;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
-;;; Copyright © 2014, 2016 John Darrington <jmd@gnu.org>
+;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org>
-;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016 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>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
+ #:use-module (guix git-download)
#:use-module (guix utils)
#:use-module (guix build utils)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
+ #:use-module (guix build-system ocaml)
#:use-module (guix build-system r)
#:use-module (gnu packages algebra)
#:use-module (gnu packages bison)
#:use-module (gnu packages guile)
#:use-module (gnu packages xorg)
#:use-module (gnu packages gl)
+ #:use-module (gnu packages imagemagick)
#:use-module (gnu packages m4)
#:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages netpbm)
+ #:use-module (gnu packages ocaml)
#:use-module (gnu packages pcre)
#:use-module (gnu packages popt)
#:use-module (gnu packages perl)
#:use-module (gnu packages python)
#:use-module (gnu packages readline)
#:use-module (gnu packages tbb)
+ #:use-module (gnu packages scheme)
#:use-module (gnu packages shells)
#:use-module (gnu packages tcl)
#:use-module (gnu packages texinfo)
#:use-module (gnu packages zip)
#:use-module (srfi srfi-1))
+(define-public aris
+ (package
+ (name "aris")
+ (version "2.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
+ (sha256 (base32
+ "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
+ (build-system gnu-build-system)
+ (inputs `(("gtk+" ,gtk+)
+ ("libxml2" ,libxml2)))
+ (native-inputs `(("pkg-config" ,pkg-config)))
+ (synopsis "Natural deduction first-order logic interface")
+ (description "Aris is a program for performing logical proofs. It supports
+propositional and predicate logic, as well as Boolean algebra and
+arithmetical logic. In addition to its predefined inference and equivalence
+rules, Aris also supports references to older proofs. Its use of standard
+logical symbols and its natural deduction interface make it easy to use for
+beginners.")
+ (license license:gpl3+)
+ (home-page "http://www.gnu.org/software/aris/")))
+
(define-public c-graph
(package
(name "c-graph")
(license license:gpl3+)
(home-page "http://www.gnu.org/software/c-graph/")))
+(define-public coda
+ (package
+ (name "coda")
+ (version "2.18")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/stcorp/coda/releases/download/"
+ version "/coda-" version ".tar.gz"))
+ (sha256
+ (base32 "11asla1ap8vd73farqjlpb179sfiy0biydcwxjfcakrp9sf8v9bs"))
+ (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")))))
+ (native-inputs
+ `(("fortran" ,gfortran)
+ ("python" ,python)
+ ("python-numpy" ,python-numpy)))
+ (inputs
+ `(("zlib" ,zlib)
+ ("pcre" ,pcre)
+ ("expat" ,expat)
+ ("hdf4" ,hdf4-alt)
+ ("hdf5" ,hdf5)))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
+ "LIBS= -lz -lpcre -lexpat")))
+ (synopsis "A common interface to various earth observation data formats")
+ (description
+ "The Common Data Access toolbox (CODA) provides a set of interfaces for
+reading remote sensing data from earth observation data files. It consists of
+command line applications and interfaces to the C, Fortran, Python, and Java
+programming languages.")
+ (home-page "https://stcorp.nl/coda")
+ (license license:gpl2+)))
+
(define-public units
(package
(name "units")
- (version "2.13")
+ (version "2.14")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/units/units-" version
".tar.gz"))
(sha256 (base32
- "1awhjw9zjlfb8s5g3yyx63f7ddfcr1sanlbxpqifmrgq24ql198b"))))
+ "1s421bxm36akjsy3qzg6da1d1g20gh094ac2slqxipgkh8yqjcwx"))))
(build-system gnu-build-system)
(synopsis "Conversion between thousands of scales")
(description
(define-public gsl
(package
(name "gsl")
- (version "2.1")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "mirror://gnu/gsl/gsl-"
- version ".tar.gz"))
- (sha256
- (base32
- "0rhcia9jhr3p1f1wybwyllwqfs9bggz99i3mi5lpyqcpff1hdbar"))))
+ (version "2.3")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://gnu/gsl/gsl-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1yxdzqjwmi2aid650fa9zyr8llw069x7lm489wx9nnfdi6vh09an"))
+ (patches (search-patches "gsl-test-i686.patch"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-tests? #f))
numbers.")
