:orphan:

.. include:: links.inc
.. _astropy-fix-example:

***********************************
Contributing Code: a Worked Example
***********************************

This example is based on fixing `Issue 1761`_ from the list
of `astropy issues on GitHub <https://github.com/astropy/astropy/issues>`_.
It resulted in `pull request 1917`_.

The issue title was "len() does not work for coordinates" with description
"It would be nice to be able to use ``len`` on coordinate arrays to know how
many coordinates are present."

This particular example was chosen because it was tagged as easy in GitHub;
seemed like the best place to start out!

Before you begin
================

Make sure you have created a development environment for astropy as described in
:ref:`contributing_environment`. The rest of this tutorial assumes you have done that
and are working in your local copy of the astropy git repository.

Grab the latest updates to astropy
==================================

A few steps in this tutorial take only a single command. They are broken out
separately to outline the process in words as well as code.

Inform your local copy of ``astropy`` about the latest changes in the development
version with::

    git fetch upstream --tags

Set up an isolated workspace
============================

+ Make a new `git`_ branch for fixing this issue and switch to the branch::

    git switch -c fix-1761 upstream/main

+ Switch to your astropy development environment::

    conda activate astropy-dev

+ Install our branch of ``astropy`` along with all development dependencies in this
  environment with::

    python -m pip install --editable . --group dev_all

If installation fails, try to upgrade ``pip`` using ``python -m pip install pip
--upgrade`` command. It is also a good practice to occasionally keep your ``conda``
up-to-date by running ``conda update conda --name base`` when prompted to do so.

Test first, please
==================

It would be hard to overstate the importance of testing in Astropy. Tests are
what gives you confidence that new code does what it should and that it
does not break old code.

You should at least run the relevant tests before you make any changes to make
sure that your Python environment is set up properly.

The first challenge is figuring out where to look for relevant tests. `Issue
1761`_ is a problem in the `~astropy.coordinates` package, so the tests for
it are in ``astropy/coordinates/tests``. The rest of ``astropy`` has a similar
layout, as described at :ref:`testing-guidelines`.

Run the current tests in that directory with::

    pytest astropy/coordinates/tests

If the bug you are working on involves remote data access, you need to run
the tests with an extra flag, i.e., ``pytest astropy/coordinates/tests --remote-data``.

In the event where all the tests passed with the bug present, new tests are
needed to expose this bug.

A subpackage organizes its tests into multiple test modules; e.g.::

    $ ls astropy/coordinates/tests
    test_angles.py
    test_angular_separation.py
    test_api_ape5.py
    test_arrays.py
    ...

`Issue 1761`_ affects arrays of coordinates, so it seems sensible to put the
new test in ``test_arrays.py``. As with all of the steps, when in doubt,
please ask on the |astropy-dev mailing list|.

The goal at this point may be a little counter-intuitive: write a test that we
know will fail with the current code. This test allows ``astropy`` to check,
in an automated way, whether our fix actually works and to prevent
regression (i.e., make sure future changes to code do not break our fix).

Looking over the existing code in ``test_arrays.py``, each test is a function
with a name that starts with ``test_``. An appropriate place to add the test is
after the last test function in the file.

Give the test a reasonably clear name; e.g., ``test_array_len``. The
easiest way to figure out what you need to import and how to set up the test
is to look at other tests. The full test is in the traceback below and in
`pull request 1917`_.

Write the test, then see if it works as expected; remember, in this case we
expect it to *fail* without the patch from `pull request 1917`_.
Running ``pytest astropy/coordinates/tests/test_arrays.py`` would give the expected failure;
an excerpt from the output is::

    ================= FAILURES =============================
    ______________ test_array_len __________________________

        def test_array_len():
            from .. import ICRS

            input_length = 5
            ra = np.linspace(0, 360, input_length)
            dec = np.linspace(0, 90, input_length)

            c = ICRS(ra, dec, unit=(u.degree, u.degree))

    >       assert len(c) == input_length
    E       TypeError: object of type 'ICRS' has no len()

    astropy/coordinates/tests/test_arrays.py:291: TypeError

Success!

