SageMath packaging work

SageMath packaging work

[Ada Stevenson]

Hi Guix, science team!

I was reaching for SageMath today and couldn't find it in the package 
repository. I notice there's a sagemath.scm file, but no actual SageMath 
package proper. Is there any work being done on packaging it at the 
moment? Are there any particular blockers preventing its packaging 
(excessive dependencies, difficult build etc.)?

Having SageMath in Guix would be really handy for me, so I'm happy to 
give packaging it a go if the only reason is that there's not enough 
interest (I will just have to wait until after exams, so in about 3-4 
weeks).

Hope you are all doing well!

Warmly,
Ada

Re: SageMath packaging work

[Sharlatan Hellseher]

Hi Ada,

It looks like it was missed in patches

https://issues.guix.gnu.org/search?query=SageMath+is%3Aopen

56729 patch[RFC PATCH 00/10] Add sagemath.
70924 patch[PATCH 00/10] Add some SageMath standard packages.

Maybe it needs some love to bring to the master branch.

I'll take a look while waiting for QA digest my Astro upate.

--
Oleg


On Wed, 22 May 2024 at 10:19, Ada Stevenson <adanskana@gmail.com> wrote:
>
> Hi Guix, science team!
>
> I was reaching for SageMath today and couldn't find it in the package
> repository. I notice there's a sagemath.scm file, but no actual SageMath
> package proper. Is there any work being done on packaging it at the
> moment? Are there any particular blockers preventing its packaging
> (excessive dependencies, difficult build etc.)?
>
> Having SageMath in Guix would be really handy for me, so I'm happy to
> give packaging it a go if the only reason is that there's not enough
> interest (I will just have to wait until after exams, so in about 3-4
> weeks).
>
> Hope you are all doing well!
>
> Warmly,
> Ada



-- 
VCS: https://github.incerto.xyz/; https://git.sr.ht/~hellseher/
GPG: 9847 81DE 689C 21C2 6418 0867 76D7 27BF F62C D2B5

… 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.

Re: SageMath packaging work

[Andreas Enge]

Am Wed, May 22, 2024 at 03:50:43PM +0100 schrieb Sharlatan Hellseher:
> https://issues.guix.gnu.org/search?query=SageMath+is%3Aopen
> 56729 patch[RFC PATCH 00/10] Add sagemath.
> 70924 patch[PATCH 00/10] Add some SageMath standard packages.
> Maybe it needs some love to bring to the master branch.

Indeed that would be welcome. Concerning #70924, we would need to check
with the python-team branch to not duplicate the patches. I will not be
available for the next two weeks, but will be happy to take part in patch
reviewing after that.

Andreas

Re: SageMath packaging work

[Vinicius Monego]

Em qua, 2024-05-22 às 09:19 +0000, Ada Stevenson escreveu:
> Hi Guix, science team!
> 
> I was reaching for SageMath today and couldn't find it in the package
> repository. I notice there's a sagemath.scm file, but no actual
> SageMath 
> package proper. Is there any work being done on packaging it at the 
> moment? Are there any particular blockers preventing its packaging 
> (excessive dependencies, difficult build etc.)?
> 
> Having SageMath in Guix would be really handy for me, so I'm happy to
> give packaging it a go if the only reason is that there's not enough 
> interest (I will just have to wait until after exams, so in about 3-4
> weeks).
> 
> Hope you are all doing well!
> 
> Warmly,
> Ada
> 

Hi Ada,

SageMath has a lot of dependencies which you can see on
https://doc.sagemath.org/html/en/reference/spkg/

These are my current notes (I'm not sure how to organize them online):

Standard packages:

+ Available in the python-team branch (not yet merged):

- fqdn (python-team)
- isoduration (python-team)
- jupyter-events (python-team)
- jupyter-server-terminals (python-team)
- notebook-shim (python-team)
- overrides (python-team)
- referencing (python-team)
- rfc3986-validator (python-team)
- uri-template (python-team)

+ Series 1 (submitted as issue 70924):

