Skipped user prompt in SM-2019.bf about hyphy

[spond]

Dear @ArtPoon,

Thanks for this highly detailed issue report. The strange behavior arises because the Slatkin-Maddison analysis has been ported to use CLI keyword arguments:

hyphy % hyphy sm --help

Available analysis command line options
---------------------------------------
Use --option VALUE syntax to invoke
If a [reqired] option is not provided on the command line, the analysis will prompt for its value
[conditionally required] options may or not be required based on the values of other options

tree [required]
	The Newick tree string defining the topology to use for testing

groups
	The number of compartments to test
	default value: 2

"description-"+(sm.i+1) [computed at run time] [required]
	"Description for sequences in compartment "+(sm.i+1) [computed at run time]

"regexp-"+(sm.i+1) [computed at run time] [required]
	"Regular expression to select the branches in compartment _"+sm.tag+"_" [computed at run time]

replicates
	The number of bootstrap replicates
	default value: 1000

weight
	Probability of branch selection for structured permutation [0-1]; 0 = classical Slatkin-Maddison, 1 = fully structured
	default value: 0.2

use-bootstrap
	Use bootstrap weights to respect well supported clades
	default value: Yes

output
	Write the JSON file here (default is to save to the same path as the tree file + '_SM.json')
	default value: sm.json_file [computed at run time]

In particular, the number of groups is given a default value of 2 which will be consumed in the interactive mode, unless you specify the -I (capital eye) flag, when you call HyPhy. So, if you do hyphy -I and then follow your workflow, then all prompts will be made.

Best,
Sergei

PS You can also specify some (or all) of the analysis arguments via CLI flags, e.g.

$hyphy sm --groups 3 

(the rest of the no-default-value prompts will be via `stdin`)

[ArtPoon]

Wow I'm so old that I was trying to run the CLI the ancient way. Thanks for the correction :-)