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The first issue I had was working out how I add PyPI packages as deps, then I was pointed towards flatpak-pip-generator which generates JSON files that you can add as modules. That works fine:
The problem I'm facing now is I want to add libusb as a dependency, but am baffled at how this is meant to work. Is there a tool similar to flatpak-pip-generator that can take a source repository and generate the manifest entry for me? Or is there a set of steps I need to take manually?
Flathub has a shared module for libusb: https://github.com/flathub/shared-modules/blob/master/libusb/libusb.json