Bee Breeding with Attributes (credit to Direwolf20 for idea)

-- BeeAnalyzer 4.0
-- Original code by Direwolf20
-- Hotfix 1 by Mandydax
-- Hotfix 2 by Mikeyhun/MaaadMike
-- Major overhaul by MacLeopold
--   Breeds bees with best attributes in this order:
--   fertility, speed, nocturnal, flyer, cave, temperature tolerance, humidity tolerance
--   other attributes are ignored (lifespawn, flowers, effect and territory)
--   Can specify multiple target species to help with keeping to the correct line

local targetSpecies = { ... }

local currslot = 1
local princess = 0
local bestDrone = 0
local data={}
local currData = {}
local princessData = {}
local droneData = {}
local countBees = 0
local beeTable = {}
local currScore = 0
local toleranceTable = {}
local toleranceString = {}
local needsUpdate = ""
local needPrincess = false

s = peripheral.wrap("right")

-- Scores for all bees

-- Mundane Bees
beeTable["Forest"] = 1
beeTable["Meadows"] = 1
beeTable["Modest"] = 2
beeTable["Tropical"] = 2
beeTable["Wintry"] = 2
beeTable["Marshy"] = 2
beeTable["Embittered"] = 2

-- End Branch
beeTable["Ender"] = 2

-- Common Branch
beeTable["Common"] = 2
beeTable["Cultivated"] = 4

-- Noble Branch
beeTable["Noble"] = 8
beeTable["Majestic"] = 16
beeTable["Imperial"] = 32

-- Industrious Branch
beeTable["Diligent"] = 8
beeTable["Unweary"] = 16
beeTable["Industrious"] = 32

-- Heroic Branch
beeTable["Steadfast"] = 8
beeTable["Valiant"] = 16
beeTable["Heroic"] = 32

-- Infernal Branch
beeTable["Sinister"] = 8
beeTable["Fiendish"] = 16
beeTable["Demonic"] = 32

-- Austere Branch
beeTable["Frugal"] = 16
beeTable["Austere"] = 32

-- Tropical Branch
beeTable["Exotic"] = 16
beeTable["Edenic"] = 32

-- Wintry Branch
beeTable["Icy"] = 16
beeTable["Glacial"] = 32
beeTable["Frigid"] = 16
beeTable["Absolute"] = 32

-- Festive Branch
beeTable["Leporine"] = 32
beeTable["Merry"] = 32
beeTable["Tipsy"] = 32
beeTable["Celebratory"] = 64

-- Agrarian Branch
beeTable["Rural"] = 8
beeTable["Farmed"] = 16

-- Boggy Branch
beeTable["Swamp"] = 16
beeTable["Boggy"] = 32
beeTable["Fungal"] = 64

-- Extra Bees

-- Agricultural Branch
beeTable["Fermented"] = 16
beeTable["Bovine"] = 16
beeTable["Caffeine"] = 16
beeTable["Citrus"] = 32
beeTable["Minty"] = 32

-- Barren Branch
beeTable["Arid"] = 8
beeTable["Barren"] = 16
beeTable["Desolate"] = 32

-- Hostile Branch
beeTable["Decaying"] = 64
beeTable["Skeletal"] = 64
beeTable["Creepy"] = 64

-- Rocky Branch
beeTable["Rocky"] = 2
beeTable["Tolerant"] = 8
beeTable["Hardy"] = 16
beeTable["Resilient"] = 32

-- Rusty Branch
beeTable["Rusty"] = 64
beeTable["Corroded"] = 64
beeTable["Tarnished"] = 64
beeTable["Leaden"] = 64

-- Metallic Branch
beeTable["Lustered"] = 64
beeTable["Galvanized"] = 128
beeTable["Invincible"] = 64

-- Alloyed Branch
beeTable["Impregnable"] = 64
beeTable["Resolute"] = 128
beeTable["Brazen"] = 256
beeTable["Fortified"] = 128
beeTable["Lustrous"] = 64

-- Precious Branch
beeTable["Shining"] = 128
beeTable["Glittering"] = 256
beeTable["Precious"] = 512
beeTable["Valuable"] = 512

-- Mineral Branch
beeTable["Lapis"] = 64
beeTable["Sodalite"] = 128
beeTable["Pyrite"] = 128
beeTable["Bauxite"] = 64
beeTable["Cinnabar"] = 64
beeTable["Sphalerite"] = 128

-- Gemstone Branch
beeTable["Emerald"] = 128
beeTable["Ruby"] = 256
beeTable["Sapphire"] = 256
beeTable["Olivine"] = 256
beeTable["Diamond"] = 512

-- Nuclear Branch
beeTable["Unstable"] = 64
beeTable["Nuclear"] = 128
beeTable["Radioactive"] = 256

