;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2013, 2014, 2015, 2016
, 2019 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, 2018, 2019 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
-;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
-;;; Copyright © 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
+;;; Copyright © 2017, 2018
, 2019 Paul Garlick <pgarlick@tourbillion-technology.com>
;;; Copyright © 2017 ng0 <ng0@n0.is>
;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
-;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2018, 2019 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 Eric Brown <brown@fastmail.com>
;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
+;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages netpbm)
+ #:use-module (gnu packages onc-rpc)
#:use-module (gnu packages pcre)
#:use-module (gnu packages popt)
#:use-module (gnu packages perl)
(define-public python-cvxopt
(package
(name "python-cvxopt")
- (version "1.2.1")
+ (version "1.2.3")
(source (origin
(method git-fetch)
(uri (git-reference
(file-name (git-file-name name version))
(sha256
(base32
- "05mnjil9palaa48xafdfh4f5pr4z7aqjr995rwl08qfyxs8y0crf"))))
+ "1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b"))))
(build-system python-build-system)
(arguments
`(#:phases
(define-public units
(package
(name "units")
- (version "2.18")
+ (version "2.19")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/units/units-" version
".tar.gz"))
(sha256 (base32
- "0y26kj349i048y4z3xrk90bvciw2j6ds3rka7r7yn3183hirr5b4"))))
+ "0mk562g7dnidjgfgvkxxpvlba66fh1ykmfd9ylzvcln1vxmi6qj2"))))
(build-system gnu-build-system)
(inputs
`(("readline" ,readline)
(define-public double-conversion
(package
(name "double-conversion")
- (version "3.1.0")
+ (version "3.1.5")
(home-page "https://github.com/google/double-conversion")
(source (origin
(method git-fetch)
- (uri (git-reference (url home-page) (commit version)))
+ (uri (git-reference (url home-page)
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "123rb2p4snqagrybw66vnapchqdwn2rfpr1wcq0ya9gwbyl7xccx"))))
+ "0csy4pjw1p8rp6g5qxi2h0ychhhp1fldv7gb761627fs2mclw9gv"))))
(build-system cmake-build-system)
(arguments
'(#:test-target "test"
(define-public gnuplot
(package
(name "gnuplot")
- (version "5.2.6")
+ (version "5.2.7")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
version "/gnuplot-"
version ".tar.gz"))
(sha256
- (base32 "1vllgap08nhvdmc03idmkdnk9cfl2bp81hps50q1pqrr640qzp9m"))))
+ (base32 "1vglp4la40f5dpj0zdj63zprrkyjgzy068p35bz5dqxjyczm1zlp"))))
(build-system gnu-build-system)
(inputs `(("readline" ,readline)
("cairo" ,cairo)
(define-public hdf4
(package
(name "hdf4")
- (version "4.2.13")
+ (version "4.2.14")
(source
(origin
(method url-fetch)
(uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
version "/src/hdf-" version ".tar.bz2"))
(sha256
- (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
+ (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
(patches (search-patches "hdf4-architectures.patch"
"hdf4-reproducibility.patch"
- "hdf4-shared-fortran.patch"))))
+ "hdf4-shared-fortran.patch"
+ "hdf4-tirpc.patch"))))
(build-system gnu-build-system)
(native-inputs
`(("gfortran" ,gfortran)
("flex" ,flex)))
(inputs
`(("zlib" ,zlib)
- ("libjpeg" ,libjpeg)))
+ ("libjpeg" ,libjpeg)
+ ("libtirpc" ,libtirpc)))
(arguments
`(#:parallel-tests? #f
- #:configure-flags '("--enable-shared")
+ #:configure-flags (list "--enable-shared"
+ (string-append "CPPFLAGS=-I"
+ (assoc-ref %build-inputs "libtirpc")
+ "/include/tirpc"))
#:phases
(modify-phases %standard-phases
;; This is inspired by two of Debian's patches.
(inputs
`(("zlib" ,zlib)))
(native-inputs
- `(("gfortran" ,gfortran)))
+ `(("gfortran" ,gfortran)
+ ("perl" ,perl))) ;part of the test machinery needs Perl
(outputs '("out" ; core library
"fortran")) ; fortran interface
(arguments
`(;; Some of the users, notably Flann, need the C++ interface.