Add this test to your local `git`_ repo
=======================================

Keep `git`_ commits small and focused on one logical piece at a time. The test
we just wrote is one logical change, so we will commit it. You could, if you
prefer, wait and commit this test along with your fix.

For this tutorial, we will commit the test separately. If you are not sure what to
do, ask on |astropy-dev mailing list|.

Check what was changed
----------------------

We can see what has changed with ``git status``::

    $ git status
    On branch fix-1761
    Your branch is up-to-date with 'astropy/main'.

    Changes not staged for commit:
      (use "git add <file>..." to update what will be committed)
      (use "git checkout -- <file>..." to discard changes in working directory)

        modified:   astropy/coordinates/tests/test_arrays.py

    no changes added to commit (use "git add" and/or "git commit -a")

There are two bits of information here:

+ one file changed; i.e., ``astropy/coordinates/tests/test_arrays.py``
+ this file has not been added to git's staging area yet, so it is listed
  under ``Changes not staged for commit``.

Use ``git diff`` to see what changes have been made::

    $ git diff
    diff --git a/astropy/coordinates/tests/test_arrays.py b/astropy/coordinates/test
    index 2785b59..7eecfbb 100644
    --- a/astropy/coordinates/tests/test_arrays.py
    +++ b/astropy/coordinates/tests/test_arrays.py
    @@ -278,3 +278,14 @@ def test_array_indexing():
         assert c2.equinox == c1.equinox
         assert c3.equinox == c1.equinox
         assert c4.equinox == c1.equinox
    +
    +
    +def test_array_len():
    +    from .. import ICRS
    +
    +    input_length = 5
    +    ra = np.linspace(0, 360, input_length)
    +    dec = np.linspace(0, 90, input_length)
    +
    +    c = ICRS(ra, dec, unit=(u.degree, u.degree))
    +
    +    assert len(c) == input_length

A graphical interface to git makes keeping track of these sorts of changes even easier;
see this `list of GUI Clients <https://git-scm.com/downloads/guis/>`_ if you are
interested. You may also find it helpful to use a full featured Interactive Development
Environment (IDE) like `PyCharm <https://www.jetbrains.com/pycharm/>`_ or `Visual Studio
Code <https://code.visualstudio.com/>`_. Both of these IDEs have built-in git support.


Stage the change
----------------

`git`_ requires you to add changes in two steps:

+ stage the change with ``git add ...``; this adds the file to
  the list of items that will be added to the repo when you are ready to
  commit.
+ commit the change with ``git commit ...``; this actually adds the changes to
  your repo.

These can be combined into one step (not recommended); the advantage of doing it in two steps
is that it is easier to undo staging than committing. As we will see later,
``git status`` even tells you how to do it.

Staging can be very handy if you are making changes in a couple of different
places that you want to commit at the same time. Make your first changes,
stage it, then make your second change and stage that. Once everything is
staged, commit the changes as one commit.

In this case, first stage the change::

    git add astropy/coordinates/tests/test_arrays.py

You get no notice at the command line that anything has changed, but
``git status`` will let you know::

    $ git status
    On branch fix-1761
    Your branch is up-to-date with 'astropy/main'.

    Changes to be committed:
      (use "git reset HEAD <file>..." to unstage)

        modified:   astropy/coordinates/tests/test_arrays.py

Note that `git`_ helpfully includes the command necessary to unstage the
change if you want to.

Commit your change
------------------

Next, we will commit the test without the fix::

    $ git commit -m "Add test for array coordinate length (issue #1761)"
    [fix-1761 dd4ef8c] Add test for array coordinate length (issue #1761)
     1 file changed, 12 insertions(+)

Commit messages should be concise. Including the GitHub issue
number allows GitHub to automatically create links to the relevant issue.

Use ``git status`` to get a recap of where we are so far::

    $ git status
    On branch fix-1761
    Your branch is ahead of 'astropy/main' by 1 commit.
      (use "git push" to publish your local commits)

    nothing to commit, working directory clean

In other words, we have made a change to our local copy of ``astropy`` but we
have not pushed (transferred) that change to our GitHub account.

