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Contributing to UniverSC development

Thank you for helping to make this package better. We value all contributions and rely on your feedback to identify problems and use cases.

TL;DR

Send your PR! Thanks!

More Details

You want to contribute? Awesome! Small changes, like fixing typos in documentation are completely fine and also most welcome. For bigger changes, we suggest that you open an issue before you start coding, so that we can maximize the probability that we can successfully merge in your code.

The goal of this guide is to help you get up and contributing to UniverSC as quickly as possible. The guide is divided into two main pieces:

  1. Filing a bug report or feature request in an issue.

  2. Suggesting a change via a pull request.

Please note that UniverSC is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Issues

When filing an issue, the most important thing is to include a minimal reproducible example so that we can quickly verify the problem, and then figure out how to fix it. There are three things you need to include to make your example reproducible: required packages, data, code.

  1. Packages should be added to the PATH at the top of the script, so it's easy to see which ones the example needs. You can see which you are using with:
echo $PATH

grep "PATH" $HOME/bash.r
  1. The easiest way to include data is to use head to show the first few rows of the files we are dealing with.
head -n 24 *R1_001.fastq
head -n 24 *R2_001.fastq
head -n 10 barcodes.txt

You can show compressed files as follows:

for file in `ls *R1_001.fastq *R2_001.fastq`
do
    zcat $file | head -n 24
done

Then simply copy these into GitHub with code blocks:

```

your code here

```

  1. Please include error messages with the full backtrace of commands that failed.
tail -n 25  my-id/outs/_log

Copy the output from the Cell Ranger logs or the terminal and paste is as a quote

> your

> quote

> here

  1. Spend a little bit of time ensuring that your code is easy for others to read:

  • make sure you've used spaces and your variable names are concise, but informative

    • use comments to indicate where your problem lies

    • do your best to remove everything that is not related to the problem.
      The shorter your code is, the easier it is to understand.

You can check you have actually made a reproducible example by starting up a fresh shell session and pasting your script in.

(Unless you've been specifically asked for it, please don't include the packages that you've installed.)

Pull requests

To contribute a change to universc, you follow these steps:

  1. Create a branch in git and make your changes.
  2. Push branch to github and issue pull request (PR).
  3. Discuss the pull request.
  4. Iterate until either we accept the PR or decide that it's not a good fit for universc.

Each of these steps are described in more detail below. This might feel overwhelming the first time you get set up, but it gets easier with practice. If you get stuck at any point, please reach out for help on the universc-dev mailing list.

If you're not familiar with git or github, please start by reading http://r-pkgs.had.co.nz/git.html

Pull requests will be evaluated against a seven point checklist:

  1. Motivation. Your pull request should clearly and concisely motivate the need for change. Unfortunately I am busy with other projects these days, so you need to describe the problem and show how your pull request solves it as concisely as possible.

    Also include this motivation in NEWS so that when a new release of UniverSC comes out it's easy for users to see what's changed. Add your item at the top of the file and use markdown for formatting. The news item should end with (@yourGithubUsername, #the_issue_number).

  2. Only related changes. Before you submit your pull request, please check to make sure that you haven't accidentally included any unrelated changes. These make it harder to see exactly what's changed, and to evaluate any unexpected side effects.

    Each PR corresponds to a git branch, so if you expect to submit multiple changes make sure to create multiple branches. If you have multiple changes that depend on each other, start with the first one and don't submit any others until the first one has been processed.

  3. Use UniverSC coding style. Please follow the Google shell style. Maintaining a consistent style across the whole code base makes it much easier to jump into the code. If you're modifying existing UniverSC code that doesn't follow the style guide, a separate pull request to fix the style would be greatly appreciated.

