pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
20 stars 7 forks source link

rename 'config_file' arg for looper init? #395

Closed nsheff closed 6 months ago

nsheff commented 11 months ago

this is confusing:

looper init
usage: looper init [-h] [-f] [-o DIR] [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-p]
                   config_file
looper init: error: the following arguments are required: config_file
looper init --help
usage: looper init [-h] [-f] [-o DIR] [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-p]
                   config_file

Initialize looper dotfile.

positional arguments:
  config_file                        Project configuration file (YAML)

it seems like there's a 'looper config' and a 'project config', but they aren't always disambiguated, make it confusing for the user as to what the arguments should be.

nsheff commented 11 months ago

maybe:'

"Initialize looper config file" positional arguments could be pep_config instead of config_file ?

looper run also has --looper-config LOOPER_CONFIG and also config_file arguments, which is confusing.

looper run --help
usage: looper run [-h] [-i] [-d] [-t S] [-x S] [-y S] [-f] [--divvy DIVCFG] [-p P] [-s S]
                  [-c K [K ...]] [-u X] [-n N] [--looper-config LOOPER_CONFIG]
                  [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-l N] [-k N]
                  [--sel-attr ATTR] [--sel-excl [E [E ...]] | --sel-incl [I [I ...]]]
                  [-a A [A ...]]
                  [config_file]
nsheff commented 11 months ago

Some related code here:

https://github.com/pepkit/looper/blob/df15cbda34767ab60da71a4261afda938b574f24/looper/utils.py#L361-L373

donaldcampbelljr commented 8 months ago

This appears to be solved.