-- Historic Branch
beeTable["Ancient"] = 16
beeTable["Primeval"] = 32
beeTable["Prehistoric"] = 64
beeTable["Relic"] = 128

-- Fossilized Branch
beeTable["Fossiled"] = 64
beeTable["Resinous"] = 64
beeTable["Oily"] = 64
beeTable["Preserved"] = 64

-- Refined Branch
beeTable["Distilled"] = 128
beeTable["Refined"] = 256
beeTable["Tarry"] = 512
beeTable["Elastic"] = 512

-- Aquatic Branch
beeTable["Water"] = 2
beeTable["River"] = 8
beeTable["Ocean"] = 8
beeTable["Stained"] = 16

-- Saccharine Branch
beeTable["Sweetened"] = 16
beeTable["Sugary"] = 32
beeTable["Fruity"] = 64

-- Classical Branch
beeTable["Marbled"] = 2
beeTable["Gothic"] = 64
beeTable["Renaissance"] = 128
beeTable["Classical"] = 256

-- Volcanic Branch
beeTable["Angry"] = 16
beeTable["Furious"] = 32
beeTable["Volcanic"] = 64
beeTable["Glowering"] = 64

-- Viscous Branch
beeTable["Viscous"] = 32
beeTable["Glutinous"] = 64
beeTable["Sticky"] = 128

-- Virulent Branch
beeTable["Malicious"] = 16
beeTable["Infectious"] = 32
beeTable["Virulent"] = 64

-- Caustic Branch
beeTable["Corrosive"] = 128
beeTable["Caustic"] = 256
beeTable["Acidic"] = 512

-- Energetic Branch
beeTable["Excited"] = 32
beeTable["Energetic"] = 64
beeTable["Ecstatic"] = 128

-- Shadow Branch
beeTable["Shadowed"] = 64
beeTable["Darkened"] = 128
beeTable["Abyssmal"] = 256

-- Primary Branch
beeTable["Maroon"] = 32
beeTable["Saffron"] = 32
beeTable["Prussian"] = 32
beeTable["Natural"] = 32
beeTable["Ebony"] = 32
beeTable["Bleached"] = 32
beeTable["Sepia"] = 32

-- Secondary Branch
beeTable["Amber"] = 64
beeTable["Turquoise"] = 64
beeTable["Indigo"] = 64
beeTable["Slate"] = 64
beeTable["Azure"] = 64
beeTable["Lavender"] = 64
beeTable["Lime"] = 64

-- Tertiary Branch
beeTable["Fuchsia"] = 128
beeTable["Ashen"] = 128

-- Hungry Branch
beeTable["Hungry"] = 16
beeTable["Starved"] = 32
beeTable["Ravenous"] = 64

-- Confused Branch
beeTable["Dazed"] = 64
beeTable["Irrational"] = 128
beeTable["Delirious"] = 256

-- Forestry Branch
beeTable["Pulped"] = 32
beeTable["Spoiled"] = 64
beeTable["Decomposed"] = 128

-- Wooden Branch
beeTable["Wooden"] = 16
beeTable["Lumbered"] = 32
beeTable["Timbered"] = 64

-- Beastly Branch
beeTable["Jaded"] = 256

-- Thaumic Bees

-- Arcane Branch
beeTable["Esoteric"] = 64
beeTable["Mysterious"] = 128
beeTable["Arcane"] = 256

-- Supernatural Branch
beeTable["Charmed"] = 32
beeTable["Enchanted"] = 64
beeTable["Supernatural"] = 128

-- Scholarly Branch
beeTable["Pupil"] = 512
beeTable["Scholarly"] = 1024
beeTable["Savant"] = 2048

-- Thaumic Branch
beeTable["Stark"] = 512
beeTable["Aura"] = 1024
beeTable["Ignis"] = 1024
beeTable["Aqua"] = 1024
beeTable["Solum"] = 1024
beeTable["Praecantatio"] = 1024

-- Skulking Branch
beeTable["Skulking"] = 256
beeTable["Brainy"] = 512
beeTable["Gossamer"] = 512
beeTable["Wispy"] = 1024
beeTable["Batty"] = 512
beeTable["Ghastly"] = 512

-- Aware Branch
beeTable["Aware"] = 64
beeTable["Vis"] = 128
beeTable["Pure"] = 256
beeTable["Flux"] = 256
beeTable["Node"] = 512
beeTable["Rejuvenating"] = 256

-- Time Branch
beeTable["Timely"] = 128
beeTable["Lordly"] = 256
beeTable["Doctoral"] = 512

