;;; 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 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
-;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017 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 Fabian Harfert <fhmgufs@web.de>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org>
+;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be>
+;;; 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 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
+;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix build-system ocaml)
#:use-module (guix build-system r)
#:use-module (gnu packages algebra)
+ #:use-module (gnu packages autotools)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages gtk)
#:use-module (gnu packages image)
+ #:use-module (gnu packages java)
#:use-module (gnu packages less)
#:use-module (gnu packages lisp)
#:use-module (gnu packages logging)
#:use-module (gnu packages tls)
#:use-module (gnu packages wxwidgets)
#:use-module (gnu packages xml)
- #:use-module (gnu packages zip)
#:use-module (srfi srfi-1))
(define-public aris
(define-public coda
(package
(name "coda")
- (version "2.18")
+ (version "2.18.2")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/stcorp/coda/releases/download/"
version "/coda-" version ".tar.gz"))
(sha256
- (base32 "11asla1ap8vd73farqjlpb179sfiy0biydcwxjfcakrp9sf8v9bs"))
+ (base32 "01fnqcby9jijvf3jxr1fk4bny059lvvq5wbqm7ns60ilykfdnm6a"))
(patches (search-patches "coda-use-system-libs.patch"))
(modules '((guix build utils)))
(snippet
(define-public gsl
(package
(name "gsl")
- (version "2.3")
+ (version "2.4")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/gsl/gsl-"
version ".tar.gz"))
(sha256
(base32
- "1yxdzqjwmi2aid650fa9zyr8llw069x7lm489wx9nnfdi6vh09an"))
+ "16yfs5n444s03np1naj6yp1fsysd42kdscxzkg0k2yvfjixx0ijd"))
(patches (search-patches "gsl-test-i686.patch"))))
(build-system gnu-build-system)
(arguments
- `(#:parallel-tests? #f
- ;; Currently there are numerous tests that fail on "exotic"
+ `(;; Currently there are numerous tests that fail on "exotic"
;; architectures such as aarch64 and ppc64le.
,@(if (string-prefix? "aarch64-linux"
(or (%current-target-system) (%current-system)))
the OCaml language.")
(license license:gpl3+)))
+(define-public ocaml4.01-gsl
+ (package-with-ocaml4.01 ocaml-gsl))
+
(define-public glpk
(package
(name "glpk")
- (version "4.61")
+ (version "4.63")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "1adbvwiaqrv9pql9ry3lhn2vfsxnff2vh4fs477d90kpfx0xwrlq"))))
+ "1xp7nclmp8inp20968bvvfcwmz3mz03sbm0v3yjz8aqwlpqjfkci"))))
(build-system gnu-build-system)
(inputs
`(("gmp" ,gmp)))
(define-public lapack
(package
(name "lapack")
- (version "3.5.0")
+ (version "3.7.1")
(source
(origin
(method url-fetch)
version ".tgz"))
(sha256
(base32
- "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))
+ "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
(build-system cmake-build-system)
(home-page "http://www.netlib.org/lapack/")
(inputs `(("fortran" ,gfortran)
("python" ,python-2)))
(arguments
- `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
- "-DLAPACKE=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)))
+ `(#: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
+ (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
(license (license:non-copyleft "file://LICENSE"
"See LICENSE in the distribution."))))
+(define-public lapack-3.5
+ (package
+ (inherit lapack)
+ (version "3.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://www.netlib.org/lapack/lapack-"
+ version ".tgz"))
+ (sha256
+ (base32
+ "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))))
+
(define-public scalapack
(package
(name "scalapack")
(define-public gnuplot
(package
(name "gnuplot")
- (version "5.0.5")
+ (version "5.0.6")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
version ".tar.gz"))
(sha256
(base32
- "0lr065qdlgss8lmy31l7hkmnk9fp4lvqq9qgb1f1209f36zy1wr5"))))
+ "0q5lr6nala3ln6f3yp6g17ziymb9r9gx9zylnw1y3hjmwl9lggjv"))))
(build-system gnu-build-system)
(inputs `(("readline" ,readline)
("cairo" ,cairo)
("pango" ,pango)
("gd" ,gd)
("lua" ,lua)))
- (native-inputs `(("pkg-config" ,pkg-config)
- ("texlive" ,texlive-minimal)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)
+ ("texlive" ,texlive-tiny)))
(home-page "http://www.gnuplot.info")
(synopsis "Command-line driven graphing utility")
(description "Gnuplot is a portable command-line driven graphing
(define-public hdf4
(package
(name "hdf4")
- (version "4.2.12")
+ (version "4.2.13")
(source
(origin
(method url-fetch)
(uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
version "/src/hdf-" version ".tar.bz2"))
(sha256
- (base32 "020jh563sjyxsgml8l809d2i1d4ms9shivwj3gbm7n0ilxbll8id"))
+ (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
(patches (search-patches "hdf4-architectures.patch"
"hdf4-reproducibility.patch"
"hdf4-shared-fortran.patch"))))
-
(build-system gnu-build-system)
(native-inputs
`(("gfortran" ,gfortran)
#:configure-flags '("--enable-shared")
#:phases
(modify-phases %standard-phases
+ ;; This is inspired by two of Debian's patches.
