I've been using player.inventory.consumeInventoryItem() but it doesn't update the stack properly, whats the best way to consume an item from the player's inventory?

What about the stack doesn't update, the current number in the stack? This can be an issue depending on where you called consumeInventoryItem() from, or if you have multiple stacks of the same item in your inventory you may not notice if it was taken from the other stack.

 

That being said, there have been times when I've had to manually check if the stack size is 0 and then set the slot contents to null, because the vanilla system somehow doesn't always update appropriately.

It doesn't visually update, I have to right click the stack to make it update, also it's getting called in my item's right click method.

If that's the case, you should be able to use --stack.stackSize without any problems. Show us your code.

I don't have my code right now but this is what I think I have

public void onItemRightClicked(ItemStack itemstack, World world, EntityPlayer player){

NBTTagCompound nbt = itemstack.stackTagCompound;

if(nbt!=null){
if(player.isSneaking){

if(player.inventory.hasItem(gammacraft.Uran235)){
player.inventory.consumeInventoryItem(gammacraft.Uran235);
nbt.setInteger("Energy",nbt.getInteger("Energy")+1);
itemstack.stackTagCompound=nbt;
}
}else{
player.addChatMessage(new ChatComponentText("Energy: "+nbt.getInteger("Energy"));
}
}
}

 

it removes the item "Uran235" from the players inventory if they are sneaking and increments the Energy tag.