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Is it possible to create a wix c# custom action project for dotnet core 3.1? The drop down shows only dotnet framework, although dotnet sdk 3.1 is installed and I have the newest wix toolset and visual studio 2019 extension.

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No. WiX DTF (Deployment Tools Foundation) only supports .NET Framework. As Windows Installer targets Windows Server and Desktop only and both of the forementioned have a version of .NET Framework already installed, I am not sure what would be accomplished by targeting .NET Core anyways.

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Only thing I can think of would be multi-plaform support? Not possible with MSI (OLE / COM file), but with a new ZIP-based package format perhaps (multi platform outright) - and a UTF8 source file in XML or JSON format compiled into a zip bundle? Anyway, just a thought - not that relevant here.
The only reason I can think of is to not have to have .NET installed or to be running an isolated .NET version. Of course your MSI would explode in terms of size. :(
We just migrated our application to net5. We have to recode all our setup and choose another solution than Wix because of that : we can't seriously release an installer requiring net472 to install an application requiring net5...
@Romka what libraries does your custom actions require? It's pretty easy to build a DTF CA for .NET 2.0 and use the CustomAction.config to specify it can run on CLR 2 or 4. In this case any version of .NET framework will work and you don't have to do anything to deploy one because every modern version of Windows has some 2+ version already installed.
Our setup has several custom actions, among them one sql database migrator exe which is part of our application, written in net5. We could make it in another target framework, but we cannot say to our clients "you must have .NET 2/4 to launch the setup, but you must have net5 runtime to launch the app"
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