;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
-;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
-;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
-;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2018 Kei Kebreau <kkebreau@posteo.net>
+;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
-;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
-;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net>
+;;; Copyright © 2017
, 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
+;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
+;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
+;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
+;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
+;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system ocaml)
+ #:use-module (guix build-system python)
#:use-module (guix build-system r)
+ #:use-module (guix build-system ruby)
#:use-module (gnu packages algebra)
+ #:use-module (gnu packages audio)
#:use-module (gnu packages autotools)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages java)
#:use-module (gnu packages less)
#:use-module (gnu packages lisp)
+ #:use-module (gnu packages linux)
#:use-module (gnu packages logging)
#:use-module (gnu packages lua)
#:use-module (gnu packages gnome)
#:use-module (gnu packages popt)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages pulseaudio)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-web)
+ #:use-module (gnu packages qt)
#:use-module (gnu packages readline)
+ #:use-module (gnu packages ruby)
#:use-module (gnu packages tbb)
#:use-module (gnu packages scheme)
#:use-module (gnu packages shells)
#:use-module (gnu packages texinfo)
#:use-module (gnu packages tex)
#:use-module (gnu packages tls)
+ #:use-module (gnu packages version-control)
#:use-module (gnu packages wxwidgets)
#:use-module (gnu packages xml)
#:use-module (srfi srfi-1))
(define-public coda
(package
(name "coda")
- (version "2.18.2")
+ (version "2.19")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/stcorp/coda/releases/download/"
version "/coda-" version ".tar.gz"))
(sha256
- (base32 "01fnqcby9jijvf3jxr1fk4bny059lvvq5wbqm7ns60ilykfdnm6a"))
+ (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
(patches (search-patches "coda-use-system-libs.patch"))
(modules '((guix build utils)))
(snippet
;; Make sure we don't use the bundled software.
- '(for-each (lambda (d)
- (delete-file-recursively (string-append "libcoda/" d)))
- '("zlib" "pcre" "expat")))))
+ '(begin
+ (for-each (lambda (d)
+ (delete-file-recursively (string-append "libcoda/" d)))
+ '("zlib" "pcre" "expat"))
+ #t))))
(native-inputs
`(("fortran" ,gfortran)
("python" ,python)
(home-page "https://stcorp.nl/coda")
(license license:gpl2+)))
+(define-public qhull
+ (package
+ (name "qhull")
+ (version "2015.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://www.qhull.org/download/qhull-"
+ (car (string-split version #\.))
+ "-src-7.2.0.tgz"))
+ (sha256
+ (base32
+ "0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
+ (build-system cmake-build-system)
+ (synopsis "Calculate convex hulls and related structures")
+ (description
+ "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
+diagram, halfspace intersection about a point, furthest-site Delaunay
+triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
+3-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
+algorithm for computing the convex hull. It handles roundoff errors from
+floating point arithmetic. It computes volumes, surface areas, and
+approximations to the convex hull.
+
+@code{Qhull} does not support triangulation of non-convex surfaces, mesh
+generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
+shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
+triangulations.")
+ (home-page "http://qhull.org")
+ (license (license:non-copyleft "file://COPYING.txt"
+ "See COPYING in the distribution."))))
+
(define-public units
(package
(name "units")
- (version "2.14")
+ (version "2.17")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/units/units-" version
".tar.gz"))
(sha256 (base32
- "1s421bxm36akjsy3qzg6da1d1g20gh094ac2slqxipgkh8yqjcwx"))))
+ "1n2xzpnxfn475zkd8rzs5gg58xszjbr4bdbgvk6hryzimvwwj0qz"))))
(build-system gnu-build-system)
+ (inputs
+ `(("readline" ,readline)
+ ("python" ,python-wrapper) ;for 'units_cur' script
+ ("python-requests" ,python-requests)))
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (add-after 'install 'wrap-units_cur
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (wrap-program (string-append bin "/units_cur")
+ `("PYTHONPATH" ":" prefix
+ ,(search-path-as-string->list (getenv "PYTHONPATH"))))
+ #t))))))
(synopsis "Conversion between thousands of scales")
(description
"GNU Units converts numeric quantities between units of measure. It
(define-public double-conversion
(package
(name "double-conversion")
- (version "1.1.5")
+ (version "3.0.0")
+ (home-page "https://github.com/google/double-conversion")
(source (origin
(method url-fetch)
- (uri (string-append
- "https://github.com/floitsch/double-conversion/archive/v"
- version ".tar.gz"))
+ (uri (string-append home-page "/archive/v" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
+ "059r1czs28ljjd388pn6l3njg1ghbf1cv3q9nkxv3dj2a8siabqm"))))
(build-system cmake-build-system)
(arguments
'(#:test-target "test"
#:configure-flags '("-DBUILD_SHARED_LIBS=ON"
"-DBUILD_TESTING=ON")))
- (home-page "https://github.com/floitsch/double-conversion")
(synopsis "Conversion routines for IEEE doubles")
(description
"The double-conversion library provides binary-decimal and decimal-binary
(define-public dionysus
(package
(name "dionysus")
- (version "1.3.0")
+ (version "1.4.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/dionysus/dionysus-" version
- ".tar.gz"))
+ ".tar.xz"))
(sha256
(base32
- "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
+ "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
(build-system gnu-build-system)
(inputs `(("tcl" ,tcl))) ;for 'tclsh'
(synopsis "Local search for universal constants and scientific values")
(define-public gsl
(package
(name "gsl")
- (version "2.4")
+ (version "2.5")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/gsl/gsl-"
version ".tar.gz"))
(sha256
(base32
- "16yfs5n444s03np1naj6yp1fsysd42kdscxzkg0k2yvfjixx0ijd"))
+ "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
(patches (search-patches "gsl-test-i686.patch"))))
(build-system gnu-build-system)
(arguments
(define-public ocaml-gsl
(package
(name "ocaml-gsl")
- (version "1.19.3")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri
(string-append
- "https://github.com/mmottl/gsl-ocaml/releases/download/v"
- version"/gsl-ocaml-" version ".tar.gz"))
+ "https://github.com/mmottl/gsl-ocaml/releases/download/"
+ version "/gsl-" version ".tbz"))
(sha256
(base32
- "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
+ "17vcswipliq1b2idbzx1z95kskn1a4q4s5v04igilg0f7lnkaarb"))))
(build-system ocaml-build-system)
(inputs
`(("gsl" ,gsl)))
(define-public glpk
(package
(name "glpk")
- (version "4.63")
+ (version "4.65")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "1xp7nclmp8inp20968bvvfcwmz3mz03sbm0v3yjz8aqwlpqjfkci"))))
+ "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
(build-system gnu-build-system)
(inputs
`(("gmp" ,gmp)))
(define-public cddlib
(package
(name "cddlib")
- (version "0.94h")
+ (version "0.94i")
(source
(origin
(method url-fetch)
(string-delete #\. version) ".tar.gz"))
(sha256
(base32
- "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
+ "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
(build-system gnu-build-system)
(inputs
`(("gmp" ,gmp)))
(define-public arpack-ng
(package
(name "arpack-ng")
- (version "3.2.0")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
- (build-system gnu-build-system)
+ (version "3.6.3")
(home-page "https://github.com/opencollab/arpack-ng")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference (url home-page) (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)))
(inputs
`(("lapack" ,lapack)
("fortran" ,gfortran)))
(license (license:non-copyleft "file://COPYING"
"See COPYING in the distribution."))))
