Packaging Sagemath

Packaging Sagemath

[Andreas Enge]

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Hello,

until Thursday evening, before joining the Guile-Guix-Perl days in
Strasbourg, I am taking part in a coding sprint around packaging Sagemath:
   https://hackmd.io/j5FzB173Q4uaExUw-6Glpg#
My personal goal is to get closer to having Sage in Guix. As usual, I have
started a package definition and am adding dependencies one by one as the
build fails; current status attached. But there is also a list of (altogether
181!) required dependencies, which I extracted here:
   https://hackmd.io/zatG6NwtTWKF5asn_fmcIw?view
So sooner or later we will need all of these packages, and if you feel
motivated to package one or the other we do not have yet, you are more
than welcome!

Andreas


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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages sagemath)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system python)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix packages)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages bdw-gc)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages graph)
  #:use-module (gnu packages lisp)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-xyz))


(define-public python-cypari2
  (package
    (name "python-cypari2")
    (version "2.1.1")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "cypari2" version))
       (sha256
        (base32
         "1nwkzgqvbw6361x0rpggy1q5nx663fswhpvg8md6xhqyfwpgc7nz"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-cython" ,python-cython)))
    (propagated-inputs
     `(("python-cysignals" ,python-cysignals)))
    (inputs
     `(("gmp" ,gmp)
       ("pari-gp", pari-gp)))
    (home-page "https://cypari2.readthedocs.io/")
    (synopsis
     "Python interface to the number theory library libpari")
    (description
     "Cypari2 provides a Python interface to the number theory library
PARI/GP.  It has been spun off from the SageMath mathematics software system,
but it can be used independently.")
    (license license:gpl2+)))

(define-public python2-cypari2
  (package-with-python2 python-cypari2))

;; The stable version of the following package is not young enough to be
;; used with Sage, since it does not support cython. One would need to
;; use an alpha release. On the other hand, Sage can be built without it.
(define-public python-gmpy2
  (package
    (name "python-gmpy2")
    (version "2.0.8")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "gmpy2" version ".zip"))
              (sha256
               (base32
                "0grx6zmi99iaslm07w6c2aqpnmbkgrxcqjrqpfq223xri0r3w8yx"))))
    (build-system python-build-system)
    (native-inputs
     `(("unzip" ,unzip)))
    (inputs
     `(("gmp" ,gmp)
       ("mpfr" ,mpfr)
       ("mpc" ,mpc)))
    (home-page "https://github.com/aleaxit/gmpy")
    (synopsis
     "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x")
    (description
     "This package provides a Python interface to the GNU multiprecision
libraries GMO, MPFR and MPC.")
    (license license:lgpl3+)))

(define-public python2-gmpy2
  (package-with-python2 python-gmpy2))

(define-public cliquer
  (package
    (name "cliquer")
    (version "1.21")
    ;; The original source package is available from the home page and
    ;; has not seen any release since 2010; it comes with only a Makefile
    ;; without an "install" target. Instead, there is an autotoolized
    ;; tarball available from the Sage project.
    (source
     (origin
       (method url-fetch)
       (uri "http://users.ox.ac.uk/~coml0531/sage/cliquer-1.21.tar.gz")
       (sha256
        (base32
         "1hdzrmrx0nvvj8kbwxrs8swqgkd284khzl623jizixcv28xb77aq"))))
    (build-system gnu-build-system)
    (synopsis "C routines for finding cliques in weighted graphs")
    (description "Cliquer is a set of reentrant C routines for finding
cliques in a weighted or unweighted graph.  It uses an exact
branch-and-bound algorithm.  It can search for maximum or maximum-weight
cliques or cliques with size or weight within a given range, restrict the
search to maximal cliques, store cliques in memory and call a user-defined
function for every found clique.")
    (license license:gpl2+)
    (home-page "https://users.aalto.fi/~pat/cliquer.html")))

(define-public libbraiding
  (package
    (name "libbraiding")
    (version "1.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url (string-append "https://github.com/miguelmarco/"
                                  name))
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0l68rikfr7k2l547gb3pp3g8cj5zzxwipm79xrb5r8ffj466ydxg"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)))
    (synopsis "Computations with braid groups")
    (description "libbraiding performs computations with braid groups,
in particular it computes normal forms of group elements.")
    (license license:gpl2+)
    (home-page "https://github.com/miguelmarco/libbraiding")))

