fix default gamma value error in command line interface

[mmolari]

Hi Pierre!
I was testing the new version of treetime and I got the following error. When calling:

treeknit examples/tree_h3n2_ha.nwk examples/tree_h3n2_na.nwk 

on the example data I got:

ERROR: LoadError: MethodError: no method matching var"#treeknit#162"(::String, ::Int64, ::String, ::Int64, ::Int64, ::Int64, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::typeof(TreeKnit.treeknit), ::String, ::String)
Closest candidates are:
  var"#treeknit#162"(::AbstractString, ::Float64, ::AbstractString, ::Int64, ::Int64, ::Int64, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::typeof(TreeKnit.treeknit), ::AbstractString, ::AbstractString, ::AbstractString...) at ~/Documents/code/TreeKnit.jl/src/cli.jl:36
Stacktrace:
 [1] treeknit(::String, ::String)
   @ TreeKnit ~/Documents/code/TreeKnit.jl/src/cli.jl:59
 [2] command_main(ARGS::Vector{String})
   @ TreeKnit ~/.julia/packages/Comonicon/AXDxW/src/codegen/julia.jl:343
 [3] command_main()
   @ TreeKnit ~/.julia/packages/Comonicon/AXDxW/src/codegen/julia.jl:90
 [4] top-level scope
   @ ~/.julia/bin/treeknit:15
in expression starting at /home/marco/.julia/bin/treeknit:15

This does not happen if I explicitly set --gamma 2 when I call treeknit.

After some investigation I think this is due to the change introduced in #38, where gamma became a float, but not in the default arguments.

The minimal change that I can make to fix the error is just to change the line:

γ::Real = 2

to

γ::Real = 2.

With this change now

treeknit examples/tree_h3n2_ha.nwk examples/tree_h3n2_na.nwk 

works.

I also changed the type of gamma to Float64 in OptArgs and set_up_optargs, but feel free to revert this if there is a reason to keep it to Real.

Hope this is helpful!

Marco

[PierreBarrat]

Hi Marco!
Thanks for spotting this issue and solving it! The change from Real to Float64 in OptArgs is what needed to be done.
This all comes from the fact that keyword arguments in the treeknit function have to have concrete types because of the cli and the Comonicon package.

Can you merge the latest commit on TreeKnit's master branch and see if all checks are successful?
Pierre

[PierreBarrat]

yay! merging