Subject: [bug#40691] [PATCH v4 0/3] gnu: Add gromacs, tng & lmfit.

From: Vincent Legoll <[email-masked]>
Date: Sat, 2 May 2020 15:46:49 +0200

Hello,

here is my latest work on adding gromacs to guix.

- rebased on latest guix master
- gromacs had a new version
- unbundling 3rdparties
- packaged some 3rdparties to have our own

I unbundled googletest by extracting our tarball in
place of the bundled copy.

Zlib got unbundled via packaging tng and unbundling
it from there.

Unbundled lmfit by packaging it separately and using that.
I put it with gromacs, but its legitimate place may be
elsewhere, like in maths.scm.

Unbundled tinyxml2 to use our version, which is newer and
broke code compatibility, so I added a patch to fix the
fallout. I am trying to get those fixes upstream, but that
may not be always practical, they may want to keep their
well tested version. I'll follow up updating the patch in
case parts of it get applied / released upstream.

The remaining bundled 3rdparties are vmd_molfile & thread_mpi.

Vmd_molfile source is behind a registration-only web form, I'm
not going there.

Thread_mpi looks like it is made to be bundled like that, and
is part of the parallelizing of gromacs which is above my
level of understanding (I'm only trying to package it, I'm not
a user). More info here:
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multithreading_with_thread-MPI

Latest license change for tng say "revised bsd", I don't know
which one to choose, I put bsd-3.

https://github.com/gromacs/tng/commit/65443992d81a8845ba3597620d84e8652e83a254

Lmfit is freebsd license, I choose bsd-2.

https://jugit.fz-juelich.de/mlz/lmfit/-/blob/master/COPYING

Gromacs itself is lgpl2.1+ and its copying file has bundled
3parties license explanations.

https://github.com/gromacs/gromacs/blob/master/COPYING

Please advise how to proceed further, this is already quite an
adventure for me.

-- 
Vincent Legoll