  4. If you're adding new parameters or a new function, you'll also need to document them in the help and manual.

  5. If fixing a bug or adding a new feature please add a test to check if it works if test data is available.

  6. If fixing a bug in the output, please give an example.

  7. If you're adding a new feature, please add a short example to the appropriate function.

This seems like a lot of work but don't worry if your pull request isn't perfect. It's a learning process and members of the UniverSC team will be on hand to help you out. A pull request ("PR") is a process, and unless you've submitted a few in the past it's unlikely that your pull request will be accepted as is. All PRs require review and approval from at least one member of the UniverSC development team before merge.

Please remember that UniverSC is package used by other people. This means that changing any existing functionality could result in breaking someone's code (or another pipeline). Please don't submit pull requests that change existing behaviour. Instead, think about how you can add a new feature in a minimally invasive way.

Making Small Changes

  • Please always use the dev branch. Choose this branch in your fork. (We build the master branch from the dev branch automatically, to make sure that the repo is compatible with the devtools R package which uses the master branch by default.)
  • Then look for the file you want to modify.
  • Click on the edit symbol (pen) on the upper right corner of the file view.
  • Make your edits.
  • Write a short commit message, less than 65 characters. E.g. "Fix manual page typo" or "Fix degree bug for loops". If needed, elaborate your changes below in the "extended description" field.
  • Commit your changes.
  • Go back to the start page of your forked repository. It is at https://github.com/<username>/universc.
  • Click on the green button before the branch name to create a pull request.
  • Click on "Create pull request".
  • Provide a more detailed description if you like. Please also indicate that you are fine with licensing your contribution under universc's license (see Legal Stuff below).
  • Click on "Create pull request".
  • That's it! It is probably a good idea to keep your forked repository until the change is accepted into universc, in case you need to modify it.
  • Now you need to wait for us, unfortunately. Please ping us, if it takes long to respond. E.g. a week is considered to be long.
  • Once your pull request is accepted, you can delete your forked repository.

Making More Involved Changes

This is mostly the same as for trivial changes, but you probably want to edit the sources on your computer, instead of online on Github.

  • Open an issue in the issue tracker about the proposed changes. This is not required for smaller things, but I suggest you do it for others. Just in case somebody is already working on the same thing, or it is something we don't want in universc.

  • Fork the repository, and clone it to the machine you'll work on.

  • We usually build UniverSC on OSX, so the dev branch is usally fine on that platform. It might have problems on other systems. If this happens, please open an issue and tell us.

  • Make sure you work on the dev branch.

  • Once ready with your changes, build universc, and run the tests. If you use the docker package, this means running:

    docker build docker build -t universc:dev .

  • Submit your pull request.

  • Now you need to wait for us, unfortunately. Please ping us, by email or mentioning the maintainer's username on GitHub if it takes longer than a week or so to respond.

Writing UniverSC Code

Some tips on writing UniverSC code. In general, look at how things are done, and try to do them similarly. (Unless you think they are not done well, in which case please tell us.)

Code Formatting

Look at the style (indentation, braces, etc.) of some recently committed bigger change, and try to mimic that. The code style within UniverSC is not stricly the same, but we want to keep it reasonably similar. If you are unsure on this, we can address this when reviewing the Pull Request so don't worry about it too much.

Documentation

Please document your new functions by editing the manual.

nano man/launch_universc.sh

nano +$(grep -n "help=" launch_universc.sh | cut -d: -f1) launch_universc.sh

Test Cases

Unless you change something trivial, please consider adding test cases. This is important! See the files in the test directory for examples.

If you are unsure how to do this please submit the PR anyway and we can discuss it. If you are able to describe the use case where this feature would be useful, please do so as best you can.

Ask Us!

In general, if you are not sure about something, please ask! You can open an issue on Github or contact the maintainer [email protected]. We to answer publicly so that others can learn from it, too. There are silly questions, if you're having trouble others probably are too.

Legal Stuff

This is a pain to deal with, but we can't avoid it, unfortunately. So, universc is licensed under the "General Public License (GPL) version 3, or later". If your contribution is bigger than a typo fix, then please indicate that you are fine with releasing your code/text under these licenses. E.g. adding a sentence that reads as "I'm fine with GPL 3" is perfectly enough.