#:configure-flags '("--enable-cxx"
"--enable-fortran"
- "--enable-fortran2003")
+ "--enable-fortran2003"
+
+ ;; Build a thread-safe library. Unfortunately,
+ ;; 'configure' invites you to either turn off C++,
+ ;; Fortran, and the high-level interface (HL), or
+ ;; to pass '--enable-unsupported'. Debian
+ ;; packagers chose to pass '--enable-unsupported'
+ ;; and we follow their lead here.
+ "--enable-threadsafe"
+ "--with-pthread"
+ "--enable-unsupported")
;; Use -fPIC to allow the R bindings to link with the static libraries
#:make-flags (list "CFLAGS=-fPIC"
"CXXFLAGS=-fPIC")
`(("gfortran" ,gfortran)))
(inputs
`(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
+ ;; XXX: These inputs are really dependencies of hdf4.
("zlib" ,zlib)
("libjpeg" ,libjpeg)
+ ("libtirpc" ,libtirpc)
+
("gctp" ,gctp)))
(arguments
`( #:configure-flags '("--enable-install-include" "--enable-shared"
(arguments
(substitute-keyword-arguments (package-arguments hdf5)
((#:configure-flags flags)
- ``("--enable-parallel" ,@(delete "--enable-cxx" ,flags)))
+ ``("--enable-parallel"
+ ,@(delete "--enable-cxx"
+ (delete "--enable-threadsafe" ,flags))))
((#:phases phases)
`(modify-phases ,phases
(add-after 'build 'mpi-setup
(lambda _
;; OpenMPI's mpirun will exit with non-zero status if it
;; detects an "abnormal termination", i.e. any process not
- ;; calling MPI_Finalize(). Since the test is explicitely
+ ;; calling MPI_Finalize(). Since the test is explicitly
;; avoiding MPI_Finalize so as not to have at_exit and thus
;; H5C_flush_cache from being called, mpirun will always
;; complain, so turn this test off.
"11wwxpy2q1bhxs2v41bqn05i2sb0905cj1xil6mg8l4k2kka4cq6"))))
(build-system gnu-build-system)
(inputs
- `(("lapack" ,lapack)
- ("qhull" ,qhull)
- ("readline" ,readline)
- ("gl2ps" ,gl2ps)
- ("glpk" ,glpk)
+ `(("alsa-lib" ,alsa-lib)
+ ("arpack" ,arpack-ng)
+ ("curl" ,curl)
("fftw" ,fftw)
("fftwf" ,fftwf)
- ("arpack" ,arpack-ng)
- ("pcre" ,pcre)
("fltk" ,fltk)
("fontconfig" ,fontconfig)
("freetype" ,freetype)
- ("hdf5" ,hdf5)
- ("libxft" ,libxft)
- ("mesa" ,mesa)
+ ("gl2ps" ,gl2ps)
+ ("glpk" ,glpk)
("glu" ,glu)
- ("zlib" ,zlib)
- ("curl" ,curl)
- ("texinfo" ,texinfo)
("graphicsmagick" ,graphicsmagick)
- ("suitesparse" ,suitesparse)
+ ("hdf5" ,hdf5)
+ ("lapack" ,lapack)
("libsndfile" ,libsndfile)
+ ("libxft" ,libxft)
+ ("mesa" ,mesa)
+ ("pcre" ,pcre)
("portaudio" ,portaudio)
- ("alsa-lib" ,alsa-lib)))
+ ("qhull" ,qhull)
+ ("readline" ,readline)
+ ("suitesparse" ,suitesparse)
+ ("texinfo" ,texinfo)
+ ("zlib" ,zlib)))
(native-inputs
`(("lzip" ,lzip)
("gfortran" ,gfortran)
,@(package-inputs octave-cli)))
(native-inputs
`(("qttools" , qttools) ;for lrelease
- ("texlive" ,texlive) ;for texi2dvi
+ ("texlive" ,(texlive-union (list texlive-epsf))) ; for texi2dvi
,@(package-native-inputs octave-cli)))
(arguments
(substitute-keyword-arguments (package-arguments octave-cli)
license:expat; file src/OpenGl/OpenGl_glext.h
license:bsd-3)))); test framework gtest
+(define-public opencascade-occt
+ (package
+ (name "opencascade-occt")
+ (version "7.3.0p3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://git.dev.opencascade.org/repos/occt.git")
+ (commit
+ (string-append "V"
+ (string-map (lambda (x) (if (eq? x #\.) #\_ x))
+ version)))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Remove files specific to non-free operating systems.
