CONTRIBUTING.md

In thomasyu888/puresynapser: R client for Sage Bionetworks' Synapse API

Contributing

We welcome all contributions! Please head to issues to either file any bugs/feature requests or find a task you want to assist with. Make sure to assign yourself the task if you decide to work on it.

The Development Life Cycle

Fork and clone this repository

1. See the Github docs for how to make a copy (a fork) of a repository to your own Github account.
2. Then, clone the repository to your local machine so you can begin making changes.
3. Add this repository as an upstream remote on your local git repository so that you are able to fetch the latest commits.

4. On your local machine make sure you have the latest version of the develop branch:

   git checkout develop git pull upstream develop

Install dependencies

We use renv for development of this package. Make sure renv is installed and run this command to load the dependencies

renv::init()

More details on how to use renv

Developing with GitHub

puresynapser follows the standard git flow development strategy.

To ensure the most fluid development, try not to push to your develop or main branch.

1. (Assuming you have followed all 4 steps above in the "fork and clone this repository" section). Navigate to your cloned repository on your computer/server.

2. Make sure your develop branch is up to date with the thomasyu888/puresynapser develop branch.

   cd {your-github-username}/puresynapser git checkout develop git pull upstream develop

3. Create a feature branch which off the develop branch. If there is a GitHub/JIRA issue that you are addressing, name the branch after the issue with some more detail (like {GH|JIRA}-123-add-some-new-feature).

   git checkout develop git checkout -b GH-123-add-some-new-feature

4. At this point, you have only created the branch locally, you need to push this to your fork on GitHub.

   ```

   git push --set-upstream origin GH-123-add-some-new-feature ```

   You should now be able to see the branch on GitHub. Make commits as you deem necessary. It helps to provide useful commit messages - a commit message saying 'Update' is a lot less helpful than saying 'Remove X parameter because it was unused'.

   git commit changed_file.txt -m "Remove X parameter because it was unused" git push

5. (Make sure you have follow instructions in "Install dependencies") Make sure to run the auto R code formatter, styler.

   styler::style_pkg(".")

6. (Make sure you have follow instructions in "Install dependencies") Once you have made your additions or changes, make sure you write tests and run the test suite. More information on testing below.

   testthat...

7. Once you have completed all the steps above, in Github, create a pull request from the feature branch of your fork to the develop branch of thomasyu888/puresynapser.

A code maintainer must review and accept your pull request. A code review ideally happens with both the contributor and the reviewer present, but is not strictly required for contributing. This can be performed remotely (e.g., Zoom, Hangout, or other video or phone conference).

Development of Package

The basic structure of this package is built off of Best Practices for API packages.

package dependency

We use renv for development of this package. Whenever a package is installed, be sure to run:

# Install package
renv::install(...)
# Snapshot
renv::snapshot()

More details on how to use renv

Testing

This package will leverage testthat to test its functions.

Documentation

We leverage roxygen2 to generate docs. To generate docs, you will want to:

roxygen2::roxygenise()

thomasyu888/puresynapser documentation built on Jan. 30, 2022, 12:14 p.m.