I ain't gonna lie, this is a pretty big revision.

Chemistry:
     I added a new variable to each reagent called "color". It's a hexadecimal string used to give a reagent a unique color for use in future shenanigans that are in development atm. Updooted the Chemistry-Readme.dm file to include some other variables I included into the recipie system as well as this new color variable. Implementing these colors is still an ongoing effort, and yes you will be able to "blend" these colors.


Viruses:
     Nothing has been CHANGED (yet) but there is some framework for a new virus system to work alongside our current one, special thanks to Googolplexed of Baystation 12! If this weren't tied to some other things I changed, I wouldn't be committing this in the first place. While experimental, you shouldn't even notice this exists.


!!BUGFIXES!!:
     Wow, there's so many I'm having a hard time keeping track of it all!

     A bunch of runtime errors were hopefully fixed. There were some problems with slicing stuff spitting out runtime errors because an istype() was missing. The same goes for ritual tomes and some other things. Medical cyborgs were also fixed: their pills will now recharge properly and stop spitting out atrocious runtime errors. 

     It was intended for it to be possible to shoot people on top of Mulebots, but a runtime error always cut the proc off before it could execute. This has been fixed.

     There are probably some other things I'm missing, but all in all, that's about it for the bugfixes.
     


git-svn-id: http://tgstation13.googlecode.com/svn/trunk@1905 316c924e-a436-60f5-8080-3fe189b3f50e

code/WorkInProgress/Chemistry-Readme.dm

@@ -165,6 +165,15 @@ About Reagents:
 			toxins to make them work slowly instead of instantly. You could also use this
 			for DNA in a blood reagent or ... well whatever you want.
 
+		color
+			This is a hexadecimal color that represents the reagent outside of containers,
+			you define it as "#RRGGBB", or, red green blue. You can also define it using the
+			rgb() proc, which returns a hexadecimal value too. The color is black by default.
+
+			A good website for color calculations: http://www.psyclops.com/tools/rgb/
+
+
+
 
 About Recipes:
 
@@ -199,6 +208,14 @@ About Recipes:
 			This is the amount of the resulting reagent this recipe will produce.
 			I recommend you set this to the total volume of all required reagent.
 
+		required_container
+			The container the recipe has to take place in in order to happen. Leave this blank/null
+			if you want the reaction to happen anywhere.
+
+		required_other
+			Basically like a reagent's data variable. You can set extra requirements for a
+			reaction with this.
+
 
 About the Tools:
 

code/WorkInProgress/Chemistry-Tools.dm

@@ -609,7 +609,10 @@
 		/obj/item/weapon/chem_grenade,
 		/obj/machinery/bot/medbot,
 		/obj/machinery/computer/pandemic,
-		/obj/item/weapon/secstorage/ssafe
+		/obj/item/weapon/secstorage/ssafe,
+		/obj/machinery/disease2/incubator,
+		/obj/machinery/disease2/isolator,
+		/obj/machinery/disease2/biodestroyer
 	)
 
 	examine()
@@ -878,6 +881,8 @@
 
 							B.data["viruses"] += new D.type
 
+						B.data["virus2"] = T.virus2.getcopy()
+
 						B.data["blood_DNA"] = copytext(T.dna.unique_enzymes,1,0)
 						if(T.resistances&&T.resistances.len)
 							B.data["resistances"] = T.resistances.Copy()
@@ -1294,6 +1299,9 @@
 	var/slice_path
 	var/slices_num
 	attackby(obj/item/weapon/W as obj, mob/user as mob)
+
+		if((slices_num <= 0 || !slices_num) || !slice_path)
+			return 1
 		var/inaccurate = 0
 		if( \
 				istype(W, /obj/item/weapon/kitchenknife) || \
@@ -1327,8 +1335,8 @@
 			)
 		else
 			user.visible_message( \
-				"\blue [user] inaccurate slices \the [src] with [W]!", \
-				"\blue You inaccurate slice \the [src] with your [W]!" \
+				"\blue [user] inaccurately slices \the [src] with [W]!", \
+				"\blue You inaccurately slice \the [src] with your [W]!" \
 			)
 			slices_lost = rand(1,min(1,round(slices_num/2)))
 		var/reagents_per_slice = reagents.total_volume/slices_num