(license license:gpl3+)))
+(define-public ocaml-gsl
+ (package
+ (name "ocaml-gsl")
+ (version "1.19.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append
+ "https://github.com/mmottl/gsl-ocaml/releases/download/v"
+ version"/gsl-ocaml-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
+ (build-system ocaml-build-system)
+ (inputs
+ `(("gsl" ,gsl)))
+ (home-page "https://mmottl.github.io/gsl-ocaml")
+ (synopsis "Bindings to the GNU Scientific Library")
+ (description
+ "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
+the OCaml language.")
+ (license license:gpl3+)))
+
(define-public glpk
(package
(name "glpk")
- (version "4.60")
+ (version "4.61")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "15z2ymzqhxwss6wgdj5f7vkyqlqdsjgrvm0x871kmlx0n0664mhk"))))
+ "1adbvwiaqrv9pql9ry3lhn2vfsxnff2vh4fs477d90kpfx0xwrlq"))))
(build-system gnu-build-system)
(inputs
`(("gmp" ,gmp)))
(arguments
`(#:configure-flags '("--with-gmp")))
- (home-page "http://www.gnu.org/software/glpk/")
+ (home-page "https://www.gnu.org/software/glpk/")
(synopsis "GNU Linear Programming Kit, supporting the MathProg language")
(description
"GLPK is a C library for solving large-scale linear programming (LP),
(source
(origin
(method url-fetch)
- (uri (string-append "ftp://ftp.ifor.math.ethz.ch/pub/fukuda/cdd/cddlib-"
+ (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
(string-delete #\. version) ".tar.gz"))
(sha256
(base32
"See LICENSE in the distribution."))))
(define-public gnuplot
- ;; Gnuplot version 5.0.4 was updated in-place, resulting in a hash mismatch.
- ;; This can be removed at the next version update.
- (let ((upstream-version "5.0.4")
- (guix-revision "1"))
- (package
- (name "gnuplot")
- (version (string-append upstream-version "-" guix-revision))
- (source
- (origin
- (method url-fetch)
- (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
- upstream-version "/gnuplot-"
- upstream-version ".tar.gz"))
- (sha256
- (base32
- "07n3w12dkcxjnhsvsliaqnkhajhi818v6q8mkpmpbplbf92vh70m"))))
- (build-system gnu-build-system)
- (inputs `(("readline" ,readline)
- ("cairo" ,cairo)
- ("pango" ,pango)
- ("gd" ,gd)))
- (native-inputs `(("pkg-config" ,pkg-config)
- ("texlive" ,texlive-minimal)))
- (home-page "http://www.gnuplot.info")
- (synopsis "Command-line driven graphing utility")
- (description "Gnuplot is a portable command-line driven graphing
+ (package
+ (name "gnuplot")
+ (version "5.0.5")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
+ version "/gnuplot-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0lr065qdlgss8lmy31l7hkmnk9fp4lvqq9qgb1f1209f36zy1wr5"))))
+ (build-system gnu-build-system)
+ (inputs `(("readline" ,readline)
+ ("cairo" ,cairo)
+ ("pango" ,pango)
+ ("gd" ,gd)))
+ (native-inputs `(("pkg-config" ,pkg-config)
+ ("texlive" ,texlive-minimal)))
+ (home-page "http://www.gnuplot.info")
+ (synopsis "Command-line driven graphing utility")
+ (description "Gnuplot is a portable command-line driven graphing
utility. It was originally created to allow scientists and students to
visualize mathematical functions and data interactively, but has grown to
support many non-interactive uses such as web scripting. It is also used as a
plotting engine by third-party applications like Octave.")
- ;; X11 Style with the additional restriction that derived works may only be
- ;; distributed as patches to the original.
