CONTRIBUTING.txt

Development process
-------------------

Here's the long and short of it:

1. If you are a first-time contributor:

   * Go to `https://github.com/scikit-image/scikit-image
     <http://github.com/scikit-image/scikit-image>`_ and click the
     "fork" button to create your own copy of the project.

   * Clone the project to your local computer::

      git clone git@github.com:your-username/scikit-image.git

   * Add the upstream repository::

      git remote add upstream git@github.com:scikit-image/scikit-image.git

   * Now, you have remote repositories named:

     - ``upstream``, which refers to the ``scikit-image`` repository
     - ``origin``, which refers to your personal fork

2. Develop your contribution:

   * Pull the latest changes from upstream::

      git checkout master
      git pull upstream master

   * Create a branch for the feature you want to work on. Since the
     branch name will appear in the merge message, use a sensible name
     such as 'transform-speedups'::

      git checkout -b transform-speedups

   * Commit locally as you progress (``git add`` and ``git commit``)

3. To submit your contribution:

   * Push your changes back to your fork on GitHub::

      git push origin transform-speedups

   * Go to GitHub. The new branch will show up with a green Pull Request
     button - click it.

   * If you want, post on the `mailing list
     <http://groups.google.com/group/scikit-image>`_ to explain your changes or
     to ask for review.

For a more detailed discussion, read these :doc:`detailed documents
<gitwash/index>` on how to use Git with ``scikit-image``
(`<http://scikit-image.org/docs/dev/gitwash/index.html>`_).

4. Review process:

   * Reviewers (the other developers and interested community members) will
     write inline and/or general comments on your Pull Request (PR) to help
     you improve its implementation, documentation and style.  Every single
     developer working on the project has their code reviewed, and we've come
     to see it as friendly conversation from which we all learn and the
     overall code quality benefits.  Therefore, please don't let the review
     discourage you from contributing: its only aim is to improve the quality
     of project, not to criticize (we are, after all, very grateful for the
     time you're donating!).

   * To update your pull request, make your changes on your local repository
     and commit. As soon as those changes are pushed up (to the same branch as
     before) the pull request will update automatically.

   * `Travis-CI <http://travis-ci.org/>`__, a continuous integration service,
     is triggered after each Pull Request update to build the code, run unit
     tests, measure code coverage and check coding style (PEP8) of your
     branch. The Travis tests must pass before your PR can be merged. If
     Travis fails, you can find out why by clicking on the "failed" icon (red
     cross) and inspecting the build and test log.

   * A pull request must be approved by two core team members before merging.

5. Document changes

   If your change introduces any API modifications, please update
   ``doc/source/api_changes.txt``.

   If your change introduces a deprecation, add a reminder to ``TODO.txt``
   for the team to remove the deprecated functionality in the future.

.. note::

   To reviewers: if it is not obvious from the PR description, add a short
   explanation of what a branch did to the merge message and, if closing a
   bug, also add "Closes #123" where 123 is the issue number.


Divergence between ``upstream master`` and your feature branch
--------------------------------------------------------------

Do *not* ever merge the main branch into yours. If GitHub indicates that the
branch of your Pull Request can no longer be merged automatically, rebase
onto master::

   git checkout master
   git pull upstream master
   git checkout transform-speedups
   git rebase master

If any conflicts occur, fix the according files and continue::

   git add conflict-file1 conflict-file2
   git rebase --continue

However, you should only rebase your own branches and must generally not
rebase any branch which you collaborate on with someone else.

Finally, you must push your rebased branch::

   git push --force origin transform-speedups

(If you are curious, here's a further discussion on the
`dangers of rebasing <http://tinyurl.com/lll385>`__.
Also see this `LWN article <http://tinyurl.com/nqcbkj>`__.)

Guidelines
----------

* All code should have tests (see `test coverage`_ below for more details).
* All code should be documented, to the same
  `standard <https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard>`_ as NumPy and SciPy.
* For new functionality, always add an example to the gallery.
* No changes are ever committed without review and approval by two core
  team members.  Ask on the
  `mailing list <http://groups.google.com/group/scikit-image>`_ if
  you get no response to your pull request.
  **Never merge your own pull request.**
* Examples in the gallery should have a maximum figure width of 8 inches.

Stylistic Guidelines
--------------------

* Set up your editor to remove trailing whitespace.  Follow `PEP08
  <http://www.python.org/dev/peps/pep-0008/>`__.  Check code with pyflakes / flake8.

* Use numpy data types instead of strings (``np.uint8`` instead of
  ``"uint8"``).

