1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882
|
.. _contributing:
**********************
Contributing to pandas
**********************
.. contents:: Table of contents:
:local:
Where to start?
===============
All contributions, bug reports, bug fixes, documentation improvements,
enhancements and ideas are welcome.
If you are simply looking to start working with the *pandas* codebase, navigate to the
`GitHub "issues" tab <https://github.com/pandas-dev/pandas/issues>`_ and start looking through
interesting issues. There are a number of issues listed under `Docs
<https://github.com/pandas-dev/pandas/issues?labels=Docs&sort=updated&state=open>`_
and `Difficulty Novice
<https://github.com/pandas-dev/pandas/issues?q=is%3Aopen+is%3Aissue+label%3A%22Difficulty+Novice%22>`_
where you could start out.
Or maybe through using *pandas* you have an idea of your own or are looking for something
in the documentation and thinking 'this can be improved'...you can do something
about it!
Feel free to ask questions on the `mailing list
<https://groups.google.com/forum/?fromgroups#!forum/pydata>`_ or on `Gitter
<https://gitter.im/pandas-dev/pandas>`_.
Bug reports and enhancement requests
====================================
Bug reports are an important part of making *pandas* more stable. Having a complete bug report
will allow others to reproduce the bug and provide insight into fixing. Because many versions of
*pandas* are supported, knowing version information will also identify improvements made since
previous versions. Trying the bug-producing code out on the *master* branch is often a worthwhile exercise
to confirm 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.
Bug reports must:
#. Include a short, self-contained Python snippet reproducing the problem.
You can format the code nicely by using `GitHub Flavored Markdown
<http://github.github.com/github-flavored-markdown/>`_::
```python
>>> from pandas import DataFrame
>>> df = DataFrame(...)
...
```
#. Include the full version string of *pandas* and its dependencies. In versions
of *pandas* after 0.12 you can use a built in function::
>>> from pandas.util.print_versions import show_versions
>>> show_versions()
and in *pandas* 0.13.1 onwards::
>>> pd.show_versions()
#. Explain why the current behavior is wrong/not desired and what you expect instead.
The issue will then show up to the *pandas* community and be open to comments/ideas from others.
Working with the code
=====================
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 *pandas* code base.
Version control, Git, and GitHub
--------------------------------
To the new user, working with Git is one of the more daunting aspects of contributing to *pandas*.
It can very quickly become overwhelming, but sticking to the guidelines below will help keep the process
straightforward and mostly trouble free. As always, if you are having difficulties please
feel free to ask for help.
The code is hosted on `GitHub <https://www.github.com/pandas-dev/pandas>`_. To
contribute you will need to sign up for a `free GitHub account
<https://github.com/signup/free>`_. We use `Git <http://git-scm.com/>`_ for
version control to allow many people to work together on the project.
Some great resources for learning Git:
* the `GitHub help pages <http://help.github.com/>`_.
* the `NumPy's documentation <http://docs.scipy.org/doc/numpy/dev/index.html>`_.
* Matthew Brett's `Pydagogue <http://matthew-brett.github.com/pydagogue/>`_.
Getting started with Git
------------------------
`GitHub has instructions <http://help.github.com/set-up-git-redirect>`__ for 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.
.. _contributing.forking:
Forking
-------
You will need your own fork to work on the code. Go to the `pandas project
page <https://github.com/pandas-dev/pandas>`_ and hit the ``Fork`` button. You will
want to clone your fork to your machine::
git clone git@github.com:your-user-name/pandas.git pandas-yourname
cd pandas-yourname
git remote add upstream git://github.com/pandas-dev/pandas.git
This creates the directory `pandas-yourname` and connects your repository to
the upstream (main project) *pandas* repository.
The testing suite will run automatically on Travis-CI once your pull request is
submitted. However, if you wish to run the test suite on a branch prior to
submitting the pull request, then Travis-CI needs to be hooked up to your
GitHub repository. Instructions for doing so are `here
<http://about.travis-ci.org/docs/user/getting-started/>`__.
Creating a branch
-----------------
You want your master branch to reflect only production-ready code, so create a
feature branch for making your changes. For example::
git branch shiny-new-feature
git checkout shiny-new-feature
The above can be simplified to::
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 *pandas*. You can have many shiny-new-features
and switch in between them using the git checkout command.
