logs as a CSV, config and tests pass

Project.toml

@@ -12,7 +12,6 @@ Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SharedArrays = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
 [compat]

src/Cambrian.jl

@@ -6,7 +6,6 @@ using Statistics
 using YAML
 using JSON
 import Formatting
-import UUIDs
 import Dates
 
 include("config.jl")

src/GA.jl

@@ -32,7 +32,7 @@ evaluate(e::GAEvo) = fitness_evaluate(e, e.fitness)
 """
 populate(e::GAEvo)
 """
-function populate(e::GAEvo)
+function ga_populate(e::AbstractEvolution)
     new_pop = Array{Individual}(undef, 0)
     if e.config.n_elite > 0
         sort!(e.population)
@@ -53,3 +53,7 @@ function populate(e::GAEvo)
     end
     e.population = new_pop
 end
+
+function populate(e::GAEvo)
+    ga_populate(e)
+end

src/config.jl

@@ -1,4 +1,4 @@
-export get_base_config, get_config
+export get_config
 
 function get_base_config()
     (seed = 0,           # evolution seed
@@ -7,17 +7,25 @@ function get_base_config()
      n_elite = 1,        # elites to carry over each generation
      n_gen = 10,         # number of generations
      log_gen = 1,        # log every x generations
-     save_gen = 1        # save population every x generation
+     save_gen = 1,       # save population every x generation
+     id = string(Dates.now()) # run id
      )
 end
 
+"convert Dict to named tuple"
+function get_config(cfg::Dict)
+    (; (Symbol(k)=>v for (k, v) in cfg)...)
+end
+
+"combine YAML file and kwargs, make sure ID is specified"
 function get_config(cfg_file::String; kwargs...)
     cfg = YAML.load_file(cfg_file)
-    f_cfg = (; (Symbol(k) => v for (k,v) in cfg)...)
-    k_cfg = (; (k=>v for (k, v) in kwargs)...)
-    cfg = merge(f_cfg, k_cfg)
+    for (k, v) in kwargs
+        cfg[String(k)] = v
+    end
+    # generate id, use date if no existing id
     if ~(:id in keys(cfg))
-        cfg = merge(cfg, (; id = string(UUIDs.uuid4())))
+        cfg["id"] = string(Dates.now())
     end
-    cfg
+    get_config(cfg)
 end

src/evolution.jl

@@ -31,7 +31,7 @@ function log_gen(e::AbstractEvolution)
     for d in 1:e.config.d_fitness
         maxs = map(i->i.fitness[d], e.population)
         with_logger(e.logger) do
-            @info Formatting.format("{1:04d} {2:e} {3:e} {4:e}",
+            @info Formatting.format("{1:04d},{2:e},{3:e},{4:e}",
                                     e.gen, maximum(maxs), mean(maxs), std(maxs))
         end
     end

src/individual.jl

@@ -1,5 +1,5 @@
 export Individual, BoolIndividual, FloatIndividual, crossover, mutate
-import Base: isless, print
+import Base: isless, show
 
 """
 every Individual subtype needs to implement:
@@ -25,23 +25,19 @@ function isless(i1::Individual, i2::Individual)
 end
 
 function ind_parse(st::String)
-    dict = JSON.Parser.parse(st)
-    for i in 1:length(dict["fitness"])
-        if dict["fitness"][i] == nothing
-            dict["fitness"][i] = -Inf
+    d = JSON.Parser.parse(st)
+    for i in 1:length(d["fitness"])
+        if d["fitness"][i] == nothing
+            d["fitness"][i] = -Inf
         end
     end
-    dict
+    d
 end
 
-function print(io::IO, ind::Individual)
+function show(io::IO, ind::Individual)
     print(io, JSON.json(ind))
 end
 
-function String(ind::Individual)
-    string(ind)
-end
-
 "default crossover method, using uniform crossover for N parents"
 function crossover(parents::Vararg{Individual})
     l = minimum(map(i->length(i.genes), parents))

src/logger.jl

@@ -34,7 +34,7 @@ function handle_message(logger::CambrianLogger, level, message, _module, group,
     iob = IOContext(buf, logger.stream)
     levelstr = level == Warn ? "Warning" : string(level)
     msglines = split(chomp(string(message)), '\n')
-    println(iob, Dates.now(), "\tCambrian ", levelstr, " ", msglines[1])
+    println(iob, Dates.now(), ",Cambrian,", levelstr, ",", msglines[1])
     for i in 2:length(msglines)
         println(iob, "│ ", msglines[i])
     end