;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
;;;
#: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 multiprecision)
+ #:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz))
(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)))
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+;; an outdated version for Sage.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 "0.7.26")
+ (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 "0.9.1")
+ (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* ((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 "1.2.5")
+ (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")))
+
+(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))
+ ;; Sage renames the include directory, so we do it also.
+ (("include/Lfunction")
+ "include/libLfunction")))
+ #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