To update this branch, you need to retrieve the changes from the master branch::
git fetch upstream
git rebase upstream/master
This will replay your commits on top of the lastest pandas git master. If this
leads to merge conflicts, you must resolve these before submitting your pull
request. If you have uncommitted changes, you will need to ``stash`` them prior
to updating. This will effectively store your changes and they can be reapplied
after updating.
.. _contributing.dev_env:
Creating a development environment
----------------------------------
An easy way to create a *pandas* development environment is as follows.
- Install either :ref:`Anaconda <install.anaconda>` or :ref:`miniconda <install.miniconda>`
- Make sure that you have :ref:`cloned the repository <contributing.forking>`
- ``cd`` to the *pandas* source directory
Tell conda to create a new environment, named ``pandas_dev``, or any other name you would like
for this environment, by running::
conda create -n pandas_dev --file ci/requirements_dev.txt
For a python 3 environment::
conda create -n pandas_dev python=3 --file ci/requirements_dev.txt
.. warning::
If you are on Windows, see :ref:`here for a fully compliant Windows environment <contributing.windows>`.
This will create the new environment, and not touch any of your existing environments,
nor any existing python installation. It will install all of the basic dependencies of
*pandas*, as well as the development and testing tools. If you would like to install
other dependencies, you can install them as follows::
conda install -n pandas_dev -c pandas pytables scipy
To install *all* pandas dependencies you can do the following::
conda install -n pandas_dev -c pandas --file ci/requirements_all.txt
To work in this environment, Windows users should ``activate`` it as follows::
activate pandas_dev
Mac OSX / Linux users should use::
source activate pandas_dev
You will then see a confirmation message to indicate you are in the new development environment.
To view your environments::
conda info -e
To return to your home root environment in Windows::
deactivate
To return to your home root environment in OSX / Linux::
source deactivate
See the full conda docs `here <http://conda.pydata.org/docs>`__.
At this point you can easily do an *in-place* install, as detailed in the next section.
.. _contributing.windows:
Creating a Windows development environment
------------------------------------------
To build on Windows, you need to have compilers installed to build the extensions. You will need to install the appropriate Visual Studio compilers, VS 2008 for Python 2.7, VS 2010 for 3.4, and VS 2015 for Python 3.5.
For Python 2.7, you can install the ``mingw`` compiler which will work equivalently to VS 2008::
conda install -n pandas_dev libpython
or use the `Microsoft Visual Studio VC++ compiler for Python <https://www.microsoft.com/en-us/download/details.aspx?id=44266>`__. Note that you have to check the ``x64`` box to install the ``x64`` extension building capability as this is not installed by default.
For Python 3.4, you can download and install the `Windows 7.1 SDK <https://www.microsoft.com/en-us/download/details.aspx?id=8279>`__. Read the references below as there may be various gotchas during the installation.
For Python 3.5, you can download and install the `Visual Studio 2015 Community Edition <https://www.visualstudio.com/en-us/downloads/visual-studio-2015-downloads-vs.aspx>`__.
Here are some references and blogs:
- https://blogs.msdn.microsoft.com/pythonengineering/2016/04/11/unable-to-find-vcvarsall-bat/
- https://github.com/conda/conda-recipes/wiki/Building-from-Source-on-Windows-32-bit-and-64-bit
- https://cowboyprogrammer.org/building-python-wheels-for-windows/
- https://blog.ionelmc.ro/2014/12/21/compiling-python-extensions-on-windows/
- https://support.enthought.com/hc/en-us/articles/204469260-Building-Python-extensions-with-Canopy
.. _contributing.getting_source:
Making changes
--------------
Before making your code changes, it is often necessary to build the code that was
just checked out. There are two primary methods of doing this.
#. The best way to develop *pandas* is to build the C extensions in-place by
running::
python setup.py build_ext --inplace
If you startup the Python interpreter in the *pandas* source directory you
will call the built C extensions
#. Another very common option is to do a ``develop`` install of *pandas*::
python setup.py develop
This makes a symbolic link that tells the Python interpreter to import *pandas*
from your development directory. Thus, you can always be using the development
version on your system without being inside the clone directory.
.. _contributing.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
*pandas* to do so! Something as simple as rewriting small passages for clarity
as you reference the docs is a simple but effective way to contribute. The
next person to read that passage will be in your debt!
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 simple way to ensure it will
help the next person.