- (license (license:fsf-free
- "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright")))))
+ ;; X11 Style with the additional restriction that derived works may only be
+ ;; distributed as patches to the original.
+ (license (license:fsf-free
+ "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
+
+(define-public gctp
+ (package
+ (name "gctp")
+ (version "2.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
+ (native-inputs
+ `(("fortran" ,gfortran)))
+ (build-system gnu-build-system)
+ (synopsis "General Cartographic Transformation Package (GCTP)")
+ (description
+ "The General Cartographic Transformation Package (GCTP) is a system of
+software routines designed to permit the transformation of coordinate pairs
+from one map projection to another. The GCTP is the standard computer
+software used by the National Mapping Division for map projection
+computations.")
+ (home-page "https://github.com/OkoSanto/GCTP")
+ (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
+
+(define-public hdf4
+ (package
+ (name "hdf4")
+ (version "4.2.12")
+ (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"))
+ (patches (search-patches "hdf4-architectures.patch"
+ "hdf4-reproducibility.patch"
+ "hdf4-shared-fortran.patch"))))
+
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)
+ ("bison" ,bison)
+ ("flex" ,flex)))
+ (inputs
+ `(("zlib" ,zlib)
+ ("libjpeg" ,libjpeg)))
+ (arguments
+ `(#:parallel-tests? #f
+ #:configure-flags '("--enable-shared")
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'patchbuild
+ (lambda _
+ (substitute*
+ '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
+ (("/bin/rm") "rm")
+ (("/bin/mkdir") "mkdir"))
+ (substitute* (find-files "." "^Makefile\\.in$")
+ (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
+-R\\$\\(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\\)") "")))))))
+ (home-page "https://www.hdfgroup.org/products/hdf4/")
+ (synopsis
+ "Library and multi-object file format for storing and managing data")
+ (description "HDF4 is a library and multi-object file format for storing
+and managing data between machines. HDF4 is an older hierarchical data format,
+incompatible with HDF5.")
+ (license
+ (license:non-copyleft
+ "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
+
+(define-public hdf4-alt
+ (package
+ (inherit hdf4)
+ (name "hdf4-alt")
+ (arguments
+ (substitute-keyword-arguments (package-arguments hdf4)
+ ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
+ (synopsis
+ "HDF4 without netCDF API, can be combined with the regular netCDF library")))
(define-public hdf5
(package
(name "hdf5")
- (version "1.8.17")
+ (version "1.8.18")
(source
(origin
(method url-fetch)
- (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-"
- version "/src/hdf5-"
- version ".tar.bz2"))
+ (uri (list (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/"
+ "hdf5-" version "/src/hdf5-"
+ version ".tar.bz2")
+ (string-append "https://support.hdfgroup.org/ftp/HDF5/"
+ "current"
+ (apply string-append
+ (take (string-split version #\.) 2))
+ "/src/hdf5-" version ".tar.bz2")))
(sha256
- (base32 "0sj8x0gfs5fb28gipnynb9wpkz113h8wq9sva9mxx66kv27xsdgw"))
+ (base32 "13542vrnl1p35n8vbq0wzk40vddmm33q5nh04j98c7r1yjnxxih1"))
(patches (list (search-patch "hdf5-config-date.patch")))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)))
(arguments
- `(#:phases
+ `(;; Some of the users, notably Flann, need the C++ interface.
+ #:configure-flags '("--enable-cxx")
+
+ #:phases
(modify-phases %standard-phases
(add-before 'configure 'patch-configure
(lambda _
(license (license:x11-style
"http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
+(define-public hdf-eos2
+ (package
+ (name "hdf-eos2")
+ (version "19.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri "ftp://edhs1.gsfc.nasa.gov\
+/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
+ (sha256
+ (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
+ (patches (search-patches "hdf-eos2-remove-gctp.patch"
+ "hdf-eos2-build-shared.patch"
+ "hdf-eos2-fortrantests.patch"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs
+ `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
+ ("zlib" ,zlib)
+ ("libjpeg" ,libjpeg)
+ ("gctp" ,gctp)))
+ (arguments
+ `( #:configure-flags '("--enable-install-include" "--enable-shared"
+ "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
+ #:parallel-tests? #f))
+ (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
+ (synopsis "HDF4-based data format for NASA's Earth Observing System")
+ (description "HDF-EOS2 is a software library built on HDF4 which supports
+the construction of data structures used in NASA's Earth Observing
+System (Grid, Point and Swath).")