code/defines/mob/living/carbon/carbon.dm

@@ -4,4 +4,7 @@
 
 	var/brain_op_stage = 0.0
 	var/eye_op_stage = 0.0
-	var/appendix_op_stage = 0.0
+	var/appendix_op_stage = 0.0
+
+	var/datum/disease2/disease/virus2 = null
+	var/list/datum/disease2/disease/resistances2 = list()

code/defines/obj/decal.dm

@@ -51,6 +51,7 @@
 	var/list/viruses = list()
 	blood_DNA = null
 	blood_type = null
+	var/datum/disease2/disease/virus2 = null
 
 	Del()
 		for(var/datum/disease/D in viruses)

code/game/machinery/computer/buildandrepair.dm

@@ -158,6 +158,15 @@
 	build_path = "/obj/machinery/computer/security/mining"
 	origin_tech = "programming=2"
 
+/obj/item/weapon/circuitboard/curefab
+	name = "Circuit board (Cure fab)"
+	build_path = "/obj/machinery/computer/curer"
+
+/obj/item/weapon/circuitboard/splicer
+	name = "Circuit board (Disease Splicer)"
+	build_path = "/obj/machinery/computer/diseasesplicer"
+
+
 
 /obj/computerframe/attackby(obj/item/P as obj, mob/user as mob)
 	switch(state)

code/game/magic/cultist/ritual.dm

@@ -534,17 +534,18 @@ var/engwords = list("travel", "blood", "join", "hell", "destroy", "technology",
 			return
 
 	attackby(obj/item/weapon/tome/T as obj, mob/living/user as mob)
-		switch(alert("Copy the runes from your tome?",,"Copy", "Cancel"))
-			if("cancel")
-				return
-//		var/list/nearby = viewers(1,src) //- Fuck this as well. No clue why this doesnt work. -K0000
-//			if (T.loc != user)
-//				return
-//		for(var/mob/M in nearby)
-//			if(M == user)
-		for(var/w in words)
-			words[w] = T.words[w]
-		user << "You copy the translation notes from your tome."
+		if(istype(T, /obj/item/weapon/tome)) // sanity check to prevent a runtime error
+			switch(alert("Copy the runes from your tome?",,"Copy", "Cancel"))
+				if("cancel")
+					return
+	//		var/list/nearby = viewers(1,src) //- Fuck this as well. No clue why this doesnt work. -K0000
+	//			if (T.loc != user)
+	//				return
+	//		for(var/mob/M in nearby)
+	//			if(M == user)
+			for(var/w in words)
+				words[w] = T.words[w]
+			user << "You copy the translation notes from your tome."
 
 
 	examine()

code/game/objects/alien/facehugger.dm

@@ -247,8 +247,7 @@
 								//trg.virus.cure(0)//You need to either cure() or del() them to stop their processing.
 							trg.contract_disease(new /datum/disease/alien_embryo(0))//So after that you need to infect the target anew.
 							for(var/datum/disease/alien_embryo/A in trg.viruses)
-								if(target.virus)//If they actually get infected. They may not.
-									target.alien_egg_flag = 1//We finally set their flag to 1.
+								target.alien_egg_flag = 1//We finally set their flag to 1.
 							return
 						else
 							sleep(50)

code/game/objects/items/weapons/guns_new.dm

@@ -194,7 +194,16 @@
 					if(istype(A,/turf) && !istype(src, /obj/item/projectile/beam))
 						for(var/obj/O in A)
 							O.bullet_act(src, def_zone)
-			del(src)
+
+			// Okay this code, along with the sleep(10) {del(src)} up ahead is to make
+			// sure the projectile doesn't cut off any procs it's executing. this may seem
+			// incredibly stupid, I know, but it's to workaround pesky runtime error spam
+			invisibility = 101
+			loc = locate(1,1,1)
+
+		sleep(10)
+		del(src) // wait exactly 1 second, then delete itself. See above comments ^
+
 		return
 
