looper cli is not taking priority if cli modifiers are used in looper config

[donaldcampbelljr]

if i use looper with a limit command
looper run --limit 2

but then place this in my looper config:

pep_config: project/project_config.yaml
output_dir: "results"
pipeline_interfaces:
  - pipeline/pipeline_interface.yaml
cli:
  run:
    limit: 1

The config file takes priority but it should be the other way around. The CLI should always take priority.

[donaldcampbelljr]

Ok, I think I see where the problem is located.

In function enrich_args_via_cfg, we take args from the CLI + any default args and then overwrite them based on what has been provided in other locations.

Here is a problem though, if I flip the sequence and have the og arguments take priority, then the non-user supplied default values will overwrite those provided in the config files.

[nsheff]

Previous versions of looper had the correct behavior, so the change must have something to do with the new arguments system.

[donaldcampbelljr]

I've pushed a fix for this.