- async-lru (review)
- calver (review)
- memory-allocator (review)
- pplpy (review)
- primecount (review)
- primecountpy (review)
- pyproject-api (review)
- types-python-dateutils (review)

+ Series 2 (currently working on, not yet submitted):

- gfan (NEXT)
- gnumake-tokenpool (v0.0.7+ needs Python 3.11+)
- jupyter-lsp (needs updated jupyter-core)
- palp http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html (NEXT)
- pytz-deprecation-shim (OK but temporary usage only)
- sympow
- tachyon: http://jedi.ks.uiuc.edu/~johns/raytracer/files/
  
+ Remaining standard packages:

- combinatorial-designs
- comm
- conway-polynomials
- elliptic-curves
- graphs
- jmol
- jsonschema-specifications
- jupyter-jsmol
- jupyterlab
- jupyterlab-mathjax2
- pari-galdata
- pari-seadata-small
- polytopes-db
- pplpy-doc
- sage-conf
- sage-docbuild
- sage-setup
- sagenb-export
- sagetex
- sphinx-inline-tabs
- threejs

Optional packages:

- admcycles
- benzene
- buckygen
- coxeter3
- csdp
- cunningham-tables
- cylp
- d3js
- database-cremona-ellcurve
- database-cubic-hecke
- database-jones-numfield
- database-knotinfo
- database-kohel
- database-mutation-class
- database-stein-watkins
- database-stein-watkins-mini
- database-symbolic-data
- dsdp
- e-antic
- frobby
- gap-jupyter
- gap-packages
- github-cli
- glucose [looks easy]
- jupymake
- kenzo
- latte-int
- libsemigroups [looks easy]
- lidia
- mathics
- mathics-scanner
- matroid-database
- mcqd
- meataxe
- msolve
- nibabel [looks easy]
- normaliz [looks easy]
- notedown
- onetbb
- ore-algebra
- p-group-cohomology
- pandoc-attributes
- papilo
- pari-elldata
- pari-galpol
- pari-nftables
- pari-seadata
- perl-cpan-polymake-prereq
- perl-mongodb
- phitigra
- plantri [looks easy]
- polymake [looks easy]
- polytopes-db-4d
- pycryptosat [looks easy]
- pynormaliz [looks easy]
- pyppeteer
- pyscipopt
- pysingular
- pyx [looks easy]
- qepcad
- rst2ipynb
- rubiks
- saclib
- sage-flatsurf
- sage-numerical-backends-coin
- sage-numerical-backends-cplex
- sage-numerical-backends-gurobi
- sage-sws2rst
- scip
- scip-sdp
- singular-jupyter
- sirocco
- slabbe
- snappy
- soplex
- tides
- topcom

As you can see, it's a lot of packages and dependencies, and these are
only the missing ones. Some of them are outdated, abandoned, or too
recent. Some of the already packaged dependencies may be too old or
need patches. We need at least the standard packages. Finally, we have
to glue them all in the sagemath package. So it's a lot of work and
nontrivial.

If you'd like to help, you can choose to package one of those "looks
easy" (but optional) packages, if you're new to Guix. Or try to help
with the more complex, yet more important, standard packages. You can
see the source link to every dependency in that sagemath packages link.
Issue 56729 is a good starting point.

The blockers are all of those you listed: excessive dependencies,
difficult building and lack of interest.

Vinicius

Re: SageMath packaging work

[Ada Stevenson]

Hi Vinicus,

On 01/06/2024 6:43 am, Vinicius Monego wrote:
> Em qua, 2024-05-22 às 09:19 +0000, Ada Stevenson escreveu:
>> Hi Guix, science team!
>>
>> I was reaching for SageMath today and couldn't find it in the package
>> repository. I notice there's a sagemath.scm file, but no actual
>> SageMath
>> package proper. Is there any work being done on packaging it at the
>> moment? Are there any particular blockers preventing its packaging
>> (excessive dependencies, difficult build etc.)?
>>
>> Having SageMath in Guix would be really handy for me, so I'm happy to
>> give packaging it a go if the only reason is that there's not enough
>> interest (I will just have to wait until after exams, so in about 3-4
>> weeks).
>>
>> Hope you are all doing well!
>>
>> Warmly,
>> Ada
>>
> 
> Hi Ada,
> 
> SageMath has a lot of dependencies which you can see on
> https://doc.sagemath.org/html/en/reference/spkg/
> 
> These are my current notes (I'm not sure how to organize them online):