+ (add-before 'configure 'add-more-aarch64-support
+ (lambda _
+ (substitute* '("mfhdf/ncgen/ncgen.l"
+ "mfhdf/ncgen/ncgenyy.c"
+ "mfhdf/libsrc/netcdf.h.in")
+ (("AIX5L64") "__aarch64__"))
+ #t))
(add-before 'configure 'patchbuild
(lambda _
(substitute*
-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
(("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
--R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")))))))
+-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
+ #t))
+ (add-after 'configure 'patch-settings
+ (lambda _
+ ;; libhdf4.settings contains the full path of the
+ ;; compilers used, and its contents are included in
+ ;; .so-files. We truncate the hashes to avoid
+ ;; unnecessary store references to those compilers:
+ (substitute* "libhdf4.settings"
+ (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
+ (string-append prefix (string-take hash 10) "...")))
+ #t))
+ )))
(home-page "https://www.hdfgroup.org/products/hdf4/")
(synopsis
"Library and multi-object file format for storing and managing data")
(define-public hdf5
(package
(name "hdf5")
- (version "1.8.18")
+ (version "1.8.19")
(source
(origin
(method url-fetch)
- (uri (list (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/"
- "hdf5-" version "/src/hdf5-"
+ (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
+ "hdf5-" (version-major+minor version)
+ "/hdf5-" version "/src/hdf5-"
version ".tar.bz2")
(string-append "https://support.hdfgroup.org/ftp/HDF5/"
"current"
(take (string-split version #\.) 2))
"/src/hdf5-" version ".tar.bz2")))
(sha256
- (base32 "13542vrnl1p35n8vbq0wzk40vddmm33q5nh04j98c7r1yjnxxih1"))
+ (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
(patches (list (search-patch "hdf5-config-date.patch")))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (outputs '("out" ; core library
+ "fortran")) ; fortran interface
(arguments
`(;; Some of the users, notably Flann, need the C++ interface.
- #:configure-flags '("--enable-cxx")
+ #:configure-flags '("--enable-cxx"
+ "--enable-fortran"
+ "--enable-fortran2003")
#:phases
(modify-phases %standard-phases
(add-before 'configure 'patch-configure
- (lambda _
+ (lambda* (#:key outputs #:allow-other-keys)
(substitute* "configure"
(("/bin/mv") "mv"))
+ (substitute* "fortran/src/Makefile.in"
+ (("libhdf5_fortran_la_LDFLAGS =")
+ (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
+ (assoc-ref outputs "fortran") "/lib")))
+ (substitute* "hl/fortran/src/Makefile.in"
+ (("libhdf5hl_fortran_la_LDFLAGS =")
+ (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
+ (assoc-ref outputs "fortran") "/lib")))
+ #t))
+ (add-after 'configure 'patch-settings
+ (lambda _
+ ;; libhdf5.settings contains the full path of the
+ ;; compilers used, and its contents are included in
+ ;; libhdf5.so. We truncate the hashes to avoid
+ ;; 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) "...")))
#t))
(add-after 'install 'patch-references
(lambda* (#:key inputs outputs #:allow-other-keys)
(substitute* (find-files bin "h5p?cc")
(("-lz" lib)
(string-append "-L" zlib "/lib " lib)))
- #t))))))
+ #t)))
+ (add-after 'install 'split
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; Move all fortran-related files
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (lib (string-append out "/lib"))
+ (inc (string-append out "/include"))
+ (ex (string-append out "/share/hdf5_examples/fortran"))
+ (fort (assoc-ref outputs "fortran"))
+ (fbin (string-append fort "/bin"))
+ (flib (string-append fort "/lib"))
+ (finc (string-append fort "/include"))
+ (fex (string-append fort "/share/hdf5_examples/fortran")))
+ (mkdir-p fbin)
+ (mkdir-p flib)
+ (mkdir-p finc)
+ (mkdir-p fex)
+ (rename-file (string-append bin "/h5fc")
+ (string-append fbin "/h5fc"))
+ (for-each (lambda (file)
+ (rename-file file
+ (string-append flib "/" (basename file))))
+ (find-files lib ".*fortran.*"))
+ (for-each (lambda (file)
+ (rename-file file
+ (string-append finc "/" (basename file))))
+ (find-files inc ".*mod"))
+ (for-each (lambda (file)
+ (rename-file file
+ (string-append fex "/" (basename file))))
+ (find-files ex ".*"))
+ (delete-file-recursively ex))
+ #t)))))
(home-page "http://www.hdfgroup.org")
(synopsis "Management suite for extremely large and complex data")
(description "HDF5 is a suite that makes possible the management of
(license (license:x11-style
"http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
+(define-public hdf-java
+ (package
+ (name "hdf-java")
+ (version "3.3.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
+ version "/src/CMake-hdfjava-" version ".tar.gz"))
+ (sha256
+ (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
+ (modules '((guix build utils)))
+ (snippet ; Make sure we don't use the bundled sources and binaries.
