;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;;
;;; This file is part of GNU Guix.
;;;
(define-module (gnu packages sagemath)
#:use-module ((guix licenses) #:prefix license:)
- #:use-module (guix packages)
- #:use-module (guix download)
+ #: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 (guix utils)
+ #:use-module (gnu 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 image)
+ #:use-module (gnu packages lisp)
#: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 "2.0.3")
+ (version "2.1.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cypari2" version))
(sha256
(base32
- "0mghbmilmy34xp1d50xdx76sijqxmpkm2bcgx2v1mdji2ff7n0yc"))))
+ "1nwkzgqvbw6361x0rpggy1q5nx663fswhpvg8md6xhqyfwpgc7nz"))))
(build-system python-build-system)
(native-inputs
`(("python-cython" ,python-cython)))
(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.
+;; used with Sage, since it does not support cython; so we use a beta
+;; release.
(define-public python-gmpy2
(package
(name "python-gmpy2")
- (version "2.0.8")
+ (version "2.1.0b1")
(source (origin
- (method url-fetch)
- (uri (pypi-uri "gmpy2" version ".zip"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/aleaxit/gmpy")
+ (commit (string-append "gmpy2-" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0grx6zmi99iaslm07w6c2aqpnmbkgrxcqjrqpfq223xri0r3w8yx"))))
+ "0ljvnmhxqdfsp0yy4c2hynhk5sggm63kkqsq4iwq4k9vsnx2xm97"))))
(build-system python-build-system)
(native-inputs
`(("unzip" ,unzip)))
(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")))
+
+;; Sage 9.1 doesn't build with ECL 20. This won't be necessary once 9.2 is
+;; released. See https://trac.sagemath.org/ticket/22191
+(define-public ecl-16
+ (package
+ (inherit ecl)
+ (version "16.1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://common-lisp.net/project/ecl/static/files/release/ecl"
+ "-" version ".tgz"))
+ (sha256
+ (base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn"))
+ (patches (search-patches
+ "ecl-16-libffi.patch"
+ "ecl-16-ignore-stderr-write-error.patch"
+ "ecl-16-format-directive-limit.patch"))))
+ ;; Current ECL uses LGPL 2.1+
+ (license license:lgpl2.0+)))
+
+(define-public pynac
+ (package
+ (name "pynac")
+ (version "0.7.26")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pynac/pynac/")
+ (commit (string-append "pynac-" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "09d2p74x1arkydlxy6pw4p4byi7r8q7f29w373h4d8a215kadc6d"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)
+ ("pkg-config" ,pkg-config)))
+ (inputs
+ `(("flint" ,flint)
+ ("gmp" ,gmp)
+ ("python" ,python)
+ ("singular" ,singular)))
+ (synopsis "Sage fork of GiNaC")
+ (description "Pynac is a derivative of the C++ library GiNaC, which
+allows manipulation of symbolic expressions. It currently provides the
+backend for symbolic expressions in Sage. The main difference between
+Pynac and GiNaC is that Pynac relies on Sage to provide the operations
+on numerical types, while GiNaC depends on CLN for this purpose.")
+ (license license:gpl2+)
+ (home-page "http://pynac.org/")))
+
+;; Sage has become upstream of the following package.
+(define-public zn-poly
+ (package
+ (name "zn-poly")
+ (version "0.9.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url (string-append "https://gitlab.com/sagemath/"
+ "zn_poly.git/"))
+ (commit version)))
+ (file-name (git-file-name "zn_poly" version))
+ (sha256
+ (base32 "1wbc3apxcldxfcw1dnwnn7fvlfb6bwvlr8glvgv6hf79p9r2s4j0"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("python" ,python-2)))
+ (inputs
+ `(("gmp" ,gmp)))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ ;; The configure script chokes on --enable-fast-install.
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (invoke "./configure"
+ (string-append "--prefix=" (assoc-ref outputs "out"))
+ "--cflags=-O3 -fPIC")))
+ (add-before 'build 'prepare-build
+ (lambda _
+ (setenv "CC" "gcc")
+ #t))
+ (add-after 'build 'build-so
+ (lambda _
+ (invoke "make" "libzn_poly.so")))
+ (add-after 'install 'install-so
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (lib (string-append out "/lib"))
+ (soname (string-append "libzn_poly-" ,version ".so"))
+ (target (string-append lib "/" soname)))
+ (install-file "libzn_poly.a" lib)
+ (install-file soname lib)
+ (symlink target
+ (string-append lib "/libzn_poly.so"))
+ (symlink target
+ (string-append lib "/libzn_poly-"
+ ,(version-major+minor version)
+ ".so")))
+ #t)))))
+ (synopsis "Arithmetic for polynomials over Z/NZ")
+ (description "zn_poly implements the arithmetic of polynomials the
+coefficients of which are modular integers.")