Thank you! This is a great resource. Sorry for not responding earlier, I 
was in the midst of exams. I just want to check if this is still up to 
date, as far as you know. I want to start helping out with this effort.

> 
> Standard packages:
> 
> + Available in the python-team branch (not yet merged):
> 
> - fqdn (python-team)
> - isoduration (python-team)
> - jupyter-events (python-team)
> - jupyter-server-terminals (python-team)
> - notebook-shim (python-team)
> - overrides (python-team)
> - referencing (python-team)
> - rfc3986-validator (python-team)
> - uri-template (python-team)
> 
> + Series 1 (submitted as issue 70924):
> 
> - async-lru (review)
> - calver (review)
> - memory-allocator (review)
> - pplpy (review)
> - primecount (review)
> - primecountpy (review)
> - pyproject-api (review)
> - types-python-dateutils (review)
> 
> + Series 2 (currently working on, not yet submitted):

How are you going with this series? Is there anything I can help with?

> 
> - gfan (NEXT)
> - gnumake-tokenpool (v0.0.7+ needs Python 3.11+)
> - jupyter-lsp (needs updated jupyter-core)
> - palp http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html (NEXT)
> - pytz-deprecation-shim (OK but temporary usage only)
> - sympow
> - tachyon: http://jedi.ks.uiuc.edu/~johns/raytracer/files/
>    
> + Remaining standard packages:
> 

I'll give these a go.

> - combinatorial-designs
> - comm
> - conway-polynomials
> - elliptic-curves
> - graphs
> - jmol
> - jsonschema-specifications
> - jupyter-jsmol
> - jupyterlab
> - jupyterlab-mathjax2
> - pari-galdata
> - pari-seadata-small
> - polytopes-db
> - pplpy-doc
> - sage-conf
> - sage-docbuild
> - sage-setup
> - sagenb-export
> - sagetex
> - sphinx-inline-tabs
> - threejs
> 
> Optional packages:

Wow, that is a lot!

> 
> - admcycles
> - benzene
> - buckygen
> - coxeter3
> - csdp
> - cunningham-tables
> - cylp
> - d3js
> - database-cremona-ellcurve
> - database-cubic-hecke
> - database-jones-numfield
> - database-knotinfo
> - database-kohel
> - database-mutation-class
> - database-stein-watkins
> - database-stein-watkins-mini
> - database-symbolic-data
> - dsdp
> - e-antic
> - frobby
> - gap-jupyter
> - gap-packages
> - github-cli
> - glucose [looks easy]
> - jupymake
> - kenzo
> - latte-int
> - libsemigroups [looks easy]
> - lidia
> - mathics
> - mathics-scanner
> - matroid-database
> - mcqd
> - meataxe
> - msolve
> - nibabel [looks easy]
> - normaliz [looks easy]
> - notedown
> - onetbb
> - ore-algebra
> - p-group-cohomology
> - pandoc-attributes
> - papilo
> - pari-elldata
> - pari-galpol
> - pari-nftables
> - pari-seadata
> - perl-cpan-polymake-prereq
> - perl-mongodb
> - phitigra
> - plantri [looks easy]
> - polymake [looks easy]
> - polytopes-db-4d
> - pycryptosat [looks easy]
> - pynormaliz [looks easy]
> - pyppeteer
> - pyscipopt
> - pysingular
> - pyx [looks easy]
> - qepcad
> - rst2ipynb
> - rubiks
> - saclib
> - sage-flatsurf
> - sage-numerical-backends-coin
> - sage-numerical-backends-cplex
> - sage-numerical-backends-gurobi
> - sage-sws2rst
> - scip
> - scip-sdp
> - singular-jupyter
> - sirocco
> - slabbe
> - snappy
> - soplex
> - tides
> - topcom
> 
> As you can see, it's a lot of packages and dependencies, and these are
> only the missing ones. Some of them are outdated, abandoned, or too
> recent. Some of the already packaged dependencies may be too old or
> need patches. We need at least the standard packages. Finally, we have
> to glue them all in the sagemath package. So it's a lot of work and
> nontrivial.
> 
> If you'd like to help, you can choose to package one of those "looks
> easy" (but optional) packages, if you're new to Guix. Or try to help
> with the more complex, yet more important, standard packages. You can
> see the source link to every dependency in that sagemath packages link.
> Issue 56729 is a good starting point.

