Add argument parsing to cli

Project.toml

@@ -4,6 +4,7 @@ authors = ["Thomas A. Christensen II <25492070+MillironX@users.noreply.github.co
 version = "0.3.0"
 
 [deps]
+ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"

beefblup

@@ -2,5 +2,51 @@
 #=
 exec julia --project="$(realpath "$(dirname "${BASH_SOURCE[0]}")")" "${BASH_SOURCE[0]}" "$@"
 =#
+# beefblup cli
+# Provides a convenient CLI for using beefblup
+# cSpell:includeRegExp #.*
+# cSpell:includeRegExp ("""|''')[^\1]*\1
+
+# Import packages
 using BeefBLUP
+using ArgParse
+
+# If this is run without arguments, catch that before parsing
+if isempty(ARGS)
     BeefBLUP.beefblup()
+    return
+end
+
+# Setup the argument table
+argsettings = ArgParseSettings()
+@add_arg_table argsettings begin
+    "datafile"
+        help = "datasheet containing the pedigree, fixed effects, and response trait formatted in CSV"
+        required = true
+        arg_type = String
+    "resultsfile"
+        help = "filename for storing the results of the analysis"
+        required = false
+        arg_type = String
+    "--heritability", "-t"
+        help = "heritability of the response trait being analyzed"
+        required = true
+        arg_type = Float64
+end
+
+arguments = parse_args(argsettings)
+
+println("Parsed args:")
+for (arg,val) in arguments
+    println("  $arg  =>  $val")
+end
+
+h2 = arguments["heritability"]
+
+if isnothing(arguments["resultsfile"])
+    BeefBLUP.beefblup(arguments["datafile"], h2)
+    exit()
+end
+
+print(arguments["datafile"], arguments["resultsfile"], string(h2))
+BeefBLUP.beefblup(arguments["datafile"], arguments["resultsfile"], h2)