+(define-public arpack-ng-3.3.0
+ (package
+ (inherit arpack-ng)
+ (version "3.3.0")
+ (name (package-name arpack-ng))
+ (home-page (package-home-page arpack-ng))
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append home-page "/archive/" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
+
(define-public arpack-ng-openmpi
(package (inherit arpack-ng)
(name "arpack-ng-openmpi")
(inputs
`(("mpi" ,openmpi)
,@(package-inputs arpack-ng)))
- (arguments `(#:configure-flags '("--enable-mpi")))
+ (arguments
+ (substitute-keyword-arguments (package-arguments arpack-ng)
+ ((#:configure-flags _ '())
+ ''("--enable-mpi"))
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
(synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
(define-public lapack
("python" ,python-2)))
(arguments
`(#:configure-flags (list
- ;; Install to PREFIX/lib (the default is
- ;; PREFIX/lib64).
- (string-append "-DCMAKE_INSTALL_LIBDIR="
- (assoc-ref %outputs "out")
- "/lib")
-
"-DBUILD_SHARED_LIBS:BOOL=YES"
"-DLAPACKE=ON"
;; Build the 'LAPACKE_clatms' functions.
"-DLAPACKE_WITH_TMG=ON")
- #:phases (alist-cons-before
- 'check 'patch-python
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((python (assoc-ref inputs "python")))
- (substitute* "lapack_testing.py"
- (("/usr/bin/env python") python))))
- %standard-phases)))
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'check 'patch-python
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((python (assoc-ref inputs "python")))
+ (substitute* "lapack_testing.py"
+ (("/usr/bin/env python") python)))
+ #t)))))
(synopsis "Library for numerical linear algebra")
(description
"LAPACK is a Fortran 90 library for solving the most commonly occurring
("fortran" ,gfortran)
("lapack" ,lapack))) ;for testing only
(arguments
- `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")))
+ `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
+ #:phases (modify-phases %standard-phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(home-page "http://www.netlib.org/scalapack/")
(synopsis "Library for scalable numerical linear algebra")
(description
(define-public gnuplot
(package
(name "gnuplot")
- (version "5.0.6")
+ (version "5.2.4")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
version ".tar.gz"))
(sha256
(base32
- "0q5lr6nala3ln6f3yp6g17ziymb9r9gx9zylnw1y3hjmwl9lggjv"))))
+ "1jvh8xmd2cvrhlsg88kxwh55wkwx31sg50v1n59slfippl0g058m"))))
(build-system gnu-build-system)
(inputs `(("readline" ,readline)
("cairo" ,cairo)
(native-inputs
`(("pkg-config" ,pkg-config)
("texlive" ,texlive-tiny)))
+ (arguments `(#:configure-flags (list (string-append
+ "--with-texdir=" %output
+ "/texmf-local/tex/latex/gnuplot"))))
(home-page "http://www.gnuplot.info")
(synopsis "Command-line driven graphing utility")
(description "Gnuplot is a portable command-line driven graphing
#:configure-flags '("--enable-cxx"
"--enable-fortran"
"--enable-fortran2003")
-
+ ;; Use -fPIC to allow the R bindings to link with the static libraries
+ #:make-flags (list "CFLAGS=-fPIC"
+ "CXXFLAGS=-fPIC")
#:phases
(modify-phases %standard-phases
(add-before 'configure 'patch-configure
;; unnecessary store references to those compilers:
(substitute* "src/libhdf5.settings"
(("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
- (string-append prefix (string-take hash 10) "...")))
+ (string-append prefix (string-take hash 10) "..."))
+ ;; Don't record the build-time kernel version to make the
+ ;; settings file reproducible.
+ (("Uname information:.*")
+ "Uname information: Linux\n"))
#t))
(add-after 'install 'patch-references
(lambda* (#:key inputs outputs #:allow-other-keys)
(for-each delete-file
(list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
"HDF4.tar.gz" "HDF5.tar.gz"))
- (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))))))
+ (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
+ #t))))
(build-system gnu-build-system)
(native-inputs
`(("jdk" ,icedtea "jdk")
(modules '((guix build utils)))
(snippet
;; Make sure we don't use the bundled software.
- '(delete-file-recursively "ThirdParty"))))
+ '(begin
+ (delete-file-recursively "ThirdParty")
+ #t))))
(build-system gnu-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
(define-public ceres
(package
(name "ceres-solver")
- (version "1.11.0")
+ (version "1.14.0")
(home-page "http://ceres-solver.org/")
(source (origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "0i7qkbf8g6pd8arxzldppga26ckv93y8zldsfz6wbd4n6b1nqrjd"))))
+ "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
(build-system cmake-build-system)
(arguments
;; TODO: Build HTML user documentation and install separately.
@end enumerate\n")
(license license:bsd-3)))
-;; For a fully featured Octave, users are strongly recommended also to install
+;; For a fully featured Octave, users are strongly recommended also to install
;; the following packages: less, ghostscript, gnuplot.
(define-public octave
(package
(name "octave")
- (version "4.2.1")
+ (version "4.4.1")
(source
(origin
(method url-fetch)
version ".tar.lz"))
(sha256
(base32
- "09zhhch79jw3ynw39vizx0i2cbd2bjz3sp38pjdzraqrbivpwp92"))))
+ "0jsdgizlv02an2ppfjwk5qf209zpwi3317yb7jvlsjzxnir3lvhy"))))
(build-system gnu-build-system)
(inputs
`(("lapack" ,lapack)
+ ("qhull" ,qhull)
("readline" ,readline)
("gl2ps" ,gl2ps)
("glpk" ,glpk)
("zlib" ,zlib)
("curl" ,curl)
("texinfo" ,texinfo)
- ("graphicsmagick" ,graphicsmagick)))
+ ("graphicsmagick" ,graphicsmagick)
+ ("suitesparse" ,suitesparse)
+ ("libsndfile" ,libsndfile)
+ ("portaudio" ,portaudio)
+ ("alsa-lib" ,alsa-lib)))
(native-inputs
`(("lzip" ,lzip)
("gfortran" ,gfortran)
script files.")