Thanks! I'll start with issue 56729, and hopefully bring it up to speed.

> 
> The blockers are all of those you listed: excessive dependencies,
> difficult building and lack of interest.
> 
> Vinicius

Warmly,
Ada

Re: SageMath packaging work

[Vinicius Monego]

Hi Ada,

Em ter, 2024-07-09 às 07:27 +0000, Ada Stevenson escreveu:
> Hi Vinicus,
> 
> On 01/06/2024 6:43 am, Vinicius Monego wrote:
> > Em qua, 2024-05-22 às 09:19 +0000, Ada Stevenson escreveu:
> > > Hi Guix, science team!
> > > 
> > > I was reaching for SageMath today and couldn't find it in the
> > > package
> > > repository. I notice there's a sagemath.scm file, but no actual
> > > SageMath
> > > package proper. Is there any work being done on packaging it at
> > > the
> > > moment? Are there any particular blockers preventing its
> > > packaging
> > > (excessive dependencies, difficult build etc.)?
> > > 
> > > Having SageMath in Guix would be really handy for me, so I'm
> > > happy to
> > > give packaging it a go if the only reason is that there's not
> > > enough
> > > interest (I will just have to wait until after exams, so in about
> > > 3-4
> > > weeks).
> > > 
> > > Hope you are all doing well!
> > > 
> > > Warmly,
> > > Ada
> > > 
> > 
> > Hi Ada,
> > 
> > SageMath has a lot of dependencies which you can see on
> > https://doc.sagemath.org/html/en/reference/spkg/
> > 
> > These are my current notes (I'm not sure how to organize them
> > online):
> 
> Thank you! This is a great resource. Sorry for not responding
> earlier, I 
> was in the midst of exams. I just want to check if this is still up
> to 
> date, as far as you know. I want to start helping out with this
> effort.
> 

Yes, it is up to date.

I am still waiting for the python-team branch to be merged because it
also introduces dependencies for jupyterlab, which I am interested in
packaging. Issue 70924 could be merged already, if anyone wants to
review, and then I merge it in the weekend.

> > 
> > Standard packages:
> > 
> > + Available in the python-team branch (not yet merged):
> > 
> > - fqdn (python-team)
> > - isoduration (python-team)
> > - jupyter-events (python-team)
> > - jupyter-server-terminals (python-team)
> > - notebook-shim (python-team)
> > - overrides (python-team)
> > - referencing (python-team)
> > - rfc3986-validator (python-team)
> > - uri-template (python-team)
> > 
> > + Series 1 (submitted as issue 70924):
> > 
> > - async-lru (review)
> > - calver (review)
> > - memory-allocator (review)
> > - pplpy (review)
> > - primecount (review)
> > - primecountpy (review)
> > - pyproject-api (review)
> > - types-python-dateutils (review)
> > 
> > + Series 2 (currently working on, not yet submitted):
> 
> How are you going with this series? Is there anything I can help
> with?
> 

I think the best approach right now is to update the packages from
issue 56729. Some of these have been submitted there but are out of
date, and some others I updated in 70924. I'll help reviewing your
submission. Also, I didn't go any further on the list since my last
message.

