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Meta-ticket: Add downstream (external user) packages as optional/experimental packages #31164

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Meta-ticket: Add downstream (external user) packages as optional/experimental packages#31164
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c: buildp: major / 3t: enhancement
@mkoeppe

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@mkoeppe
mkoeppe
opened on Jan 2, 2021

Since Sage 9.2, the spkg section of the Sage reference manual is automatically generated from the information in the SAGE_ROOT/build/pkgs/ directory. Each SPKG is represented by a subdirectory. The structure of these subdirectories is explained in the Developer's Guide.

This meta-ticket tracks the task of adding external packages, in particular those that used to be listed at https://wiki.sagemath.org/SageMathExternalPackages, as optional/experimental packages.
By including them as optional/experimental packages in build/pkgs:

  • They are automatically included in our reference manual (see Improve build/pkgs/*/SPKG.rst #29655)
  • Information about them can be obtained using the commands
    • Optional packages available: ./sage -optional
    • Experimental packages available: ./sage -experimental
    • Details about an SPKG: ./sage -info <SPKG>
  • The GH Actions workflows CI Linux and CI macOS will run them on every Sage development release, providing continuous integration that will allow use to catch unintended breaking changes during the Sage development cycle

Already added as packages, see spkg section of the Sage reference manual:

Tickets for pip-installable packages:

The packages will typically be added as pip packages instead of normal packages.
These do not come with tarball information and do not have to pin the version, so by default the latest version on PyPI would be installed.
Hence there is no additional maintenance burden from updating the packages.
Adding the packages is made easy by the new sage -package create commands, added in Sage 9.3.

No ticket yet:

  • sage_acsv: Algorithms for analytic combinatorics in several variables by Benjamin Hackl et al.

  • oriented_matroids by Aram Dermenjian

  • flagmatic: Tool for researchers in extremal graph theory by Emil R. Vaughan et al. (orig GitHub repo, GitHub repo)

  • stallings_graphs: experiment with finitely generated subgroups of infinite groups by Pascal Weil (self-hosted GitLab repo)

  • addcombq: Fast Additive Combinatorics functions by Matt Torrence (GitHub repo)

  • arithmat: Implementation of arithmetic matroids and toric arrangements by Roberto Pagaria and Giovanni Paolini (GitHub repo)

  • gcaops: Kontsevich Graph Complex Action on Poisson Structures by Ricardo Buring (GitHub repo)

  • cvolume: Compute completed volumes of strata of quadratic differentials with odd zeros by Eduard Duryev
    (GitHub repo)

  • badic: Beta-adic tools and automata by Paul Mercat (GitLab.com repo)

  • abelfunctions: Computing with Abelian functions, Riemann surfaces, and algebraic curves by Chris Swierczewski (GitHub repo, discussion)

  • carlin: Carleman linearization of polynomial differential equations by Marcelo Forets (GitHub repo)

  • elementary_vectors: Elementary vectors, sign vectors, oriented matroids and vectors with components in intervals and sign_vector_conditions by @MarcusAichmayr

  • adeles: Computing with adèles and idèles by Mathé Hertogh (GitHub repo)

  • yacop_sage: Steenrod algebra cohomology by Christian Nassau (GitHub repo)

  • FlexRiLog: Flexible and rigid labelings of graphs by Jan Legerský (GitHub repo)

  • sage_cluster_pictures: Cluster pictures, BY-trees, models and local invariants of hyperelliptic curves by Alex J. Best and Raymond van Bommel (GitHub repo)

  • dual-pairs: Computing with dual pairs of algebras by Peter Bruin (GitLab.com repo)

  • msinvar: Computation of moduli space invariants by Sergey Mozgovoy (GitHub repo)

  • comb_walks: Walk Models with elliptic kernel function by Frédéric Chyzak, Antonio Jiménez-Pastor, Pierre Lairez (self-hosted GitLab repo)

  • kerrgeodesic_gw: Computing geodesics of the Kerr spacetime as well as gravitational waves from bodies orbiting a Kerr black hole by Eric Gourgoulhon, Alexandre Le Tiec, Frédéric H. Vincent and Niels Warburton (GitHub repo)

  • dd_functions: Computation with DD-finite functions by Antonio Jiménez-Pastor (GitHub repo)

  • sherali_adams: Sherali-Adams relaxation on a numpy system of the form Ax <= b by Matthew Drescher (GitHub repo)

  • conrey-dirichlet-characters: Working with Dirichlet characters using a numbering scheme described by Brian Conrey by Jonathan Bober (GitHub repo)

  • pychebfun: Python Chebyshev Functions by Olivier Verdier, Chris Swierczewski (GitHub repo, orig GitHub repo)

  • pysemigroup: Automata and semigroups by Charles Paperman (self-hosted GitLab repo)

  • zetalib: Computing zeta functions of groups, algebras, and modules by Tobias Rossmann, Tomer Bauer (GitLab.com repo; orig website (404))

  • hypigu: Compute the Igusa local zeta function and flag Hilbert–Poincaré series of hyperplane arrangements by Joshua Maglione (GitHub repo)

  • mclf: Computing with Models of Curves over Local Fields by Stefan Wewers, Julian Rüth (GitHub repo)

  • hilbert-modular-group: Computing with Hilbert modular groups, including a reduction algorithm by Fredrik Stromberg (GitHub repo)

Not pip-installable:

In this ticket, only pip-installable packages will be added.
This adds an incentive to package authors to bring their packages to this form.

