document that --pretend doesn't include arguments passed after "--"

[atravitz]

No description provided.

[mikemhenry]

I love all of these issues @atravitz! Can you add an example of what your running into?

[vyasr]

Alyssa is using the feature of flow that allows you to pass arbitrary arguments to the scheduler, e.g. python project.py submit -n 1 -- -A=MY_ACCOUNT -l OTHER_RESOURCE. The way that we implement this is to literally pass these arguments through to the scheduler, e.g. sbatch -A=MY_ACCOUNT -l OTHER_RESOURCE script.sh, without actually modifying script.sh. As a result, using --pretend doesn't show the changes. I think the most straightforward option here is to simply print the submission command along with the script if flags is not None (or maybe all the time). I'm not inclined to actually change the behavior to actually modify the script, since I don't know if we can guarantee that all command line options actually map to scheduler directives that would be placed in a script and it would also require some extra template hackery to substitute existing lines with new ones if any directives were being overridden.