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Bug#1019890: ITP: oxdna-cuda -- coarse-grained simulation software for DNA, RNA, and related systems

Package: wnpp
Severity: wishlist
Owner: Constantine Evans <const@costi.eu>
X-Debbugs-Cc: debian-devel@lists.debian.org

* Package name    : oxdna-cuda
  Version         : 3.4.2
  Upstream Author : Lorenzo Rovigatti <lorenzo.rovigatti@uniroma1.it>
* URL             : https://dna.physics.ox.ac.uk/
* License         : GPL-3
  Programming Lang: C++, Python
  Description     : coarse-grained simulation software for DNA, RNA, and related systems

oxDNA is a simulation code that was initially conceived as an
implementation of the coarse-grained DNA model introduced by
T. E. Ouldridge, J. P. K. Doye and A. A. Louis. It has been since
reworked and it is now an extensible simulation+analysis framework. It
natively supports DNA, RNA, Lennard-Jones and patchy particle
simulations of different kinds on both single CPU cores and NVIDIA


oxDNA is research software, but is reasonably established (around
since 2010), stable, and widely used within DNA nanotechnology and
related fields, not just within the authors' research groups (for
example, I'm not connected to them, there are around 200 papers listed
on their website, and there is oxdna.org that provides cloud-based
simulations using it).

I currently maintain the oxDNA installations on a Debian (11) research
group server, where oxDNA used by a few people, and on my own Arch and
Debian (sid) systems; maintaining this more general package would not
add too much to what I am already doing, as keeping an unmanaged
installation on a long-term, multi-user system would be asking for

oxDNA has CUDA and CPU simulation backends. I've only made a package
so far including CUDA support, which would thus need to go in
contrib, because I primarily use the CUDA backend, and have mostly
seen others using it and presenting results with it.  It also has two
python libraries, oxpy and oxDNA_analysis_tools, which I have packaged
as separate binary packages.

I have not made a serious Debian package before, and would need a
sponsor for this; I'd plan to upload it to mentors.  Like much
research software, it was not built with standard system-wide
installation as a priority, and has needed some tweaking to its
build process in that regard, but it is reasonably simple, and the
upstream authors are responsive to changes to make things easier.

Note that above, I have listed the maintainer of the current
repository.  The core developers are more generally listed at
<https://dna.physics.ox.ac.uk/index.php/Contact_information> as Thomas
Ouldridge, Petr Šulc, Flavio Romano, and Lorenzo Rovigatti.  The
current upstream codebase is at
<https://github.com/lorenzo-rovigatti/oxDNA>, and current license at

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