.. _developers-tips:

===========================
Developers' Tips and Tricks
===========================

Productivity and sanity-preserving tips
=======================================

In this section we gather some useful advice and tools that may increase your
quality-of-life when reviewing pull requests, running unit tests, and so forth.
Some of these tricks consist of userscripts that require a browser extension
such as `TamperMonkey`_ or `GreaseMonkey`_; to set up userscripts you must have
one of these extensions installed, enabled and running.  We provide userscripts
as GitHub gists; to install them, click on the "Raw" button on the gist page.

.. _TamperMonkey: https://tampermonkey.net/
.. _GreaseMonkey: https://www.greasespot.net/


.. _viewing_rendered_html_documentation:

Viewing the rendered HTML documentation for a pull request
----------------------------------------------------------

We use CircleCI to build the HTML documentation for every pull request. To
access that documentation, instructions are provided in the :ref:`documentation
section of the contributor guide <contribute_documentation>`. To save you a few
clicks, we provide a `userscript
<https://raw.githubusercontent.com/lesteve/userscripts/master/add-button-for-pr-circleci-doc.user.js>`__
that adds a button to every PR. After installing the userscript, navigate to
any GitHub PR; a new button labeled "See CircleCI doc for this PR" should
appear in the top-right area.

Folding and unfolding outdated diffs on pull requests
-----------------------------------------------------

GitHub hides discussions on PRs when the corresponding lines of code have been
changed in the mean while. This `userscript
<https://raw.githubusercontent.com/lesteve/userscripts/master/github-expand-all.user.js>`__
provides a shortcut (Control-Alt-P at the time of writing but look at the code
to be sure) to unfold all such hidden discussions at once, so you can catch up.

Checking out pull requests as remote-tracking branches
------------------------------------------------------

In your local fork, add to your ``.git/config``, under the ``[remote
"upstream"]`` heading, the line::

  fetch = +refs/pull/*/head:refs/remotes/upstream/pr/*

You may then use ``git checkout pr/PR_NUMBER`` to navigate to the code of the
pull-request with the given number. (`Read more in this gist.
<https://gist.github.com/piscisaureus/3342247>`_)

Display code coverage in pull requests
--------------------------------------

To overlay the code coverage reports generated by the CodeCov continuous
integration, consider `this browser extension
<https://github.com/codecov/browser-extension>`_. The coverage of each line
will be displayed as a color background behind the line number.


.. _pytest_tips:

Useful pytest aliases and flags
-------------------------------

The full test suite takes fairly long to run. For faster iterations,
it is possibly to select a subset of tests using pytest selectors.
In particular, one can run a `single test based on its node ID
<https://docs.pytest.org/en/latest/example/markers.html#selecting-tests-based-on-their-node-id>`_::

  pytest -v sklearn/linear_model/tests/test_logistic.py::test_sparsify

or use the `-k pytest parameter
<https://docs.pytest.org/en/latest/example/markers.html#using-k-expr-to-select-tests-based-on-their-name>`_
to select tests based on their name. For instance,::

  pytest sklearn/tests/test_common.py -v -k LogisticRegression

will run all :term:`common tests` for the ``LogisticRegression`` estimator.

When a unit test fails, the following tricks can make debugging easier:

  1. The command line argument ``pytest -l`` instructs pytest to print the local
     variables when a failure occurs.

  2. The argument ``pytest --pdb`` drops into the Python debugger on failure. To
     instead drop into the rich IPython debugger ``ipdb``, you may set up a
     shell alias to::

         pytest --pdbcls=IPython.terminal.debugger:TerminalPdb --capture no

Other `pytest` options that may become useful include:

  - ``-x`` which exits on the first failed test
  - ``--lf`` to rerun the tests that failed on the previous run
  - ``--ff`` to rerun all previous tests, running the ones that failed first
  - ``-s`` so that pytest does not capture the output of ``print()``
    statements
  - ``--tb=short`` or ``--tb=line`` to control the length of the logs

Since our continuous integration tests will error if
``FutureWarning`` isn't properly caught,
it is also recommended to run ``pytest`` along with the
``-Werror::FutureWarning`` flag.

.. _saved_replies:

Standard replies for reviewing
------------------------------

It may be helpful to store some of these in GitHub's `saved
replies <https://github.com/settings/replies/>`_ for reviewing:

.. highlight:: none

..
    Note that putting this content on a single line in a literal is the easiest way to make it copyable and wrapped on screen.

Issue: Usage questions
    ::

        You're asking a usage question. The issue tracker is mainly for bugs and new features. For usage questions, it is recommended to try [Stack Overflow](https://stackoverflow.com/questions/tagged/scikit-learn) or [the Mailing List](https://mail.python.org/mailman/listinfo/scikit-learn).

Issue: You're welcome to update the docs
    ::

        Please feel free to offer a pull request updating the documentation if you feel it could be improved.

Issue: Self-contained example for bug
    ::

        Please provide [self-contained example code](https://stackoverflow.com/help/mcve), including imports and data (if possible), so that other contributors can just run it and reproduce your issue. Ideally your example code should be minimal.

Issue: Software versions
    ::

        To help diagnose your issue, please paste the output of:
        ```py
        import sklearn; sklearn.show_versions()
        ```
        Thanks.