+ (delete-file-recursively "samples/ios")
+ (delete-file-recursively "samples/mfc")
+ (delete-file-recursively "samples/qt/FuncDemo")
+ (delete-file "genconf.bat")
+ (delete-file "gendoc.bat")
+ (delete-file "genproj.bat")
+ (delete-file "upgrade.bat")
+ ;; Remove references to deleted files.
+ (substitute* "dox/FILES_HTML.txt"
+ ((".*standard.*") "" )
+ ((".*UIKitSample.*") ""))
+ #t))))
+ (build-system cmake-build-system)
+ (arguments
+ '(;; There is no test target for make. OCCT provides an
+ ;; 'Automated Testing System', which may be accessed after
+ ;; installation via the draw.sh script. draw.sh is located in
+ ;; the bin directory. For details see:
+ ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
+ ;; occt_dev_guides__tests.html
+ #:tests? #f
+ ;; Configure without freeimage: attempting to link against the
+ ;; freeimage version 3.17 library leads to 'undefined
+ ;; reference' errors.
+ #:configure-flags
+ (list "-DUSE_FREEIMAGE:BOOL=OFF"
+ "-DUSE_TBB:BOOL=ON"
+ "-DUSE_VTK:BOOL=OFF"
+ "-DBUILD_DOC_Overview:BOOL=OFF"
+ "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
+ "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
+ "-UCMAKE_INSTALL_LIBDIR")))
+ (inputs
+ `(("doxygen" ,doxygen)
+ ;("freeimage" ,freeimage)
+ ("freetype" ,freetype)
+ ("glu" ,glu)
+ ("libxext" ,libxext)
+ ("libxi" ,libxi)
+ ("libxmu" ,libxmu)
+ ("mesa" ,mesa)
+ ("tbb" ,tbb)
+ ("tcl" ,tcl)
+ ("tk" ,tk)))
+ ;; TODO: build Overview documentation and add 'doc' output.
+ (home-page "https://www.opencascade.com")
+ (synopsis "Libraries for 3D modeling and numerical simulation")
+ (description
+ "Open CASCADE is a set of libraries for the development of applications
+dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
+C++ class libraries providing services for 3D surface and solid modeling, CAD
+data exchange, and visualization. It is used for development of specialized
+software dealing with 3D models in design (CAD), manufacturing (CAM),
+numerical simulation (CAE), measurement equipment (CMM), and quality
+control (CAQ) domains.
+
+This is the certified version of the Open Cascade Technology (OCCT) library.")
+ (license (list ;; OCCT library:
+ license:lgpl2.1; with an exception for the use of header
+ ; files, see OCCT_LGPL_EXCEPTION.txt.
+ ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
+ ;; src/OpenGl/OpenGl_HaltonSampler.hxx:
+ license:expat
+ ;; Files src/ExprIntrp/ExprIntrp.tab.* and
+ ;; src/StepFile/step.tab.*:
+ license:gpl3+ ; with Bison 2.2 exception.
+ ;; File src/NCollection/NCollection_UtfIterator.lxx:
+ (license:non-copyleft
+ "https://www.unicode.org/license.html")
+ ;; File src/NCollection/NCollection_StdAllocator.hxx:
+ license:public-domain))))
+
(define-public gmsh
(package
(name "gmsh")
(version "2.16.0")
(source
(origin
- (method url-fetch)
- (uri (string-append "http://gmsh.info/src/gmsh-"
- version "-source.tgz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.onelab.info/gmsh/gmsh.git")
+ (commit
+ (string-append "gmsh_"
+ (string-map (lambda (x) (if (eq? x #\.) #\_ x))
+ version)))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
+ (base32 "08rq4jajwmlpivnm9yifz2jhaivnz065lnk0h2zv773nwl9wf162"))
(modules '((guix build utils)))
(snippet
;; Remove non-free METIS code
`(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
"-DENABLE_BUILD_SHARED:BOOL=ON"
"-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
- (home-page "http://www.geuz.org/gmsh/")
+ (home-page "http://gmsh.info/")
(synopsis "3D finite element grid generator")
(description "Gmsh is a 3D finite element grid generator with a built-in
CAD engine and post-processor. Its design goal is to provide a fast, light
(define-public maxflow
(package
(name "maxflow")
- (version "3.04")
+ ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
+ ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
+ (version "3.0.5")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gerddie/maxflow.git")
- (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
- (file-name (string-append name "-" version "-checkout"))
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
