;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2017, 2018, 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2017, 2019 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
+;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
+;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
+;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
+;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (gnu packages graphviz)
#:use-module (gnu packages image)
#:use-module (gnu packages java)
+ #:use-module (gnu packages llvm)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
implemented. On the other hand, these comprise asymptotically fast
multiplication routines such as Toom–Cook and the FFT.")
(license license:lgpl3+)
- (home-page "http://mpfrcx.multiprecision.org/")))
+ (home-page "http://www.multiprecision.org/mpfrcx/")))
(define-public gf2x
(package
that can be called from within a C program and of executable command
line applications.")
(license license:gpl3+)
- (home-page "http://cm.multiprecision.org/")))
+ (home-page "http://www.multiprecision.org/cm/")))
(define-public fplll
(package
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/fplll/fplll.git")
+ (url "https://github.com/fplll/fplll")
(commit version)))
(file-name (git-file-name name version))
(sha256
;; Github instead.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/fplll/fpylll.git")
+ (url "https://github.com/fplll/fpylll")
(commit (string-append version "dev"))))
+ (file-name (git-file-name name version))
(sha256
(base32
"01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w"))))
(define-public pari-gp
(package
(name "pari-gp")
- (version "2.11.2")
+ (version "2.11.4")
(source (origin
(method url-fetch)
(uri (string-append
version ".tar.gz"))
(sha256
(base32
- "0fck8ssmirl8fy7s4mspgrxjs5sag76xbshqlqzkcl3kqyrk4raa"))))
+ "070bjw4kg7r6lqs1hfs08n5fmjv90cpwflp3wr04hbrmyz28zj5z"))))
(build-system gnu-build-system)
(native-inputs
`(("texlive" ,(texlive-union
(define-public gp2c
(package
(name "gp2c")
- (version "0.0.11pl2")
+ (version "0.0.11pl4")
(source (origin
(method url-fetch)
(uri (string-append
version ".tar.gz"))
(sha256
(base32
- "0wqsf05wgkqvmmsx7jinvzdqav6rl56sr8haibgs31nzz4x9xz9g"))))
+ "1cnnh7diqc97q76q5pyhpbljbhc0sz8mlrbqgiwi0sjkgh8iqsj0"))))
(build-system gnu-build-system)
(native-inputs `(("perl" ,perl)))
(inputs `(("pari-gp" ,pari-gp)))
(define-public giac
(package
(name "giac")
- (version "1.5.0-69")
- (source (origin
- (method url-fetch)
- ;; "~parisse/giac" is not used because the maintainer regularly
- ;; overwrites the release tarball there, introducing a checksum
- ;; mismatch every time. See
- ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
- (uri (string-append "https://www-fourier.ujf-grenoble.fr/"
- "~parisse/debian/dists/stable/main/"
- "source/giac_" version ".tar.gz"))
- (sha256
- (base32
- "05l1qa2kfmvsbp0iqjmg3ixkcqa3h9ry1mjpcps52bxw05s3k1z9"))))
+ (version "1.6.0-7")
+ (source
+ (origin
+ (method url-fetch)
+ ;; "~parisse/giac" is not used because the maintainer regularly
+ ;; overwrites the release tarball there, introducing a checksum
+ ;; mismatch every time. See
+ ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
+ (uri (string-append "https://www-fourier.ujf-grenoble.fr/"
+ "~parisse/debian/dists/stable/main/source/"
+ "giac_" version ".tar.gz"))
+ (sha256
+ (base32 "1pvgp137zcl0rbhdn1j41xxfml7fp771a7x4ph8qrhhlx0hxzn3p"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((ice-9 ftw)
(delete-file (string-append out "/bin/xcasnew"))
#t))))))
(inputs
- ;;; TODO: Add libnauty.
+;;; TODO: Add libnauty.
`(("fltk" ,fltk)
("glpk" ,glpk)
("gmp" ,gmp)
("gsl" ,gsl)
("lapack" ,lapack)
("libao" ,ao)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("libpng" ,libpng)
("libsamplerate" ,libsamplerate)
("libx11" ,libx11)
or text interfaces) or as a C++ library.")
(license license:gpl3+)))
-(define-public giac-xcas
- (deprecated-package "giac-xcas" giac))
-
(define-public flint
(package
(name "flint")
- (version "2.5.2")
- (source (origin
- (method url-fetch)
- (uri (string-append
- "http://flintlib.org/flint-"
- version ".tar.gz"))
- (sha256 (base32
- "11syazv1a8rrnac3wj3hnyhhflpqcmq02q8pqk2m6g2k6h0gxwfb"))
- (patches (search-patches "flint-ldconfig.patch"))))
+ ;; When updating this package, change its licence to lgpl2.1+.