(license license:gpl3+)))
+(define-public qtoctave
+ (package (inherit octave)
+ (name "qtoctave")
+ (source (origin
+ (inherit (package-source octave))))
+ (inputs
+ `(("qscintilla" ,qscintilla)
+ ("qt" ,qtbase)
+ ,@(package-inputs octave)))
+ (native-inputs
+ `(("qttools" , qttools) ;for lrelease
+ ("texlive" ,texlive) ;for texi2dvi
+ ,@(package-native-inputs octave)))
+ (arguments
+ (substitute-keyword-arguments (package-arguments octave)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-before 'configure 'patch-qscintilla-library-name
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; The QScintilla library that the Octave configure script tries
+ ;; to link with should be named libqscintilla-qt5.so, but the
+ ;; QScintilla input provides the shared library as
+ ;; libqscintilla2_qt5.so.
+ (substitute* "configure"
+ (("qscintilla2-qt5")
+ "qscintilla2_qt5"))
+ #t))))))))
+
(define-public opencascade-oce
(package
(name "opencascade-oce")
"https://github.com/tpaviot/oce/archive/OCE-"
version
".tar.gz"))
+ (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
(sha256
(base32
"0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
(modules '((guix build utils)))
(snippet
;; Remove non-free METIS code
- '(delete-file-recursively "contrib/Metis"))))
+ '(begin
+ (delete-file-recursively "contrib/Metis")
+ #t))))
(build-system cmake-build-system)
(propagated-inputs
`(("fltk" ,fltk)
(define-public petsc
(package
(name "petsc")
- (version "3.7.6")
+ (version "3.9.3")
(source
(origin
(method url-fetch)
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
"petsc-lite-" version ".tar.gz"))
(sha256
- (base32 "1y3f5jjq0v5b62i3sabp4kp5mgfyp3vnk0dxhwkrhpypax77nzxh"))))
+ (base32 "1fwkbwv4g7zf2lc8fw865xd0bl9anb6jaczfis5dff7h449gwa48"))))
+ (outputs '("out" ;libraries and headers
+ "examples")) ;~30MiB of examples
(build-system gnu-build-system)
(native-inputs
- `(("python" ,python-2)
- ("perl" ,perl)))
+ `(("python" ,python-2)))
(inputs
`(("gfortran" ,gfortran)
("lapack" ,lapack)
#:configure-flags
`("--with-mpi=0"
"--with-openmp=1"
- "--with-superlu=1"
- ,(string-append "--with-superlu-include="
- (assoc-ref %build-inputs "superlu") "/include")
- ,(string-append "--with-superlu-lib="
- (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
+ "--with-superlu=1")
#:make-flags
;; Honor (parallel-job-count) for build. Do not use --with-make-np,
;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
,@configure-flags)))
(format #t "build directory: ~s~%" (getcwd))
(format #t "configure flags: ~s~%" flags)
- (zero? (apply system* "./configure" flags)))))
+ (apply invoke "./configure" flags))))
(add-after 'configure 'clean-local-references
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
"PETScBuildInternal.cmake"
;; Once installed, should uninstall with Guix
"uninstall.py"))
+ #t)))
+ (add-after 'install 'move-examples
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (examples (assoc-ref outputs "examples"))
+ (exdir (string-append out "/share/petsc/examples"))
+ (exdir' (string-append examples "/share/petsc/examples")))
+ (copy-recursively exdir exdir')
+ (delete-file-recursively exdir)
#t))))))
(home-page "http://www.mcs.anl.gov/petsc")
(synopsis "Library to solve PDEs")
(name "petsc-openmpi")
(inputs
`(("openmpi" ,openmpi)
+ ("hdf5" ,hdf5-parallel-openmpi)
,@(package-inputs petsc)))
(arguments
(substitute-keyword-arguments (package-arguments petsc)
``("--with-mpiexec=mpirun"
,(string-append "--with-mpi-dir="
(assoc-ref %build-inputs "openmpi"))
- ,@(delete "--with-mpi=0" ,cf)))))
+ ,(string-append "--with-hdf5-include="
+ (assoc-ref %build-inputs "hdf5") "/include")
+ ,(string-append "--with-hdf5-lib="
+ (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
+ ,@(delete "--with-mpi=0" ,cf)))
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
(synopsis "Library to solve PDEs (with MPI support)")))
(define-public petsc-complex-openmpi
,@(delete "--with-mpi=0" ,cf)))))
(synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
+
+(define-public python-kiwisolver
+ (package
+ (name "python-kiwisolver")
+ (version "1.0.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "kiwisolver" version))
+ (sha256
+ (base32
+ "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/nucleic/kiwi")
+ (synopsis "Fast implementation of the Cassowary constraint solver")
+ (description
+ "Kiwi is an efficient C++ implementation of the Cassowary constraint
+solving algorithm. Kiwi has been designed from the ground up to be
+lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
+Cassowary solver with typical use cases gaining a 40x improvement. Memory
+savings are consistently > 5x.")
+ (license license:bsd-3)))
+
+(define-public python2-kiwisolver
+ (package-with-python2 python-kiwisolver))
+
(define-public slepc
(package
(name "slepc")
- (version "3.7.4")
+ (version "3.9.2")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "12pbl8yd6r8k9xjlr1qw25rs0k1acgic7hw1s6l6bhiv9s285drg"))))
+ "0gmhdqac8zm3jx43h935z7bflazjnpvqxjv4jh5za2y1z2rqax94"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)))
(format #t "configure flags: ~s~%" flags)
(setenv "SLEPC_DIR" (getcwd))
(setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
- (zero? (apply system* "./configure" flags)))))
+ (apply invoke "./configure" flags))))
(add-after 'install 'delete-doc
;; TODO: SLEPc installs HTML documentation alongside headers in
;; $out/include. We'd like to move them to share/doc, but delete
;; documentation is difficult.
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")))
- (for-each delete-file (find-files out "\\.html$")))))
+ (for-each delete-file (find-files out "\\.html$"))
+ #t)))
(add-after 'install 'clean-install
;; Clean up unnecessary build logs from installation.
(lambda* (#:key outputs #:allow-other-keys)
(delete-file f))))
'("configure.log" "make.log" "gmake.log"
"test.log" "error.log" "RDict.db"
- "uninstall.py"))))))))
+ "uninstall.py"))
+ #t))))))
(home-page "http://slepc.upv.es")
(synopsis "Scalable library for eigenproblems")
(description "SLEPc is a software library for the solution of large sparse
The emphasis of the software is on methods and techniques appropriate for
problems in which the associated matrices are sparse, for example, those
arising after the discretization of partial differential equations.")
