Contributions are welcome and can
come in different forms, including but not limited to:
- Adding new features.
- Improving documentation.
- Addressing one of the open issues.
- Creating new issues.
- Even fixing typos.
Please read the following documents before making changes to the
codebase.
Environment Setup
In order to contribute to the project, it is a better idea to have
your own local copy of CausalGPS on your Github account. Here
are the steps:
- Navigate to CausalGPS Github repository, and
at the top right corner, click on the
Fork button. This
will add a clone of the project to your Github account.
- Open your terminal (or Gitbash for Windows, Anaconda prompt, …) and
run the following command (brackets are not included):
git clone git@github.com:[your user name]/CausalGPS.git
- If you do not already have an SSH key, you need to generate one.
Read more here.
- Now, you can modify the codebase and track your modification.
- It is a good idea to create a new branch to work on the codebase.
Read the following instructions for git branching.
Git Branching Model
Although, in your personal repository, you can pick any branch name,
however, in order to keep consistency and also understand who is working
on what, the following convention is strongly recommended. In this
project, we follow the convention that is proposed by Vincent Driessen
in his A
successful Git branching model post.
Here is the summary of the branches:
- master: master branch only hosts the released
software packages. Only project maintainers have write access on the
master branch.
- develop: develop branch is considered the main
branch where the source code of HEAD always reflects a state with the
latest delivered development changes for the next release.
- supporting branch: There are different supporting
branches, three main supporting branches that we suggest the
contributors to follow the naming convention includes:
- feature: we start a new feature branch to add new features
to the software. The naming convention is
iss[issue_number]_short_description. For example, if I need to add
unittest to one of the functions in the package and the issue number is
12, iss12_add_unittest can be a valid git branch name. We start it with
the issue number to go back and take a look at the issue details if
necessary. Although feature branches are temporary, this naming
convention helps developers to understand the situation while working on
the codebase. If you are working on some features that there is no open
issue for that, please open an issue here and
assign it to yourself. You can also make a comment that you are working
on that.
- hotfix: hotfix branches will be only used for fixing a bug
on a released package. After fixing the bug, the third digit of the
version number should be incremented by one. For example, 2.3.5 –>
2.3.6. These branches will be prefixed with hotfix and followed by the
upcoming version number (e.g., in this case, hotfix_2.3.6)
- release: Release branches support the preparation of a new
production release.
Where to submit pull requests?
All pull requests should be submitted to
base repository: NSAPH-Software/CausalGPS and
base: develop branch.
Pull request checklist
- Please run
devtools::document(),
devtools::load_all() after your final modifications.
- Make sure that your modified code passes all checks and tests (you
can run
devtools::check() in RStudio)
- Your PR should pass all the CI and reviews so we can merge it.
- Add a line(s) about the modification to the NEWS.md file.
- If you are adding new features, please make sure that appropriate
documentation is added or updated.
- Please clean up white spaces. Read more here.
Reporting bugs
Please report potential bugs by creating a new issue
or sending us an email. Please include the following information in your
bug report:
- A brief description of what you are doing, what you expected to
happen, and what happened.
- OS that you are using and whether you are using a personal computer
or HPC cluster.
- The version of the package that you have installed.
Style Guide
In this project, we follow the tidyverse style guide.
Summary
Names
- File names all snake_case and ends with .R (e.g.,
create_matching.R)
- variable names small letter and separate with _ if need (e.g.,
delta_n)
- Function names should follow snake_case style (e.g.,
generate_data)
- Function names follow verb+output convention (e.g.,
compute_resid)
Spaces and Indentation
- Indentations are two spaces (do not use tab)
- Place space around binary operators (e.g., x + y)
#Acceptable:
z <- x + y
#Not recommended:
z<-x+y # (no space)
z<- x+y
z<-x +y
#Acceptable:
a <- matrix(c(1:100), nrow = 5)
#Not recommended:
a <- matrix(c(1:100),nrow = 5) # (no space after comma)
a <- matrix( c(1:100), nrow = 5 ) # (extra space after and before parentheses)
a<-matrix(c(1:100), nrow = 5) # (no space around unary operator <- )
- Place space after # and before commenting and avoid multiple
###
#Acceptable:
# This is a comment
#Not recommended:
#This is a comment
# This is a comment (more than one space after #)
## This is a comment (multiple #)
### This is a comment (multiple # and more than one space)
- Do not put space at the opening and closing the parenthesis
#Acceptable:
x <- (z + y)
#Not recommended:
x <- ( z + y ) # (unnecessary space)
x <- (z + y )
x <- ( z + y)
- Place a space before and after
() when used with
if, for, or while.
#Acceptible
if (x > 2) {
print(x)
}
# Not recommended
if(x > 2){
print(x)
}
Other notes
- Maximum line length is 80 character
- Use explicit returns
- Use explicit tags in documentation (e.g., @title, @description, …)
Notes on SuperLearner
In this package we create a customized wrapper for the SuperLearner
internal libraries. Please read Notes on SL Wrappers for more
details.
Logger
Use logger to investigate the internal process. The default level is
“INFO”, which writes messages into “CausalGPS.log” file. You can use
update_logger function to change the log file location and
level.