+ ;; https://github.com/wbhart/flint2/issues/812
+ (version "2.6.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://flintlib.org/flint-" version ".tar.gz"))
+ (sha256
+ (base32 "1np1p8dx4g3jnlfr1sxmi1jdk2pb57crskm0ch2w2l1v7h8lb6sz"))))
(build-system gnu-build-system)
+ (inputs
+ `(("ntl" ,ntl)))
(propagated-inputs
`(("gmp" ,gmp)
("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
(arguments
- `(#:parallel-tests? #f ; seems to be necessary on arm
+ `(#:parallel-tests? #f ; seems to be necessary on arm
#:phases
(modify-phases %standard-phases
+ (add-before 'configure 'newer-c++
+ (lambda _
+ (substitute* "configure"
+ (("-ansi") ""))
+ #t))
(replace 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(gmp (assoc-ref inputs "gmp"))
- (mpfr (assoc-ref inputs "mpfr")))
- ;; do not pass "--enable-fast-install", which makes the
- ;; homebrew configure process fail
+ (mpfr (assoc-ref inputs "mpfr"))
+ (ntl (assoc-ref inputs "ntl")))
+ ;; Do not pass "--enable-fast-install", which makes the
+ ;; homebrew configure process fail.
(invoke "./configure"
(string-append "--prefix=" out)
(string-append "--with-gmp=" gmp)
- (string-append "--with-mpfr=" mpfr))
+ (string-append "--with-mpfr=" mpfr)
+ (string-append "--with-ntl=" ntl))
#t))))))
(synopsis "Fast library for number theory")
(description
(define-public arb
(package
(name "arb")
- (version "2.17.0")
+ (version "2.18.1")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/fredrik-johansson/arb.git")
+ (url "https://github.com/fredrik-johansson/arb")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
- "05lpy3hkl5f8ik19aw40cqydrb932xaf2n8hbq9ib5dnk7f010p1"))))
+ "15fx3dcbzgwddw9p1nysmx0dbh058afv5m8cj5pdjkcmcl7kw7z9"))))
(build-system gnu-build-system)
(propagated-inputs
`(("flint" ,flint))) ; flint.h is included by arf.h
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/fredrik-johansson/python-flint.git")
+ (url "https://github.com/fredrik-johansson/python-flint")
(commit version)))
(file-name (git-file-name name version))
(sha256
(define-public ntl
(package
(name "ntl")
- (version "9.7.0")
+ (version "11.4.3")
(source (origin
(method url-fetch)
- (uri (string-append "http://shoup.net/ntl/ntl-"
+ (uri (string-append "https://shoup.net/ntl/ntl-"
version ".tar.gz"))
- (sha256 (base32
- "115frp5flyvw9wghz4zph1b3llmr5nbxk1skgsggckr81fh3gmxq"))))
+ (sha256
+ (base32
+ "1lisp3064rch3jaa2wrhy1s9kll7i3ka3d0y6lj6l3l4ckfcrhdp"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file-recursively "src/libtool-origin")
+ #t))))
(build-system gnu-build-system)
(native-inputs
`(("libtool" ,libtool)
("perl" ,perl))) ; for configuration
- ;; FIXME: Add optional input gf2x once available; then also add
- ;; configure flag "NTL_GF2X_LIB=on".
(inputs
- `(("gmp" ,gmp)))
+ `(("gmp" ,gmp)
+ ("gf2x" ,gf2x)))
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'configure
- (lambda* (#:key outputs #:allow-other-keys)
+ (lambda* (#:key inputs outputs #:allow-other-keys)
(chdir "src")
- (system* "./configure"
+ (invoke "./configure"
(string-append "PREFIX=" (assoc-ref outputs "out"))
+ (string-append "LIBTOOL=" (assoc-ref inputs "libtool") "/bin/libtool")
+ ;; set the library prefixes explicitly so that they get
+ ;; embedded in the .la file
+ (string-append "GMP_PREFIX=" (assoc-ref inputs "gmp"))
+ (string-append "GF2X_PREFIX=" (assoc-ref inputs "gf2x"))
;; Do not build especially for the build machine.