-- Soulful Branch
beeTable["Spirit"] = 128
beeTable["Soul"] = 256

-- Alchemical Branch
beeTable["Minium"] = 256

-- Metallic Branch
beeTable["Iron"] = 64
beeTable["Copper"] = 64
beeTable["Tin"] = 64
beeTable["Silver"] = 64
beeTable["Lead"] = 64
beeTable["Gold"] = 128

-- Gem Branch
beeTable["Diamond"] = 512
beeTable["Emerald"] = 128

-- Fleshy Branch
beeTable["Poultry"] = 512
beeTable["Beefy"] = 512
beeTable["Porcine"] = 512

-- Only scores species that you specify on the command line
local targeting = false
local targetFound = false
if #targetSpecies > 0 then
  for key, value in pairs(beeTable) do
    targetFound = false
    for i, target in ipairs(targetSpecies) do
      if key == target then
        print("Targeting "..key.." species.")
        targeting = true
        targetFound = true
        break
      end
    end
    if not targetFound then
      beeTable[key] = 0
    end
  end
  if not targeting then
    print("Did not find target species")
    return
  end
end

-- Fix for some versions returning bees.species.*
function fixName(name)
  return name:gsub("bees%.species%.",""):gsub("^.", string.upper)
end

toleranceTable["NONE"] = 0
toleranceTable["UP_1"] = 1
toleranceTable["UP_2"] = 2
toleranceTable["DOWN_1"] = 1
toleranceTable["DOWN_2"] = 2
toleranceTable["BOTH_1"] = 2
toleranceTable["BOTH_2"] = 4

toleranceString["NONE"] = "    "
toleranceString["UP_1"] = " +1 "
toleranceString["UP_2"] = " +2 "
toleranceString["DOWN_1"] = " -1 "
toleranceString["DOWN_2"] = " -2 "
toleranceString["BOTH_1"] = "+-1 "
toleranceString["BOTH_2"] = "+-2 "


function getBees()
  io.write("waiting for bees.")
  -- catalog bees in own inventory
  local free = {}
  for i = 1,16 do
    turtle.select(i)
    if turtle.getItemCount(i) > 0 then
      countBees = countBees + 1
      if #free > 0 then
        j = table.remove(free, 1)
        turtle.transferTo(j)
        table.insert(free, i)
      end
    else
      table.insert(free, i)
    end
  end
  -- get any bees from apiary
  if countBees < 2 or needPrincess then
    turtle.select(1)
    while not turtle.suck() do
      sleep(10)
      io.write(".")
    end
    countBees = countBees + 1
  end
  for i = 1,6 do
    if turtle.suck() then countBees = countBees + 1 end
  end
  print()
end

function returnBees()
   turtle.select(princess)
   s.dropSneaky(1,1)
   turtle.select(bestDrone)
   s.dropSneaky(0,1)
end

function ditchCombs()
  turtle.turnLeft()
  m = peripheral.wrap("front")
  for i = 1,8 do
    turtle.suck()
    while (not m.isBee()) and (turtle.getItemCount(i) > 0) do
      turtle.select(i)
      turtle.drop()
      if not m.isBee() then
        turtle.suck()
        turtle.dropDown()
        turtle.select(countBees)
        turtle.transferTo(i, 1)
        countBees = countBees - 1
      end
    end
  end
  turtle.turnRight()
end

function scanBees()
   turtle.turnLeft()
   turtle.turnLeft()
   for i = 1, countBees do
     turtle.select(i)
     turtle.drop()
   end
end

function determineBest(slot)
  local primScore = beeTable[data["speciesPrimary"]]
  local secScore = beeTable[data["speciesSecondary"]]
  if primScore == nil or secScore == nil then
    needsUpdate = data["speciesPrimary"]..":"..data["speciesSecondary"]
  end
  primScore = (primScore ~= nil and primScore or 0)
  secScore = (secScore ~= nil and secScore or 0)
  local useNew = false
  local score = 0
  score = primScore + secScore
  if(bestDrone == 0) then
    useNew = true
  else
    if (score > currScore) then
      useNew = true
    elseif (score == currScore) then
      if data["fertility"] > currData["fertility"] then
        useNew = true
      elseif data["fertility"] < currData["fertility"] then
        useNew = false

      elseif data["speed"] > currData["speed"] then
        useNew = true
      elseif data["speed"] < currData["speed"] then
        useNew = false

      elseif data["nocturnal"] and not currData["nocturnal"] then
        useNew = true
      elseif not data["nocturnal"] and currData["nocturnal"] then
        useNew = false

      elseif data["tolerantFlyer"] and not currData["tolerantFlyer"] then
        useNew = true
      elseif not data["tolerantFlyer"] and currData["tolerantFlyer"] then
        useNew = false

      elseif data["caveDwelling"] and not currData["caveDwelling"] then
        useNew = true
      elseif not data["caveDwelling"] and currData["caveDwelling"] then
        useNew = false

