Github issues tracker has increasingly become my research to-do list. Far beyond bugs and features of the code associated with the project, the issues sign-post different directions for investigation and the progress I’ve made in each. Tags serve to group issues related to a common sub-project (as in my pdg-control) repo or priotize tasks (as in my nonparametric-bayes repo.
Issues not only have title and tags, but support a comment thread for progress and discussion of the issue. Thanks to github-flavored-markdown, issues can reference each other simply by number, and can be updated or closed automatically by mentioning the issue number in a commit.
Issues can also be grouped into shared deadlines, or milestones; a feature I haven’t fully exploited (but see our ews-review paper). In any collaborative project the issues can be assigned to different people, (though currently this requires they have a Github account).
A consequence of this workflow is a conveniently numbered, color-coded and cross-linked collection of steps involved in a given research project. This tends to be a higher-level overview than the individual commit log, particularly as I often use commits to track multiple runs with different parameters, or move code across to different supercomputers that do the actual runs.
I am still figuring out the right level or “resolution” on which to create and track issues.1 On one extreme, almost every commit could be seen as resolving an issue. The ideal use for me is probably nearer the other extreme, where individual issues are rather big-picture, and may be referenced by many commits. Perhaps the right way to think about it is that the questions addressed by resolving an issue are on the level of what is interesting to others, while changes in individual commits are more for me. Hopefully I get better at finding this relevant level.
Another nice feature of issues is that they can be closed when a particular line of investigation hits a dead-end, or stalls, or when the problem is resolved. Unlike the resulting paper from an investigation which essentially summarizes the issues that were closed successfully, the issues tracker also reveals the dead-ends, as well as those issues that were not closed a time of publication (but perhaps left to “further research”). Hopefully I will have some decent examples of this in the repositories accompanying my next papers.
Unlike issues, commits do not have a native tag structure (so-called “tags” mark important events in the commit history rather than grouping common commits). So at least this would group commits by the tag of the associated issue.↩