"NATIVE=off"
- ;; Also do not tune to the build machine.
- "WIZARD=off"
- "SHARED=on")
- #t)))))
+ "NTL_GF2X_LIB=on"
+ "SHARED=on"))))))
(synopsis "C++ library for number theory")
(description
"NTL is a C++ library providing data structures and algorithms
for manipulating signed, arbitrary length integers, and for vectors,
matrices, and polynomials over the integers and over finite fields.")
(license license:gpl2+)
- (home-page "http://shoup.net/ntl/")))
+ (home-page "https://shoup.net/ntl/")))
(define-public singular
(package
(name "singular")
- (version "4.1.2p1")
+ (version "4.1.3p2")
(source
(origin
(method url-fetch)
#\.) "-")
"/singular-" version ".tar.gz"))
(sha256 (base32
- "0kvd55353fiqyq1msmi0kka66n5h0aqs7m3km60r01b1w2f8085m"))))
+ "1524yrni7gh0hir5ckridq671q5s6avfjdsdyahj51kzdl3wcypf"))))
(build-system gnu-build-system)
(native-inputs
`(("doxygen" ,doxygen)
(uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
(sha256
(base32
- "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))))
+ "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))
+ (patches (search-patches "bc-fix-cross-compilation.patch"))))
(build-system gnu-build-system)
(native-inputs
- `(("ed" ,ed)
+ `(("automake" ,automake)
+ ("autoconf" ,autoconf)
+ ("ed" ,ed)
("flex" ,flex)
("texinfo" ,texinfo)))
(arguments
'(#:configure-flags
- (list "--with-readline")))
+ (list "--with-readline")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'autogen
+ (lambda _
+ (invoke "autoreconf" "-vif"))))))
(home-page "https://www.gnu.org/software/bc/")
(synopsis "Arbitrary precision numeric processing language")
(description
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/extemporelang/kiss_fft.git")
+ (url "https://github.com/extemporelang/kiss_fft")
(commit version)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/vkostyukov/la4j.git")
+ (url "https://github.com/vkostyukov/la4j")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(version "1.6")
(source (origin
(method url-fetch)
- (uri (string-append "http://search.maven.org/remotecontent?"
- "filepath=pl/edu/icm/JLargeArrays/"
+ (uri (string-append "https://repo1.maven.org/maven2/"
+ "pl/edu/icm/JLargeArrays/"
version "/JLargeArrays-" version
"-sources.jar"))
(file-name (string-append name "-" version ".jar"))
(version "3.1")
(source (origin
(method url-fetch)
- (uri (string-append "http://search.maven.org/remotecontent?"
- "filepath=com/github/wendykierp/JTransforms/"
+ (uri (string-append "https://repo1.maven.org/maven2/"
+ "com/github/wendykierp/JTransforms/"
version "/JTransforms-" version "-sources.jar"))
(sha256
(base32
Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
(license license:bsd-2)))
+(define-public lmfit
+ (package
+ (name "lmfit")
+ (version "8.2.2")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://jugit.fz-juelich.de/mlz/lmfit.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "00bch77a6qgnw6vzsjn2a42n8n683ih3xm0wpr454jxa15hw78vf"))))
+ (build-system cmake-build-system)
+ (native-inputs
+ `(("perl" ,perl))) ; for pod2man
+ (home-page "https://jugit.fz-juelich.de/mlz/lmfit")
+ (synopsis "Levenberg-Marquardt minimization and least-squares fitting")
+ (description "lmfit is a C library for Levenberg-Marquardt least-squares
+minimization and curve fitting. It is mature code, based on decades-old
+algorithms from the FORTRAN library MINPACK.")
+ (license license:bsd-2)))
+
+(define-public symengine
+ (package
+ (name "symengine")
+ (version "0.6.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/symengine/symengine")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "129iv9maabmb42ylfdv0l0g94mcbf3y4q3np175008rcqdr8z6h1"))))
+ (build-system cmake-build-system)
+ (arguments
+ '(#:configure-flags
+ ;; These are the suggested build options in the README.