      elseif toleranceTable[data["toleranceTemperature"]] > toleranceTable[currData["toleranceTemperature"]] then
        useNew = true
      elseif toleranceTable[data["toleranceTemperature"]] < toleranceTable[currData["toleranceTemperature"]] then
        useNew = false

      elseif toleranceTable[data["toleranceHumidity"]] > toleranceTable[currData["toleranceHumidity"]] then
        useNew = true
      elseif toleranceTable[data["toleranceHumidity"]] < toleranceTable[currData["toleranceHumidity"]] then
        useNew = false

      end
    end
  end
  if useNew then
    bestDrone = slot
    currScore = score
    currData = data
  end
  return score, useNew
end

function log2(num)
  return num == 0 and 0.0 or math.log(num)/math.log(2)
end

function analyzeBees()
  print("analyzing "..countBees.." bees...")
  local score = 0
  local useNew = false
  print()
  print("typ species f spd n f c tmp hmd score")
  print("-|-|-------|-|---|-|-|-|---|---|-----")
  for i = 1, countBees do
    turtle.select(i)
    while not s.suckSneaky(0,1) do
      sleep(5)
    end
    turtle.turnRight()
    turtle.drop()
    m = peripheral.wrap("front")
    data = m.analyze()
    data["speciesPrimary"] = fixName(data["speciesPrimary"])
    data["speciesSecondary"] = fixName(data["speciesSecondary"])
    io.write(i.." ")
    if (data["type"] == "princess") then
      princess = i
      princessData = data
      io.write("P ")
      useNew = false
      score = 0
    else
      io.write("d ")
      score, useNew = determineBest(i)
    end
    io.write(data["speciesPrimary"]:gsub("bees%.species%.",""):sub(1,3)..":"..data["speciesSecondary"]:gsub("bees%.species%.",""):sub(1,3).." ")
    io.write(tostring(data["fertility"]).." ")
    io.write(data["speed"] == 1 and "1.0 " or tostring(data["speed"]).." ")
    if data["nocturnal"] then
      io.write("n ")
    else
      io.write("  ")
    end
    if data["tolerantFlyer"] then
      io.write("f ")
    else
      io.write("  ")
    end
    if data["caveDwelling"] then
      io.write("c ")
    else
      io.write("  ")
    end
    io.write(toleranceString[data["toleranceTemperature"]])
    io.write(toleranceString[data["toleranceHumidity"]])
    io.write(string.format("%5.1d", log2(score)).." ")
    if useNew then
      io.write("*")
      droneData = data
    end
    print()
    turtle.suck()
    turtle.turnLeft()
  end
  if princess ~= 0 then
    print("breeding princess ("..princess..") with drone ("..bestDrone..")")
  else
    print("no princess")
  end
  print()
end

function dropExcess()
  for i = 1, 16 do
    turtle.select(i)
    turtle.dropDown()
   end
end

-- Drop same drones so they won't interfere
function dropDupe()
  for i = 1, countBees do
    turtle.select(i)
    local count = turtle.getItemCount(i)
    if count > 1 then
      print("dropping "..tostring(turtle.getItemCount(i)-1).." excess drones...")
      turtle.dropDown(count - 1)
    end
  end
  turtle.select(1)
end

function isPurebred()
  if princessData["speciesPrimary"] ~= princessData["speciesSecondary"] then
    return false
  end
  for key, value in pairs(princessData) do
    if value ~= droneData[key] and key ~= "territory" and key ~= "type" then
      return false
    end
  end
  return true
end
------=============================

-- clear out system
while turtle.detect() do
  turtle.turnRight()
end
local i = 1
turtle.select(i)
while turtle.getItemCount(i) > 0 do
  i = i + 1
  turtle.select(i)
end
turtle.turnRight()
while s.suckSneaky(0,1) do
  i = i + 1
  turtle.select(i)
end
turtle.turnRight()
turtle.suck()
turtle.turnRight()
while turtle.suck() do
end

-- start breeding loop
while true do
  currslot = 1
  princess = 0
  bestDrone = 0
  data = {}
  currData = {}
  princessData = {}
  droneData = {}
  countBees = 0
  currScore = 0

  getBees()
  ditchCombs()
  if (turtle.getItemCount(2) > 0) then
    dropDupe()
    scanBees()
    analyzeBees()
    if countBees <= 2 and isPurebred() then
      print("Bees are purebred")
      turtle.turnLeft()
      return
    end
    if needsUpdate == "" then
      turtle.turnRight()
      turtle.turnRight()
      if princess ~= 0 then
        returnBees()
        dropExcess()
      else
        needPrincess = true
      end
    else
      turtle.turnLeft()
      print("Please add new species to bee table: "..needsUpdate)
      return
    end
  end
  sleep(5)
end