"0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
(build-system cmake-build-system)
- (home-page "http://pub.ist.ac.at/~vnk/software.html")
+ (home-page "https://pub.ist.ac.at/~vnk/software.html")
(synopsis "Library implementing Maxflow algorithm")
(description "An implementation of the maxflow algorithm described in
@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
(define-public petsc
(package
(name "petsc")
- (version "3.10.4")
+ (version "3.11.2")
(source
(origin
(method url-fetch)
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
"petsc-lite-" version ".tar.gz"))
(sha256
- (base32 "0fk16944zh3473ra198kdkxdn08rq7b6ap838hxy1mh1i0hb488r"))))
+ (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
(outputs '("out" ; libraries and headers
"examples")) ; ~30MiB of examples
(build-system gnu-build-system)
``("--with-mpiexec=mpirun"
,(string-append "--with-mpi-dir="
(assoc-ref %build-inputs "openmpi"))
- ,@(delete "--with-mpi=0" ,cf)))))
+ ,@(delete "--with-mpi=0" ,cf)))
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-before 'configure 'mpi-setup
+ ,%openmpi-setup)))))
(synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
(define-public python-petsc4py
(define-public slepc
(package
(name "slepc")
- (version "3.10.1")
+ (version "3.11.1")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn"))))
+ "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
(build-system gnu-build-system)
(native-inputs
- `(("python" ,python-2)))
+ `(("python" ,python-2)
+ ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
(inputs
`(("arpack" ,arpack-ng)
("gfortran" ,gfortran)))
`(,(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)))
+ `(,(format #f "MAKE_NP=~a" (parallel-job-count))
+ ,(string-append "PETSCCONFIGDIR="
+ (assoc-ref %build-inputs "petsc:examples")
+ "/share/petsc/examples/config"))
#:phases
(modify-phases %standard-phases
(replace 'configure
(synopsis "Multifrontal sparse direct solver")
(description
"MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
-sparse system of linear equations A x = b using Guassian elimination.")
+sparse system of linear equations A x = b using Gaussian elimination.")
(license license:cecill-c)))
(define-public mumps-metis
(define-public r-quadprog
(package
(name "r-quadprog")
- (version "1.5-5")
+ (version "1.5-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "quadprog" version))
(sha256
(base32
- "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
+ "0vg7i9p241bwvfdspjbydjrsvgipl6nsb8bjigp0hbbgvxbixx0s"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(define-public maxima
(package
(name "maxima")
- (version "5.42.2")
+ (version "5.43.0")
(source
(origin
(method url-fetch)
version "-source/" name "-" version ".tar.gz"))
(sha256
(base32
- "0kdncy6137sg3rradirxzj10mkcvafxd892zlclwhr9sa7b12zhn"))
+ "0xyahp4c6509haxh4n1swiqm3421gplkdisa0zypclh3252sbzfw"))
(patches (search-patches "maxima-defsystem-mkdir.patch"))))
(build-system gnu-build-system)
(inputs
(let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed"))
(coreutils (assoc-ref inputs "coreutils"))
(dirname (string-append coreutils "/bin/dirname"))
- (head (string-append coreutils "/bin/head")))
+ (head (string-append coreutils "/bin/head"))
+ (perl (string-append (assoc-ref inputs "perl") "/bin/perl"))
+ (python (string-append (assoc-ref inputs "python")
+ "/bin/python3")))
(substitute* "src/maxima.in"
(("sed ") (string-append sed " "))
(("dirname") dirname)
(("head") head))
+ (substitute* "doc/info/Makefile.in"
+ (("/usr/bin/env perl") perl))
+ (substitute* "doc/info/build_html.sh.in"
+ (("python") python))
#t)))
(add-before 'check 'pre-check
(lambda _
;; of Debian's Maxima package.
;; If Maxima can successfully run this, the binary to be installed
;; should be fine.
- (zero?
- (system
- (string-append "./maxima-local "
- "--lisp=gcl "
- "--batch-string=\"run_testsuite();\" "
- "| grep -q \"No unexpected errors found\"")))))
+ (invoke "sh" "-c"
+ (string-append
+ "./maxima-local "
+ "--lisp=gcl "
+ "--batch-string=\"run_testsuite();\" "
+ "| grep -q \"No unexpected errors found\""))))
;; 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.