Fix the issue
=============

Write the code
--------------

Now that we have a test written, we will fix the issue. A full discussion of
the fix is beyond the scope of this tutorial, but the fix is to add a
``__len__`` method to ``astropy.coordinates.SphericalCoordinatesBase`` in
``coordsystems.py`` (the code has since been refactored, if you try to look
for it). All of the spherical coordinate systems inherit from
this base class and it is this base class that implements the
``__getitem__`` method that allows indexing of coordinate arrays.

See `pull request 1917`_ to view the changes to the code.

.. _test_changes:

Test your change
----------------

There are a few levels at which you want to test:

+ Does this code change make the test we wrote succeed now? Check
  by running ``pytest astropy/coordinates/tests/test_arrays.py``.
  In this case, yes!
+ Do the rest of the coordinate tests still pass? Check by running
  ``pytest astropy/coordinates/``. In this case, yes, we have not broken
  anything!
+ Do all of the astropy tests still succeed? Check by running ``pytest``
  from the top-level directory.
  This may take a while depending on the speed of your system.
  Success again!

.. note::
    Tests that are skipped or xfailed are fine. A fail or an error is not
    fine. If you get stuck, ask on |astropy-dev mailing list| for help!

Stage and commit your change
----------------------------

Add the file to your `git`_ repo in two steps: stage, then commit.

To make this a little different than the commit we did above, make sure you
are still in the top level directory and check the ``git status``::

    $ git status
    On branch fix-1761
    Your branch is ahead of 'astropy/main' by 1 commit.
      (use "git push" to publish your local commits)

    Changes not staged for commit:
      (use "git add <file>..." to update what will be committed)
      (use "git checkout -- <file>..." to discard changes in working directory)

        modified:   astropy/coordinates/coordsystems.py

    no changes added to commit (use "git add" and/or "git commit -a")

Note that git knows what has changed no matter what directory you are in (as
long as you are in one of the directories in the repo, that is).

Stage the change with::

    git add astropy/coordinates/coordsystems.py

For this commit, it is helpful to use a multi-line commit message that will
automatically close the issue on GitHub when this change is accepted. The
snippet below accomplishes that in bash (and similar shells)::

    $ git commit -m"
    > Add len() to coordinates
    >
    > Closes #1761"
    [fix-1761 f196771] Add len() to coordinates
     1 file changed, 4 insertions(+)

Another option for multi-line commit message is to use a
`Git GUI Client <https://git-scm.com/downloads/guis/>`_ or to run
``git commit`` without a message to get prompted by an editor.

The message after committing should look like this when you inspect with
``git log``::

    Add len() to coordinates

    Closes #1761

If the commit message does not look right, run ``git commit --amend``.
If you still run into problems, please ask about fixing it at
|astropy-dev mailing list|.

At this point, none of the Astropy maintainers know anything about
your changes.

We will take care of that in a moment with a "pull request", but first,
see :ref:`astropy-fix-add-tests`.

.. _astropy-fix-add-tests:

Stop and think: Any more tests or other changes?
================================================

It never hurts to pause at this point and review whether your proposed
changes are complete. In this case, there are some more tests that could
be included, such as:

+ What happens when ``len()`` is called on a coordinate that is *not* an
  array?
+ Does ``len()`` work when the coordinate is an array with one entry?

Both of these are mentioned in `pull request 1917`_, so it does not hurt to check
them. In this case, they also provide an opportunity to illustrate a feature
of the |pytest| framework.

The second case is easier, so it will be handled first following the
development cycle we used above:

+ Make the change in ``astropy/coordinates/tests/test_arrays.py``
+ Test the change

The test passed; but rather than committing this one change, we will also
implement the check for the scalar case.

One could imagine two different desirable outcomes here:

+ ``len(scalar_coordinate)`` behaves just like ``len(scalar_angle)``, raising
  a `TypeError` for a scalar coordinate.
+ ``len(scalar_coordinate)`` returns 1 since there is one coordinate.

If you encounter a case like this and are not sure what to do, ask. The best
place to ask is on GitHub on the page for the issue you are fixing.

Alternatively, make a choice and be clear in your pull request on GitHub what
you chose and why; instructions for that are below.

