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 Assuming one has an own instance of ntfy running, is there a decent guide on how to set up the whole notification thing properly? 
 In theory, all you need to do is to have the notification app running on your phone, connected with your server.

Then go to Amethyst's Fdroid version, go to Settings in the left drawer and select the app as a distributor. That will create a topic in the Notification app and you should be able to see our server sending notifications.  
 The "connected with your server" part is the issue. 
Do I need to create a Topic on the server first? And then have the app subscribe to it?

Anyway if there was a simple step guide, that would help 
 It depends on the server implementation. With NTFY, you don't need to create a topic.  
 Yes, ntfy. Alright figured it out. Here are the steps:

1) Install ntfy from F-Droid
2) If you have already done so, and there are entries that are of the form ntfy.sh/xGH... ➡️ Delete them
3) In ntfy app > Settings > Default Server: change to your self hosted url (e.g https://ntfy.mydomain.tld)
4) In Amethyst, log in with Amber, and follow the poop up steps. The process will make the ntfy app to create a new subscription, but this time to your server (not ntfy.sh) 
 Did it work?  
 Hmm, I was able to sign into Amethyst, and browse, open DMs etc. 

But in the ntfy app, where it did automatically create the subscription, it also just says "Connecting..."

Is there any specific way to test it's doing what it's supposed to? I literally learned Amber + ntfy .. and have little clue what to do 
 So I have a similar problem too, I am definitely not seeing any notifications coming from Amethyst  
 Do you see from anything else?  
 So earlier today I got one notification from Amethyst and it was a message saying I got zapped from one person but I have not seen anything else since then 
 Can you force close the app and reopen it? I want to see if there is a caching issue 
 Go to the phone's Settings/Apps/Amethyst and hit force close.  
 Force close ntfy or amethyst  
 Amethyst 
 Sure I'll force close 
 I just got a notification from your zap ⚡ 
 I think it worked now. But keep an eye on it. I am watching for the timeout behavior from the NTFY server  
 Okay  
 But that was the only notification I saw , should I get all notifications not just zaps  
 No, you should get only DMs and Zaps. The other stuff is too heavy.  
 Can't figure out Zaps... What are they? 
 Oh okay