CONTRIBUTING.md

Contributing to micronota

micronota is an open source software package and we welcome community contributions. You can find the micronota source code on GitHub here.

This document covers what you should do to get started with contributing to micronota. You should read the entire document before contributing code to micronota. This will save time for both you and the micronota developers.

Types of contributions

We're interested in many different types of contributions, including feature additions, bug fixes, continuous integration improvements, and documentation/website updates, additions, and fixes.

When considering contributing to micronota, you should begin by posting an issue to the micronota issue tracker. The information that you include in that post will differ based on the type of contribution. Your contribution will also need to be fully tested where applicable (discussed further below).

• For feature additions, please describe why the functionality that you are proposing to add is relevant. For it to be relevant, it should be demonstrably useful to micronota users and it should also fit within the biology/bioinformatics domain. This typically means that a new analytic method is implemented (you should describe why it's useful, ideally including a link to a paper that uses this method), or an existing method is enhanced (e.g., improved performance). We will request benchmark results comparing your method to the pre-existing methods (which would also be required for publication of your method) so pointing to a paper or other document containing benchmark results, or including benchmark results in your issue, will speed up the process.

• For bug fixes, please provide a detailed description of the bug so other developers can reproduce it. We take bugs in micronota very seriously. Bugs can be related to errors in code, documentation, or tests. Errors in documentation or tests are usually updated in the next scheduled release of micronota. Errors in code that could result in incorrect results or inability to access certain functionality may result in a bug fix release of micronota that is released ahead of schedule.

You should include the following information in your bug report:

1. The exact command(s) necessary to reproduce the bug.
2. A link to all necessary input files for reproducing the bug. These files should only be as large as necessary to create the bug. For example, if you have an input file with 10,000 FASTA-formatted sequences but the error only arises due to one of the sequences, create a new FASTA file with only that sequence, run the command that was giving you problems, and verify that you still get an error. Then post that command and link to the trimmed FASTA file. This is extremely useful to other developers and it is likely that if you don't provide this information you'll get a response asking for it. Often this process helps you to better understand the bug as well.

When you post your issue, the micronota developers will respond to let you know if we agree with the addition or change. It's very important that you go through this step to avoid wasting time working on a feature that we are not interested in including in micronota. This initial discussion with the developers is important because micronota is rapidly changing, including complete re-writes of some of the core objects. If you don't get in touch first you could easily waste time by working on an object or interface that is deprecated.

Getting started

"quick fixes"

Some of our issues are labeled as quick fix. Working on these issues is a good way to get started with contributing to micronota. These are usually small bugs or documentation errors that will only require one or a few lines of code to fix. Getting started by working on one of these issues will allow you to familiarize yourself with our development process before committing to a large amount of work (e.g., adding a new feature to micronota). Please post a comment on the issue if you're interested in working on one of these "quick fixes".

Joining development

Once you are more comfortable with our development process, you can check out the on deck label on our issue tracker. These issues represent what our current focus is in the project. As such, they are probably the best place to start if you are looking to join the conversation and contribute code.

Code review

When you submit code to micronota, it will be reviewed by one or more micronota developers. These reviews are intended to confirm a few points:

• Your code provides relevant changes or additions to micronota (Types of contributions).
• Your code adheres to our coding guidelines (Coding guidelines).
• Your code is sufficiently well-tested (Testing guidelines).
• Your code is sufficiently well-documented (Documentation guidelines).

This process is designed to ensure the quality of micronota and can be a very useful experience for new developers.

Particularly for big changes, if you'd like feedback on your code in the form of a code review as you work, you should request help in the issue that you created and one of the micronota developers will work with you to perform regular code reviews. This can greatly reduce development time (and frustration) so we highly recommend that new developers take advantage of this rather than submitting a pull request with a massive amount of code. That can lead to frustration when the developer thinks they are done but the reviewer requests large amounts of changes, and it also makes it harder to review.

Submitting code to micronota

micronota is hosted on GitHub, and we use GitHub's Pull Request mechanism for reviewing and accepting submissions. You should work through the following steps to submit code to micronota.

Note: We recommend developing micronota in a Python 3 environment because doctests must be written (and pass) in Python 3.