* Use the following import conventions::

   import numpy as np
   import matplotlib.pyplot as plt
   from scipy import ndimage as ndi

   cimport numpy as cnp  # in Cython code

* When documenting array parameters, use ``image : (M, N) ndarray``
  and then refer to ``M`` and ``N`` in the docstring, if necessary.

* Refer to array dimensions as (plane), row, column, not as x, y, z. See
  :ref:`Coordinate conventions <numpy-images-coordinate-conventions>`
  in the user guide for more information.

* Functions should support all input image dtypes.  Use utility functions such
  as ``img_as_float`` to help convert to an appropriate type.  The output
  format can be whatever is most efficient.  This allows us to string together
  several functions into a pipeline, e.g.::

   hough(canny(my_image))

* Use ``Py_ssize_t`` as data type for all indexing, shape and size variables
  in C/C++ and Cython code.

* Use relative module imports, i.e. ``from .._shared import xyz`` rather than
  ``from skimage._shared import xyz``.

* Wrap Cython code in a pure Python function, which defines the API. This
  improves compatibility with code introspection tools, which are often not
  aware of Cython code.

* For Cython functions, release the GIL whenever possible, using
  ``with nogil:``.


Test coverage
-------------

Tests for a module should ideally cover all code in that module,
i.e., statement coverage should be at 100%.

To measure the test coverage, install
`coverage.py <http://nedbatchelder.com/code/coverage/>`__
(using ``easy_install coverage``) and then run::

  $ make coverage

This will print a report with one line for each file in `skimage`,
detailing the test coverage::

  Name                                             Stmts   Exec  Cover   Missing
  ------------------------------------------------------------------------------
  skimage/color/colorconv                             77     77   100%
  skimage/filter/__init__                              1      1   100%
  ...


Activate Travis-CI for your fork (optional)
-------------------------------------------

Travis-CI checks all unittests in the project to prevent breakage.

Before sending a pull request, you may want to check that Travis-CI
successfully passes all tests. To do so,

* Go to `Travis-CI <http://travis-ci.org/>`__ and follow the Sign In link at
  the top

* Go to your `profile page <https://travis-ci.org/profile>`__ and switch on
  your scikit-image fork

It corresponds to steps one and two in
`Travis-CI documentation <http://about.travis-ci.org/docs/user/getting-started/>`__
(Step three is already done in scikit-image).

Thus, as soon as you push your code to your fork, it will trigger Travis-CI,
and you will receive an email notification when the process is done.

Every time Travis is triggered, it also calls on `Coveralls
<http://coveralls.io>`_ to inspect the current test overage.


Building docs
-------------

To build docs, run ``make`` from the ``docs`` directory. ``make help`` lists
all targets.

Requirements
~~~~~~~~~~~~

Sphinx (>= 1.3) and Latex is needed to build doc.

**Sphinx:**

.. code:: sh

    pip install sphinx

**Latex Ubuntu:**

.. code:: sh

    sudo apt-get install -qq texlive texlive-latex-extra dvipng

**Latex Mac:**

Install the full `MacTex <http://www.tug.org/mactex/>`__ installation or
install the smaller
`BasicTex <http://www.tug.org/mactex/morepackages.html>`__ and add *ucs*
and *dvipng* packages:

.. code:: sh

    sudo tlmgr install ucs dvipng

Fixing Warnings
~~~~~~~~~~~~~~~

-  "citation not found: R###" There is probably an underscore after a
   reference in the first line of a docstring (e.g. [1]\_). Use this
   method to find the source file: $ cd doc/build; grep -rin R####

-  "Duplicate citation R###, other instance in..."" There is probably a
   [2] without a [1] in one of the docstrings

-  Make sure to use pre-sphinxification paths to images (not the
   \_images directory)

Auto-generating dev docs
~~~~~~~~~~~~~~~~~~~~~~~~

This set of instructions was used to create
scikit-image/tools/deploy-docs.sh

-  Go to Github account settings -> personal access tokens
-  Create a new token with access rights ``public_repo`` and
   ``user:email only``
-  Install the travis command line tool: ``gem install travis``. On OSX,
   you can get gem via ``brew install ruby``.
-  Take then token generated by Github and run
   ``travis encrypt GH_TOKEN=<token>`` from inside a scikit-image repo
-  Paste the output into the secure: field of ``.travis.yml``.
-  The decrypted GH\_TOKEN env var will be available for travis scripts

https://help.github.com/articles/creating-an-access-token-for-command-line-use/
http://docs.travis-ci.com/user/encryption-keys/


Bugs
----

Please `report bugs on GitHub <https://github.com/scikit-image/scikit-image/issues>`_.