- (license license:lgpl3)))
+ (license license:bsd-2)))
(define-public slepc-complex
(package (inherit slepc)
(define-public slepc-openmpi
(package (inherit slepc)
(name "slepc-openmpi")
+ (arguments
+ (substitute-keyword-arguments (package-arguments slepc)
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
(inputs
`(("mpi" ,openmpi)
("arpack" ,arpack-ng-openmpi)
(define-public mumps
(package
(name "mumps")
- (version "5.0.2")
+ (version "5.1.2")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp"))
+ "1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b"))
(patches (search-patches "mumps-build-parallelism.patch"))))
(build-system gnu-build-system)
(inputs
;; By default only the d-precision library is built. Make with "all"
;; target so that all precision libraries and examples are built.
(lambda _
- (zero? (system* "make" "all"
- (format #f "-j~a" (parallel-job-count))))))
+ (invoke "make" "all"
+ (format #f "-j~a" (parallel-job-count)))))
(replace 'check
;; Run the simple test drivers, which read test input from stdin:
;; from the "real" input for the single- and double-precision
(substitute-keyword-arguments (package-arguments mumps)
((#:phases phases)
`(modify-phases ,phases
- (replace
- 'check
- (lambda _
- ((assoc-ref ,phases 'check)
- #:exec-prefix '("mpirun" "-n" "2"))))))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)
+ (replace 'check
+ (lambda _
+ ((assoc-ref ,phases 'check)
+ #:exec-prefix '("mpirun" "-n" "2"))))))))
(synopsis "Multifrontal sparse direct solver (with MPI)")))
(define-public mumps-metis-openmpi
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
- (home-page "http://cran.r-project.org/web/packages/quadprog")
+ (home-page "https://cran.r-project.org/web/packages/quadprog")
(synopsis "Functions to solve quadratic programming problems")
(description
"This package contains routines and documentation for solving quadratic
(define-public r-pracma
(package
(name "r-pracma")
- (version "2.0.7")
+ (version "2.1.5")
(source (origin
(method url-fetch)
(uri (cran-uri "pracma" version))
(sha256
- (base32 "0hxa0rbbp54j0c05qj7vfwhqfdmiz5ax8vhqxd09g33x7c0hqbc5"))))
+ (base32 "18cv7c2gvagbmggfbsy2xk9bpn47izd0qrmqnc3q7afvj6pr6nf9"))))
(build-system r-build-system)
(propagated-inputs
`(("r-quadprog" ,r-quadprog)))
- (home-page "http://cran.r-project.org/web/packages/pracma")
+ (home-page "https://cran.r-project.org/web/packages/pracma")
(synopsis "Practical numerical math functions")
(description "This package provides functions for numerical analysis and
linear algebra, numerical optimization, differential equations, plus some
porting.")
(license license:gpl3+)))
+(define-public ruby-asciimath
+ (package
+ (name "ruby-asciimath")
+ (version "1.0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "asciimath" version))
+ (sha256
+ (base32
+ "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
+ (build-system ruby-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ ;; Apply this patch
+ ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
+ (add-after 'unpack 'patch-remove-spurious-backslashes
+ (lambda _
+ (substitute* "spec/parser_spec.rb"
+ (("\\\\\"")
+ "\"")))))))
+ (native-inputs
+ `(("bundler" ,bundler)
+ ("ruby-rspec" ,ruby-rspec)))
+ (synopsis "AsciiMath parsing and conversion library")
+ (description
+ "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
+easy-to-write markup language for mathematics.")
+ (home-page "https://github.com/asciidoctor/asciimath")
+ (license license:expat)))
+
(define-public superlu
(package
(name "superlu")
(let ((line (read-line in 'concat)))
(unless (regexp-exec rx line)
(display line out)
- (loop)))))))))))
+ (loop))))
+ #t)))))))
(build-system cmake-build-system)
(native-inputs
`(("tcsh" ,tcsh)))
(arguments
`(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
"-DTPL_BLAS_LIBRARIES=openblas"
- "-DBUILD_SHARED_LIBS:BOOL=YES"
- "-DCMAKE_INSTALL_LIBDIR=lib")))
+ "-DBUILD_SHARED_LIBS:BOOL=YES")))
(home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
(synopsis "Supernodal direct solver for sparse linear systems")
(description
(define-public superlu-dist
(package
(name "superlu-dist")
- (version "3.3")
+ (version "5.3.0")
(source
(origin
(method url-fetch)
(uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
"superlu_dist_" version ".tar.gz"))
(sha256
- (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
- (modules '((guix build utils)))
+ (base32 "0ja5ihqivkda1wd58y4lmzvmwssm9g91f70c5q0fzwhng6580h6y"))
+ (modules '((guix build utils)))
(snippet
;; Replace the non-free implementation of MC64 with a stub
'(begin
(use-modules (ice-9 regex)
(ice-9 rdelim))
- (call-with-output-file "SRC/mc64ad.c"
+ (call-with-output-file "SRC/mc64ad_dist.c"
(lambda (port)
(display "
#include <stdio.h>
#include <stdlib.h>
-void mc64id_(int *a) {
+void mc64id_dist(int *a) {
fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
abort ();
}
-void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
+void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
abort ();
}\n" port)))
- (delete-file "SRC/mc64ad.f.bak")
(substitute* "SRC/util.c" ;adjust default algorithm
(("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
- "RowPerm = NOROWPERM"))))
+ "RowPerm = NOROWPERM"))
+ #t))
(patches (search-patches "superlu-dist-scotchmetis.patch"))))
(build-system gnu-build-system)
(native-inputs
(arguments
`(#:parallel-build? #f ;race conditions using ar
#:phases
- (alist-replace
- 'configure
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (call-with-output-file "make.inc"
- (lambda (port)
- (format port "
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (call-with-output-file "make.inc"
+ (lambda (port)
+ (format port "
PLAT =
DSuperLUroot = ~a
DSUPERLULIB = ~a/lib/libsuperlu_dist.a
FFLAGS = -O2 -g $(PIC)
LOADER = $(CC)
CDEFS = -DAdd_"
- (getcwd)
- (assoc-ref outputs "out")
- (assoc-ref inputs "lapack")
- (assoc-ref inputs "pt-scotch")))))
- (alist-cons-after
- 'unpack 'remove-broken-symlinks
- (lambda _
- (for-each delete-file
- (find-files "MAKE_INC" "\\.#make\\..*")))
- (alist-cons-before
- 'build 'create-install-directories
- (lambda* (#:key outputs #:allow-other-keys)
- (for-each
- (lambda (dir)
- (mkdir-p (string-append (assoc-ref outputs "out")
- "/" dir)))
- '("lib" "include")))
- (alist-replace
- 'check
+ (getcwd)
+ (assoc-ref outputs "out")
+ (assoc-ref inputs "lapack")
+ (assoc-ref inputs "pt-scotch"))))
+ #t))
+ (add-after 'unpack 'remove-broken-symlinks
+ (lambda _
+ (for-each delete-file
+ (find-files "MAKE_INC" "\\.#make\\..*"))
+ #t))
+ (add-before 'build 'create-install-directories
+ (lambda* (#:key outputs #:allow-other-keys)
+ (for-each
+ (lambda (dir)
+ (mkdir-p (string-append (assoc-ref outputs "out")
+ "/" dir)))
+ '("lib" "include"))
+ #t))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)
+ (replace 'check
(lambda _
(with-directory-excursion "EXAMPLE"
- (and
- (zero? (system* "mpirun" "-n" "2"
- "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
- (zero? (system* "mpirun" "-n" "2"
- "./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
- (alist-replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- ;; Library is placed in lib during the build phase. Copy over
- ;; headers to include.