+ `(begin
+ (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"))))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("jdk" ,icedtea "jdk")
+ ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
+ ;; For tests:
+ ("hamcrest-core" ,java-hamcrest-core)
+ ("junit" ,java-junit)
+ ("slf4j-simple" ,java-slf4j-simple)))
+ (inputs
+ `(("hdf4" ,hdf4)
+ ("hdf5" ,hdf5)
+ ("zlib" ,zlib)
+ ("libjpeg" ,libjpeg)
+ ("slf4j-api" ,java-slf4j-api)))
+ (arguments
+ `(#:configure-flags
+ (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
+ (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
+ (assoc-ref %build-inputs "jdk") "/lib" )
+ (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
+ (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
+
+ #:make-flags
+ (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
+ (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
+ (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
+ (string-append "JPEGLIB="
+ (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
+ "LLEXT=so")
+
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'chdir-to-source
+ (lambda _ (chdir ,(string-append "hdfjava-" version))))
+ (add-before 'configure 'patch-build
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* "configure"
+ (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
+ (("/bin/cat") (which "cat")))
+ ;; Set classpath for compilation
+ (substitute* '("hdf/hdf5lib/Makefile.in"
+ "hdf/hdf5lib/exceptions/Makefile.in"
+ "hdf/hdflib/Makefile.in")
+ (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
+ (string-append (assoc-ref inputs "slf4j-api")
+ "/share/java/slf4j-api.jar")))
+ ;; Replace outdated config.sub and config.guess:
+ (with-directory-excursion "config"
+ (for-each (lambda (file)
+ (copy-file
+ (string-append (assoc-ref inputs "automake")
+ "/share/automake-1.15/" file) file))
+ '("config.sub" "config.guess")))
+ (mkdir-p (string-append (assoc-ref outputs "out")))
+ ;; Set classpath for tests
+ (let* ((build-dir (getcwd))
+ (lib (string-append build-dir "/lib"))
+ (jhdf (string-append lib "/jhdf.jar"))
+ (jhdf5 (string-append lib "/jhdf5.jar"))
+ (testjars
+ (map (lambda (i)
+ (string-append (assoc-ref inputs i)
+ "/share/java/" i ".jar"))
+ '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
+ (class-path
+ (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
+
+ (substitute* '("test/hdf5lib/Makefile.in"
+ "test/hdf5lib/junit.sh.in"
+ "examples/runExample.sh.in")
+ (("/usr/bin/test")
+ (string-append (assoc-ref inputs "coreutils")
+ "/bin/test"))
+ (("/usr/bin/uname")
+ (string-append (assoc-ref inputs "coreutils")
+ "/bin/uname"))
+ (("CLASSPATH=[^\n]*")
+ (string-append "CLASSPATH=" class-path)))
+ (setenv "CLASSPATH" class-path))
+ #t))
+ (add-before 'check 'build-examples
+ (lambda _
+ (zero? (apply system* `("javac"
+ ,@(find-files "examples" ".*\\.java")))))))
+
+ #:parallel-build? #f
+
+ #:parallel-tests? #f ))
+ (home-page "https://support.hdfgroup.org/products/java")
+ (synopsis "Java interface for the HDF4 and HDF5 libraries")
+ (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
+the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
+implemented in C.")
+
+ ;; BSD-style license:
+ (license (license:x11-style
+ "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
+/current/src/unpacked/COPYING"))))
+
(define-public hdf-eos2
(package
(name "hdf-eos2")
(arguments `(#:tests? #f)) ; Tests require googletest *sources*
(inputs `(("lapack" ,lapack)
("fftw" ,fftw)))
- (native-inputs `(("texlive-minimal" ,texlive-minimal)
- ("doxygen" ,doxygen)))
+ ;; FIXME: Even though the fonts are available dvips complains:
+ ;; "Font cmmi10 not found; characters will be left blank."
+ (native-inputs
+ `(("texlive" ,texlive-tiny)
+ ("ghostscript" ,ghostscript)
+ ("doxygen" ,doxygen)))
(home-page "http://itpp.sourceforge.net")
(synopsis "C++ library of maths, signal processing and communication classes")
(description "IT++ is a C++ library of mathematical, signal processing and
("libjpeg" ,libjpeg)))
(arguments
`(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
+
+ #:phases (modify-phases %standard-phases
+ (add-before 'configure 'fix-source-date
+ (lambda _
+ ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
+ ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
+ ;; to '1st hour of the current day', and therefore makes the
+ ;; package not reproducible.
+ (substitute* "./configure"
+ (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
+ "date --date='@0'"))
+ #t))
+ (add-after 'configure 'patch-settings
+ (lambda _
+ ;; libnetcdf.settings contains the full filename of the compilers
+ ;; used to build the library. We truncate the hashes of those
+ ;; filenames to avoid unnecessary references to the corresponding
+ ;; store items.
+ (substitute* "libnetcdf.settings"
+ (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
+ (string-append prefix (string-take hash 10) "...")))