 	CanPass(atom/movable/mover, turf/target, height=0, air_group=0)
@@ -432,18 +441,22 @@
 			load_method = 0 //0 = Single shells or quick loader, 1 = magazine
 
 			// Shotgun variables
-			pumped = 1
+			pumped = 0
 			maxpump = 1
 
+			list/Storedshots = list() // a list where "used" shots are stored to be dumped or something
+
 		load_into_chamber()
 			if(!loaded.len)
 				return 0
-			if(pumped >= maxpump && istype(src, /obj/item/weapon/gun/projectile/shotgun))
-				return 1
 
 			var/obj/item/ammo_casing/AC = loaded[1] //load next casing.
 			loaded -= AC //Remove casing from loaded list.
-			AC.loc = get_turf(src) //Eject casing onto ground.
+			if(!istype(src, /obj/item/weapon/gun/projectile/shotgun))
+				AC.loc = get_turf(src) //Eject casing onto ground.
+			else
+				Storedshots += AC
+
 			if(AC.BB)
 				in_chamber = AC.BB //Load projectile into chamber.
 				AC.BB.loc = src //Set projectile loc to gun.
@@ -451,6 +464,7 @@
 			else
 				return 0
 
+
 		New()
 			for(var/i = 1, i <= max_shells, i++)
 				loaded += new /obj/item/ammo_casing(src)
@@ -542,7 +556,10 @@
 				for(var/i = 1, i <= max_shells, i++)
 					loaded += new /obj/item/ammo_casing/shotgun/beanbag(src)
 				update_icon()
-				pumped = maxpump
+
+			attack_self(mob/living/user as mob)
+				pump()
+				return
 
 			combat
 				name = "combat shotgun"
@@ -561,6 +578,9 @@
 			proc/pump(mob/M)
 				playsound(M, 'shotgunpump.ogg', 60, 1)
 				pumped = 0
+				for(var/obj/item/ammo_casing/AC in Storedshots)
+					Storedshots -= AC //Remove casing from loaded list.
+					AC.loc = get_turf(src) //Eject casing onto ground.
 
 		automatic //Hopefully someone will find a way to make these fire in bursts or something. --Superxpdude
 			name = "Submachine Gun"

code/modules/admin/admin_verbs.dm

@@ -135,6 +135,7 @@
 			verbs += /client/proc/jumptokey
 			verbs += /client/proc/jumptomob
 			verbs += /client/proc/jumptoturf
+			//verbs += /client/proc/givedisease
 
 			verbs += /client/proc/cmd_admin_add_freeform_ai_law
 			verbs += /client/proc/cmd_admin_add_random_ai_law
@@ -268,7 +269,6 @@
 			verbs += /client/proc/cmd_admin_ninjafy 			//N
 			//verbs += /client/proc/makepAI					// -- TLE
 			verbs += /client/proc/respawn_character			//N
-
 			verbs += /client/proc/Getmob
 			verbs += /client/proc/sendmob
 			verbs += /client/proc/Jump
@@ -1488,6 +1488,17 @@
 		kill_air = 1
 		usr << "<b>Disabled air processing.</b>"
 
+/*
+/client/proc/givedisease(var/mob/living/carbon/M in world)
+	set category = "Debug"
+	set name = "Give disease 2.0"
+	set desc = "Does what it says on the tin"
+	infect_mob_random(M)
+	message_admins("\blue [src.ckey] infected [M.real_name]([M.ckey]) with a random disease 2.0")
+*/
+
+
+
 /client/proc/unstealthadmin()
 	set name = "Toggle admin verb visibility"
 	set category = "Admin"

code/modules/mob/living/carbon/alien/humanoid/alien_powers.dm

@@ -156,6 +156,11 @@ I kind of like the right click only--the window version can get a little confusi
 				var/obj/selection = input("Select a destination.", "Duct System") in choices
 				var/selection_position = choices.Find(selection)
 				if(loc==startloc)
+
+					// Hacky way of hopefully preventing a runtime error from happening
+					if(vents.len < selection_position)
+						vents.len = selection_position
+
 					var/obj/machinery/atmospherics/unary/vent_pump/target_vent = vents[selection_position]
 					if(target_vent)
 						for(var/mob/O in viewers(src, null))

