From 20caeea4838ed0cf92452b6f7cf4cb9b42cd4ba8 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Mon, 17 Jun 2019 15:11:21 +0200 Subject: gnu: Add cliquer. * gnu/packages/sagemath.scm (cliquer): New variable. --- gnu/packages/sagemath.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/sagemath.scm') diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index baa79ab1c0..42b2bbdb94 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -20,6 +20,7 @@ #: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 (gnu packages algebra) #:use-module (gnu packages compression) @@ -89,3 +90,29 @@ 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"))) -- cgit v1.2.3 From 1e1a65a63349d1d2bd272738304a1d9f3b128a84 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Mon, 17 Jun 2019 15:59:14 +0200 Subject: gnu: python-cypari2: Update to 2.1.1. * gnu/packages/sagemath.scm (python-cypari2): Update to 2.1.1. --- gnu/packages/sagemath.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/sagemath.scm') diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 42b2bbdb94..f7d695049c 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -32,14 +32,14 @@ (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))) -- cgit v1.2.3 From 972ef8f591fcdbd5d5bb33d0f8dc6f6c40adf952 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 18 Jun 2019 00:04:55 +0200 Subject: gnu: Add libbraiding. * gnu/packages/sagemath.scm (libbraiding): New variable. --- gnu/packages/sagemath.scm | 32 ++++++++++++++++++++++++++++++-- 1 file changed, 30 insertions(+), 2 deletions(-) (limited to 'gnu/packages/sagemath.scm') diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index f7d695049c..91b46a8890 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -18,11 +18,13 @@ (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 (gnu packages algebra) + #:use-module (gnu packages autotools) #:use-module (gnu packages compression) #:use-module (gnu packages multiprecision) #:use-module (gnu packages python) @@ -116,3 +118,29 @@ 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"))) -- cgit v1.2.3 From 4c32f116cd89d158960c93ada28c32f3738e7b16 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 18 Jun 2019 00:12:36 +0200 Subject: gnu: Add libhomfly. * gnu/packages/sagemath.scm (libhomfly): New variable. --- gnu/packages/sagemath.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages/sagemath.scm') diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 91b46a8890..9736f79dc3 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -25,6 +25,7 @@ #:use-module (guix packages) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) + #:use-module (gnu packages bdw-gc) #:use-module (gnu packages compression) #:use-module (gnu packages multiprecision) #:use-module (gnu packages python) @@ -144,3 +145,31 @@ function for every found clique.") 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"))) -- cgit v1.2.3 From 80a70da7fc6732341f184dbbbd50f2441d8cee3f Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 18 Jun 2019 19:32:18 +0200 Subject: gnu: givaro: Add version 4.0.4. * gnu/packages/sagemath.scm (givaro-4.0.4): New variable. --- gnu/packages/sagemath.scm | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) (limited to 'gnu/packages/sagemath.scm') diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 9736f79dc3..4e1b51c023 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -173,3 +173,20 @@ in particular it computes normal forms of group elements.") 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")))))) -- cgit v1.2.3 From 9fafb0d21fb584cdc7dd1a92ce6646e07d16efcd Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 18 Jun 2019 19:48:41 +0200 Subject: gnu: fflas-ffpack: Add version 2.3.2. * gnu/packages/sagemath.scm (fflas-ffpack-2.3.2): New variable. --- gnu/packages/sagemath.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages/sagemath.scm') diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 4e1b51c023..b24f3411b1 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -23,6 +23,7 @@ #: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) @@ -190,3 +191,24 @@ represented as strings.") (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))))) -- cgit v1.2.3 From e27ae2db008d081f2cfce14e14320b3b76a9fefb Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Tue, 18 Jun 2019 19:54:59 +0200 Subject: gnu: linbox: Add version 1.5.2. * gnu/packages/sagemath.scm (linbox-1.5.2): New variable. --- gnu/packages/sagemath.scm | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) (limited to 'gnu/packages/sagemath.scm') diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index b24f3411b1..732011bf36 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -212,3 +212,19 @@ represented as strings.") (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))))) -- cgit v1.2.3 From 538230c9331b64844f1f2bdb884ae9a88d3ac537 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Wed, 19 Jun 2019 09:55:42 +0200 Subject: gnu: python-gmpy2: Update to 2.1.0b1. The gmpy2 package has become a standard package in sage-8.7, and the latest stable release is too old. * gnu/packages/sagemath.scm (python-gmpy2): Update to 2.1.0b1. --- gnu/packages/sagemath.scm | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) (limited to 'gnu/packages/sagemath.scm') diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 732011bf36..82b73d7811 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -65,18 +65,21 @@ 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))) -- cgit v1.2.3 From 3923e9d9421f2608c900d7815896e5809b154fec Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Wed, 19 Jun 2019 15:33:01 +0200 Subject: gnu: Add pynac. * gnu/packages/sagemath.scm (pynac): New variable. --- gnu/packages/sagemath.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu/packages/sagemath.scm') diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 82b73d7811..07c13582de 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -29,6 +29,7 @@ #:use-module (gnu packages bdw-gc) #:use-module (gnu packages compression) #:use-module (gnu packages multiprecision) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz)) @@ -231,3 +232,37 @@ represented as strings.") "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/"))) -- cgit v1.2.3 From 01822e3ebf24031d6438fc4e7ad3a869ea12fdf4 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Wed, 19 Jun 2019 16:54:09 +0200 Subject: gnu: Add zn_poly. * gnu/packages/sagemath.scm (zn_poly): New variable. --- gnu/packages/sagemath.scm | 47 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) (limited to 'gnu/packages/sagemath.scm') diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 07c13582de..6cf1badb3c 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -266,3 +266,50 @@ 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/" + name ".git/")) + (commit version))) + (file-name (git-file-name name 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"))) -- cgit v1.2.3 From a1dcaacb7b790668fd8cce6ce29a004587f50218 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Wed, 19 Jun 2019 23:57:49 +0200 Subject: gnu: Add brial. * gnu/packages/sagemath.scm (brial): New variable. --- gnu/packages/sagemath.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/sagemath.scm') diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 6cf1badb3c..8ae3cf77ff 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -27,7 +27,9 @@ #: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) @@ -313,3 +315,41 @@ on numerical types, while GiNaC depends on CLN for this purpose.") 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"))) -- cgit v1.2.3 From 80ee7c4a48cdab4afa4d8eb4b7b8873d47841830 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Thu, 20 Jun 2019 00:03:46 +0200 Subject: gnu: zn_poly: Rename to zn-poly, according to our naming conventions. Reported by Nicolas Goaziou . This is a follow-up to commit 01822e3ebf24031d6438fc4e7ad3a869ea12fdf4. * gnu/packages/sagemath.scm (zn_poly): Rename to... * gnu/packages/sagemath.scm (zn-poly): ...this. --- gnu/packages/sagemath.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu/packages/sagemath.scm') diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 8ae3cf77ff..63d1281668 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -270,18 +270,18 @@ on numerical types, while GiNaC depends on CLN for this purpose.") (home-page "http://pynac.org/"))) ;; Sage has become upstream of the following package. -(define-public zn_poly +(define-public zn-poly (package - (name "zn_poly") + (name "zn-poly") (version "0.9.1") (source (origin (method git-fetch) (uri (git-reference (url (string-append "https://gitlab.com/sagemath/" - name ".git/")) + "zn_poly.git/")) (commit version))) - (file-name (git-file-name name version)) + (file-name (git-file-name "zn_poly" version)) (sha256 (base32 "0ra5vy585bqq7g3317iw6fp44iqgqvds3j0l1va6mswimypq4vxb")))) -- cgit v1.2.3