+
+ ;; Source files carry a permissive license header.
+ (license (license:non-copyleft home-page))))
+
+(define-public hdf-eos5
+ (package
+ (name "hdf-eos5")
+ (version "1.15")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
+/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
+ (sha256
+ (base32
+ "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
+ (patches (search-patches "hdf-eos5-build-shared.patch"
+ "hdf-eos5-remove-gctp.patch"
+ "hdf-eos5-fix-szip.patch"
+ "hdf-eos5-fortrantests.patch"))))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (build-system gnu-build-system)
+ (inputs
+ `(("hdf5" ,hdf5)
+ ("zlib" ,zlib)
+ ("gctp" ,gctp)))
+ (arguments
+ `(#:configure-flags '("--enable-install-include" "--enable-shared"
+ "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
+ #:parallel-tests? #f))
+ (synopsis "HDF5-based data format for NASA's Earth Observing System")
+ (description
+ "HDF-EOS5 is a software library built on HDF5 to support the construction
+of data structures used in NASA's Earth Observing System (Grid, Point and
+Swath).")
+ (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
+
+ ;; Source files carry a permissive license header.
+ (license (license:non-copyleft home-page))))
+
(define-public hdf5-parallel-openmpi
(package (inherit hdf5)
(name "hdf5-parallel-openmpi")
HDF5 file is encoded according to the HDF File Format Specification.")
(license (license:x11-style "file://COPYING"))))
+(define-public itpp
+ (package
+ (name "itpp")
+ (version "4.3.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/itpp/itpp/"
+ version "/itpp-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
+ (build-system cmake-build-system)
+ (arguments `(#:tests? #f)) ; Tests require googletest *sources*
+ (inputs `(("lapack" ,lapack)
+ ("fftw" ,fftw)))
+ (native-inputs `(("texlive-minimal" ,texlive-minimal)
+ ("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
+communication classes and functions. Its main use is in simulation of
+communication systems and for performing research in the area of
+communications. The kernel of the library consists of generic vector and
+matrix classes, and a set of accompanying routines. Such a kernel makes IT++
+similar to MATLAB, GNU Octave or SciPy.")
+ (license license:gpl3+)))
+
(define-public netcdf
(package
(name "netcdf")
- (version "4.4.0")
+ (version "4.4.1.1")
(source
(origin
(method url-fetch)
"netcdf-" version ".tar.gz"))
(sha256
(base32
- "0y6gdcplarwqqnrav2xg1xd6ih732rzzbmdw78v3rl5b8mwcnh0d"))
- (patches (list (search-patch "netcdf-config-date.patch")))))
+ "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
+ (patches (search-patches "netcdf-date-time.patch"
+ "netcdf-tst_h_par.patch"))))
(build-system gnu-build-system)
(native-inputs
`(("m4" ,m4)
("doxygen" ,doxygen)
("graphviz" ,graphviz)))
(inputs
- `(("hdf5" ,hdf5)
- ("zlib" ,zlib)))
+ `(("hdf4" ,hdf4-alt)
+ ("hdf5" ,hdf5)
+ ("zlib" ,zlib)
+ ("libjpeg" ,libjpeg)))
(arguments
- `(#:configure-flags '("--enable-doxygen" "--enable-dot")
+ `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
#:parallel-tests? #f)) ;various race conditions
(home-page "http://www.unidata.ucar.edu/software/netcdf/")
(synopsis "Library for scientific data")
(define-public octave
(package
(name "octave")
- (version "4.0.3")
+ (version "4.2.1")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://gnu/octave/octave-"
- version ".tar.xz"))
+ version ".tar.lz"))
(sha256
(base32
- "11day29k4yfvxh4101x5yf26ld992x5n6qvmhjjk6mzsd26fqayw"))))
+ "09zhhch79jw3ynw39vizx0i2cbd2bjz3sp38pjdzraqrbivpwp92"))))
(build-system gnu-build-system)
(inputs
`(("lapack" ,lapack)
("libxft" ,libxft)
("mesa" ,mesa)
("glu" ,glu)
- ("zlib" ,zlib)))
+ ("zlib" ,zlib)
+ ("curl" ,curl)
+ ("graphicsmagick" ,graphicsmagick)))
(native-inputs
- `(("gfortran" ,gfortran)
+ `(("lzip" ,lzip)
+ ("gfortran" ,gfortran)
("pkg-config" ,pkg-config)
("perl" ,perl)
;; The following inputs are not actually used in the build process.
