate merge conflicts that you need to resolve. See
:ref:`below<recovering-from-mess-up>` for help in this case.

Finally, remove the backup branch upon a successful rebase::

   git branch -D tmp


.. note::

   Rebasing on main is preferred over merging upstream back to your
   branch. Using ``git merge`` and ``git pull`` is discouraged when
   working on feature branches.

.. _recovering-from-mess-up:

Recovering from mess-ups
========================

Sometimes, you mess up merges or rebases. Luckily, in Git it is
relatively straightforward to recover from such mistakes.

If you mess up during a rebase::

   git rebase --abort

If you notice you messed up after the rebase::

   # reset branch back to the saved point
   git reset --hard tmp

If you forgot to make a backup branch::

   # look at the reflog of the branch
   git reflog show my-feature-branch

   8630830 my-feature-branch@{0}: commit: BUG: io: close file handles immediately
   278dd2a my-feature-branch@{1}: rebase finished: refs/heads/my-feature-branch onto 11ee694744f2552d
   26aa21a my-feature-branch@{2}: commit: BUG: lib: make seek_gzip_factory not leak gzip obj
   ...

   # reset the branch to where it was before the botched rebase
   git reset --hard my-feature-branch@{2}

If you didn't actually mess up but there are merge conflicts, you need to
resolve those.


Additional things you might want to do
######################################

.. _rewriting-commit-history:

Rewriting commit history
========================

.. note::

   Do this only for your own feature branches.

There's an embarrassing typo in a commit you made? Or perhaps you
made several false starts you would like the posterity not to see.

This can be done via *interactive rebasing*.

Suppose that the commit history looks like this::

    git log --oneline
    eadc391 Fix some remaining bugs
    a815645 Modify it so that it works
    2dec1ac Fix a few bugs + disable
    13d7934 First implementation
    6ad92e5 * masked is now an instance of a new object, MaskedConstant
    29001ed Add pre-nep for a couple of structured_array_extensions.
    ...

and ``6ad92e5`` is the last commit in the ``main`` branch. Suppose we
want to make the following changes:

* Rewrite the commit message for ``13d7934`` to something more sensible.
* Combine the commits ``2dec1ac``, ``a815645``, ``eadc391`` into a single one.

We do as follows::

    # make a backup of the current state
    git branch tmp HEAD
    # interactive rebase
    git rebase -i 6ad92e5

This will open an editor with the following text in it::

    pick 13d7934 First implementation
    pick 2dec1ac Fix a few bugs + disable
    pick a815645 Modify it so that it works
    pick eadc391 Fix some remaining bugs

    # Rebase 6ad92e5..eadc391 onto 6ad92e5
    #
    # Commands:
    #  p, pick = use commit
    #  r, reword = use commit, but edit the commit message
    #  e, edit = use commit, but stop for amending
    #  s, squash = use commit, but meld into previous commit
    #  f, fixup = like "squash", but discard this commit's log message
    #
    # If you remove a line here THAT COMMIT WILL BE LOST.
    # However, if you remove everything, the rebase will be aborted.
    #

To achieve what we want, we will make the following changes to it::

    r 13d7934 First implementation
    pick 2dec1ac Fix a few bugs + disable
    f a815645 Modify it so that it works
    f eadc391 Fix some remaining bugs

This means that (i) we want to edit the commit message for
``13d7934``, and (ii) collapse the last three commits into one. Now we
save and quit the editor.

Git will then immediately bring up an editor for editing the commit
message. After revising it, we get the output::

    [detached HEAD 721fc64] FOO: First implementation
     2 files changed, 199 insertions(+), 66 deletions(-)
    [detached HEAD 0f22701] Fix a few bugs + disable
     1 files changed, 79 insertions(+), 61 deletions(-)
    Successfully rebased and updated refs/heads/my-feature-branch.

and the history looks now like this::

     0f22701 Fix a few bugs + disable
     721fc64 ENH: Sophisticated feature
     6ad92e5 * masked is now an instance of a new object, MaskedConstant

If it went wrong, recovery is again possible as explained :ref:`above
<recovering-from-mess-up>`.