- (let* ((out (assoc-ref outputs "out"))
- (incdir (string-append out "/include")))
- (for-each (lambda (file)
- (let ((base (basename file)))
- (format #t "installing `~a' to `~a'~%"
- base incdir)
- (copy-file file
- (string-append incdir "/" base))))
- (find-files "SRC" ".*\\.h$"))))
- %standard-phases)))))))
+ (invoke "mpirun" "-n" "2"
+ "./pddrive" "-r" "1" "-c" "2" "g20.rua")
+ (invoke "mpirun" "-n" "2"
+ "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Library is placed in lib during the build phase. Copy over
+ ;; headers to include.
+ (let* ((out (assoc-ref outputs "out"))
+ (incdir (string-append out "/include")))
+ (for-each (lambda (file)
+ (let ((base (basename file)))
+ (format #t "installing `~a' to `~a'~%"
+ base incdir)
+ (copy-file file
+ (string-append incdir "/" base))))
+ (find-files "SRC" ".*\\.h$")))
+ #t)))))
(home-page (package-home-page superlu))
(synopsis "Parallel supernodal direct solver")
(description
(define-public scotch
(package
(name "scotch")
- (version "6.0.4")
+ (version "6.0.5a")
(source
(origin
(method url-fetch)
- (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/"
- "scotch_" version ".tar.gz"))
+ (uri (string-append "https://gforge.inria.fr/frs/download.php/"
+ "latestfile/298/scotch_" version ".tar.gz"))
(sha256
- (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
+ (base32 "0vsmgjz8qv80di3ljmc7hbdsizxxxwy2b9rgd2fl1mdc6dgbj8av"))
(patches (search-patches "scotch-test-threading.patch"
- "pt-scotch-build-parallelism.patch"))))
+ "scotch-build-parallelism.patch"
+ "scotch-graph-induce-type-64.patch"
+ "scotch-graph-diam-64.patch"))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)
(modify-phases %standard-phases
(add-after
'unpack 'chdir-to-src
- (lambda _ (chdir "src")))
+ (lambda _ (chdir "src") #t))
(replace
'configure
(lambda _
;; XXX: Causes invalid frees in superlu-dist tests
;; "SCOTCH_PTHREAD"
;; "SCOTCH_PTHREAD_NUMBER=2"
- "restrict=__restrict"))))))
- (add-after
- 'build 'build-esmumps
+ "restrict=__restrict"))))
+ #t))
+ (add-after 'build 'build-esmumps
(lambda _
- (zero? (system* "make"
- (format #f "-j~a" (parallel-job-count))
- "esmumps"))))
+ (invoke "make"
+ (format #f "-j~a" (parallel-job-count))
+ "esmumps")))
(replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(mkdir out)
- (zero? (system* "make"
- (string-append "prefix=" out)
- "install"))
+ (invoke "make"
+ (string-append "prefix=" out)
+ "install")
;; esmumps files are not installed with the above
(for-each (lambda (f)
(copy-file f (string-append out "/include/" f)))
(find-files "../include" ".*esmumps.h$"))
(for-each (lambda (f)
(copy-file f (string-append out "/lib/" f)))
- (find-files "../lib" "^lib.*esmumps.*"))))))))
+ (find-files "../lib" "^lib.*esmumps.*"))
+ #t))))))
(home-page "http://www.labri.fr/perso/pelegrin/scotch/")
(synopsis "Programs and libraries for graph algorithms")
(description "SCOTCH is a set of programs and libraries which implement
(define-public p4est
(package
(name "p4est")
- (version "1.1")
+ (version "2.0")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "0faina2h5qsx3m2izbzaj9bbakma1krbbjmq43wrp1hcbyijflqb"))))
+ "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
(build-system gnu-build-system)
(inputs
`(("fortran" ,gfortran)
" -lopenblas")
,(string-append "LAPACK_LIBS=-L"
(assoc-ref %build-inputs "lapack")
- " -llapack"))))
+ " -llapack"))
+ #:phases (modify-phases %standard-phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(home-page "http://www.p4est.org")
(synopsis "Adaptive mesh refinement on forests of octrees")
(description
(define-public maxima
(package
(name "maxima")
- (version "5.40.0")
+ (version "5.41.0")
(source
(origin
(method url-fetch)
version "-source/" name "-" version ".tar.gz"))
(sha256
(base32
- "15pp35ayglv723bjbqc60gcdv2bm54s6pywsm4i4cwbjsf64dzkl"))
+ "0x0n81z0s4pl8nwpf7ivlsbvsdphm9w42250g7qdkizl0132by6s"))
(patches (search-patches "maxima-defsystem-mkdir.patch"))))
(build-system gnu-build-system)
(inputs
(define-public wxmaxima
(package
(name "wxmaxima")
- (version "17.05.1")
+ (version "18.02.0")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0dv0cy0cf46v0cbw32izscpkdmpxg1qhwq1f4cz46kkqd8k4yfbj"))))
- (build-system gnu-build-system)
+ "03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj"))
+ (patches
+ (search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch"))))
+ (build-system cmake-build-system)
(native-inputs
- `(("autoconf" ,autoconf)
- ("automake" ,automake)
- ("gettext" ,gettext-minimal)))
+ `(("gettext" ,gettext-minimal)))
(inputs
`(("wxwidgets" ,wxwidgets)
("maxima" ,maxima)
("gtk+" ,gtk+)
("shared-mime-info" ,shared-mime-info)))
(arguments
- `(#:phases
+ `(#:tests? #f ; no check target
+ #:phases
(modify-phases %standard-phases
- (add-after 'unpack 'autoconf
- (lambda _
- (zero? (system* "sh" "bootstrap"))))
(add-after 'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
(wrap-program (string-append (assoc-ref outputs "out")
(define-public armadillo
(package
(name "armadillo")
- (version "7.800.2")
+ (version "9.100.5")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/arma/armadillo-"
version ".tar.xz"))
(sha256
(base32
- "1qqzy7dp891j9v7062mv1599hdwr97vqzrd3j2fl8c3gmc00dmzg"))))
+ "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
(build-system cmake-build-system)
- (arguments `(#:tests? #f)) ;no test target
+ (arguments `(#:tests? #f)) ; no test target
(inputs
`(("openblas" ,openblas)
("lapack" ,lapack)
(define-public openblas
(package
(name "openblas")
- (version "0.2.19")
+ (version "0.3.2")
(source
(origin
(method url-fetch)
- (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
- version))
+ (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
+ version "%20version.tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "071zqnmnxhh0c9phzyn3f198yxa0hjxda7016azdbq2056sm70w7"))))
+ "0b20km2jv7m6qiylrlvhq2vnmkmilb633mr8rhqmgbn1wqrp58jq"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ;no "check" target
+ `(#:test-target "test"
;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
;; TARGET is specified, OpenBLAS will tune itself to the build host, so
;; we need to disable substitutions.
