The easiest way to do the tarball cleaning is with Files-Excluded in the copyright file, uscan will involve something (mkorigtargz?) that uses it to repack. That's a technical answer to the technical side of the question.
On the "policy"/legal question of whether it's permissible to package the internal open source in this larger source for the Debian project, I have no specific opinion but it sounds complicated. You might gauge upstream's feelings by asking if they can provide a tarball with just the open source parts. If not, even if your interpretation of the license situation is that you can package the inner code, it may not be worth it if it's fought by upstream. (E.g. they may see their more restrictive license as "additional terms" on top of the license in the inner files, thus basically creating a non-open source license.) Of course I am not a lawyer, just noting that it's much more pleasant to package when upstream is cooperative or at least not hostile :)
Good luck!
Ryan
Hi Niels,
Thanks for prompt reply.
On 2022-08-30 17:40, Niels Thykier wrote:
> From the description you have provided, I would assume yes with the
> following assumptions:
>
> 1) By "Extract AmberTools" you mean repackage the orig tarball.
Yes, that is what I meant.
> 2) AmberTools consists entirely of open sourced files that have a
> compatible license. Probably it does, but I would double check that
> no non-free files made their way into AmberTools.
Absolutely.
> (Plus of course that AmberTools does not Depend or Build-Depend on any
> non-free components whether third-party or from ambermd.org)
Right, this was implied.
> For reference, I did not check the upstream site.
ACK.
Best,
Andrius