> > 
> > - gfan (NEXT)
> > - gnumake-tokenpool (v0.0.7+ needs Python 3.11+)
> > - jupyter-lsp (needs updated jupyter-core)
> > - palp http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html (NEXT)
> > - pytz-deprecation-shim (OK but temporary usage only)
> > - sympow
> > - tachyon: http://jedi.ks.uiuc.edu/~johns/raytracer/files/
> >    
> > + Remaining standard packages:
> > 
> 
> I'll give these a go.
> 

Sounds good.

> > - combinatorial-designs
> > - comm
> > - conway-polynomials
> > - elliptic-curves
> > - graphs
> > - jmol
> > - jsonschema-specifications
> > - jupyter-jsmol
> > - jupyterlab
> > - jupyterlab-mathjax2
> > - pari-galdata
> > - pari-seadata-small
> > - polytopes-db
> > - pplpy-doc
> > - sage-conf
> > - sage-docbuild
> > - sage-setup
> > - sagenb-export
> > - sagetex
> > - sphinx-inline-tabs
> > - threejs
> > 
> > Optional packages:
> 
> Wow, that is a lot!
> > 
> > - admcycles
> > - benzene
> > - buckygen
> > - coxeter3
> > - csdp
> > - cunningham-tables
> > - cylp
> > - d3js
> > - database-cremona-ellcurve
> > - database-cubic-hecke
> > - database-jones-numfield
> > - database-knotinfo
> > - database-kohel
> > - database-mutation-class
> > - database-stein-watkins
> > - database-stein-watkins-mini
> > - database-symbolic-data
> > - dsdp
> > - e-antic
> > - frobby
> > - gap-jupyter
> > - gap-packages
> > - github-cli
> > - glucose [looks easy]
> > - jupymake
> > - kenzo
> > - latte-int
> > - libsemigroups [looks easy]
> > - lidia
> > - mathics
> > - mathics-scanner
> > - matroid-database
> > - mcqd
> > - meataxe
> > - msolve
> > - nibabel [looks easy]
> > - normaliz [looks easy]
> > - notedown
> > - onetbb
> > - ore-algebra
> > - p-group-cohomology
> > - pandoc-attributes
> > - papilo
> > - pari-elldata
> > - pari-galpol
> > - pari-nftables
> > - pari-seadata
> > - perl-cpan-polymake-prereq
> > - perl-mongodb
> > - phitigra
> > - plantri [looks easy]
> > - polymake [looks easy]
> > - polytopes-db-4d
> > - pycryptosat [looks easy]
> > - pynormaliz [looks easy]
> > - pyppeteer
> > - pyscipopt
> > - pysingular
> > - pyx [looks easy]
> > - qepcad
> > - rst2ipynb
> > - rubiks
> > - saclib
> > - sage-flatsurf
> > - sage-numerical-backends-coin
> > - sage-numerical-backends-cplex
> > - sage-numerical-backends-gurobi
> > - sage-sws2rst
> > - scip
> > - scip-sdp
> > - singular-jupyter
> > - sirocco
> > - slabbe
> > - snappy
> > - soplex
> > - tides
> > - topcom
> > 
> > As you can see, it's a lot of packages and dependencies, and these
> > are
> > only the missing ones. Some of them are outdated, abandoned, or too
> > recent. Some of the already packaged dependencies may be too old or
> > need patches. We need at least the standard packages. Finally, we
> > have
> > to glue them all in the sagemath package. So it's a lot of work and
> > nontrivial.
> > 
> > If you'd like to help, you can choose to package one of those
> > "looks
> > easy" (but optional) packages, if you're new to Guix. Or try to
> > help
> > with the more complex, yet more important, standard packages. You
> > can
> > see the source link to every dependency in that sagemath packages
> > link.
> > Issue 56729 is a good starting point.
> 
> Thanks! I'll start with issue 56729, and hopefully bring it up to
> speed.
> 

Have fun :)

> > 
> > The blockers are all of those you listed: excessive dependencies,
> > difficult building and lack of interest.
> > 
> > Vinicius
> 
> Warmly,
> Ada

Vinicius