#:make-flags
(list (string-append "PREFIX=" (assoc-ref %outputs "out"))
"SHELL=bash"
- "NO_LAPACK=1"
;; Build the library for all supported CPUs. This allows
;; switching CPU targets at runtime with the environment variable
;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
'("TARGET=ARMV8"))
(else '()))))
;; no configure script
- #:phases (alist-delete 'configure %standard-phases)))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'build 'set-extralib
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; Get libgfortran found when building in utest.
+ (setenv "FEXTRALIB"
+ (string-append "-L" (assoc-ref inputs "fortran-lib")
+ "/lib"))
+ #t)))))
(inputs
- `(("fortran" ,gfortran)))
+ `(("fortran-lib" ,gfortran "lib")))
(native-inputs
`(("cunit" ,cunit)
+ ("fortran" ,gfortran)
("perl" ,perl)))
(home-page "http://www.openblas.net/")
(synopsis "Optimized BLAS library based on GotoBLAS")
"OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
(license license:bsd-3)))
+(define-public openblas-ilp64
+ (package (inherit openblas)
+ (name "openblas-ilp64")
+ (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
+ (arguments
+ (substitute-keyword-arguments (package-arguments openblas)
+ ((#:make-flags flags '())
+ `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
+ ,flags))))
+ (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
+ (license license:bsd-3)))
+
(define* (make-blis implementation #:optional substitutable?)
"Return a BLIS package with the given IMPLEMENTATION (see config/ in the
source tree for a list of implementations.)
(define-public openlibm
(package
(name "openlibm")
- (version "0.5.1")
+ (version "0.6.0")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq"))))
+ "0a5fpm8nra5ldhjk0cqd2rx1qh32wiarkxmcqcm5xl8z7l4kjm6l"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
(list (string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
;; no configure script
- (alist-delete 'configure %standard-phases)
+ (modify-phases %standard-phases (delete 'configure))
#:tests? #f)) ;the tests are part of the default target
(home-page "http://openlibm.org/")
(synopsis "Portable C mathematical library (libm)")
(define-public openspecfun
(package
(name "openspecfun")
- (version "0.5.2")
+ (version "0.5.3")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1y5b2h6f2k72536kym3vzy3li3bhpd23x463g7hdmjdi3cncavz1"))))
+ "1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m"))))
(build-system gnu-build-system)
(arguments
- '(#:tests? #f ;no "check" target
+ '(#:tests? #f ; no "check" target
#:make-flags
(list (string-append "prefix=" (assoc-ref %outputs "out")))
- ;; no configure script
- #:phases (alist-delete 'configure %standard-phases)))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)))) ; no configure script
(inputs
`(("fortran" ,gfortran)))
(home-page "https://github.com/JuliaLang/openspecfun")
(modules '((guix build utils)))
(snippet
;; Remove bundled metis source
- '(delete-file-recursively "metis-5.1.0"))))
+ '(begin
+ (delete-file-recursively "metis-5.1.0")
+ #t))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
(define-public glm
(package
(name "glm")
- (version "0.9.6.3")
+ (version "0.9.9.1")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://sourceforge/ogl-math/glm-" version
- "/glm-" version ".zip"))
+ (uri (string-append "https://github.com/g-truc/glm/releases/download/"
+ version "/glm-" version ".zip"))
(sha256
(base32
- "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
+ "042a23hmxfs429czkmlg5ixf28aikzfbw18780prj2gcd4flgw8h"))))
(build-system cmake-build-system)
(native-inputs
`(("unzip" ,unzip)))
- (home-page "http://glm.g-truc.net")
+ (home-page "https://glm.g-truc.net/")
(synopsis "OpenGL Mathematics library")
(description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
library for graphics software based on the OpenGL Shading Language (GLSL)
(define-public lpsolve
(package
(name "lpsolve")
- (version "5.5.2.0")
+ (version "5.5.2.5")
(source
(origin
(method url-fetch)
"/lp_solve_" version "_source.tar.gz"))
(sha256
(base32
- "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq"))
+ "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
(modules '((guix build utils)))
(snippet
- '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
- (("^c=cc") "c=gcc")
- ;; Pretend to be on a 64 bit platform to obtain a common directory
- ;; name for the build results on all architectures; nothing else
- ;; seems to depend on it.
- (("^PLATFORM=.*$") "PLATFORM=ux64\n")
-
- ;; The check for 'isnan' as it is written fails with
- ;; "non-floating-point argument in call to function
- ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
- ;; definition, which in turn leads to bad things. Fix the feature
- ;; test.
- (("isnan\\(0\\)") "isnan(0.)")))))
+ '(begin
+ (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
+ (("^c=cc") "c=gcc")
+ ;; Pretend to be on a 64 bit platform to obtain a common directory
+ ;; name for the build results on all architectures; nothing else
+ ;; seems to depend on it.
+ (("^PLATFORM=.*$") "PLATFORM=ux64\n")
+
+ ;; The check for 'isnan' as it is written fails with
+ ;; "non-floating-point argument in call to function
+ ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
+ ;; definition, which in turn leads to bad things. Fix the feature
+ ;; test.
+ (("isnan\\(0\\)") "isnan(0.)"))
