I thought I'd share this and save other people searching!
I hadn't driven my car in a while and the battery went flat, I took the battery into the house and charged it up using a portable charger. When I reconnected the battery the alarm immediately began to sound. I did lots of searchs and came up with many proposed solutions such as putting the key in the door and locking -> unlocking -> locking. None of these worked. Finally I found a solution and it's very simple!
Reconnect the battery and let the alarm go off, they make sure that every door, boot and bonnet is closed and locked. After about 30 seconds the siren will stop and shortly after the indicators will all start flashing. (I assume this is the alarm system performing a self check and reseting)
Once the indicators have stopped flash I opened the car using the key fob and success the alarm didnt go off!