diff options
Diffstat (limited to 'gnu/packages/sagemath.scm')
| -rw-r--r-- | gnu/packages/sagemath.scm | 284 |
1 files changed, 274 insertions, 10 deletions
diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index baa79ab1c0..63d1281668 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -18,12 +18,20 @@ (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 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 multiprecision) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz)) @@ -31,14 +39,14 @@ (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))) @@ -60,18 +68,21 @@ but it can be used independently.") (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))) @@ -89,3 +100,256 @@ libraries GMO, MPFR and MPC.") (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"))) + +;; The following three packages from the Linbox group are needed in +;; an outdated version for Sage. + +(define-public givaro-4.0.4 + (package (inherit givaro) + (name "givaro") + (version "4.0.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linbox-team/givaro") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "199p8wyj5i63jbnk7j8qbdbfp5rm2lpmcxyk3mdjy9bz7ygx3hhy")))))) + +(define-public fflas-ffpack-2.3.2 + (package (inherit fflas-ffpack) + (name "fflas-ffpack") + (version "2.3.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linbox-team/fflas-ffpack") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1cqhassj2dny3gx0iywvmnpq8ca0d6m82xl5rz4mb8gaxr2kwddl")))) + (propagated-inputs + `(("givaro" ,givaro-4.0.4))) + ;; A test fails, but since all tests pass in the latest version, + ;; there is not much point in investigating. + (arguments + (substitute-keyword-arguments (package-arguments fflas-ffpack) + ((#:tests? _ #f) #f))))) + +(define-public linbox-1.5.2 + (package (inherit linbox) + (version "1.5.2") + (name "linbox") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linbox-team/linbox") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1wfivlwp30mzdy1697w7rzb8caajim50mc8h27k82yipn2qc5n4i")))) + (inputs + `(("fflas-ffpack" ,fflas-ffpack-2.3.2))))) + +(define-public pynac + (package + (name "pynac") + (version "0.7.25") + (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 + "0nnifvg6kzx0lq6gz7znind8g30v3d2pjfwgsdiks3vv9kv9nbj3")))) + (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 "0.9.1") + (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 + "0ra5vy585bqq7g3317iw6fp44iqgqvds3j0l1va6mswimypq4vxb")))) + (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 ((lib (string-append (assoc-ref outputs "out") "/lib"))) + (install-file "libzn_poly.so" lib))))))) + (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 "1.2.5") + (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 + "1nv56fp3brpzanxj7vwvxqdafqfsfhdgq5imr3m94psw5gdfqwja")))) + (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://gitlab.com/sagemath/zn_poly"))) |