+ #t))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ; no check target
+ `(#:tests? #f ; no check target
#:phases
(modify-phases %standard-phases
- (delete 'configure)
+ (delete 'configure) ; no configure script
(replace 'build
(lambda _
- (and (with-directory-excursion "lpsolve55"
- (zero? (system* "bash" "ccc")))
- (with-directory-excursion "lp_solve"
- (zero? (system* "bash" "ccc"))))))
+ (with-directory-excursion "lpsolve55"
+ (invoke "bash" "ccc"))
+ (with-directory-excursion "lp_solve"
+ (invoke "bash" "ccc"))
+ #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
;; This is where LibreOffice expects to find the header
;; files, and where they are installed by Debian.
(include (string-append out "/include/lpsolve")))
- (mkdir-p lib)
- (copy-file "lpsolve55/bin/ux64/liblpsolve55.a"
- (string-append lib "/liblpsolve55.a"))
- (copy-file "lpsolve55/bin/ux64/liblpsolve55.so"
- (string-append lib "/liblpsolve55.so"))
+ (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
+ (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
(install-file "lp_solve/bin/ux64/lp_solve" bin)
;; Install a subset of the header files as on Debian
(define-public dealii
(package
(name "dealii")
- (version "8.5.0")
+ (version "8.5.1")
(source
(origin
(method url-fetch)
"download/v" version "/dealii-" version ".tar.gz"))
(sha256
(base32
- "0yfpy4zh8j7hmqakw17zdlmvfdcmhwgs66wcb716plc4y7v3z4g6"))
+ "1bh9rsmkrg0zi70n27b11djmac9lximghsiy7mg7w7x544n82gnk"))
(modules '((guix build utils)))
(snippet
;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
- '(delete-file-recursively "bundled"))))
+ '(begin
+ (delete-file-recursively "bundled")
+ #t))))
(build-system cmake-build-system)
(inputs
`(("tbb" ,tbb)
version "-src.zip"))
(sha256
(base32
- "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
+ "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
+ (patches (search-patches "flann-cmake-3.11.patch"))))
(build-system cmake-build-system)
(outputs '("out"
"octave")) ;46 MiB .mex file that pulls Octave
(define-public hypre
(package
(name "hypre")
- (version "2.11.0")
+ (version "2.14.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/LLNL/hypre/archive/"
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
+ "0v515i73bvaz378h5465b1dy9v2gf924zy2q94cpq4qqarawvkqh"))
(modules '((guix build utils)))
(snippet
'(begin
;; substitute the tarball creation time.
(substitute* "src/utilities/HYPRE_utilities.h"
(("Date Compiled: .*$")
- "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
+ "Date Compiled: Apr 11 2018 16:24:59 +0000\"\n"))
#t))))
(build-system gnu-build-system)
(outputs '("out" ;6.1 MiB of headers and libraries
(native-inputs
`(("doc++" ,doc++)
("netpbm" ,netpbm)
+ ("perl" ,perl) ;needed to run 'ppmquant' during tests
("texlive" ,texlive) ;full package required for fonts
("ghostscript" ,ghostscript)))
(inputs
(substitute-keyword-arguments (package-arguments hypre)
((#:configure-flags flags)
``("--with-MPI"
- ,@(delete "--without-MPI" ,flags)))))
+ ,@(delete "--without-MPI" ,flags)))
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
(synopsis "Parallel solvers and preconditioners for linear equations")
(description
"HYPRE is a software library of high performance preconditioners and
supports compressed MAT files, as well as newer (version 7.3) MAT files.")
(license license:bsd-2)))
-(define-public libhilbert
- (package
- (name "libhilbert")
- (version "0.2-1")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "http://web.cs.dal.ca/~chamilto/hilbert/"
- "libhilbert-" version ".tar.gz"))
- (sha256
- (base32
- "0v48x8405dj95gjn2saja4bzhw86d6zl6d3dg8h7dzac2qr97s34"))))
- (build-system gnu-build-system)
- (home-page "http://web.cs.dal.ca/~chamilto/hilbert")
- (synopsis "Hilbert indices for multidimensional data")
- (description "The libhilbert library can efficiently calculate Hilbert
-curves and order-preserving representations of Hilbert curve indices that use
-the same amount of space as the original point representation. This is useful
-when using the Gilbert curve as a space filling curve through a
-high-dimensional space where not all demensions have the same cardinality.")
- (license license:lgpl2.1+)))
-
(define-public vc
(package
(name "vc")
- (version "1.2.0")
+ (version "1.3.3")
(source
(origin (method url-fetch)
(uri (string-append "https://github.com/VcDevel/Vc/releases/"
"download/" version "/Vc-" version ".tar.gz"))
(sha256
(base32
- "1rh6dhqar3y07n4xqyml0sa0v48qv3ch9dc3yc2in855hlh4vnqi"))))
+ "1zmlpn32jzb38smp3j834llmbix3whsrbw0h397qxysbw792kih8"))))
(build-system cmake-build-system)
(arguments
'(#:configure-flags
- '("-DBUILD_TESTING=ON")))
+ '("-DBUILD_TESTING=ON"
+ ;; By default, Vc will optimize for the CPU of the build machine.
+ ;; Setting this to "none" makes it create portable binaries. See
+ ;; "cmake/OptimizeForArchitecture.cmake".
+ "-DTARGET_ARCHITECTURE=none")))
(synopsis "SIMD vector classes for C++")
(description "Vc provides portable, zero-overhead C++ types for explicitly
data-parallel programming. It is a library designed to ease explicit
"-DINSTALL_PYTHON_BINDINGS=true"
(string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR="
%output
- "/lib/python2.7/site-packages")
- (string-append "-DCMAKE_INSTALL_LIBDIR="
- %output
- "/lib"))
-
+ "/lib/python2.7/site-packages"))
#:phases
(modify-phases %standard-phases
(add-before 'configure 'bootstrap
(("\\\\n") "")))))))
(home-page "http://cubicle.lri.fr/")
(synopsis "Model checker for array-based systems")
- (description "Cubicle is an open source model checker for verifying safety
-properties of array-based systems. This is a syntactically restricted class of
-parametrized transition systems with states represented as arrays indexed by an
-arbitrary number of processes. Cache coherence protocols and mutual exclusion
-algorithms are typical examples of such systems.")
+ (description "Cubicle is a model checker for verifying safety properties
+of array-based systems. This is a syntactically restricted class of
+parametrized transition systems with states represented as arrays indexed by
+an arbitrary number of processes. Cache coherence protocols and mutual
+exclusion algorithms are typical examples of such systems.")