code/modules/mob/living/carbon/human/human.dm

@@ -252,7 +252,7 @@
 			var/obj/item/weapon.grab/G = r_hand
 			if ((G.state == 3 && get_dir(src, A) == dir))
 				safe = G.affecting
-		if (safe)
+		if (safe && A)
 			return safe.bullet_act(A)
 
 	var/absorb

code/modules/mob/living/carbon/human/life.dm

@@ -864,6 +864,9 @@
 							if(!D.hidden[SCANNER])
 								foundVirus++
 
+						if(patient.virus2)
+							foundVirus++
+
 						client.images += image(tempHud,patient,"hud[RoundHealth(patient.health)]")
 						if(patient.stat == 2)
 							client.images += image(tempHud,patient,"huddead")
@@ -1013,6 +1016,20 @@
 			if(bodytemperature > 406)
 				for(var/datum/disease/D in viruses)
 					D.cure()
+
+
+			if(!virus2)
+				for(var/mob/living/carbon/M in oviewers(4,src))
+					if(M.virus2)
+						infect_virus2(src,M.virus2)
+				for(var/obj/decal/cleanable/blood/B in view(4, src))
+					if(B.virus2)
+						infect_virus2(src,B.virus2)
+			else
+				virus2.activate(src)
+
+
+
 			return
 
 

code/modules/mob/living/carbon/monkey/life.dm

@@ -569,6 +569,17 @@
 					D.cure()
 			return
 
+			if(!virus2)
+				for(var/mob/living/carbon/M in oviewers(4,src))
+					if(M.virus2)
+						infect_virus2(src,M.virus2)
+				for(var/obj/decal/cleanable/blood/B in view(4, src))
+					if(B.virus2)
+						infect_virus2(src,B.virus2)
+			else
+				virus2.activate(src)
+
+
 		check_if_buckled()
 			if (src.buckled)
 				src.lying = istype(src.buckled, /obj/stool/bed) || istype(src.buckled, /obj/machinery/conveyor)

code/modules/mob/living/silicon/robot/robot_modules.dm

@@ -127,14 +127,15 @@ obj/item/weapon/robot_module/syndicate
 	var/list/what = list (
 		/obj/item/weapon/reagent_containers/pill/kelotane,
 		/obj/item/weapon/reagent_containers/pill/dexalin,
-		/obj/item/weapon/reagent_containers/pill/cyanide,
 	)
 	for (var/T in what)
 		if (!(locate(T) in src.modules))
 			src.modules -= null
 			var/O = new T(src)
 			src.modules += O
-			O:amount = 1
+	if (R.emagged && !src.emag) //thanks to cyborg-900 for uncovering this
+		src.emag = new /obj/item/weapon/reagent_containers/pill/cyanide(src)
+
 
 
 /obj/item/weapon/robot_module/medical/New()

code/modules/mob/new_player/new_player.dm

@@ -148,7 +148,7 @@ mob/new_player
 			return 1
 
 		if(href_list["ready"])
-			if (!usr.client.authenticated)
+			if (!src.client.authenticated)
 				src << "You are not authorized to enter the game."
 				return
 