.. contents:: Documentation:
:local:
About the *pandas* documentation
--------------------------------
The documentation is written in **reStructuredText**, which is almost like writing
in plain English, and built using `Sphinx <http://sphinx.pocoo.org/>`__. The
Sphinx Documentation has an excellent `introduction to reST
<http://sphinx.pocoo.org/rest.html>`__. Review the Sphinx docs to perform more
complex changes to the documentation as well.
Some other important things to know about the docs:
- The *pandas* documentation consists of two parts: the docstrings in the code
itself and the docs in this folder ``pandas/doc/``.
The docstrings 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. See `this document
<https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt>`_
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
<http://matplotlib.org/sampledoc/ipython_directive.html>`_ sphinx extension.
This directive lets you put code in the documentation which will be run
during the doc build. For example::
.. 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 the doc building a bit more complex.
.. note::
The ``.rst`` files are used to automatically generate Markdown and HTML versions
of the docs. For this reason, please do not edit ``CONTRIBUTING.md`` directly,
but instead make any changes to ``doc/source/contributing.rst``. Then, to
generate ``CONTRIBUTING.md``, use `pandoc <http://johnmacfarlane.net/pandoc/>`_
with the following command::
pandoc doc/source/contributing.rst -t markdown_github > CONTRIBUTING.md
The utility script ``scripts/api_rst_coverage.py`` can be used to compare
the list of methods documented in ``doc/source/api.rst`` (which is used to generate
the `API Reference <http://pandas.pydata.org/pandas-docs/stable/api.html>`_ page)
and the actual public methods.
This will identify methods documented in in ``doc/source/api.rst`` that are not actually
class methods, and existing methods that are not documented in ``doc/source/api.rst``.
How to build the *pandas* documentation
---------------------------------------
Requirements
~~~~~~~~~~~~
First, you need to have a development environment to be able to build pandas
(see the docs on :ref:`creating a development environment above <contributing.dev_env>`).
Further, to build the docs, there are some extra requirements: you will need to
have ``sphinx`` and ``ipython`` installed. `numpydoc
<https://github.com/numpy/numpydoc>`_ is used to parse the docstrings that
follow the Numpy Docstring Standard (see above), but you don't need to install
this because a local copy of numpydoc is included in the *pandas* source
code.
`nbconvert <https://nbconvert.readthedocs.io/en/latest/>`_ and
`nbformat <https://nbformat.readthedocs.io/en/latest/>`_ are required to build
the Jupyter notebooks included in the documentation.
If you have a conda environment named ``pandas_dev``, you can install the extra
requirements with::
conda install -n pandas_dev sphinx ipython nbconvert nbformat
Furthermore, it is recommended to have all :ref:`optional dependencies <install.optional_dependencies>`.
installed. This is not strictly necessary, but be aware that you will see some error
messages when building the docs. This happens because all the code in the documentation
is executed during the doc build, and so code examples using optional dependencies
will generate errors. Run ``pd.show_versions()`` to get an overview of the installed
version of all dependencies.
.. warning::
You need to have ``sphinx`` version >= 1.3.2.
Building the documentation
~~~~~~~~~~~~~~~~~~~~~~~~~~
So how do you build the docs? Navigate to your local
``pandas/doc/`` directory in the console and run::
python make.py html
Then you can find the HTML output in the folder ``pandas/doc/build/html/``.
The first time you build the docs, it will take quite a while because it has to run
all the code examples and build all the generated docstring pages. In subsequent
evocations, sphinx will try to only build the pages that have been modified.
If you want to do a full clean build, do::
python make.py clean
python make.py build
Starting with *pandas* 0.13.1 you can tell ``make.py`` to compile only a single section
of the docs, greatly reducing the turn-around time for checking your changes.
You will be prompted to delete ``.rst`` files that aren't required. This is okay because
the prior versions of these files can be checked out from git. However, you must make sure
not to commit the file deletions to your Git repository!
::
#omit autosummary and API section
python make.py clean
python make.py --no-api
# compile the docs with only a single
# section, that which is in indexing.rst
python make.py clean
python make.py --single indexing
For comparison, a full documentation build may take 10 minutes, a ``-no-api`` build
may take 3 minutes and a single section may take 15 seconds. Subsequent builds, which
only process portions you have changed, will be faster. Open the following file in a web
browser to see the full documentation you just built::
pandas/docs/build/html/index.html
And you'll have the satisfaction of seeing your new and improved documentation!