(license license:asl2.0)))
+
+(define-public elemental
+ (package
+ (name "elemental")
+ (version "0.87.7")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/elemental/Elemental/"
+ "archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1nfp82w22pi8x8fg9sc37z8kf84dqi1dhxp8bbk7571y4aygvv3v"))))
+ (build-system cmake-build-system)
+ (home-page "http://libelemental.org")
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs
+ `(("blas" ,openblas)
+ ("gfortran:lib" ,gfortran "lib")
+ ("gmp" ,gmp)
+ ("lapack" ,lapack)
+ ("metis" ,metis)
+ ("mpc" ,mpc)
+ ("mpfr" ,mpfr)
+ ("mpi" ,openmpi)
+ ("qd" ,qd)))
+ (arguments
+ `(#:build-type "Release" ;default RelWithDebInfo not supported
+ #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
+ "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
+ "-DEL_CACHE_WARNINGS:BOOL=YES"
+ "-DEL_TESTS:BOOL=YES"
+ "-DCMAKE_INSTALL_LIBDIR=lib"
+ "-DGFORTRAN_LIB=gfortran")
+ #:phases (modify-phases %standard-phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)
+ (add-before 'check 'setup-tests
+ (lambda _
+ ;; Parallelism is done at the MPI layer.
+ (setenv "OMP_NUM_THREADS" "1")
+ #t))
+ (add-after 'install 'remove-tests
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Tests are installed, with no easy configuration
+ ;; switch to prevent this, so delete them.
+ (delete-file-recursively
+ (string-append (assoc-ref outputs "out") "/bin"))
+ #t)))))
+ (synopsis "Dense and sparse-direct linear algebra and optimization")
+ (description "Elemental is a modern C++ library for distributed-memory
+dense and sparse-direct linear algebra, conic optimization, and lattice
+reduction.")
+ (license license:bsd-2)))
+
+(define-public mcrl2
+ (package
+ (name "mcrl2")
+ (version "201707.1.15162")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
+ version
+ ".tar.gz"))
+ (sha256
+ (base32
+ "1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
+ (native-inputs
+ `(("subversion" ,subversion)))
+ (inputs
+ `(("boost" ,boost)
+ ("glu" ,glu)
+ ("mesa" ,mesa)
+ ("qtbase" ,qtbase)))
+ (build-system cmake-build-system)
+ (synopsis "Toolset for the mCRL2 formal specification language")
+ (description
+ "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
+specification language for describing concurrent discrete event systems. Its
+toolset supports analysis and automatic verification, linearisation, simulation,
+state-space exploration and generation, and tools to optimise and analyse
+specifications. Also, state spaces can be manipulated, visualised and
+analysed.")
+ (home-page "https://mcrl2.org")
+ (license license:boost1.0)))
+
+(define-public r-subplex
+ (package
+ (name "r-subplex")
+ (version "1.5-4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "subplex" version))
+ (sha256
+ (base32
+ "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "https://cran.r-project.org/web/packages/subplex")
+ (synopsis "Unconstrained optimization using the subplex algorithm")
+ (description "This package implements the Subplex optimization algorithm.
+It solves unconstrained optimization problems using a simplex method on
+subspaces. The method is well suited for optimizing objective functions that
+are noisy or are discontinuous at the solution.")
+ (license license:gpl3+)))
+
+(define-public r-desolve
+ (package
+ (name "r-desolve")
+ (version "1.21")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "deSolve" version))
+ (sha256
+ (base32
+ "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
+ (properties `((upstream-name . "deSolve")))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "https://desolve.r-forge.r-project.org/")
+ (synopsis "Solvers for initial value problems of differential equations")
+ (description "This package provides functions that solve initial
+value problems of a system of first-order ordinary differential equations (ODE),
+of partial differential equations (PDE), of differential algebraic equations
+(DAE), and of delay differential equations. The functions provide an interface
+to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
+to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
+the Runge-Kutta family with fixed or variable time steps. The package contains
+routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
+differential equations (PDE) that have been converted to ODEs by numerical
+differencing.")
+ (license license:gpl2+)))
+
+(define-public tcalc
+ (package
+ (name "tcalc")
+ (version "2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
+ (build-system gnu-build-system)
+ (synopsis "The terminal calculator")
+ (description
+ "The terminal calculator is a small program to help users of the GNU/Linux
+terminal do calculations simply and quickly. The formula to be calculated can
+be fed to @command{tcalc} through the command line.")
+ (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
+ (license license:gpl3+)))
+
+(define-public sundials
+ (package
+ (name "sundials")
+ (version "3.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
+ "sundials-" version ".tar.gz"))
+ (sha256
+ (base32
+ "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
+ (build-system cmake-build-system)
+ (native-inputs
+ `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
+ (inputs
+ `(("fortran" ,gfortran) ;for fcmix
+ ("blas" ,openblas)
+ ("suitesparse" ,suitesparse))) ;TODO: Add hypre
+ (arguments
+ `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
+ "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
+ "-DEXAMPLES_ENABLE_F77:BOOL=ON"
+ "-DEXAMPLES_ENABLE_F90:BOOL=ON"
+ "-DEXAMPLES_INSTALL:BOOL=OFF"
+
+ "-DFCMIX_ENABLE:BOOL=ON"
+
+ "-DKLU_ENABLE:BOOL=ON"
+ ,(string-append "-DKLU_INCLUDE_DIR="
+ (assoc-ref %build-inputs "suitesparse")
+ "/include")
+ ,(string-append "-DKLU_LIBRARY_DIR="
+ (assoc-ref %build-inputs "suitesparse")
+ "/lib"))))
+ (home-page "https://computation.llnl.gov/projects/sundials")
+ (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
+ (description "SUNDIALS is a family of software packages implemented with
+the goal of providing robust time integrators and nonlinear solvers that can
+easily be incorporated into existing simulation codes.")
+ (license license:bsd-3)))
+
+(define-public sundials-openmpi
+ (package (inherit sundials)
+ (name "sundials-openmpi")
+ (inputs
+ `(("mpi" ,openmpi)
+ ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
+ ,@(package-inputs sundials)))
+ (arguments
+ (substitute-keyword-arguments (package-arguments sundials)
+ ((#:configure-flags flags '())
+ `(cons* "-DMPI_ENABLE:BOOL=ON"
+ "-DPETSC_ENABLE:BOOL=ON"
+ (string-append "-DPETSC_INCLUDE_DIR="
+ (assoc-ref %build-inputs "petsc")
+ "/include")
+ (string-append "-DPETSC_LIBRARY_DIR="
+ (assoc-ref %build-inputs "petsc")
+ "/lib")
+ ,flags))
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
+ (synopsis "SUNDIALS with OpenMPI support")))
HCoop / jackhill / guix / guix.git / blobdiff