+ #t)))
+
#:parallel-tests? #f)) ;various race conditions
(home-page "http://www.unidata.ucar.edu/software/netcdf/")
(synopsis "Library for scientific data")
"--disable-shared" "--with-pic"
,flags))))))
+(define-public netcdf-fortran
+ (package
+ (name "netcdf-fortran")
+ (version "4.4.4")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:parallel-tests? #f))
+ (inputs
+ `(("netcdf" ,netcdf)))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (synopsis "Fortran interface for the netCDF library")
+ (description (package-description netcdf))
+ (home-page (package-home-page netcdf))
+ (license (package-license netcdf))))
+
(define-public nlopt
(package
(name "nlopt")
(license license:bsd-3)))
;; For a fully featured Octave, users are strongly recommended also to install
-;; the following packages: texinfo, less, ghostscript, gnuplot.
+;; the following packages: less, ghostscript, gnuplot.
(define-public octave
(package
(name "octave")
("glu" ,glu)
("zlib" ,zlib)
("curl" ,curl)
+ ("texinfo" ,texinfo)
("graphicsmagick" ,graphicsmagick)))
(native-inputs
`(("lzip" ,lzip)
;; will still run without them, albeit without the features they
;; provide.
("less" ,less)
- ("texinfo" ,texinfo)
("ghostscript" ,ghostscript)
("gnuplot" ,gnuplot)))
(arguments
`(#:configure-flags
(list (string-append "--with-shell="
(assoc-ref %build-inputs "bash")
- "/bin/sh"))))
+ "/bin/sh"))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'configure 'configure-makeinfo
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "libinterp/corefcn/help.cc"
+ (("Vmakeinfo_program = \"makeinfo\"")
+ (string-append "Vmakeinfo_program = \""
+ (assoc-ref inputs "texinfo")
+ "/bin/makeinfo\"")))
+ #t)))))
(home-page "https://www.gnu.org/software/octave/")
(synopsis "High-level language for numerical computation")
(description "GNU Octave is a high-level interpreted language that is
(define-public petsc
(package
(name "petsc")
- (version "3.7.2")
+ (version "3.8.0")
(source
(origin
(method url-fetch)
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
"petsc-lite-" version ".tar.gz"))
(sha256
- (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d"))))
+ (base32 "1lajbk3c29hnh83v6cbmm3a8wv6bdykh0p70kwrr4vrnizalk88s"))))
(build-system gnu-build-system)
(native-inputs
- `(("python" ,python-2)
- ("perl" ,perl)))
+ `(("python" ,python-2)))
(inputs
`(("gfortran" ,gfortran)
("lapack" ,lapack)
(assoc-ref %build-inputs "superlu") "/include")
,(string-append "--with-superlu-lib="
(assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
+ #:make-flags
+ ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
+ ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
+ (list (format #f "MAKE_NP=~a" (parallel-job-count)))
#:phases
(modify-phases %standard-phases
(replace 'configure
(format #t "configure flags: ~s~%" flags)
(zero? (apply system* "./configure" flags)))))
(add-after 'configure 'clean-local-references
- (lambda* (#:key inputs outputs #:allow-other-keys)
+ (lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* (find-files "." "^petsc(conf|machineinfo).h$")
;; Prevent build directory from leaking into compiled code
(((getcwd)) out)
;; Scrub timestamp for reproducibility
((".*Libraries compiled on.*") ""))
+ (substitute* (find-files "." "petscvariables")
+ ;; Do not expose build machine characteristics, set to defaults.
+ (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
+ (("NPMAX = [:digit:]+") "NPMAX = 2"))
#t)))
(add-after 'install 'clean-install
;; Try to keep installed files from leaking build directory names.
(define-public slepc
(package
(name "slepc")
- (version "3.7.1")
+ (version "3.8.0")
(source
(origin
(method url-fetch)
- (uri (string-append "http://slepc.upv.es/download/download.php?"
