Work items for the mini-hackathon

[winni2k]

This issue tracks the work items of the mini-hackathon.

Abbreviations

SM=snakemake CI=continuous integration

Procedure

Grab a work item and create an issue for it. Mention this issue in the issue you create so that we can track progress toward each issue and who is working on what. Updates on issue progress go in the comments of the new issue. Each work item can be broken down into smaller work items by creating more issues. Each new issue should mention the issue that it is a part of. When you are ready to start working on an issue, assign yourself to it on github. Happy coding!

Work Items

Job tracking and Slurm interaction

SM still has some rough edges when interacting with the slurm scheduler.

Problems

• On ctrl-c SM does not run scancel to cancel jobs that it has kicked off
• SM does not appear to take note when jobs are killed by slurm through certain ways (for example OOM kills and alloted time expiration)

Fredrik's PR on pathlib support

Fredrik has written a PR for native support of pathlib.Path objects in SM that needs to be shepherded through the PR acceptance process.

Todos

• Is pathlib support still a problem with python >= 3.6?
• The PR has gotten stale and needs rebasing onto upstream's master branch

Get an SM CI for testing slurm interactions up and running

Without tests, our wonderful new features can/will regress, and we will only find out that they have regressed after a new version of SM has shipped. No one wants that ;)

Problems

• Survey current SM CI landscape
  • Is SM being tested continuously?
  • Is SM being tested continuously for slurm interactions?
  • Can we shoehorn the current SM CI to also test our new slurm features?

Solutions

• Properly testing slurm integration will likely require some sort of VM/container to spin up slurm and run our tests

[winni2k]

Naming anonymous rules

Anonymous rules are great, but they have no name. It would be really cool to be able to specify the name of each rule programmatically, perhaps through a docstring.