+ '("-DCMAKE_BUILD_TYPE=Release"
+ "-DWITH_GMP=on"
+ "-DWITH_MPFR=on"
+ "-DWITH_MPC=on"
+ "-DINTEGER_CLASS=flint"
+ "-DWITH_LLVM=on"
+ "-DWITH_SYMENGINE_THREAD_SAFE=on"
+ "-DBUILD_SHARED_LIBS=on"))) ;also build libsymengine
+ (native-inputs
+ `(("llvm" ,llvm)))
+ (inputs
+ `(("flint" ,flint)
+ ("gmp" ,gmp)
+ ("mpc" ,mpc)
+ ("mpfr" ,mpfr)))
+ (home-page "https://github.com/symengine/symengine")
+ (synopsis "Fast symbolic manipulation library")
+ (description
+ "SymEngine is a standalone fast C++ symbolic manipulation library.
+Optional thin wrappers allow usage of the library from other languages.")
+ (license (list license:expat ;SymEngine
+ license:bsd-3)))) ;3rd party code
+
(define-public eigen
(package
(name "eigen")
- (version "3.3.5")
+ (version "3.3.7")
(source (origin
(method url-fetch)
(uri (string-append "https://bitbucket.org/eigen/eigen/get/"
version ".tar.bz2"))
(sha256
(base32
- "1qh3yrwn78ms5yhwbpl5wvblk4gbz02cacdygxylr7i9xbrvylkk"))
+ "1km3fyfzyqfdvmnl79drps3fjwnz3zbh0c7l34mfbqyvvs8cy4wz"))
(file-name (string-append name "-" version ".tar.bz2"))
+ (patches (search-patches "eigen-stabilise-sparseqr-test.patch"))
(modules '((guix build utils)))
(snippet
;; There are 3 test failures in the "unsupported" directory,
(define-public xtensor
(package
(name "xtensor")
- (version "0.20.9")
+ (version "0.20.10")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/QuantStack/xtensor.git")
+ (url "https://github.com/QuantStack/xtensor")
(commit version)))
(sha256
(base32
- "1rw04bdi7mzp362dhkxr9m4rafnvb47xjsi9p3fp4vfif8v0jij8"))
+ "1fmv2hpx610xwhxrndfsfvlbqfyk4l3gi5q5d7pa9m82kblxjj9l"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
(native-inputs
("libtool" ,libtool)))
(propagated-inputs
`(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-before 'bootstrap 'setenv
- ;; Prevent the autogen.sh script to carry out the configure
- ;; script, which has not yet been patched to replace /bin/sh.
- (lambda _
- (setenv "NOCONFIGURE" "yes")
- #t)))))
(synopsis "Algebraic computations with exact rings and fields")
(description
"Givaro is a C++ library implementing the basic arithmetic of various
`(#:configure-flags
(list (string-append "--with-blas-libs="
(assoc-ref %build-inputs "openblas")
- "/lib/libopenblas.so"))
- #:phases
- (modify-phases %standard-phases
- (add-before 'bootstrap 'setenv
- ;; Prevent the autogen.sh script to carry out the configure
- ;; script, which has not yet been patched to replace /bin/sh.
- (lambda _
- (setenv "NOCONFIGURE" "yes")
- #t)))))
+ "/lib/libopenblas.so"))))
(synopsis "C++ library for linear algebra over finite fields")
(description
"FFLAS-FFPACK is a C++ template library for basic linear algebra
(file-name (git-file-name name version))
(sha256
(base32
- "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))))
+ "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))
+ (patches (search-patches "linbox-fix-pkgconfig.patch"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)
("pkg-config" ,pkg-config)))
- (inputs
+ (propagated-inputs
`(("fflas-ffpack" ,fflas-ffpack)))
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-before 'bootstrap 'setenv
- ;; Prevent the autogen.sh script to carry out the configure
- ;; script, which has not yet been patched to replace /bin/sh.
- (lambda _
- (setenv "NOCONFIGURE" "yes")
- #t)))))
(synopsis "C++ library for linear algebra over exact rings")
(description
"LinBox is a C++ template library for exact linear algebra computation
("automake" ,automake)
("libtool" ,libtool)))
(inputs
- `(("gmp" ,gmp)
- ("ntl" ,ntl)
+ `(("ntl" ,ntl)
("pari-gp" ,pari-gp)))
(synopsis "Ranks of elliptic curves and modular symbols")
(description "The eclib package includes mwrank (for 2-descent on
a program that performs fast computation of the more general multiplicative
structure constants of Schubert polynomials.")
(license license:gpl2+)
- (home-page "http://sites.math.rutgers.edu/~asbuch/lrcalc/")))
+ (home-page "https://sites.math.rutgers.edu/~asbuch/lrcalc/")))
(define-public iml
(package
HCoop / jackhill / guix / guix.git / blobdiff