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Contributing guide for cw-eval

This guide is based on scikit-image's CONTRIBUTING.txt.

Thank you for contributing to the cw-eval codebase. The technical details of the development process is summed up below.

Development process

1. If you are a first-time contributor:

  • Go to https://github.com/cosmiq/cw-eval and click the "fork" button to create your own copy of the project.

  • Clone the project to your local computer: git clone https://github.com/your-username/cw-eval.git

  • Change the directory: cd cw-eval

  • Add the upstream repository::

    git remote add upstream https://github.com/cosmiq/cw-eval.git

  • Now, you have remote repositories named:

    • upstream, which refers to the CosmiQ 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 'add-apls': git checkout -b add-apls
  • Commit locally as you progress (you may push to your fork if you wish).

3. To submit your contribution:

  • Push your changes back to your fork on GitHub: git push origin add-apls
  • Go to your fork of cw-eval on GitHub. The new branch will show up with a green Pull Request button - click it. When you prepare your pull request, please merge to the dev branch in the upstream remote.

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 see it as a conversation from which we all learn and the overall code quality benefits.
  • 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, 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 X) and inspecting the build and test log.
  • Codecov will run to check how your PR affects test coverage. See the Tests section below for more information.
  • A pull request must be approved by a reviewer before merging.

5. Document changes

  • If your change introduces any API modifications, please update doc/api_changes.txt. Note that we don't allow API modifications that remove existing parameters or alter required arguments except in major releases, and if your PR introduces these changes, it will not be merged until the next x.0.0 release.
  • 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

If GitHub indicates that the branch of your Pull Request can no longer be merged automatically, merge the master branch into yours:

git fetch upstream master
git merge upstream/master

If any conflicts occur, they need to be fixed before continuing. See which files are in conflict using git status, which displayes a message like:

Unmerged paths:
  (use "git add <file>..." to mark resolution)

  both modified:   file_with_conflict.txt

Inside the conflicted file, you'll find sections like these::

<<<<<<< HEAD
The way the text looks in your branch
=======
The way the text looks in the master branch
>>>>>>> master

Choose one version of the text that should be kept, and delete the rest:

The way the text looks in your branch

Now, add the fixed file with git add file_with_conflict.txt, and once you have fixed all of the merge conficts, git commit.

Note: Advanced Git users are encouraged to rebase instead of merge, but we squash most commits either way.

Guidelines

  • For new functionality, always add an example to the cookbook (docs/cookbook/) using a jupyter notebook. Build the docs using Sphinx before you create a PR to make sure your notebook renders properly.
  • We encourage you to solicit review from another team member before merging.

Stylistic Guidelines

  • Follow PEP08. Check code with pyflakes / flake8.
  • Please use the same import conventions as used throughout the rest of the package.

Testing

scikit-image has an extensive test suite that ensures correct execution on your system. The test suite has to pass before a pull request can be merged, and tests should be added to cover any modifications to the code base.

We make use of the pytest testing framework, with tests located in the cw-eval/tests folder. You can run the tests yourself (see below) or use Travis-CI test runs in your PR. If you do the latter, begin your PR name with "[WIP]" to mark it as a work in progress until all tests pass.

To use pytest, ensure that the library is installed in development mode using pip install -e .

Now, run all tests using PYTHONPATH=. pytest cw-eval

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 pytest-cov (using easy_install pytest-cov) and then run make coverage. This will print a report with one line for each file in cw_eval, 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,

This corresponds to steps one and two in Travis-CI documentation (Step three is already done in cw-eval).

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 Codecov to inspect the current test overage.

Building docs

To build docs, run make html from the cw-eval/docs directory.

Then, all the HTML files will be generated in cw-eval/docs/_build/. To rebuild a full clean documentation, run:

make clean
make html

Requirements: [Sphinx] (http://www.sphinx-doc.org/en/stable/) is needed to build the documentation. Sphinx and other python packages needed to build the documentation can be installed using pip install . from within the cw-eval folder.

Deprecation cycle

If the behavior of the library has to be changed, a deprecation cycle must be followed to warn users.

  • a deprecation cycle is not necessary when:

    • adding a new function, or
    • adding a new keyword argument to the end of a function signature, or
    • fixing what was buggy behavior

  • a deprecation cycle is necessary for any breaking API change, meaning a change where the function, invoked with the same arguments, would return a different result after the change. This includes:

    • changing the order of arguments or keyword arguments, or
    • adding arguments or keyword arguments to a function, or
    • changing a function's name or submodule, or
    • changing the default value of a function's arguments.

Usually, our policy is to put in place a deprecation cycle over two releases.

For the sake of illustration, we consider the modification of a default value in a function signature. In version N (therefore, next release will be N+1), we have

def a_function(image, rescale=True):
    out = do_something(image, rescale=rescale)
    return out

that has to be changed to

def a_function(image, rescale=None):
    if rescale is None:
        warn('The default value of rescale will change to `False` in version N+3')
        rescale = True
    out = do_something(image, rescale=rescale)
    return out

and in version N+3:

def a_function(image, rescale=False):
    out = do_something(image, rescale=rescale)
      return out

Here is the process for a 2-release deprecation cycle:

  • In the signature, set default to None, and modify the docstring to specify that it's True.
  • In the function, if rescale is set to None, set to True and warn that the default will change to False in version N+3.
  • In doc/release/release_dev.rst, under deprecations, add "In a_function, the rescale argument will default to False in N+3."
  • In TODO.txt, create an item in the section related to version N+3 and write "change rescale default to False in a_function".

Note that the 2-release deprecation cycle is not a strict rule and in some cases, the developers can agree on a different procedure upon justification (like when we can't detect the change, or it involves moving or deleting an entire function for example).

Bugs

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