Contributing to py_entitymatching

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This document is adapted from pandas how to contribute guidelines for py_entitymatching package.

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 py_entitymatching codebase, navigate to the GitHub “issues” tab and start looking through interesting issues.

Or maybe through using py_entitymatching 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

Bug reports and enhancement requests

Bug reports are an important part of making py_entitymatching more stable.Having a complete bug report will allow others to reproduce the bug and provide insight into fixing. We use GitHub issue tracker to track bugs. It is important that you provide the exact version of py_entitymatching where the bug is found. 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:

  1. Include a short, self-contained Python snippet reproducing the problem. You can format the code nicely by using GitHub Flavored Markdown:

    ```python
>>> import py_entitymatching as em
>>> em.down_sample(...)
...
```

  2. Include the full version string of py_entitymatching. You can find the version as follows:

    >>> import py_entitymatching as em
>>> em.__version__

  3. Explain why the current behavior is wrong/not desired and what you expect instead.

The issue will then show up to the py_entitymatching 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 py_entitymatching code base.

Version control, Git, and GitHub

To the new user, working with Git is one of the more daunting aspects of contributing to py_entitymatching. 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. To contribute you will need to sign up for a free GitHub account. We use Git for version control to allow many people to work together on the project.

Some great resources for learning Git:

Getting started with Git

GitHub has instructions 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.

Forking

You will need your own fork to work on the code. Go to the py_entitymatching project page and hit the Fork button. You will want to clone your fork to your machine:

git clone git@github.com:<your-user-name>/py_entitymatching.git <local-repo-name>
cd <local-repo-name>
git remote add upstream git://github.com/anhaidgroup/py_entitymatching.git

This creates the directory local-repo-name and connects your repository to the upstream (main project) py_entitymatching 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.

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 new_feature
git checkout new_feature

The above can be simplified to:

git checkout -b new_feature

This changes your working directory to the new_feature branch. Keep any changes in this branch specific to one bug or feature so it is clear what the branch brings to py_entitymatching. You can have many 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 py_entitymatching git master. If this leads to merge conflicts, you must resolve them 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.

Creating a development environment

An easy way to create a py_entitymatching development environment is as follows.

  • Install either Anaconda or miniconda

  • Make sure that you have cloned the repository

  • cd to the py_entitymatching source directory

Tell conda to create a new environment, named py_entitymatching_dev, or any other name you would like for this environment, by running:

conda create -n py_entitymatching_dev --file requirements.yml

For a python 3 environment:

conda create -n py_entitymatching_dev python=3 --file requirements.yml

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 py_entitymatching. You need to install the nose package which is used for testing, as follows:

conda install -n py_entitymatching_dev nose

To work in this environment, Windows users should activate it as follows:

activate py_entitymatching_dev

Mac OSX / Linux users should use:

source activate py_entitymatching_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.

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 py_entitymatching 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.

About the py_entitymatching documentation

The documentation is written in reStructuredText, which is almost like writing in plain English, and built using Sphinx. The Sphinx Documentation has an excellent introduction to reST. Review the Sphinx docs to perform more complex changes to the documentation as well.

Some other important things to know about the docs:

  • The py_entitymatching documentation consists of two parts: the docstrings in the code itself and the docs in this folder py_entitymatching/docs/.

    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 Google Docstring Standard. This standard specifies the format of the different sections of the docstring. See this document for a detailed explanation, or look at some of the existing functions to extend it in a similar manner.

How to build the py_entitymatching documentation

Requirements

To build the py_entitymatching docs there are some extra requirements: you will need to have sphinx and ipython installed.

It is easiest to create a development environment, then install:

conda install -n py_entitymatching_dev sphinx sphinx_rtd_theme ipython

Building the documentation

So how do you build the docs? Navigate to your local py_entitymatching/docs/ directory in the console and run:

make html

Then you can find the HTML output in the folder py_entitymatching/docs/_build/html/.

If you want to do a full clean build, do:

make clean html

Contributing to the code base

Code standards

py_entitymatching follows Google Python Style Guide.

Please try to maintain backward compatibility. py_entitymatching 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.

Writing tests

Adding tests is one of the most common requests after code is pushed to py_entitymatching. Therefore, it is worth getting in the habit of writing tests ahead of time so this is never an issue.

Unit testing

Like many packages, py_entitymatching uses the Nose testing system.

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.

The tests can then be run directly inside your Git clone (without having to install py_entitymatching) by typing:

nosetests

Performance testing

Performance matters and it is worth considering whether your code has introduced performance regressions. py_entitymatching uses asv for performance testing. The benchmark test cases are all found in the benchmarks/asv_benchmarks directory. asv supports both python2 and python3.

To install asv:

pip install git+https://github.com/spacetelescope/asv

If you need to run a benchmark, run the following from the benchmarks directory:

asv run

This command uses conda by default for creating the benchmark environments.

Information on how to write a benchmark and how to use asv can be found in the asv documentation.

Contributing your changes to py_entitymatching

Committing your code

Finally, commit your changes to your local repository with an explanatory message.

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 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 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>/py_entitymatching.git (fetch)
origin  git@github.com:<yourname>/py_entitymatching.git (push)
upstream        git://github.com/anhaidgroup/py_entitymatching.git (fetch)
upstream        git://github.com/anhaidgroup/py_entitymatching.git (push)

Now your code is on GitHub, but it is not yet a part of the py_entitymatching 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:

  1. Navigate to your repository on GitHub – https://github.com/<your-user-name>/py_entitymatching

  2. Click on Branches

  3. Click on the Compare button for your feature branch

  4. Select the base and compare branches, if necessary. This will be master and 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:

  1. Navigate to your repository on GitHub

  2. Click on the Pull Request button

  3. You can then click on Commits and Files Changed to make sure everything looks okay one last time

  4. Write a description of your changes.

  5. 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 new_feature

This will automatically update your pull request with the latest code and restart the Travis-CI tests.

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 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 new_feature