Cli fix (#90)

* flip add_cli_args! optunderscores

* actually assign results

* update other humann function calls

* add tests

* add tests

docs/src/humann.md

@@ -426,7 +426,6 @@ See [Using Conda.jl](@ref using-conda)
 
 You can attach names to features using [`humann_rename`](@ref).
 
-
 ## HUMAnN for multiple samples
 
 [Official tutorial link](https://github.com/biobakery/biobakery/wiki/humann3#42-humann-for-multiple-samples)

src/humann.jl

@@ -28,7 +28,7 @@ function humann(inputfile, output; kwargs...)
         append!(c, ["--metaphlan-options", "'--bowtie2db $(ENV["METAPHLAN_BOWTIE2_DB"])'"])
     end
 
-    add_cli_kwargs!(c, kwargs)
+    add_cli_kwargs!(c, kwargs; optunderscores=false)
 
     @info "Running command: $(Cmd(c))"
     return run(Cmd(c))
@@ -271,6 +271,6 @@ function humann_barplot(comm::CommunityProfile, outpath; kwargs...)
     cmd = ["humann_barplot", "--i", tmp, "-o", outpath,
             "--last-metadata", string(last(keys(first(metadata(comm)))))]
 
-    add_cli_kwargs!(cmd, kwargs)
+    add_cli_kwargs!(cmd, kwargs; optunderscores=false)
     run(Cmd(cmd))
 end

src/utils.jl

@@ -34,7 +34,7 @@ function install_deps(env=:BiobakeryUtils; force=false)
     return nothing
 end
 
-function add_cli_kwargs!(cmd, kwargs; optunderscores=false)
+function add_cli_kwargs!(cmd, kwargs; optunderscores=true)
     for (key,val) in pairs(kwargs)
         if val isa Bool
             val && push!(cmd, string("--", key))
@@ -44,7 +44,7 @@ function add_cli_kwargs!(cmd, kwargs; optunderscores=false)
             append!(cmd, [string("--", key), string(val)])
         end
     end
-    !optunderscores && map(c-> startswith(c, "--") ? replace(c, "_"=>"-") : c, cmd)
+    !optunderscores && map!(c-> startswith(c, "--") ? replace(c, "_"=>"-") : c, cmd, cmd)
     return cmd
 end
 

test/runtests.jl

@@ -10,6 +10,16 @@ isdir(Conda.bin_dir(:BiobakeryUtils)) || BiobakeryUtils.install_deps()
 ENV["PATH"] = ENV["PATH"] * ":" * Conda.bin_dir(:BiobakeryUtils)
 
 @testset "CLI" begin
+    @testset "Utilities" begin
+        cmd = ["thing", "foo_bar"]         
+        cmd2 = copy(cmd)
+
+        BiobakeryUtils.add_cli_kwargs!(cmd, Dict(:some_thing=> "foo", :bool=> true))
+        @test all(cmd .== ["thing", "foo_bar", "--some_thing", "foo", "--bool"])
+        BiobakeryUtils.add_cli_kwargs!(cmd2, Dict(:some_thing=> "foo", :bool=> true); optunderscores=false)
+        @test all(cmd2 .== ["thing", "foo_bar", "--some-thing", "foo", "--bool"])
+    end
+
     @testset "Metaphlan" begin
         @test BiobakeryUtils.check_for_install("metaphlan") |> isnothing
         @test BiobakeryUtils.check_for_install("merge_metaphlan_tables.py") |> isnothing