.. _contributing.dev_docs:
Building master branch documentation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When pull requests are merged into the *pandas* ``master`` branch, the main parts of
the documentation are also built by Travis-CI. These docs are then hosted `here
<http://pandas-docs.github.io/pandas-docs-travis>`__.
Contributing to the code base
=============================
.. contents:: Code Base:
:local:
Code standards
--------------
*pandas* uses the `PEP8 <http://www.python.org/dev/peps/pep-0008/>`_ standard.
There are several tools to ensure you abide by this standard. Here are *some* of
the more common ``PEP8`` issues:
- we restrict line-length to 80 characters to promote readability
- passing arguments should have spaces after commas, e.g. ``foo(arg1, arg2, kw1='bar')``
The Travis-CI will run `flake8 <http://pypi.python.org/pypi/flake8>`_ tool and report
any stylistic errors in your code. Generating any warnings will cause the build to fail;
thus these are part of the requirements for submitting code to *pandas*.
It is helpful before submitting code to run this yourself on the diff::
git diff master | flake8 --diff
Furthermore, we've written a tool to check that your commits are PEP8 great, `pip install pep8radius
<https://github.com/hayd/pep8radius>`_. Look at PEP8 fixes in your branch vs master with::
pep8radius master --diff
and make these changes with::
pep8radius master --diff --in-place
Additional standards are outlined on the `code style wiki
page <https://github.com/pandas-dev/pandas/wiki/Code-Style-and-Conventions>`_.
Please try to maintain backward compatibility. *pandas* has lots 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. Also, be careful when changing method
signatures and add deprecation warnings where needed.
Test-driven development/code writing
------------------------------------
*pandas* is serious about testing and strongly encourages contributors to embrace
`test-driven development (TDD) <http://en.wikipedia.org/wiki/Test-driven_development>`_.
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 *pandas*. Therefore,
it is worth getting in the habit of writing tests ahead of time so this is never an issue.
Like many packages, *pandas* uses the `Nose testing system
<https://nose.readthedocs.io/en/latest/index.html>`_ and the convenient
extensions in `numpy.testing
<http://docs.scipy.org/doc/numpy/reference/routines.testing.html>`_.
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. If your test requires working with files or
network connectivity, there is more information on the `testing page
<https://github.com/pandas-dev/pandas/wiki/Testing>`_ of the wiki.
The ``pandas.util.testing`` module has many special ``assert`` functions that
make it easier to make statements about whether Series or DataFrame objects are
equivalent. The easiest way to verify that your code is correct is to
explicitly construct the result you expect, then compare the actual result to
the expected correct result::
def test_pivot(self):
data = {
'index' : ['A', 'B', 'C', 'C', 'B', 'A'],
'columns' : ['One', 'One', 'One', 'Two', 'Two', 'Two'],
'values' : [1., 2., 3., 3., 2., 1.]
}
frame = DataFrame(data)
pivoted = frame.pivot(index='index', columns='columns', values='values')
expected = DataFrame({
'One' : {'A' : 1., 'B' : 2., 'C' : 3.},
'Two' : {'A' : 1., 'B' : 2., 'C' : 3.}
})
assert_frame_equal(pivoted, expected)
Running the test suite
~~~~~~~~~~~~~~~~~~~~~~
The tests can then be run directly inside your Git clone (without having to
install *pandas*) by typing::
nosetests pandas
The tests suite is exhaustive and takes around 20 minutes to run. Often it is
worth running only a subset of tests first around your changes before running the
entire suite. This is done using one of the following constructs::
nosetests pandas/tests/[test-module].py
nosetests pandas/tests/[test-module].py:[TestClass]
nosetests pandas/tests/[test-module].py:[TestClass].[test_method]
.. versionadded:: 0.18.0
Furthermore one can run
.. code-block:: python
pd.test()
with an imported pandas to run tests similarly.
Running the performance test suite
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Performance matters and it is worth considering whether your code has introduced
performance regressions. *pandas* is in the process of migrating to
`asv benchmarks <https://github.com/spacetelescope/asv>`__
to enable easy monitoring of the performance of critical *pandas* operations.
These benchmarks are all found in the ``pandas/asv_bench`` directory. asv
supports both python2 and python3.
.. note::
The asv benchmark suite was translated from the previous framework, vbench,
so many stylistic issues are likely a result of automated transformation of the
code.
To use all features of asv, you will need either ``conda`` or
``virtualenv``. For more details please check the `asv installation
webpage <https://asv.readthedocs.io/en/latest/installing.html>`_.