Deleting a branch on GitHub
===========================

::

   git checkout main
   # delete branch locally
   git branch -D my-unwanted-branch
   # delete branch on github
   git push origin --delete my-unwanted-branch

See also:
https://stackoverflow.com/questions/2003505/how-do-i-delete-a-git-branch-locally-and-remotely


Several people sharing a single repository
==========================================

If you want to work on some stuff with other people, where you are all
committing into the same repository, or even the same branch, then just
share it via GitHub.

First fork NumPy into your account, as from :ref:`development-process-summary`.

Then, go to your forked repository github page, say
``https://github.com/your-user-name/numpy``

Click on the 'Admin' button, and add anyone else to the repo as a
collaborator:

.. image:: pull_button.png

Now all those people can do::

    git clone git@github.com:your-user-name/numpy.git

Remember that links starting with ``git@`` use the ssh protocol and are
read-write; links starting with ``git://`` are read-only.

Your collaborators can then commit directly into that repo with the
usual::

     git commit -am 'ENH - much better code'
     git push origin my-feature-branch # pushes directly into your repo


Checkout changes from an existing pull request
==============================================

If you want to test the changes in a pull request or continue the work in a
new pull request, the commits are to be cloned into a local branch in your
forked repository

First ensure your upstream points to the main repo, as from
:ref:`development-process-summary`

Then, fetch the changes and create a local branch. Assuming ``$ID`` is the pull request number
and ``$BRANCHNAME`` is the name of the *new local* branch you wish to create::

    git fetch upstream pull/$ID/head:$BRANCHNAME

Checkout the newly created branch::

    git checkout $BRANCHNAME

You now have the changes in the pull request.


Exploring your repository
=========================

To see a graphical representation of the repository branches and
commits::

   gitk --all

To see a linear list of commits for this branch::

   git log


Backporting
===========

Backporting is the process of copying new feature/fixes committed in NumPy's
``main`` branch back to stable release branches. To do this you make a branch
off the branch you are backporting to, cherry pick the commits you want from
``numpy/main``, and then submit a pull request for the branch containing the
backport.

1. First, you need to make the branch you will work on. This needs to be
   based on the older version of NumPy (not main)::

    # Make a new branch based on numpy/maintenance/1.8.x,
    # backport-3324 is our new name for the branch.
    git checkout -b backport-3324 upstream/maintenance/1.8.x

2. Now you need to apply the changes from main to this branch using
   ``git cherry-pick``::

    # Update remote
    git fetch upstream
    # Check the commit log for commits to cherry pick
    git log upstream/main
    # This pull request included commits aa7a047 to c098283 (inclusive)
    # so you use the .. syntax (for a range of commits), the ^ makes the
    # range inclusive.
    git cherry-pick aa7a047^..c098283
    ...
    # Fix any conflicts, then if needed:
    git cherry-pick --continue

3. You might run into some conflicts cherry picking here. These are
   resolved the same way as merge/rebase conflicts. Except here you can
   use ``git blame`` to see the difference between main and the
   backported branch to make sure nothing gets screwed up.

4. Push the new branch to your GitHub repository::

    git push -u origin backport-3324

5. Finally make a pull request using GitHub. Make sure it is against the
   maintenance branch and not main, GitHub will usually suggest you
   make the pull request against main.

.. _pushing-to-main:

Pushing changes to the main repo
================================

*Requires commit rights to the main NumPy repo.*

When you have a set of "ready" changes in a feature branch ready for
NumPy's ``main`` or ``maintenance`` branches, you can push
them to ``upstream`` as follows:

1. First, merge or rebase on the target branch.

   a) Only a few, unrelated commits then prefer rebasing::

        git fetch upstream
        git rebase upstream/main

      See :ref:`rebasing-on-main`.

   b) If all of the commits are related, create a merge commit::

        git fetch upstream
        git merge --no-ff upstream/main

2. Check that what you are going to push looks sensible::

        git log -p upstream/main..
        git log --oneline --graph

3. Push to upstream::

        git push upstream my-feature-branch:main

.. note::

    It's usually a good idea to use the ``-n`` flag to ``git push`` to check
    first that you're about to push the changes you want to the place you
    want.