Maintained/abandoned on a Trac ticket:

Outdated (disappeared or does not work with current Sage):

  • sage-semigroups: A semigroup (representation) theory library by Nicolas M. Thiéry (GitHub repo, broken as of 2022-09, Sage 9.7)
  • CHA: Combinatorial Hopf algebras by Nicolas Borie (Bitbucket repo - 404)
  • cryptosage: Cryptography algorithms by Sara Forouhar (GitHub repo with .sage files, last updated 2015)
  • sage-drg: Checking the feasibility of distance-regular graph parameter sets by Janos Vidali (GitHub repo, not pip-installable, no Python 3 support)
  • SchottkyUniformization: SK prime function, Riemann Theta function built from a RS via Schottky uniformization by Jeremy Upsal (GitHub repo, last updated 2016)
  • ss-isogeny-software: Quantum-Resistant Cryptosystems from Supersingular Elliptic Curve Isogenies by Luca De Feo (GitHub repo, marked as obsolete by the author)
  • lecf: Lyapunov exponents for multidimensional continued fractions by Vincent Delecroix and Sébastien Labbé (GitHub repo - last updated 2014, GitHub repo - 404)
  • harmonic-modules: Computing the bicharacter of diagonal harmonic polynomials by Nicolas Thiéry (GitHub repo)

Discussions:

-------------------------
List of external packages 
-------------------------

This list used to be maintained at https://wiki.sagemath.org/SageMathExternalPackages

'''Please help by moving packages to one of the sections above!'''

See also https://github.com/slel/external-packages
for another collection

`Modular Abelian Varieties <https://github.com/williamstein/sage_modabvar>`_
-----------------------------------------------------------------------------

  by William Stein and Hao Chen

  Links:

  - https://github.com/williamstein/sage_modabvar
  - https://github.com/haochenuw/sage_modabvar


`Purple Sage <https://github.com/fredstro/psage>`_
------------------------------------------------------

  by William Stein, Fredrik Stromberg, Stephan Ehlen, Martin Raum and others

  A Library of Number Theory Code that depends on Sage.



`fgb_sage <https://github.com/mwageringel/fgb_sage>`_
-----------------------------------------------------

  by Markus Wageringel

  Sage interface for computing Gröbner bases with FGb.

`guptri_py <https://github.com/mwageringel/guptri_py>`_
-------------------------------------------------------

  by Markus Wageringel

  Sage/NumPy interface for solving generalized eigenvalue problems of singular matrix pencils with GUPTRI.


Brocoli
-------

  by Jean-Philippe Labbé

  Package dealing with LImit ROots of COxeter groups (eternal Beta version)

  - home: http://page.mi.fu-berlin.de/labbe/pages/brocoli.html
  - docs-html: https://jplab.github.io/brocoli/doc/html
  - docs-pdf: http://page.mi.fu-berlin.de/labbe/pdfs/brocoli.pdf
  - gallery: http://page.mi.fu-berlin.de/labbe/gallery.html
  - repo: https://github.com/jplab/brocoli

`sagemath-polytope-tikz <http://page.mi.fu-berlin.de/labbe/polytope.html>`_
---------------------------------------------------------------------------

  by Jean-Philippe Labbé

`SFBpresentation <https://github.com/jplab/SFBpresentation>`_
-------------------------------------------------------------

  by Jean-Philippe Labbé
  
  

--------
See also
--------

- `Packages on PyPI matching 'sagemath'
  <https://pypi.org/search/?q=sagemath>`_
- `Packages on PyPI matching 'sage' and Mathematics <https://pypi.org/search/?q=sage&o=&c=Topic+%3A%3A+Scientific%2FEngineering+%3A%3A+Mathematics>`_
- `Packages on PyPI matching 'sage' and Science <https://pypi.org/search/?q=sage&o=&c=Intended+Audience+%3A%3A+Science%2FResearch>`_

- `Packages on github matching "Sage code" <https://github.com/search?q=%22Sage+code%22>`_
- `Packages on gitlab matching "sagemath" <https://gitlab.com/search?search=sagemath>`_
- `Packages on Google Code Archive with tag "SAGE" <https://code.google.com/archive/search?q=domain:code.google.com%20label:SAGE>`_
- `Packages on Bitbucket matching "sagemath" <https://bitbucket.org/repo/all?name=sagemath>`_

CC: @slel @mwageringel @videlec @seblabbe @sagetrac-tmonteil @jplab @fredstro @fchapoton @sagetrac-srobik @williamstein @nthiery @saraedum @edgarcosta @sorger-c @mforets @pjbruin @rburing @mathzeta

Component: build

Issue created by migration from https://trac.sagemath.org/ticket/31164

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