(define-public libhomfly
  (package
    (name "libhomfly")
    (version "1.02r6")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url (string-append "https://github.com/miguelmarco/"
                                  name))
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0sv3cwrf9v9sb5a8wbhjmarxvya13ma3j8y8592f9ymxlk5y0ldk"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)))
    (inputs
     `(("libgc" ,libgc)))
    (synopsis "Computation of homfly polynomials of links")
    (description "libhomfly computes homfly polynomials of links,
represented as strings.")
    (license license:public-domain)
    (home-page "https://github.com/miguelmarco/libhomfly")))

(define-public sage
  (package
    (name "sage")
    (version "8.6")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "ftp://ftp.fu-berlin.de/unix/misc/sage/src/sage-"
                    version ".tar.gz"))
              (sha256
               (base32
                "1ylpd0ziln50bfghqkgbn1n4gd7w2hl8g1gvg94igkbrknahjb44"))
              (modules '((guix build utils)))
              (snippet '(begin (delete-file-recursively "upstream")
                               (delete-file-recursively ".git")
                               #t))))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2
       #:phases
       (modify-phases %standard-phases
         (add-before 'build 'setup
           (lambda _
             (setenv "SAGE_ROOT" (getcwd))
             (setenv "SAGE_LOCAL" (getcwd))
             (setenv "SAGE_SHARE" (string-append (getcwd) "/share"))
             (setenv "PATH" (string-append (getcwd) "/build/bin:" (getcwd) "/src/bin:" (getenv "PATH")))
             (setenv "SAGE_NUM_THREADS" "4")
             (mkdir-p "var/lib/sage/installed")
             (chdir "src")
             #t)))))
    (inputs
     `(("boost" ,boost)
       ("cliquer" ,cliquer)
       ("ecl" ,ecl)
       ("edge-addition-planarity-suite" ,edge-addition-planarity-suite)
       ("flint" ,flint)
       ("gap" ,gap)
       ; ("givaro" ,givaro)
       ("glpk" ,glpk)
       ("gmp" ,gmp)
       ("gsl" ,gsl)
       ("libbraiding" ,libbraiding)
       ("libgc" ,libgc)
       ("libhomfly" ,libhomfly)
       ("mpc" ,mpc)
       ("ntl" ,ntl)
       ("pari-gp" ,pari-gp)
       ("python-cypari2" ,python2-cypari2)
       ("python-numpy" ,python2-numpy)
       ("python-six" ,python2-six)
       ("rw" ,rw)
       ("singular" ,singular)))
    (native-inputs
     `(("cython" ,python2-cython)
       ("pkg-config" ,pkg-config)
       ("python-cysignals" ,python2-cysignals)
       ("python-pkgconfig" ,python2-pkgconfig)
       ("python-jinja2" ,python2-jinja2)))
    (synopsis "SageMath computer algebra system")
    (description
     "SageMath is a mathematics software built on top of many existing
packages such as NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT,
R and others. Their combined power may be accessed through a common,
Python-based language or directly via interfaces or wrappers.")
    ;; documentation under cc-by-sa3.0, bundled packages under various
    ;; other licenses, see COPYING.txt in the distribution
    (license license:gpl3)
    (home-page "https://www.sagemath.org/")))

Re: Packaging Sagemath

[Nicolas Goaziou]

Hello,

Andreas Enge <andreas@enge.fr> writes:

> My personal goal is to get closer to having Sage in Guix. 

Very nice!

> But there is also a list of (altogether 181!) required dependencies,
> which I extracted here: https://hackmd.io/zatG6NwtTWKF5asn_fmcIw?view

I followed the link, but, IIUC, it is not up-to-date. For example, we
already have packaged many of them. Would it be useful to set-up
a world-writable document (e.g., a pad) somewhere, with a list of the
packages yet to be packaged, or a checklist with all packages that we
could tick-off?

For example, here is such an up-to-date list, barring a few FIXME
I wasn't sure about:

