Tim Coalson

flirt aborting when the reference isn't a single frame sounds like a very silly change, but less likely to be accidental. Maybe it was a quick hack to prevent the...

I agree that user-editable stuff would be best to keep in as few sections as possible, and closer to the top of the script is better (but not if it...

As a preview, here is some example code that uses the new parameter functions I wrote (the example will be at the top of the new shlib file): ``` opts_AddOptional...

It doesn't seem like a good idea to have two copies/versions of the error checking and job launching code, so if those can be moved outside of the conditional, that...

Separate example launch scripts with settings for YA and lifespan does seem like a possibility worth exploring, given the large number of differences in parameters. The user is expected to...

I can live with a separate example file for lifespan when there are a large number of parameters to change (and in the interest of time). I don't know if...

Also, I think it may be beneficial to reference JSON sidecars, especially if that is the definitive source of those values for some datasets. I don't follow why @mharms would...

As for "--Session" and "--session", etc, I am not a fan of supporting mixed capitalization of option flags (I would go all lower case). Other than compatibility concerns, I think...

I often run locally when editing and testing the pipelines, though I have typically edited the default rather than using the --runlocal option. My new options code doesn't currently accept...

If you use quotes, you can do that on the command line, too. Or, the option can set a different variable and you can test that for nonempty.