+ (license (list license:gpl2 license:gpl3)) ; dual licensed
+ (home-page "https://gitlab.com/sagemath/zn_poly")))
+
+(define-public brial
+ (package
+ (name "brial")
+ (version "1.2.8")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BRiAl/BRiAl/")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0qhgckd4fvbs40jw14mvw89rccv94d3df27kipd27hxd4cx7y80y"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)
+ ("pkg-config" ,pkg-config)))
+ (inputs
+ `(("boost" ,boost)
+ ("libpng" ,libpng)
+ ("m4ri" ,m4ri)))
+ (arguments
+ ;; We are missing the boost unit test framework.
+ `(#:tests? #f
+ #:configure-flags (list "--without-boost-unit-test-framework")))
+ (synopsis "Arithmetic of polynomials over boolean rings")
+ (description "BRiAl is the successor to PolyBoRi maintained by the
+Sage community. Its core is a C++ library, which provides high-level data
+types for Boolean polynomials and monomials, exponent vectors, as well as
+for the underlying polynomial rings and subsets of the powerset of the
+Boolean variables. As a unique approach, binary decision diagrams are
+used as internal storage type for polynomial structures.")
+ (license license:gpl2+)
+ (home-page "https://github.com/BRiAl/BRiAl/")))
+
+(define-public lcalc
+ (package
+ (name "lcalc")
+ (version "1.23")
+ ;; The original home page of the project has disappeared, as well as
+ ;; code hosted by the original author on Google Code. The latter has
+ ;; been copied to gitlab.com/sagemath and purportedly contains patches
+ ;; for a never released version 1.3, that supposedly follows 1.23.
+ ;; We use the tarball as well as the patches hosted inside the sage
+ ;; package system distributed with the sage tarball.
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "ftp://ftp.fu-berlin.de/unix/misc/sage/spkg/"
+ "upstream/lcalc/lcalc-1.23.tar.bz2"))
+ (sha256
+ (base32
+ "1c6dsdshgxhqppjxvxhp8yhpxaqvnz3d1mlh26r571gkq8z2bm43"))
+ (patches (search-patches "lcalc-lcommon-h.patch"
+ "lcalc-default-parameters-1.patch"
+ "lcalc-default-parameters-2.patch"
+ "lcalc-using-namespace-std.patch"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;no tests
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'build 'prepare-build
+ (lambda* (#:key outputs #:allow-other-keys)
+ (chdir "src")
+ (let ((out (assoc-ref outputs "out")))
+ (substitute* "Makefile"
+ (("^INSTALL_DIR= /usr/local")
+ (string-append "INSTALL_DIR=" out))))
+ #t))
+ (add-before 'install 'make-output-dirs
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (lib (string-append out "/lib"))
+ (include (string-append out "/include")))
+ (mkdir-p bin)
+ (mkdir-p lib)
+ (mkdir-p include))
+ #t)))))
+ ;; FIXME:
+ ;; We need to add pari-gp and probably pari related patches from the
+ ;; sage project, as well as uncomment the line setting PARI_DEFINE in
+ ;; the Makefile to get the full functionality of this package.
+ ;; For the time being, we hope that sage can be compiled without.
+ (synopsis "C++ library for L-functions")
+ (description "Lcalc computes L-functions, in particular the Riemann
+zeta function and its twists by quadratic characters.")
+ (license license:gpl2+)
+ (home-page "https://gitlab.com/sagemath/sage")))
+
+(define-public ratpoints
+ (package
+ (name "ratpoints")
+ (version "2.1.3")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://www.mathe2.uni-bayreuth.de/stoll/programs/"
+ "ratpoints-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4"))
+ (patches
+ ;; Taken from
+ ;; <https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/>
+ (search-patches "ratpoints-sturm_and_rp_private.patch"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:test-target "test"
+ #:make-flags
+ (list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out"))
+ "CCFLAGS=-fPIC")
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ;no configure script
+ (add-before 'install 'create-install-directories
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (mkdir-p out)
+ (with-directory-excursion out
+ (for-each (lambda (d) (mkdir-p d))
+ '("bin" "include" "lib"))))
+ #t)))))
+ (inputs
+ `(("gmp" ,gmp)))
+ (home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/")
+ (synopsis "Find rational points on hyperelliptic curves")
+ (description "Ratpoints tries to find all rational points within
+a given height bound on a hyperelliptic curve in a very efficient way,
+by using an optimized quadratic sieve algorithm.")
+ (license license:gpl2+)))
HCoop / jackhill / guix / guix.git / blobdiff