Re: Astronomy related software in Guix

Re: Astronomy related software in Guix

[Sharlatan Hellseher]

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Hi,

Thank you Ole for your reply.

I'd pin this thread in Guix Science mailing list to attract anyone
interested in this subject.

Some of the listed projects are already available (cfitsio, wcslib,
wcstools, astropy, sunpy, jwst, ...) some are still in review (GDL, plplot).

Working in collaboration with Iliya to bring Nemo to Guix.

Regards,
Oleg

On Mon, 16 Oct 2023, 14:09 Ole Streicher, <olebole@debian.org> wrote:

> Dear Oleg,
>
> when we started with Debian Astro, we mainly had the same problem. At
> the end, it depends on your needs, and the needs of your (potential)
> community. I started with what seemed to be needed in my institute; that
> was mainly ds9, wcslib, wcstools, cfitsio, ftools-fv. ds9 and ftool-fv
> give the main functionality to display FITS images and tables; however
> they are quite old now, and wcslib+cfitsio are the basic libraries.
>
> Then, there is the astropy ecosystem, which is today one of the building
> blocks for data analysis; including ipython, jupyter notebooks,
> matplotlib, scipy, numpy etc. This is however not a "game changer"
> because people can (and will) install it from PyPI.
>
> Definitely worthwile to package is also Source-Extractor, and maybe
> other software from astromatic.
>
> One other constituent is Topcat, which bring together with the program
> itself brings a whole Java infrastructure to handle astronomy data files.
>
> Finally people are very happy to get older legacy packages ready-to-run:
> IRAF, x11iraf, pyRAF, ESO-MIDAS. The GNU Datalanguage is a replacement
> for the legacy IDL, which is also helpful for some people.
>
> I hope this small list helps you somehow :-)
>
> Cheers
>
> Ole
>
> On 10.10.23 02:50, Sharlatan Hellseher wrote:
> > Hi Ole,
> >
> > I hope this message finds you well. I came across your name as a
> contributor to
> > Debian Astro.
> >
> > I follow your updates  in https://salsa.debian.org/debian-astro-team
> > and would like to ask for advise on priority you picked to prepare
> packages.
> >
> > I am also interested in using Guix for astronomy software and was
> wondering if
> > you could offer some advice. Specifically, as an expert in astronomical
> software
> > priority list for packaging, I was wondering if you could provide a list
> of
> > priority astronomical/astrophysical software that would be beneficial to
> include
> > in Guix. I understand that this may vary depending on the needs and
> interests of
> > the community, but any guidance would be greatly appreciated.
> >
> > Guix provides source base destribution of software and
> > which may be reproduced very strictly. It was successfully deployed in
> > Bioinformatics researches already.
> >
> > Thank you for your time and contributions to Debian Astro.
> >
> > Regards,
> > Oleg
> >
> > P.S. Some reference links
> > - https://guix.gnu.org/en/about/ About the project.
> > -
> https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages/astronomy.scm
> > Available packages definition related to astronomy, astrophysics, solar
> dynamics
> > or galaxy dynamics.
> > - https://packages.guix.gnu.org/ Packages search (26472 availalbe)
> > - https://git.sr.ht/~hellseher/ffab/tree/main/item/TODO.md My personal
> list of
> >    software queued to be packed.
> >
> > --
> > … наш разум - превосходная объяснительная машина которая способна
> > найти смысл почти в чем угодно, истолковать любой феномен, но
> > совершенно не в состоянии принять мысль о непредсказуемости.
> >
>

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Re: Astronomy related software in Guix

[Hugo Buddelmeijer]

Hi Oleg, Ole,

I love Guix, and astronomy, so I'm willing to do some of the work to
get astronomy software working.

I concur with Ole in the priority list; to summarize and to add some:
- Python stuff, which is mostly already in Guix, or can otherwise (for
now) be installed through pip
- ds9, wcslib, wcstools, cfitsio, ftools-fv
- Source-Extractor and other astrometic [1] software (SWarp, SCAMP for me)
- Java tools, Topcat [3] / Aladin [4], those are also just a jar-file
away in the meantime
- ESO (European Southern Observatory) software [2]: cpl, esorex
- Older stuff, IRAF, x11iraf, pyRAF, ESO-MIDAS

My plan was/is to contribute some of these packages, but so far have
not yet gotten to it. Most of my 'Guix-time' is spent trying to get
everything that already exists to work the way I want. For example,
getting power management to work on my laptop is next on my list.
However, what I would certainly do is send patches to keep these
packages updated if they would be in guix, because I would use most of
them.

I did manage to compile some of the software on a clean Guix system
(like cfitsio IIRC). I noticed that some of the old libraries rely on
/bin/cp and similar paths. I recall finding some release notes from
the 90s explicitly stating these paths are hardcoded to prevent
problems that probably don't exist anymore. I didn't know how to fix
those path-dependencies properly in a Guix package since at that point
I never made a Guix package, so I just added symlinks in my
config.scm. I realized that starting with converting those old
libraries would be biting off more than I could chew, so I'm planning
to first create some simpler Guix packages, like some more Python
libraries; I did my first 'guix import' experiments last week.