Testing for an expected error
-----------------------------

In this case, we opted for raising a `TypeError`, because
the user needs to know that the coordinate they created is not going to
behave like an array of one coordinate if they try to index it later on.

The |pytest| framework makes testing for an exception relatively
easy; you put the code you expect to fail in a ``with`` block::

    c = ICRS(0, 0, unit=(u.degree, u.degree))

    with pytest.raises(TypeError):
        len(c)

A test like this can be added ``test_array_len`` in ``test_arrays.py``.
In your own work, you may also choose to put that into a new test function,
if you wish.

Aside: Python lesson--let others do your work
---------------------------------------------

The actual fix to this issue was very, very short. In ``coordsystems.py``, two
lines were added::

    def __len__(self):
        return len(self.lonangle)

``lonangle`` contains the ``Angle`` objects that represent longitude (sometimes this
is an RA, sometimes a longitude). By simply calling ``len()`` on one of the
angles in the array you get, for free, whatever behavior has been defined in
the ``Angle`` class for handling the case of a scalar.

Adding an explicit check for the case of a scalar here would have the very
big downside of having two things that need to be kept in sync: handling of
scalars in ``Angle`` and in coordinates.

Commit any additional changes
=============================

Continue to follow the development cycle above for other files that you need
to modify, including changelog (see :ref:`git_edit_changelog`) and
documentation, as needed:

+ Check that **all** ``astropy`` tests still pass; see :ref:`test_changes`
+ ``git status`` to see what needs to be staged and committed
+ ``git add ...`` to stage the changes
+ ``git commit ...`` to commit the changes
+ ``git log`` to inspect the change history

The `git`_ commands, without their output, are::

    git status
    git add astropy/coordinates/tests/test_arrays.py
    git commit -m "Add tests of len() for scalar coordinate and length 1 coordinate"
    git log

Push your changes to your GitHub fork of astropy
================================================

Use this command to push your local changes out to your copy of ``astropy``
on GitHub before asking for the changes to be reviewed::

    git push origin fix-1761

Propose your changes as a pull request
======================================

This stage requires going to your GitHub account and navigate to *your* copy
of ``astropy``; the url will be something like
``https://github.com/your-user-name/astropy``.

Once there, select the branch that contains your fix from the branches
dropdown:

    .. image:: worked_example_switch_branch.png

After selecting the correct branch, click on the "Pull Request" button,
as shown below:

    .. image:: pull_button.png

Name your pull request something sensible. Include the issue number with a
leading ``#`` in the description of the pull request so that a link is
created to the original issue, as stated in ``astropy``'s pull request template.

Please see `pull request 1917`_ for the pull request showcased in this tutorial.

.. _git_edit_changelog:

Edit the changelog
==================

Keeping the list of changes up to date is nearly impossible unless each
contributor makes the appropriate updates as they propose changes.

Create a file ``docs/changes/coordinates/<PULL REQUEST>.feature.rst``, where
``<PULL REQUEST>`` is the pull request number (1917 for this example).  The
content of this file should summarize what you did. For writing changelog
entries, you do not need to know much about the markup language being used
(though you can read as much as you want about it at the `Sphinx primer`_); look
at other entries and emulate.

For this issue, the file would contain::

    Implemented ``len()`` for coordinate objects.

Putting ``len()`` in double-backtick makes that text render in a monospaced
font.

Commit your changes and push
----------------------------

You can use ``git status`` as above or jump right to staging and committing::

    git add docs/changes/coordinates/<PULL REQUEST>.feature.rst
    git commit -m "Add changelog entry"
    git push

Revise and push as necessary
============================

You may be asked to make changes in the discussion of the pull request. Make
those changes in your local copy, commit them to your local repo, and push them
to GitHub. GitHub will automatically update your pull request.

.. _Issue 1761: https://github.com/astropy/astropy/issues/1761
.. _pull request 1917: https://github.com/astropy/astropy/pull/1917
.. _Sphinx primer: https://www.sphinx-doc.org/
.. _test commit: https://github.com/mwcraig/astropy/commit/cf7d5ac15d7c63ae28dac638c6484339bac5f8de