- "filename=slepc-" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
+ version ".tar.gz"))
(sha256
(base32
- "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7"))))
+ "0qyrsdndfdw2g0jmj9iskxj3j20zlkplhv26288s079dhm7cr365"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)))
#:configure-flags
`(,(string-append "--with-arpack-dir="
(assoc-ref %build-inputs "arpack") "/lib"))
+ #:make-flags ;honor (parallel-job-count)
+ `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
#:phases
(modify-phases %standard-phases
(replace 'configure
(define-public r-pracma
(package
(name "r-pracma")
- (version "2.0.4")
+ (version "2.0.7")
(source (origin
(method url-fetch)
(uri (cran-uri "pracma" version))
(sha256
- (base32 "1z3i90mkzwvp9di17caf4934z2xlb2imm3hwxllcrbwvmnmhrwyc"))))
+ (base32 "0hxa0rbbp54j0c05qj7vfwhqfdmiz5ax8vhqxd09g33x7c0hqbc5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-quadprog" ,r-quadprog)))
(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 = $(CC)
CDEFS = -DAdd_"
- (getcwd)
- (assoc-ref outputs "out")
- (assoc-ref inputs "lapack")
- (assoc-ref inputs "pt-scotch")))))
- (alist-cons-after
- 'unpack 'remove-broken-symlinks
- (lambda _
- (for-each delete-file
- (find-files "MAKE_INC" "\\.#make\\..*")))
- (alist-cons-before
- 'build 'create-install-directories
- (lambda* (#:key outputs #:allow-other-keys)
- (for-each
- (lambda (dir)
- (mkdir-p (string-append (assoc-ref outputs "out")
- "/" dir)))
- '("lib" "include")))
- (alist-replace
- 'check
+ (getcwd)
+ (assoc-ref outputs "out")
+ (assoc-ref inputs "lapack")
+ (assoc-ref inputs "pt-scotch"))))
+ #t))
+ (add-after 'unpack 'remove-broken-symlinks
+ (lambda _
+ (for-each delete-file
+ (find-files "MAKE_INC" "\\.#make\\..*"))
+ #t))
+ (add-before 'build 'create-install-directories
+ (lambda* (#:key outputs #:allow-other-keys)
+ (for-each
+ (lambda (dir)
+ (mkdir-p (string-append (assoc-ref outputs "out")
+ "/" dir)))
+ '("lib" "include"))
+ #t))
+ (replace 'check
(lambda _
(with-directory-excursion "EXAMPLE"
(and
(zero? (system* "mpirun" "-n" "2"
"./pddrive" "-r" "1" "-c" "2" "g20.rua"))
(zero? (system* "mpirun" "-n" "2"
- "./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
- (alist-replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- ;; Library is placed in lib during the build phase. Copy over
- ;; headers to include.
- (let* ((out (assoc-ref outputs "out"))
- (incdir (string-append out "/include")))
- (for-each (lambda (file)
- (let ((base (basename file)))
- (format #t "installing `~a' to `~a'~%"
- base incdir)
- (copy-file file
- (string-append incdir "/" base))))
- (find-files "SRC" ".*\\.h$"))))
- %standard-phases)))))))
+ "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))))))
+ (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
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)
- ("flex" ,flex-2.6.1) ; A bug in flex prevents building with flex-2.6.3.
+ ("flex" ,flex)
("bison" ,bison)))
(arguments
`(#:phases
'("COMMON_FILE_COMPRESS_GZ"
"COMMON_PTHREAD"
"COMMON_RANDOM_FIXED_SEED"
+ "INTSIZE64" ;use 'long' instead of 'int'
;; Prevents symbolc clashes with libesmumps
"SCOTCH_RENAME"
;; XXX: Causes invalid frees in superlu-dist tests
;; See LICENSE_en.txt
(license license:cecill-c)))
+(define-public scotch32
+ ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
+ ;; some applications.
+ (package (inherit scotch)
+ (name "scotch32")
+ (arguments
+ (substitute-keyword-arguments (package-arguments scotch)
+ ((#:phases scotch-phases)
+ `(modify-phases ,scotch-phases
+ (replace
+ 'configure
+ (lambda _
+ (call-with-output-file "Makefile.inc"
+ (lambda (port)
+ (format port "
+EXE =
+LIB = .a
+OBJ = .o
+MAKE = make
+AR = ar
+ARFLAGS = -ruv
+CAT = cat
+CCS = gcc
+CCP = mpicc
+CCD = gcc
+CPPFLAGS =~{ -D~a~}
+CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
+LDFLAGS = -lz -lm -lrt -lpthread
+CP = cp
+LEX = flex -Pscotchyy -olex.yy.c
+LN = ln
+MKDIR = mkdir
+MV = mv
+RANLIB = ranlib
+YACC = bison -pscotchyy -y -b y
+"
+ '("COMMON_FILE_COMPRESS_GZ"
+ "COMMON_PTHREAD"
+ "COMMON_RANDOM_FIXED_SEED"
+ "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
+ ;; Prevents symbolc clashes with libesmumps
+ "SCOTCH_RENAME"
+ ;; XXX: Causes invalid frees in superlu-dist tests
+ ;; "SCOTCH_PTHREAD"
+ ;; "SCOTCH_PTHREAD_NUMBER=2"
+ "restrict=__restrict"))))))))))
+ (synopsis
+ "Programs and libraries for graph algorithms (32-bit integers)")))
+
(define-public pt-scotch
(package (inherit scotch)
(name "pt-scotch")
(lambda _ (zero? (system* "make" "ptcheck"))))))))
(synopsis "Programs and libraries for graph algorithms (with MPI)")))
+(define-public pt-scotch32
+ (package (inherit scotch32)
+ (name "pt-scotch32")
+ (propagated-inputs
+ `(("openmpi" ,openmpi))) ;headers include MPI headers
+ (arguments
+ (substitute-keyword-arguments (package-arguments scotch32)
+ ((#:phases scotch32-phases)
+ `(modify-phases ,scotch32-phases
+ (replace 'build
+ (lambda _
+ (and
+ (zero? (system* "make"
+ (format #f "-j~a" (parallel-job-count))
+ "ptscotch" "ptesmumps"))
+ ;; Install the serial metis compatibility library
+ (zero? (system* "make" "-C" "libscotchmetis" "install")))))
+ (replace 'check
+ (lambda _
+ (zero? (system* "make" "ptcheck"))))))))
+ (synopsis
+ "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
+
(define-public metis
(package
(name "metis")
(define-public maxima
(package
(name "maxima")
- (version "5.39.0")
+ (version "5.41.0")
(source
(origin
(method url-fetch)
version "-source/" name "-" version ".tar.gz"))
(sha256
(base32
- "1cvignn5y6qzrby6qb885yc8zdcdqdr1d50vcvc3gapw2f0gk3zm"))
+ "0x0n81z0s4pl8nwpf7ivlsbvsdphm9w42250g7qdkizl0132by6s"))
(patches (search-patches "maxima-defsystem-mkdir.patch"))))
(build-system gnu-build-system)
(inputs
;; '/tmp/nix-build-maxima-*', which won't exist at run time.