To install asv::
pip install git+https://github.com/spacetelescope/asv
If you need to run a benchmark, change your directory to ``asv_bench/`` and run::
asv continuous -f 1.1 upstream/master HEAD
You can replace ``HEAD`` with the name of the branch you are working on,
and report benchmarks that changed by more than 10%.
The command uses ``conda`` by default for creating the benchmark
environments. If you want to use virtualenv instead, write::
asv continuous -f 1.1 -E virtualenv upstream/master HEAD
The ``-E virtualenv`` option should be added to all ``asv`` commands
that run benchmarks. The default value is defined in ``asv.conf.json``.
Running the full test suite can take up to one hour and use up to 3GB of RAM.
Usually it is sufficient to paste only a subset of the results into the pull
request to show that the committed changes do not cause unexpected performance
regressions. You can run specific benchmarks using the ``-b`` flag, which
takes a regular expression. For example, this will only run tests from a
``pandas/asv_bench/benchmarks/groupby.py`` file::
asv continuous -f 1.1 upstream/master HEAD -b ^groupby
If you want to only run a specific group of tests from a file, you can do it
using ``.`` as a separator. For example::
asv continuous -f 1.1 upstream/master HEAD -b groupby.groupby_agg_builtins
will only run the ``groupby_agg_builtins`` benchmark defined in ``groupby.py``.
You can also run the benchmark suite using the version of ``pandas``
already installed in your current Python environment. This can be
useful if you do not have virtualenv or conda, or are using the
``setup.py develop`` approach discussed above; for the in-place build
you need to set ``PYTHONPATH``, e.g.
``PYTHONPATH="$PWD/.." asv [remaining arguments]``.
You can run benchmarks using an existing Python
environment by::
asv run -e -E existing
or, to use a specific Python interpreter,::
asv run -e -E existing:python3.5
This will display stderr from the benchmarks, and use your local
``python`` that comes from your ``$PATH``.
Information on how to write a benchmark and how to use asv can be found in the
`asv documentation <https://asv.readthedocs.io/en/latest/writing_benchmarks.html>`_.
.. _contributing.gbq_integration_tests:
Running Google BigQuery Integration Tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
You will need to create a Google BigQuery private key in JSON format in
order to run Google BigQuery integration tests on your local machine and
on Travis-CI. The first step is to create a `service account
<https://console.developers.google.com/iam-admin/serviceaccounts/>`__.
Integration tests for ``pandas.io.gbq`` are skipped in pull requests because
the credentials that are required for running Google BigQuery integration
tests are `encrypted <https://docs.travis-ci.com/user/encrypting-files/>`__
on Travis-CI and are only accessible from the pandas-dev/pandas repository. The
credentials won't be available on forks of pandas. Here are the steps to run
gbq integration tests on a forked repository:
#. Go to `Travis CI <https://travis-ci.org/>`__ and sign in with your GitHub
account.
#. Click on the ``+`` icon next to the ``My Repositories`` list and enable
Travis builds for your fork.
#. Click on the gear icon to edit your travis build, and add two environment
variables:
- ``GBQ_PROJECT_ID`` with the value being the ID of your BigQuery project.
- ``SERVICE_ACCOUNT_KEY`` with the value being the contents of the JSON key
that you downloaded for your service account. Use single quotes around
your JSON key to ensure that it is treated as a string.
For both environment variables, keep the "Display value in build log" option
DISABLED. These variables contain sensitive data and you do not want their
contents being exposed in build logs.
#. Your branch should be tested automatically once it is pushed. You can check
the status by visiting your Travis branches page which exists at the
following location: https://travis-ci.org/your-user-name/pandas/branches .
Click on a build job for your branch. Expand the following line in the
build log: ``ci/print_skipped.py /tmp/nosetests.xml`` . Search for the
term ``test_gbq`` and confirm that gbq integration tests are not skipped.
Running the vbench performance test suite (phasing out)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Historically, *pandas* used `vbench library <https://github.com/pydata/vbench>`_
to enable easy monitoring of the performance of critical *pandas* operations.
These benchmarks are all found in the ``pandas/vb_suite`` directory. vbench
currently only works on python2.