1. Begin by creating an issue describing your proposed change (see Types of contributions for details).

2. Fork the micronota repository on the GitHub website.

3. Clone your forked repository to the system where you'll be developing with git clone. cd into the micronota directory that was created by git clone.

4. Ensure that you have the latest version of all files. This is especially important if you cloned a long time ago, but you'll need to do this before submitting changes regardless. You should do this by adding micronota as a remote repository and then pulling from that repository. You'll only need to run the git remote command the first time you do this:

git remote add upstream https://github.com/biocore/micronota.git
git checkout master
git pull upstream master

5. Install micronota in "development mode" so that your changes are reflected in the installed package without having to reinstall the package each time:

pip install -e .

6. Create a new topic branch that you will make your changes in with git checkout -b:

git checkout -b my-topic-branch

What you name your topic branch is up to you, though we recommend including the issue number in the topic branch, since there is usually already an issue associated with the changes being made in the pull request. For example, if you were addressing issue number 42, you might name your topic branch issue-42.

7. Run make all to confirm that the tests pass before you make any changes. It will run the test code, docstring tests, pep8 check, and html doc build.

8. Make your changes, add them (with git add), and commit them (with git commit). Don't forget to update associated tests and documentation as necessary. Write descriptive commit messages to accompany each commit. We recommend following NumPy's commit message guidelines, including the usage of commit tags (i.e., starting commit messages with acronyms such ENH, BUG, etc.).

9. Please mention your changes in CHANGELOG.md. This file informs micronota users of changes made in each release, so be sure to describe your changes with this audience in mind. It is especially important to note API additions and changes, particularly if they are backward-incompatible, as well as bug fixes. Be sure to make your updates under the section designated for the latest development version of micronota (this will be at the top of the file). Describe your changes in detail under the most appropriate section heading(s). For example, if your pull request fixes a bug, describe the bug fix under the "Bug fixes" section of CHANGELOG.md. Please also include a link to the issue(s) addressed by your changes. See CHANGELOG.md for examples of how we recommend formatting these descriptions.

10. When you're ready to submit your code, ensure that you have the latest version of all files in case some changed while you were working on your edits. You can do this by merging master into your topic branch:

git checkout master
git pull upstream master
git checkout my-topic-branch
git merge master

11. Run make all to ensure that your changes did not cause anything expected to break.

12. Once the tests pass, you should push your changes to your forked repository on GitHub using:

git push origin my-topic-branch

13. Issue a pull request on the GitHub website to request that we merge your branch's changes into micronota's master branch. Be sure to include a description of your changes in the pull request, as well as any other information that will help the micronota developers involved in reviewing your code. Please include fixes #<issue-number> in your pull request description or in one of your commit messages so that the corresponding issue will be closed when the pull request is merged (see here for more details). One of the micronota developers will review your code at this stage. If we request changes (which is very common), don't issue a new pull request. You should make changes on your topic branch, and commit and push them to GitHub. Your pull request will update automatically.

Coding guidelines

We adhere to the PEP 8 Python style guidelines. We also follow the coding guidelines of scikit-bio. Before submitting code to micronota, you should read this document carefully and apply the guidelines in your code.

Testing guidelines

All code that is added to micronota must be unit tested, and the unit test code must be submitted in the same pull request as the library code that you are submitting. We will only merge code that is unit tested and that passes the continuous integration build. This build includes, but is not limited to, the following checks:

• Full unit test suite executes without errors in Python 3.
• Doctests execute correctly in Python 3.
• C code can be correctly compiled.
• Cython code is correctly generated.
• All the dependecies of external software are correctly installed.
• All tests import functionality from the appropriate minimally deep API.
• Documentation can be built.
• Current code coverage is maintained or improved.
• Code passes pep8/flake8 checks.

Running make test locally during development will include a subset of the full checks performed by Travis-CI. To report test coverage besides running unit tests, run:

WITH_COVERAGE=TRUE make test
coverage html && open htmlcov/index.html

The coding guidelines describe our expectations for unit tests. You should review the unit test section before working on your test code.

Tests can be executed by running make test from the base directory of the project.

Documentation guidelines

We strive to keep micronota well-documented, particularly its public-facing API. See our documentation guide for more details.

Getting help with git

If you're new to git, you'll probably find gitref.org helpful.