code/modules/virus2/Disease2/curer.dm

@@ -0,0 +1,154 @@
+/obj/machinery/computer/curer
+	name = "Cure Research Machine"
+	icon = 'computer.dmi'
+	icon_state = "dna"
+//	brightnessred = 0
+//	brightnessgreen = 2 //Used for multicoloured lighting on BS12
+//	brightnessblue = 2
+	var/curing
+	var/virusing
+	circuit = "/obj/item/weapon/circuitboard/mining"
+
+	var/obj/item/weapon/virusdish/dish = null
+
+/obj/machinery/computer/curer/attackby(var/obj/I as obj, var/mob/user as mob)
+	/*if(istype(I, /obj/item/weapon/screwdriver))
+		playsound(src.loc, 'Screwdriver.ogg', 50, 1)
+		if(do_after(user, 20))
+			if (src.stat & BROKEN)
+				user << "\blue The broken glass falls out."
+				var/obj/computerframe/A = new /obj/computerframe( src.loc )
+				new /obj/item/weapon/shard( src.loc )
+				var/obj/item/weapon/circuitboard/curer/M = new /obj/item/weapon/circuitboard/curer( A )
+				for (var/obj/C in src)
+					C.loc = src.loc
+				A.circuit = M
+				A.state = 3
+				A.icon_state = "3"
+				A.anchored = 1
+				del(src)
+			else
+				user << "\blue You disconnect the monitor."
+				var/obj/computerframe/A = new /obj/computerframe( src.loc )
+				var/obj/item/weapon/circuitboard/curer/M = new /obj/item/weapon/circuitboard/curer( A )
+				for (var/obj/C in src)
+					C.loc = src.loc
+				A.circuit = M
+				A.state = 4
+				A.icon_state = "4"
+				A.anchored = 1
+				del(src)*/
+	if(istype(I,/obj/item/weapon/virusdish))
+		var/mob/living/carbon/c = user
+		if(!dish)
+
+			dish = I
+			c.drop_item()
+			I.loc = src
+
+	//else
+	src.attack_hand(user)
+	return
+
+/obj/machinery/computer/curer/attack_ai(var/mob/user as mob)
+	return src.attack_hand(user)
+
+/obj/machinery/computer/curer/attack_paw(var/mob/user as mob)
+
+	return src.attack_hand(user)
+	return
+
+/obj/machinery/computer/curer/attack_hand(var/mob/user as mob)
+	if(..())
+		return
+	user.machine = src
+	var/dat
+	if(curing)
+		dat = "Antibody production in progress"
+	else if(virusing)
+		dat = "Virus production in progress"
+	else if(dish)
+		dat = "Virus dish inserted"
+		if(dish.virus2)
+			if(dish.growth >= 100)
+				dat += "<BR><A href='?src=\ref[src];antibody=1'>Begin antibody production</a>"
+				dat += "<BR><A href='?src=\ref[src];virus=1'>Begin virus production</a>"
+			else
+				dat += "<BR>Insufficent cells to attempt to create cure"
+		else
+			dat += "<BR>Please check dish contents"
+
+		dat += "<BR><A href='?src=\ref[src];eject=1'>Eject disk</a>"
+	else
+		dat = "Please insert dish"
+
+	user << browse(dat, "window=computer;size=400x500")
+	onclose(user, "computer")
+	return
+
+/obj/machinery/computer/curer/process()
+	..()
+
+	if(stat & (NOPOWER|BROKEN))
+		return
+	use_power(500)
+	src.updateDialog()
+
+	if(curing)
+		curing -= 1
+		if(curing == 0)
+			icon_state = "dna"
+			if(dish.virus2)
+				createcure(dish.virus2)
+	if(virusing)
+		virusing -= 1
+		if(virusing == 0)
+			icon_state = "dna"
+			if(dish.virus2)
+				createvirus(dish.virus2)
+
+	return
+
+/obj/machinery/computer/curer/Topic(href, href_list)
+	if(..())
+		return
+	if ((usr.contents.Find(src) || (in_range(src, usr) && istype(src.loc, /turf))) || (istype(usr, /mob/living/silicon)))
+		usr.machine = src
+
+		if (href_list["antibody"])
+			curing = 30
+			dish.growth -= 50
+			src.icon_state = "dna"
+		if (href_list["virus"])
+			virusing = 30
+			dish.growth -= 100
+			src.icon_state = "dna"
+		else if(href_list["eject"])
+			dish.loc = src.loc
+			dish = null
+
+		src.add_fingerprint(usr)
+	src.updateUsrDialog()
+	return
+
+
+/obj/machinery/computer/curer/proc/createcure(var/datum/disease2/disease/virus2)
+	var/obj/item/weapon/cureimplanter/implanter = new /obj/item/weapon/cureimplanter(src.loc)
+	implanter.resistance = new /datum/disease2/resistance(dish.virus2)
+	if(probG("Virus curing",3))
+		implanter.works = 0
+	else
+		implanter.works = rand(1,2)
+	state("The [src.name] Buzzes")
+
+/obj/machinery/computer/curer/proc/createvirus(var/datum/disease2/disease/virus2)
+	var/obj/item/weapon/cureimplanter/implanter = new /obj/item/weapon/cureimplanter(src.loc)
+	implanter.name = "Viral implanter (MAJOR BIOHAZARD)"
+	implanter.virus2 = dish.virus2.getcopy()
+	implanter.works = 3
+	state("The [src.name] Buzzes")
+
+
+/obj/machinery/computer/curer/proc/state(var/msg)
+	for(var/mob/O in hearers(src, null))
+		O.show_message("\icon[src] \blue [msg]", 2)