(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"))
(define-public wxmaxima
(package
(name "wxmaxima")
- (version "19.03.1")
+ (version "19.09.0")
(source
(origin
(method git-fetch)
(commit (string-append "Version-" version))))
(file-name (git-file-name name version))
(sha256
- (base32
- "1qkf4jg86xnn3wk3782ffmfz12axb92dkjagcz3ffzw2wi1rclml"))))
+ (base32 "195j6j8z0jd6xg3a63ywbrbsc6dany795m3fb95nbx1vq0bqqvvn"))))
(build-system cmake-build-system)
(native-inputs
`(("gettext" ,gettext-minimal)))
(version (string-append upstream-version "-" revision))
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
- upstream-version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/beltoforion/muparser.git")
+ (commit (string-append "v" upstream-version))))
+ (file-name (git-file-name name version))
(sha256
- (base32
- "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
+ (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags '("--enable-samples=no")
(define-public openblas
(package
+ ;; TODO: Incorporate 'openblas/fixed-num-threads' changes on the next
+ ;; rebuild cycle.
+ (replacement openblas/fixed-num-threads)
+
(name "openblas")
- (version "0.3.4")
+ (version "0.3.6")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1s56lgilyyw86dzmj3jkci9zsg24n60wq4d0zri1hrxlxb6ihimj"))))
+ "1r2g9zzwq5dm8vjd19pxwggfvfzy56cvkmpmp5d014qr3svgmsap"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
#:make-flags
(list (string-append "PREFIX=" (assoc-ref %outputs "out"))
"SHELL=bash"
+ "MAKE_NB_JOBS=0" ;use jobserver for submakes
;; 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.
(license license:bsd-3)))
(define-public openblas-ilp64
- (package (inherit openblas)
+ (package/inherit openblas
(name "openblas-ilp64")
(supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
(arguments
(synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
(license license:bsd-3)))
+(define openblas/fixed-num-threads
+ ;; TODO: Move that to 'openblas' proper on the next rebuild cycle.
+ (package
+ (inherit openblas)
+ (version (match (string-split (package-version openblas) #\.)
+ ((numbers ... (= string-length len))
+ (string-join (append numbers
+ (list (make-string len #\a)))
+ "."))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments openblas)
+ ((#:make-flags flags ''())
+ ;; This is the maximum number of threads OpenBLAS will ever use (that
+ ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
+ ;; is used.) If we don't set it, the makefile sets it to the number
+ ;; of cores of the build machine, which is obviously wrong.
+ `(cons "NUM_THREADS=128" ,flags))))))
+
(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.)
(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"
+ (invoke "./configure" "-p" out
+ "-d" "opt"
+ "--disable-static"
+ "--enable-shared"
+ "--enable-threading=openmp"
- ,implementation)))))
+ ,implementation))))
(add-before 'check 'show-test-output
(lambda _
;; By default "make check" is silent. Make it verbose.
(version "0.5.3")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JuliaLang/openspecfun.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32
- "1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m"))))
+ (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ; no "check" target
#:substitutable? #f
#:modules ((srfi srfi-26)
- (srfi srfi-1)
(guix build gnu-build-system)
(guix build utils))
#:configure-flags
(let ((doc (string-append (assoc-ref outputs "doc")
"/share/doc/atlas")))
(mkdir-p doc)
- (fold (lambda (file previous)
- (and previous (zero? (system* "cp" file doc))))
- #t (find-files "../ATLAS/doc" ".*")))))
+ (for-each (cut install-file <> doc)
+ (find-files "../ATLAS/doc" ".*"))
+ #t)))
(add-after 'check 'check-pt
- (lambda _ (zero? (system* "make" "ptcheck"))))
+ (lambda _ (invoke "make" "ptcheck")))
;; Fix files required to run configure.
(add-before 'configure 'fix-/bin/sh
(lambda _
;; Use `sh', not `/bin/sh'.
(substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
(("/bin/sh")
- "sh"))))
+ "sh"))
+ #t))
;; Fix /bin/sh in generated make files.
(add-after 'configure 'fix-/bin/sh-in-generated-files
(lambda _
(substitute* (find-files "." "^[Mm]ake\\.inc.*")
(("/bin/sh")
- "sh"))))
+ "sh"))
+ #t))
;; ATLAS configure program does not accepts the default flags
;; passed by the 'gnu-build-system'.
