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It is possible but it would require work on both auto-pts and NimBLE side. On autopts you'd have to create support in autoptsclient for new project - there is one for Mynewt, but it supports Mynewt running on board - it uses BSPs from ptsprojects/boards. Linux (native) build is host only, and app uses controller provided by Linux. Because such app runs on Linux system and not physical board, it renders current BTP communication useless - there is no UART. I tried building bttester app on native with config:
and there are some compilation errors. Maybe they could be resolved by apache/mynewt-core#3042 , or by modifying app code.
Besides that, another communication channel for BTP commands would have to be made, AFAIK TCP could work. You could take a look at uart_pipe.c - we would have to make similar one for TCP.
I'm not sure it would be worth to implement all of this, because PTS is used to qualify Host itself - it does not depend on what platform Host is built. And all tests can be run or nRF52 or nRF53, and other BSP support could be added more easily - it would require only adding board support in autopts, which basically tells autopts how to restart board, and optionally build and flash image onto it.
I notice that Nimble already provides a linux port. I wonder if it is possible to perform auto-pts on linux too?
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