;; Work around that.
#:make-flags (list "TMPDIR=/tmp")
- #:phases (alist-cons-before
- 'check 'pre-check
- (lambda _
- (chmod "src/maxima" #o555))
- ;; Make sure the doc and emacs files are found in the
- ;; standard location. Also configure maxima to find gnuplot
- ;; without having it on the PATH.
- (alist-cons-after
- 'install 'post-install
- (lambda* (#:key outputs inputs #:allow-other-keys)
- (let* ((gnuplot (assoc-ref inputs "gnuplot"))
- (out (assoc-ref outputs "out"))
- (datadir (string-append out "/share/maxima/" ,version)))
- (with-directory-excursion out
- (mkdir-p "share/emacs")
- (mkdir-p "share/doc")
- (symlink
- (string-append datadir "/emacs/")
- (string-append out "/share/emacs/site-lisp"))
- (symlink
- (string-append datadir "/doc/")
- (string-append out "/share/doc/maxima"))
- (with-atomic-file-replacement
- (string-append datadir "/share/maxima-init.lisp")
- (lambda (in out)
- (format out "~a ~s~a~%"
- "(setf $gnuplot_command "
- (string-append gnuplot "/bin/gnuplot") ")")
- (dump-port in out))))))
- %standard-phases))))
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'check 'pre-check
+ (lambda _
+ (chmod "src/maxima" #o555)
+ #t))
+ ;; Make sure the doc and emacs files are found in the
+ ;; standard location. Also configure maxima to find gnuplot
+ ;; without having it on the PATH.
+ (add-after 'install 'post-install
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ (let* ((gnuplot (assoc-ref inputs "gnuplot"))
+ (out (assoc-ref outputs "out"))
+ (datadir (string-append out "/share/maxima/" ,version))
+ (binutils (string-append (assoc-ref inputs "binutils")
+ "/bin")))
+ (with-directory-excursion out
+ (mkdir-p "share/emacs")
+ (mkdir-p "share/doc")
+ (symlink
+ (string-append datadir "/emacs/")
+ (string-append out "/share/emacs/site-lisp"))
+ (symlink
+ (string-append datadir "/doc/")
+ (string-append out "/share/doc/maxima"))
+ (with-atomic-file-replacement
+ (string-append datadir "/share/maxima-init.lisp")
+ (lambda (in out)
+ (format out "~a ~s~a~%"
+ "(setf $gnuplot_command "
+ (string-append gnuplot "/bin/gnuplot") ")")
+ (dump-port in out))))
+ ;; Ensure that Maxima will have access to the GNU binutils
+ ;; components at runtime.
+ (wrap-program (string-append out "/bin/maxima")
+ `("PATH" prefix (,binutils))))
+ #t)))))
(home-page "http://maxima.sourceforge.net")
(synopsis "Numeric and symbolic expression manipulation")
(description "Maxima is a system for the manipulation of symbolic and
(define-public wxmaxima
(package
(name "wxmaxima")
- ;; Versions 16.12.0 to 16.12.2 have a bug which causes output lines to
- ;; overlap. See <https://debbugs.gnu.org/25793>
- (version "16.04.2")
+ (version "17.05.1")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://sourceforge/wxmaxima/wxMaxima/"
- version "/" name "-" version ".tar.gz"))
+ (uri (string-append "https://github.com/andrejv/" name "/archive"
+ "/Version-" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1fpqzk1921isiqrpgpf433ldq41924qs9sy99fl1zn5661b2l73n"))))
+ "0dv0cy0cf46v0cbw32izscpkdmpxg1qhwq1f4cz46kkqd8k4yfbj"))))
(build-system gnu-build-system)
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("gettext" ,gettext-minimal)))
(inputs
`(("wxwidgets" ,wxwidgets)
("maxima" ,maxima)
("gtk+" ,gtk+)
("shared-mime-info" ,shared-mime-info)))
(arguments
- `(#:phases (modify-phases %standard-phases
- (add-after
- 'install 'wrap-program
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (wrap-program (string-append (assoc-ref outputs "out")
- "/bin/wxmaxima")
- `("PATH" ":" prefix
- (,(string-append (assoc-ref inputs "maxima")
- "/bin")))
- ;; For GtkFileChooserDialog.