(replace 'configure
(chdir "../build")
(format #t "build directory: ~s~%" (getcwd))
(format #t "configure flags: ~s~%" flags)
- (zero? (apply system* bash
- (string-append srcdir "/configure")
- flags))))))))
+ (apply invoke bash
+ (string-append srcdir "/configure")
+ flags)))))))
(synopsis "Automatically Tuned Linear Algebra Software")
(description
"ATLAS is an automatically tuned linear algebra software library
(define-public glm
(package
(name "glm")
- (version "0.9.9.5")
+ (version "0.9.9.6")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/g-truc/glm/releases/download/"
version "/glm-" version ".zip"))
(sha256
- (base32
- "1vmg7hb4xvsa77zpbwiw6lqc7pyaj56dihx6xriny5b9rrh4iqsg"))))
+ (base32 "1l0pi1qi37mk6s0yrkrw07lspv4gcqnr9ryg3521hrl77ff37dwx"))
+ (patches (search-patches "glm-restore-install-target.patch"))))
(build-system cmake-build-system)
(native-inputs
`(("unzip" ,unzip)))
(define-public dealii
(package
(name "dealii")
- (version "9.0.1")
+ (version "9.1.1")
(source
(origin
(method url-fetch)
"download/v" version "/dealii-" version ".tar.gz"))
(sha256
(base32
- "0r7f8rhl3xr94imd372plizdcbqk0a70w73lwc3vw912dxk0sbyz"))
- (patches (search-patches "dealii-mpi-deprecations.patch"))
+ "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw"))
(modules '((guix build utils)))
(snippet
;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
(inputs
`(("mpi" ,openmpi)
;;Supported only with MPI:
+ ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate?
("p4est" ,p4est-openmpi)
("petsc" ,petsc-openmpi)
("slepc" ,slepc-openmpi)
(define-public hypre
(package
(name "hypre")
- (version "2.14.0")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/LLNL/hypre/archive/"
- "v" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "0v515i73bvaz378h5465b1dy9v2gf924zy2q94cpq4qqarawvkqh"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- ;; Remove use of __DATE__ and __TIME__ for reproducibility;
- ;; substitute the tarball creation time.
- (substitute* "src/utilities/HYPRE_utilities.h"
- (("Date Compiled: .*$")
- "Date Compiled: Apr 11 2018 16:24:59 +0000\"\n"))
- #t))))
+ (version "2.15.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/LLNL/hypre.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1lvh4ybqkriyqfg2zmic6mrg1981qv1i9vry1fdgsabn81hb71g4"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Remove use of __DATE__ and __TIME__ for reproducibility;
+ ;; substitute the release date.
+ (substitute* "src/utilities/HYPRE_utilities.h"
+ (("Date Compiled: .*$")
+ "Date Compiled: Oct 19 2018 15:23:00 +0000\"\n"))
+ #t))))
(build-system gnu-build-system)
- (outputs '("out" ;6.1 MiB of headers and libraries
- "doc")) ;4.8 MiB of documentation
+ (outputs '("out" ; 6.1 MiB of headers and libraries
+ "doc")) ; 4.8 MiB of documentation
(native-inputs
`(("doc++" ,doc++)
("netpbm" ,netpbm)
- ("perl" ,perl) ;needed to run 'ppmquant' during tests
- ("texlive" ,(texlive-union (list texlive-generic-xypic
- texlive-fonts-xypic
+ ("perl" ,perl) ; needed to run 'ppmquant' during tests
+ ("texlive" ,(texlive-union (list texlive-xypic
+ texlive-cm
texlive-latex-hyperref
texlive-bibtex)))
("ghostscript" ,ghostscript)))
(lambda _
(setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
(setenv "PATH" (string-append "." ":" (getenv "PATH")))
- (and (system* "make" "check" "CHECKRUN=")
- (fold (lambda (filename result)
- (and result
- (let ((size (stat:size (stat filename))))
- (when (not (zero? size))
- (format #t "~a size ~d; error indication~%"
- filename size))
- (zero? size))))
- #t
- (find-files "test" ".*\\.err$")))))
+ (invoke "make" "check" "CHECKRUN=")
+ (for-each (lambda (filename)
+ (let ((size (stat:size (stat filename))))
+ (when (positive? size)
+ (error (format #f "~a size ~d; error indication~%"
+ filename size)))))
+ (find-files "test" ".*\\.err$"))
+ #t))
(add-after 'install 'install-docs
(lambda* (#:key outputs #:allow-other-keys)
;; Custom install because docs/Makefile doesn't honor ${docdir}.