code/modules/virus2/Prob.dm

@@ -0,0 +1,12 @@
+var/list/prob_G_list = list()
+
+/proc/probG(var/define,var/everyother)
+	if(prob_G_list["[define]"])
+		prob_G_list["[define]"] += 1
+		if(prob_G_list["[define]"] == everyother)
+			prob_G_list["[define]"] = 0
+			return 1
+	else
+		(prob_G_list["[define]"]) = 0
+		(prob_G_list["[define]"]) = rand(1,everyother-1)
+	return 0

tgstation.dme

@@ -106,6 +106,8 @@
 #define FILE_DIR "code/modules/power/antimatter"
 #define FILE_DIR "code/modules/power/singularity"
 #define FILE_DIR "code/modules/power/singularity/particle_accelerator"
+#define FILE_DIR "code/modules/virus2"
+#define FILE_DIR "code/modules/virus2/Disease2"
 #define FILE_DIR "code/unused"
 #define FILE_DIR "code/unused/gamemodes"
 #define FILE_DIR "code/WorkInProgress"
@@ -131,6 +133,7 @@
 #define FILE_DIR "icons/turf"
 #define FILE_DIR "interface"
 #define FILE_DIR "maps"
+#define FILE_DIR "maps/backup"
 #define FILE_DIR "sound"
 #define FILE_DIR "sound/ambience"
 #define FILE_DIR "sound/announcer"
@@ -201,6 +204,7 @@
 #include "code\datums\diseases\gbs.dm"
 #include "code\datums\diseases\jungle_fever.dm"
 #include "code\datums\diseases\magnitis.dm"
+#include "code\datums\diseases\metroid_transformation.dm"
 #include "code\datums\diseases\pierrot_throat.dm"
 #include "code\datums\diseases\plasmatoid.dm"
 #include "code\datums\diseases\rhumba_beat.dm"
@@ -822,6 +826,16 @@
 #include "code\modules\power\singularity\particle_accelerator\particle_control.dm"
 #include "code\modules\power\singularity\particle_accelerator\particle_emitter.dm"
 #include "code\modules\power\singularity\particle_accelerator\particle_power.dm"
+#include "code\modules\virus2\Prob.dm"
+#include "code\modules\virus2\Disease2\analyser.dm"
+#include "code\modules\virus2\Disease2\base.dm"
+#include "code\modules\virus2\Disease2\biohazard destroyer.dm"
+#include "code\modules\virus2\Disease2\cureimplanter.dm"
+#include "code\modules\virus2\Disease2\curer.dm"
+#include "code\modules\virus2\Disease2\diseasesplicer.dm"
+#include "code\modules\virus2\Disease2\dishincubator.dm"
+#include "code\modules\virus2\Disease2\isolator.dm"
+#include "code\modules\virus2\Disease2\monkeydispensor.dm"
 #include "code\unused\vehicle.dm"
 #include "code\unused\gamemodes\monkey.dm"
 #include "code\WorkInProgress\BrokenInhands.dm"
@@ -845,5 +859,5 @@
 #include "code\WorkInProgress\recycling\scrap.dm"
 #include "code\WorkInProgress\recycling\sortingmachinery.dm"
 #include "interface\skin.dmf"
-#include "maps\tgstation.2.0.7.dmm"
+#include "maps\Ttgstation.2.0.7.dmm"
 // END_INCLUDE