- `("GSETTINGS_SCHEMA_DIR" =
- (,(string-append (assoc-ref inputs "gtk+")
- "/share/glib-2.0/schemas")))
- `("XDG_DATA_DIRS" ":" prefix
- (;; Needed by gdk-pixbuf to know supported icon formats.
- ,(string-append
- (assoc-ref inputs "shared-mime-info") "/share")
- ;; The default icon theme of GTK+.
- ,(string-append
- (assoc-ref inputs "adwaita-icon-theme") "/share"))))
- #t)))))
+ `(#: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")
+ "/bin/wxmaxima")
+ `("PATH" ":" prefix
+ (,(string-append (assoc-ref inputs "maxima")
+ "/bin")))
+ ;; For GtkFileChooserDialog.
+ `("GSETTINGS_SCHEMA_DIR" =
+ (,(string-append (assoc-ref inputs "gtk+")
+ "/share/glib-2.0/schemas")))
+ `("XDG_DATA_DIRS" ":" prefix
+ (;; Needed by gdk-pixbuf to know supported icon formats.
+ ,(string-append
+ (assoc-ref inputs "shared-mime-info") "/share")
+ ;; The default icon theme of GTK+.
+ ,(string-append
+ (assoc-ref inputs "adwaita-icon-theme") "/share"))))
+ #t)))))
(home-page "https://andrejv.github.io/wxmaxima/")
(synopsis "Graphical user interface for the Maxima computer algebra system")
(description
"OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD 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.)
+
+SUBSTITUTABLE? determines whether the package is made available as a
+substitute.
+
+Currently the specialization must be selected at configure-time, but work is
+underway to allow BLIS to select the right optimized kernels at run time:
+<https://github.com/flame/blis/issues/129>."
+ (package
+ (name (if (string=? implementation "reference")
+ "blis"
+ (string-append "blis-" implementation)))
+ (version "0.2.2")
+ (home-page "https://github.com/flame/blis")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference (url home-page) (commit version)))
+ (sha256
+ (base32
+ "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
+ (file-name (git-file-name "blis" version))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:test-target "test"
+
+ #:substitutable? ,substitutable?
+
+ #:phases (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; This is a home-made 'configure' script.
+ (let ((out (assoc-ref outputs "out")))
+ (zero? (system* "./configure" "-p" out
+ "-d" "opt"
+ "--disable-static"
+ "--enable-shared"
+ "--enable-threading=openmp"
+
+ ,implementation)))))
+ (add-before 'check 'show-test-output
+ (lambda _
+ ;; By default "make check" is silent. Make it verbose.
+ (system "tail -F output.testsuite &")
+ #t)))))
+ (synopsis "High-performance basic linear algebra (BLAS) routines")
+ (description
+ "BLIS is a portable software framework for instantiating high-performance
+BLAS-like dense linear algebra libraries. The framework was designed to
+isolate essential kernels of computation that, when optimized, immediately
+enable optimized implementations of most of its commonly used and
+computationally intensive operations. While BLIS exports a new BLAS-like API,
+it also includes a BLAS compatibility layer which gives application developers
+access to BLIS implementations via traditional BLAS routine calls.")
+ (license license:bsd-3)))
+
+(define-public blis
+ ;; This is the "reference" implementation, which is the non-optimized but
+ ;; portable variant (no assembly).
+ (make-blis "reference" #t))
+
+(define ignorance blis)
+
+(define-syntax-rule (blis/x86_64 processor)
+ "Expand to a package specialized for PROCESSOR."
+ (package
+ (inherit (make-blis processor))
+ (supported-systems '("x86_64-linux"))))
+
+(define-public blis-sandybridge
+ ;; BLIS specialized for Sandy Bridge processors (launched 2011):
+ ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
+ (blis/x86_64 "sandybridge"))
+
+(define-public blis-haswell
+ ;; BLIS specialized for Haswell processors (launched 2013):
+ ;; <http://ark.intel.com/products/codename/42174/Haswell>.
+ (blis/x86_64 "haswell"))
+
+(define-public blis-knl
+ ;; BLIS specialized for Knights Landing processor (launched 2016):
+ ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
+ (blis/x86_64 "knl"))
+
+
(define-public openlibm
(package
(name "openlibm")
(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)")
#: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))))
(inputs
`(("fortran" ,gfortran)))
(home-page "https://github.com/JuliaLang/openspecfun")
(define-public suitesparse
(package
(name "suitesparse")
- (version "4.4.3")
+ (version "4.5.5")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5"))))
+ "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Remove bundled metis source
+ '(delete-file-recursively "metis-5.1.0"))))
(build-system gnu-build-system)
(arguments
- '(#:parallel-build? #f ;cholmod build fails otherwise
- #:tests? #f ;no "check" target
+ '(#:tests? #f ;no "check" target
#:make-flags
(list "CC=gcc"
"BLAS=-lblas"
"TBB=-ltbb"
- "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used
+ "MY_METIS_LIB=-lmetis"
(string-append "INSTALL_LIB="
(assoc-ref %outputs "out") "/lib")
(string-append "INSTALL_INCLUDE="
- (assoc-ref %outputs "out") "/include"))
+ (assoc-ref %outputs "out") "/include")
+ "library")
#:phases
- (alist-cons-before
- 'install 'prepare-out
- ;; README.txt states that the target directories must exist prior to
- ;; running "make install".