Issue: Code blocks
    ::

        Readability can be greatly improved if you [format](https://help.github.com/articles/creating-and-highlighting-code-blocks/) your code snippets and complete error messages appropriately. For example:

            ```python
            print(something)
            ```
        generates:
        ```python
        print(something)
        ```
        And:

            ```pytb
            Traceback (most recent call last):
              File "<stdin>", line 1, in <module>
            ImportError: No module named 'hello'
            ```
        generates:
        ```pytb
        Traceback (most recent call last):
          File "<stdin>", line 1, in <module>
        ImportError: No module named 'hello'
        ```
        You can edit your issue descriptions and comments at any time to improve readability. This helps maintainers a lot. Thanks!

Issue/Comment: Linking to code
    ::

        Friendly advice: for clarity's sake, you can link to code like [this](https://help.github.com/articles/creating-a-permanent-link-to-a-code-snippet/).

Issue/Comment: Linking to comments
    ::

        Please use links to comments, which make it a lot easier to see what you are referring to, rather than just linking to the issue. See [this](https://stackoverflow.com/questions/25163598/how-do-i-reference-a-specific-issue-comment-on-github) for more details.

PR-NEW: Better description and title
    ::

        Thanks for the pull request! Please make the title of the PR more descriptive. The title will become the commit message when this is merged. You should state what issue (or PR) it fixes/resolves in the description using the syntax described [here](http://scikit-learn.org/dev/developers/contributing.html#contributing-pull-requests).

PR-NEW: Fix #
    ::

        Please use "Fix #issueNumber" in your PR description (and you can do it more than once). This way the associated issue gets closed automatically when the PR is merged. For more details, look at [this](https://github.com/blog/1506-closing-issues-via-pull-requests).

PR-NEW or Issue: Maintenance cost
    ::

        Every feature we include has a [maintenance cost](http://scikit-learn.org/dev/faq.html#why-are-you-so-selective-on-what-algorithms-you-include-in-scikit-learn). Our maintainers are mostly volunteers. For a new feature to be included, we need evidence that it is often useful and, ideally, [well-established](http://scikit-learn.org/dev/faq.html#what-are-the-inclusion-criteria-for-new-algorithms) in the literature or in practice. That doesn't stop you implementing it for yourself and publishing it in a separate repository, or even [scikit-learn-contrib](https://scikit-learn-contrib.github.io).

PR-WIP: What's needed before merge?
    ::

        Please clarify (perhaps as a TODO list in the PR description) what work you believe still needs to be done before it can be reviewed for merge. When it is ready, please prefix the PR title with `[MRG]`.

PR-WIP: Regression test needed
    ::

        Please add a [non-regression test](https://en.wikipedia.org/wiki/Non-regression_testing) that would fail at master but pass in this PR.

PR-WIP: PEP8
    ::

        You have some [PEP8](https://www.python.org/dev/peps/pep-0008/) violations, whose details you can see in the Circle CI `lint` job. It might be worth configuring your code editor to check for such errors on the fly, so you can catch them before committing.

PR-MRG: Patience
    ::

        Before merging, we generally require two core developers to agree that your pull request is desirable and ready. [Please be patient](http://scikit-learn.org/dev/faq.html#why-is-my-pull-request-not-getting-any-attention), as we mostly rely on volunteered time from busy core developers. (You are also welcome to help us out with [reviewing other PRs](http://scikit-learn.org/dev/developers/contributing.html#code-review-guidelines).)

PR-MRG: Add to what's new
    ::

        Please add an entry to the change log at `doc/whats_new/v*.rst`. Like the other entries there, please reference this pull request with `:pr:` and credit yourself (and other contributors if applicable) with `:user:`.

PR: Don't change unrelated
    ::

        Please do not change unrelated lines. It makes your contribution harder to review and may introduce merge conflicts to other pull requests.

.. highlight:: default

Debugging memory errors in Cython with valgrind
===============================================

While python/numpy's built-in memory management is relatively robust, it can
lead to performance penalties for some routines. For this reason, much of
the high-performance code in scikit-learn in written in cython. This
performance gain comes with a tradeoff, however: it is very easy for memory
bugs to crop up in cython code, especially in situations where that code
relies heavily on pointer arithmetic.

Memory errors can manifest themselves a number of ways. The easiest ones to
debug are often segmentation faults and related glibc errors. Uninitialized
variables can lead to unexpected behavior that is difficult to track down.
A very useful tool when debugging these sorts of errors is
valgrind_.


Valgrind is a command-line tool that can trace memory errors in a variety of
code. Follow these steps:

  1. Install `valgrind`_ on your system.

  2. Download the python valgrind suppression file: `valgrind-python.supp`_.

  3. Follow the directions in the `README.valgrind`_ file to customize your
     python suppressions. If you don't, you will have spurious output coming
     related to the python interpreter instead of your own code.

  4. Run valgrind as follows::

       $> valgrind -v --suppressions=valgrind-python.supp python my_test_script.py

.. _valgrind: http://valgrind.org
.. _`README.valgrind`: https://svn.python.org/projects/python/trunk/Misc/README.valgrind
.. _`valgrind-python.supp`: https://svn.python.org/projects/python/trunk/Misc/valgrind-python.supp


The result will be a list of all the memory-related errors, which reference
lines in the C-code generated by cython from your .pyx file. If you examine
the referenced lines in the .c file, you will see comments which indicate the
corresponding location in your .pyx source file. Hopefully the output will
give you clues as to the source of your memory error.

For more information on valgrind and the array of options it has, see the
tutorials and documentation on the `valgrind web site <http://valgrind.org>`_.