(with-directory-excursion "docs"
(for-each (lambda (base)
(install-file (string-append base ".pdf") docdir)
- (copy-recursively base docdir)) ;html docs
+ (copy-recursively base docdir)) ; html docs
'("HYPRE_usr_manual"
"HYPRE_ref_manual")))
#t))))))
(assoc-ref outputs "out"))
(chmod wrapper #o555))))
(replace 'configure
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (zero? (system* "./configure"
- (string-append "--prefix="
- (assoc-ref outputs "out")))))))))
+ (lambda* (#:key outputs #:allow-other-keys)
+ (invoke "./configure"
+ (string-append "--prefix="
+ (assoc-ref outputs "out"))))))))
(inputs `(("scm" ,scm)))
(native-inputs `(("unzip" ,unzip)
("texinfo" ,texinfo)))
(define-public z3
(package
(name "z3")
- (version "4.8.4")
+ (version "4.8.6")
(home-page "https://github.com/Z3Prover/z3")
(source (origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "014igqm5vwswz0yhz0cdxsj3a6dh7i79hvhgc3jmmmz3z0xm1gyn"))))
+ "1sywcqj5y8yp28m4cdvzsgw74kd6zr1s3y1x17ky8pr9prvpvl6x"))))
(build-system gnu-build-system)
(arguments
`(#:phases
#t))
(add-before 'configure 'bootstrap
(lambda _
- (zero?
- (system* "python" "scripts/mk_make.py"))))
+ (invoke "python" "scripts/mk_make.py")))
;; work around gnu-build-system's setting --enable-fast-install
;; (z3's `configure' is a wrapper around the above python file,
;; which fails when passed --enable-fast-install)
(add-before 'check 'make-test-z3
(lambda _
;; Build the test suite executable.
- (zero? (system* "make" "test-z3" "-j"
- (number->string (parallel-job-count))))))
+ (invoke "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")))))))
+ (invoke "./test-z3" "/a"))))))
(native-inputs
`(("which" ,which)
("python" ,python-wrapper)))
(define-public mcrl2
(package
(name "mcrl2")
- (version "201707.1.15162")
+ (version "201908.0")
(source (origin
(method url-fetch)
(uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
".tar.gz"))
(sha256
(base32
- "1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
- (native-inputs
- `(("subversion" ,subversion)))
+ "1i4xgl2d5fgiz1mwi50cyfkrrcpm8nxfayfjgmhq7chs58wlhfsz"))))
(inputs
`(("boost" ,boost)
("glu" ,glu)
(home-page "https://mcrl2.org")
(license license:boost1.0)))
+(define-public mcrl2-minimal
+ (package
+ (inherit mcrl2)
+ (name "mcrl2-minimal")
+ (inputs
+ `(("boost" ,boost)))
+ (arguments
+ '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
+
(define-public r-subplex
(package
(name "r-subplex")
(define-public r-desolve
(package
(name "r-desolve")
- (version "1.21")
+ (version "1.24")
(source
(origin
(method url-fetch)
(uri (cran-uri "deSolve" version))
(sha256
(base32
- "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
+ "0hkvspq0fp8j64l9zayab2l2nazazhwfgfym0jllh0xv5a12r99s"))))
(properties `((upstream-name . "deSolve")))
(build-system r-build-system)
(native-inputs
(add-after 'build 'build-tests
(lambda* (#:key inputs make-flags #:allow-other-keys)
(setenv "CPLUS_INCLUDE_PATH"
- (string-append (assoc-ref inputs "dune-grid") "/share:"
- (getenv "CPLUS_INCLUDE_PATH")))
+ (string-append (assoc-ref inputs "dune-grid") "/share"))
(apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
(uri (string-append
"https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
(sha256
- (base32
- "1ax12qj9lyvnx4vs3gx7l8r3wx5gjbsdswp5f00ik9z0wz7xf297"))))
+ (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
(build-system gnu-build-system)
(inputs
`(("python2" ,python-2)))
(arguments
- `(#:tests? #f ; no tests
+ `(#:tests? #f ; no tests
#:phases
(modify-phases %standard-phases
(replace 'configure
Search (GIMPS). Mlucas also includes a simple Python script for assignment
management via the GIMPS project's Primenet server.")
(license license:gpl2+)))
+
+(define-public nauty
+ (package
+ (name "nauty")
+ (version "2.6r11")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pallini.di.uniroma1.it/"
+ "nauty" (string-join (string-split version #\.) "")
+ ".tar.gz"))
+ (sha256
+ (base32
+ "05z6mk7c31j70md83396cdjmvzzip1hqb88pfszzc6k4gy8h3m2y"))))
+ (build-system gnu-build-system)
+ (outputs '("out" "lib"))
+ (arguments
+ `(#:test-target "checks"
+ #:phases
+ (modify-phases %standard-phases
+ ;; Default make target does not build all available
+ ;; executables. Create them now.