I do co-maintain some astronomy related conda-forge packages (some
with Ole), and those recipes (=build scripts) occasionally contain
some comments about problematic behaviour of these software, e.g. for
cpl [5]. I suppose the debian packages might also include some
workarounds that we could consult when creating Guix packages.

FWIW, I didn't mind becoming a conda-forge maintainer, because almost
everything is automated. E.g. a bot automatically creates a merge
request when a new version of a package is out and it is usually only
a single click ('merge') to get the conda package updated. I realized
I need at least some automation to commit to being a package
maintainer (even though that doesn't seem to be an official role in
Guix). So my goal is to first set up my own Cuirass server, and then
see what I can automate from there; but I haven't gotten to that yet,
because I'm still in the get-my-work-machine-comfortable-phase.

Hugo

[1] https://www.astromatic.net/software/
[2] https://www.eso.org/sci/software.html
[3] https://www.star.bris.ac.uk/~mbt/topcat/
[4] https://aladin.cds.unistra.fr/
[5] https://github.com/conda-forge/cpl-feedstock/blob/main/recipe/meta.yaml

On Mon, 16 Oct 2023 at 20:59, Sharlatan Hellseher <sharlatanus@gmail.com> wrote:
>
> Hi,
>
> Thank you Ole for your reply.
>
> I'd pin this thread in Guix Science mailing list to attract anyone interested in this subject.
>
> Some of the listed projects are already available (cfitsio, wcslib, wcstools, astropy, sunpy, jwst, ...) some are still in review (GDL, plplot).
>
> Working in collaboration with Iliya to bring Nemo to Guix.
>
> Regards,
> Oleg
>
> On Mon, 16 Oct 2023, 14:09 Ole Streicher, <olebole@debian.org> wrote:
>>
>> Dear Oleg,
>>
>> when we started with Debian Astro, we mainly had the same problem. At
>> the end, it depends on your needs, and the needs of your (potential)
>> community. I started with what seemed to be needed in my institute; that
>> was mainly ds9, wcslib, wcstools, cfitsio, ftools-fv. ds9 and ftool-fv
>> give the main functionality to display FITS images and tables; however
>> they are quite old now, and wcslib+cfitsio are the basic libraries.
>>
>> Then, there is the astropy ecosystem, which is today one of the building
>> blocks for data analysis; including ipython, jupyter notebooks,
>> matplotlib, scipy, numpy etc. This is however not a "game changer"
>> because people can (and will) install it from PyPI.
>>
>> Definitely worthwile to package is also Source-Extractor, and maybe
>> other software from astromatic.
>>
>> One other constituent is Topcat, which bring together with the program
>> itself brings a whole Java infrastructure to handle astronomy data files.
>>
>> Finally people are very happy to get older legacy packages ready-to-run:
>> IRAF, x11iraf, pyRAF, ESO-MIDAS. The GNU Datalanguage is a replacement
>> for the legacy IDL, which is also helpful for some people.
>>
>> I hope this small list helps you somehow :-)
>>
>> Cheers
>>
>> Ole
>>
>> On 10.10.23 02:50, Sharlatan Hellseher wrote:
>> > Hi Ole,
>> >
>> > I hope this message finds you well. I came across your name as a contributor to
>> > Debian Astro.
>> >
>> > I follow your updates  in https://salsa.debian.org/debian-astro-team
>> > and would like to ask for advise on priority you picked to prepare packages.
>> >
>> > I am also interested in using Guix for astronomy software and was wondering if
>> > you could offer some advice. Specifically, as an expert in astronomical software
>> > priority list for packaging, I was wondering if you could provide a list of
>> > priority astronomical/astrophysical software that would be beneficial to include
>> > in Guix. I understand that this may vary depending on the needs and interests of
>> > the community, but any guidance would be greatly appreciated.
>> >
>> > Guix provides source base destribution of software and
>> > which may be reproduced very strictly. It was successfully deployed in
>> > Bioinformatics researches already.
>> >
>> > Thank you for your time and contributions to Debian Astro.
>> >
>> > Regards,
>> > Oleg
>> >
>> > P.S. Some reference links
>> > - https://guix.gnu.org/en/about/ About the project.
>> > - https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages/astronomy.scm
>> > Available packages definition related to astronomy, astrophysics, solar dynamics
>> > or galaxy dynamics.
>> > - https://packages.guix.gnu.org/ Packages search (26472 availalbe)
>> > - https://git.sr.ht/~hellseher/ffab/tree/main/item/TODO.md My personal list of
>> >    software queued to be packed.
>> >
>> > --
>> > … наш разум - превосходная объяснительная машина которая способна
>> > найти смысл почти в чем угодно, истолковать любой феномен, но
>> > совершенно не в состоянии принять мысль о непредсказуемости.
>> >