- [ ] appnope
- [X] arb
- [X] babel
- [X] backports_abc
- [X] backports_functools_lru_cache
- [X] backports_shutil_get_terminal_size
- [X] backports_ssl_match_hostname
- [X] bleach
- [ ] brial
- [X] bzip2
- [X] cddlib
- [X] certifi
- [ ] combinatorial_designs
- [X] configparser
- [ ] conway_polynomials
- [X] curl
- [X] cvxopt
- [X] cycler
- [X] dateutil
- [X] decorator
- [X] docutils
- [ ] eclib
- [X] ecm
- [ ] elliptic_curves
- [X] entrypoints
- [X] enum34
- [ ] fflas_ffpack
- [ ] flask_autoindex
- [X] flask_babel
- [ ] flask_oldsessions
- [ ] flask_openid
- [ ] flask_silk
- [X] flask
- [ ] flintqs
- [ ] fplll FIXME: available in version 4, so what?
- [ ] fpylll
- [X] freetype
- [X] functools32
- [X] future
- [ ] gf2x
- [ ] gfan
- [X] giac
- [X] git
- [ ] givaro (next missing, in the works)
- [ ] graphs
- [X] html5lib
- [X] iconv
- [X] imagesize
- [ ] iml FIXME: imlib2?
- [X] ipaddress
- [X] ipykernel
- [X] ipython_genutils
- [X] ipython
- [X] ipywidgets
- [X] itsdangerous
- [X] jinja2
- [ ] jmol
- [X] jsonschema
- [X] jupyter_client
- [X] jupyter_core
- [X] kiwisolver
- [ ] lcalc
- [X] libatomic_ops
- [ ] libgd FIXME: libgdata?
- [X] libpng
- [ ] linbox
- [ ] lrcalc
- [ ] m4rie
- [ ] m4ri
- [X] markupsafe
- [X] mathjax
- [X] matplotlib
- [X] maxima
- [X] mistune
- [X] mpfi
- [X] mpmath
- [X] nauty
- [X] nbconvert
- [X] nbformat
- [X] ncurses
- [X] networkx
- [X] notebook
- [X] openblas
- [X] packaging
- [ ] palp
- [ ] pandocfilters
- [ ] pari_galdata
- [ ] pari_seadata_small
- [X] patch
- [X] pathlib2
- [X] pathpy
- [X] pcre
- [X] pexpect
- [X] pickleshare
- [X] pillow
- [X] pip
- [X] pkgconfig
- [ ] pkgconf
- [ ] polytopes_db
- [ ] ppl
- [X] prometheus_client
- [X] prompt_toolkit
- [X] psutil
- [X] ptyprocess
- [ ] pycygwin
- [X] pygments
- [ ] pynac FIXME: pynacl?
- [X] pyparsing
- [X] python_openid
- [X] pytz
- [X] pyzmq
- [ ] ratpoints
- [X] readline
- [X] requests
- [X] rpy2
- [X] r
- [ ] rubiks
- [ ] sagenb_export
- [ ] sagenb
- [ ] sagetex
- [X] scandir
- [X] scipy
- [X] send2trash
- [X] setuptools_scm
- [X] setuptools
- [X] simplegeneric
- [X] singledispatch
- [X] snowballstemmer
- [ ] speaklater
- [X] sphinxcontrib_websupport
- [X] sphinx
- [X] sqlite
- [X] subprocess32
- [ ] symmetrica
- [ ] sympow
- [X] sympy
- [ ] tachyon
- [X] terminado
- [X] testpath
- [ ] thebe
- [ ] threejs FIXME: r-threejs?
- [X] tornado
- [X] traitlets
- [X] twisted
- [X] typing
- [X] vcversioner
- [X] wcwidth
- [X] webencodings
- [X] werkzeug
- [X] widgetsnbextension
- [X] xz
- [X] yasm
- [X] zeromq
- [X] zlib
- [ ] zn_poly
- [X] zope_interface

> So sooner or later we will need all of these packages, and if you feel
> motivated to package one or the other we do not have yet, you are more
> than welcome!

I'll try to help when I have time.

Regards,

-- 
Nicolas Goaziou

Re: Packaging Sagemath

[Andreas Enge]

On Tue, Jun 18, 2019 at 11:47:29AM +0200, Nicolas Goaziou wrote:
> I followed the link, but, IIUC, it is not up-to-date. For example, we
> already have packaged many of them. Would it be useful to set-up
> a world-writable document (e.g., a pad) somewhere, with a list of the
> packages yet to be packaged, or a checklist with all packages that we
> could tick-off?

Indeed, many of them are already available, this is the list of all
dependencies that we will (probably) have to add to the Sage recipe at
some point. I did not go through it to check which ones we already have.

> For example, here is such an up-to-date list, barring a few FIXME
> I wasn't sure about:

Thanks for the work on the list! As far as I can tell, the web page is
already a world-writable pad; just click on the pencil or the split-page
icons at the top left of the page. We may as well delete the packaged
items (as I have been doing for two or three I just packaged now), and
leave only TODO items.

> I'll try to help when I have time.

Great, I was actually thinking of you when I wrote the message, since
you added a few mathematical software packages already :-)

Andreas

Re: Packaging Sagemath

[Andreas Enge]

On Tue, Jun 18, 2019 at 01:30:06PM +0200, Andreas Enge wrote:
> We may as well delete the packaged
> items (as I have been doing for two or three I just packaged now), and
> leave only TODO items.

Well, no; I have actually kept packages that I did not yet add to my
preliminary sage recipe, be they available or not. It is just that I have
been packaging "in order", with every new package immediately added to
sage and then deleted from the list.

Andreas