To install vbench::
pip install git+https://github.com/pydata/vbench
Vbench also requires ``sqlalchemy``, ``gitpython``, and ``psutil``, which can all be installed
using pip. If you need to run a benchmark, change your directory to the *pandas* root and run::
./test_perf.sh -b master -t HEAD
This will check out the master revision and run the suite on both master and
your commit. Running the full test suite can take up to one hour and use up
to 3GB of RAM. Usually it is sufficient to paste a subset of the results into the Pull Request to show that the committed changes do not cause unexpected
performance regressions.
You can run specific benchmarks using the ``-r`` flag, which takes a regular expression.
See the `performance testing wiki <https://github.com/pandas-dev/pandas/wiki/Performance-Testing>`_ for information
on how to write a benchmark.
Documenting your code
---------------------
Changes should be reflected in the release notes located in ``doc/source/whatsnew/vx.y.z.txt``.
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 following the section
regarding documentation :ref:`above <contributing.documentation>`.
Further, to let users know when this feature was added, the ``versionadded``
directive is used. The sphinx syntax for that is:
.. code-block:: rst
.. versionadded:: 0.17.0
This will put the text *New in version 0.17.0* wherever you put the sphinx
directive. This should also be put in the docstring when adding a new function
or method (`example <https://github.com/pandas-dev/pandas/blob/v0.16.2/pandas/core/generic.py#L1959>`__)
or a new keyword argument (`example <https://github.com/pandas-dev/pandas/blob/v0.16.2/pandas/core/frame.py#L1171>`__).
Contributing your changes to *pandas*
=====================================
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
#
Finally, commit your changes to your local repository with an explanatory message. *Pandas*
uses a convention for commit message prefixes and layout. Here are
some common prefixes along with general guidelines for when to use them:
* ENH: Enhancement, new functionality
* BUG: Bug fix
* DOC: Additions/updates to documentation
* TST: Additions/updates to tests
* BLD: Updates to the build process/scripts
* PERF: Performance improvement
* CLN: Code cleanup
The following defines how a commit message should be structured. Please reference the
relevant GitHub issues in your commit message using GH1234 or #1234. Either style
is fine, but the former is generally preferred:
* a subject line with `< 80` chars.
* One blank line.
* Optionally, a commit message body.
Now you can commit your changes in your local repository::
git commit -m
Combining commits
-----------------
If you have multiple commits, you may want to combine them into one commit, often
referred to as "squashing" or "rebasing". This is a common request by package maintainers
when submitting a pull request as it maintains a more compact commit history. To rebase
your commits::
git rebase -i HEAD~#
Where # is the number of commits you want to combine. Then you can pick the relevant
commit message and discard others.
To squash to the master branch do::
git rebase -i master
Use the ``s`` option on a commit to ``squash``, meaning to keep the commit messages,
or ``f`` to ``fixup``, meaning to merge the commit messages.
Then you will need to push the branch (see below) forcefully to replace the current
commits with the new ones::
git push origin shiny-new-feature -f
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/pandas.git (fetch)
origin git@github.com:yourname/pandas.git (push)
upstream git://github.com/pandas-dev/pandas.git (fetch)
upstream git://github.com/pandas-dev/pandas.git (push)
Now your code is on GitHub, but it is not yet a part of the *pandas* project. For that to
happen, a pull request needs to be submitted on GitHub.
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/pandas
#. Click on ``Branches``
#. Click on the ``Compare`` button for your feature branch
#. Select the ``base`` and ``compare`` branches, if necessary. This will be ``master`` and
``shiny-new-feature``, respectively.
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 master version. This pull request and its associated
changes will eventually be committed to the master 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 need to make more changes, you can make them in
your branch, push them to GitHub, and the pull request will be automatically
updated. Pushing them to GitHub again is done by::
git push -f origin shiny-new-feature
This will automatically update your pull request with the latest code and restart the
Travis-CI tests.
If your pull request is related to the ``pandas.io.gbq`` module, please see
the section on :ref:`Running Google BigQuery Integration Tests
<contributing.gbq_integration_tests>` to configure a Google BigQuery service
account for your pull request on Travis-CI.
Delete your merged branch (optional)
------------------------------------
Once your feature branch is accepted into upstream, you'll probably want to get rid of
the branch. First, merge upstream master into your branch so git knows it is safe to
delete your branch::
git fetch upstream
git checkout master
git merge upstream/master
Then you can just do::
git branch -d shiny-new-feature
Make sure you use a lower-case ``-d``, or else git won't warn you if your feature
branch has not actually been merged.
The branch will still exist on GitHub, so to delete it there do::
git push origin --delete shiny-new-feature
|