+ (add-after 'build 'build-extra-programs
+ (lambda _
+ (for-each (lambda (target) (invoke "make" target))
+ '("blisstog" "bliss2dre" "checks6" "sumlines"))
+ #t))
+ ;; Upstream does not provide any install target.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (lib-output (assoc-ref outputs "lib"))
+ (bin (string-append out "/bin"))
+ (doc (string-append out "/share/doc/nauty/"))
+ (include (string-append lib-output "/include/nauty"))
+ (lib (string-append lib-output "/lib/nauty")))
+ (for-each (lambda (f) (install-file f bin))
+ '("dreadnaut" "NRswitchg" "addedgeg" "amtog" "biplabg"
+ "blisstog" "bliss2dre" "catg" "checks6" "complg"
+ "converseg" "copyg" "countg" "cubhamg" "deledgeg"
+ "delptg" "directg" "dretodot" "dretog" "genbg"
+ "genbgL" "geng" "genquarticg" "genrang" "genspecialg"
+ "gentourng" "gentreeg" "hamheuristic" "labelg"
+ "linegraphg" "listg" "multig" "newedgeg" "pickg"
+ "planarg" "ranlabg" "shortg" "showg" "subdivideg"
+ "sumlines" "twohamg" "vcolg" "watercluster2"))
+ (for-each (lambda (f) (install-file f include))
+ (find-files "." "\\.h$"))
+ (for-each (lambda (f) (install-file f lib))
+ (find-files "." "\\.a$"))
+ (for-each (lambda (f) (install-file f doc))
+ (append '("formats.txt" "README" "schreier.txt")
+ (find-files "." "\\.pdf$")))))))))
+ (inputs
+ `(("gmp" ,gmp))) ;for sumlines
+ (home-page "https://pallini.di.uniroma1.it/")
+ (synopsis "Library for graph automorphisms")
+ (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
+procedures for computing automorphism groups of graphs and digraphs.
+
+@code{nauty} computes graph information in the form of a set of
+generators, the size of the group, and the orbits of the group; it can
+also produce a canonical label. The @code{nauty} suite is written in
+C and comes with a command-line interface, a collection of
+command-line tools, and an Application Programming Interface (API).
+
+This package provides the static libraries required to run programs
+compiled against the nauty library.")
+ (license license:asl2.0)))
+
+(define-public ppl
+ (package
+ (name "ppl")
+ (version "1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://www.bugseng.com/products/ppl/download/"
+ "ftp/releases/" version
+ "/ppl-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("m4", m4)))
+ (inputs
+ `(("glpk" ,glpk)
+ ("gmp", gmp)))
+ (home-page "https://www.bugseng.com/parma-polyhedra-library")
+ (synopsis
+ "Parma Polyhedra Library for computations with polyhedra")
+ (description
+ "The Parma Polyhedra Library (PPL) provides numerical abstractions
+especially targeted at applications in the field of analysis and
+verification of complex systems. These abstractions include convex
+polyhedra, defined as the intersection of a finite number of (open or
+closed) halfspaces, each described by a linear inequality (strict or
+non-strict) with rational coefficients; some special classes of polyhedra
+shapes that offer interesting complexity/precision tradeoffs; and grids
+which represent regularly spaced points that satisfy a set of linear
+congruence relations. The library also supports finite powersets and
+products of (any kind of) polyhedra and grids, a mixed integer linear
+programming problem solver using an exact-arithmetic version of the simplex
+algorithm, a parametric integer programming solver, and primitives for
+termination analysis via the automatic synthesis of linear ranking
+functions.")
+ (license license:gpl3+)))
+
+(define-public speedcrunch
+ (package
+ (name "speedcrunch")
+ (version "0.12.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://bitbucket.org/heldercorreia/speedcrunch.git")
+ (commit (string-append "release-" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
+ (build-system cmake-build-system)
+ (inputs `(("qtbase" ,qtbase)))
+ (native-inputs `(("qttools" ,qttools)))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'chdir-to-src
+ (lambda _ (chdir "src") #t)))))
+ (synopsis "High-precision scientific calculator")
+ (description
+ "SpeedCrunch is a high-precision scientific calculator. It features a
+syntax-highlighted scrollable display and is designed to be fully used via
+keyboard. Some distinctive features are auto-completion of functions and
+variables, a formula book, and quick insertion of constants from various
+fields of knowledge.")
+ (home-page "http://speedcrunch.org/")
+ (license license:gpl2+)))
+
HCoop / jackhill / guix / guix.git / blobdiff