Deciphering Life: One Bit at a Time - Package Version Increment Pre- and Post-Commit Hooks

If you just want the hook scripts, check this gist. If you want to know some of the motivation behind writing them, and about the internals, then read on.

Package Version Incrementing

A good practice to get into is incrementing the minor version number (i.e. going from 0.0.1 to 0.0.2) after each git commit when developing packages (this is recommended by the Bioconductor devs as well ). This makes it very easy to know what changes are in your currently installed version, and if you remembered to actually install the most recent version for testing.

If you are like me, this is a hard habit to get into, especially because I have to manually remember to go over to the DESCRIPTION file and up the version number when I make a commit. It seems I am not the only one according to this tweet from Kevin Ushey:

Is there a git hook / alias that can auto-increment a package patch number (in DESCRIPTION) with each commit? #rstats #lazyweb
— Kevin Ushey (@kevin_ushey) February 6, 2014

I thought it sounded like a good idea, and got to work.

Git Hooks

For those who don’t know, git allows you to have custom scripts (hooks) that are run at different steps in an overall git workflow. These are essentially executable scripts stored in the .git/hooks/ folder of an individual repo.

For our purposes, we would want something that runs either just before commit (pre-commit hook) or just after (post-commit hook), because we want to make modifications that are associated with commits themselves. The pre-commit hook is most appropriate, because we can make file modifications before our actual commit. However, if the user is already using a validation pre-commit hook, or wants the version change separate, a post-commit hook might be better. Both are available in the gist.

I suppose this could have been done using an alias to run a script, but the nice thing about commit hooks is they are tied to the action of committing itself, instead of as a separate action.

Rscript & read and write.dcf

R already has some nice functionality for reading and writing the debian control format (dcf) DESCRIPTION files that are required at the root of an R package. So ideally we could write our script in R and not have to do parsing from the bash shell. Rscript lets us do this easily by defining in the shebang (#!) where to find the executable to run the script.

#!/path/2/Rscript

The rest is simply reading the DESCRIPTION file (read.dcf), getting the current version, incrementing, writing a new DESCRIPTION file (write.dcf), and making the changes to the git commit.

currDCF <- read.dcf("DESCRIPTION")
currVersion <- currDCF[1,"Version"]
splitVersion <- strsplit(currVersion, ".", fixed=TRUE)[[1]]
nVer <- length(splitVersion)
currEndVersion <- as.integer(splitVersion[nVer])
newEndVersion <- as.character(currEndVersion + 1)
splitVersion[nVer] <- newEndVersion
newVersion <- paste(splitVersion, collapse=".")
currDCF[1,"Version"] <- newVersion
write.dcf(currDCF, "DESCRIPTION")

In order to add the new DESCRIPTION file (pre-commit), or do a subsequent commit, we do need a couple of system calls to git itself.

system("git add DESCRIPTION")

We also need to check that there are files to actually be commited (for the pre-commit) before we go ahead and increment the version. The git diff command will tell us if there is anything or not.

fileDiff <- system("git diff HEAD --name-only", intern=TRUE)

Overriding Increment

There is two wrinkles to this process. What if you don’t want to increment the version of your package for a good reason, like you’ve just changed the major version number? Or, in the case of the post-commit, you don’t want to end up in an infinite loop of incrementing.

But you can’t pass arguments from the git call to the script. It turns out we can prepend an environment variable definition, and then get it using Sys.getenv. So our script checks for the environment variable, and if it is defined, sets it. Otherwise it uses the default that is initialized at the beginning of the script.

doIncrement <- TRUE # default
 
# get the environment variable and modify if necessary
tmpEnv <- as.logical(Sys.getenv("doIncrement"))
if (!is.na(tmpEnv)){
  doIncrement <- tmpEnv
}

So to change the default value of doIncrement, you make your commit like this:

doIncrement=FALSE git commit -m "commit message"

This same behavior is used to keep from making an infinite number of increments in the post-commit script.

Installation

To install the hooks, create the pre-commit or post-commit file in your .git/hooks directory, paste in the commands from the appropriate one in the gist, save the file, and make it executable (chmod on ’nix systems). I have been able to use both of these on ’nix and Windows systems. Also don’t forget to provide the path to your Rscript executable (either in the same directory as your R binary, or at /usr/bin/Rscript).

Just in testing these scripts I have become surprised at the potential utility, and I hope you find them useful as well if you are developing R packages (which you should be if you are writing any analysis).

If you have comments, suggestions, or improvements feel free to modify the gist, or leave a comment, contact me on twitter, or send me an email (check the About link above).

Caveats

The script assumes the version separator is “.”, and that you always are incrementing the last value. If you don’t like it, feel free to change it.

Reuse

https://creativecommons.org/licenses/by/4.0/

Citation

BibTeX citation:

@online{mflight2014,
  author = {Robert M Flight},
  title = {Package {Version} {Increment} {Pre-} and {Post-Commit}
    {Hooks}},
  date = {2014-02-07},
  url = {https://rmflight.github.io/posts/2014-02-07-package-version-increment-pre-and-post-commit-hooks},
  langid = {en}
}

For attribution, please cite this work as:

Robert M Flight. 2014. “Package Version Increment Pre- and Post-Commit Hooks.” February 7, 2014. https://rmflight.github.io/posts/2014-02-07-package-version-increment-pre-and-post-commit-hooks.