- (lambda _
- (mkdir-p (string-append (assoc-ref %outputs "out") "/lib"))
- (mkdir-p (string-append (assoc-ref %outputs "out") "/include")))
- ;; no configure script
- (alist-delete 'configure %standard-phases))))
+ (modify-phases %standard-phases
+ (delete 'configure)))) ;no configure script
(inputs
`(("tbb" ,tbb)
- ("lapack" ,lapack)))
+ ("lapack" ,lapack)
+ ("metis" ,metis)))
(home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
(synopsis "Suite of sparse matrix software")
(description
(define-public dealii
(package
(name "dealii")
- (version "8.4.1")
+ (version "8.5.0")
(source
(origin
(method url-fetch)
"download/v" version "/dealii-" version ".tar.gz"))
(sha256
(base32
- "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800"))
+ "0yfpy4zh8j7hmqakw17zdlmvfdcmhwgs66wcb716plc4y7v3z4g6"))
(modules '((guix build utils)))
(snippet
;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
("suitesparse" ,suitesparse))) ;for UMFPACK
(arguments
`(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
- #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure
- #:phases (modify-phases %standard-phases
- (add-after
- 'install 'hint-example-prefix
- ;; Set Cmake hints in examples so that they can find this
- ;; deal.II when configuring.
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref %outputs "out"))
- (exmpl (string-append out "/share/doc"
- "/dealii/examples")))
- (substitute* (find-files exmpl "CMakeLists.txt")
- (("([[:space:]]*HINTS.*)\n" _ line)
- (string-append line " $ENV{HOME}/.guix-profile "
- out "\n")))
- #t))))))
+ #:configure-flags
+ ;; Work around a bug in libsuitesparseconfig linking
+ ;; see https://github.com/dealii/dealii/issues/4745
+ '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
(home-page "https://www.dealii.org")
(synopsis "Finite element library")
(description
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")
@item NVIDIA GPUs / CUDA (in development)
@end enumerate\n")
(home-page "https://github.com/VcDevel/Vc")
+ ;; "No support_???.cpp file exists for this architecture."
+ (supported-systems '("x86_64-linux" "i686-linux"))
(license license:bsd-3)))
(define-public reducelcs
(home-page "https://www.gnu.org/software/jacal/")
(license license:gpl3+)))
+(define-public z3
+ (package
+ (name "z3")
+ (version "4.5.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/Z3Prover/z3/archive/z3-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags
+ (list "-DBUILD_PYTHON_BINDINGS=true"
+ "-DINSTALL_PYTHON_BINDINGS=true"
+ (string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR="
+ %output
+ "/lib/python2.7/site-packages")
+ (string-append "-DCMAKE_INSTALL_LIBDIR="
+ %output
+ "/lib"))
+
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'bootstrap
+ (lambda _
+ (zero?
+ (system* "python" "contrib/cmake/bootstrap.py" "create"))))
+ (add-before 'check 'make-test-z3
+ (lambda _
+ ;; Build the test suite executable.
+ (zero? (system* "make" "test-z3" "-j"
+ (number->string (parallel-job-count))))))
+ (replace 'check
+ (lambda _
+ ;; Run all the tests that don't require arguments.
+ (zero? (system* "./test-z3" "/a")))))))
+ (native-inputs
+ `(("python" ,python-2)))
+ (synopsis "Theorem prover")
+ (description "Z3 is a theorem prover and @dfn{satisfiability modulo
+theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
+ (home-page "https://github.com/Z3Prover/z3")
+ (license license:expat)))
+
+(define-public cubicle
+ (package
+ (name "cubicle")
+ (version "1.1.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://cubicle.lri.fr/cubicle-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("ocaml" ,ocaml)
+ ("which" ,(@@ (gnu packages base) which))))
+ (propagated-inputs
+ `(("z3" ,z3)))
+ (arguments
+ `(#:configure-flags (list "--with-z3")
+ #:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'configure-for-release
+ (lambda _
+ (substitute* "Makefile.in"
+ (("SVNREV=") "#SVNREV="))))
+ (add-before 'configure 'fix-/bin/sh
+ (lambda _
+ (substitute* "configure"
+ (("/bin/sh") (which "sh")))))
+ (add-before 'configure 'fix-smt-z3wrapper.ml
+ (lambda _
+ (substitute* "Makefile.in"
+ (("\\\\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.")
+ (license license:asl2.0)))
HCoop / jackhill / guix / guix.git / blobdiff