(list (string-append "--with-shell="
(assoc-ref %build-inputs "bash")
"/bin/sh"))))
- (home-page "http://www.gnu.org/software/octave/")
+ (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
specialized for numerical computations. It can be used for both linear and
script files.")
(license license:gpl3+)))
+(define-public opencascade-oce
+ (package
+ (name "opencascade-oce")
+ (version "0.17.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/tpaviot/oce/archive/OCE-"
+ version
+ ".tar.gz"))
+ (sha256
+ (base32
+ "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
+ (build-system cmake-build-system)
+ (arguments
+ '(#:configure-flags
+ (list "-DOCE_TESTING:BOOL=ON"
+ "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
+ "-DOCE_DRAW:BOOL=ON"
+ (string-append "-DOCE_INSTALL_PREFIX:PATH="
+ (assoc-ref %outputs "out"))
+ "-UCMAKE_INSTALL_RPATH")))
+ (inputs
+ `(("freetype" ,freetype)
+ ("glu" ,glu)
+ ("libxmu" ,libxmu)
+ ("mesa" ,mesa)
+ ("tcl" ,tcl)
+ ("tk" ,tk)))
+ (native-inputs
+ `(("python" ,python-wrapper)))
+ (home-page "https://github.com/tpaviot/oce")
+ (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 ``Community Edition'' (OCE) of Open CASCADE, which gathers
+patches, improvements, and experiments contributed by users over the official
+Open CASCADE library.")
+ (license (list license:lgpl2.1; OCE libraries, with an exception for the
+ ; use of header files; see
+ ; OCCT_LGPL_EXCEPTION.txt
+ license:public-domain; files
+ ; src/Standard/Standard_StdAllocator.hxx and
+ ; src/NCollection/NCollection_StdAllocator.hxx
+ license:expat; file src/OpenGl/OpenGl_glext.h
+ license:bsd-3)))); test framework gtest
+
(define-public gmsh
(package
(name "gmsh")
- (version "2.11.0")
+ (version "2.16.0")
(source
(origin
(method url-fetch)
- (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-"
+ (uri (string-append "http://gmsh.info/src/gmsh-"
version "-source.tgz"))
(sha256
- (base32 "1ilplibvjgf7a905grpnclrvkmqy9fgrpl7xyp3w4yl1qc682v9b"))
+ (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
(modules '((guix build utils)))
(snippet
;; Remove non-free METIS code
("lapack" ,lapack)
("mesa" ,mesa)
("glu" ,glu)
+ ("opencascade-oce" ,opencascade-oce)
("libx11" ,libx11)
("libxext" ,libxext)))
(inputs
(arguments
`(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
"-DENABLE_BUILD_SHARED:BOOL=ON"
- "-DENABLE_BUILD_DYNAMIC:BOOL=ON")
- #:phases (modify-phases %standard-phases
- (replace
- 'check
- (lambda _
- (zero? (system* "make" "test"
- ;; Disable this test. See
- ;; https://geuz.org/trac/gmsh/ticket/271
- "ARGS=-E component8_in_a_box")))))))
+ "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
(home-page "http://www.geuz.org/gmsh/")
(synopsis "3D finite element grid generator")
(description "Gmsh is a 3D finite element grid generator with a built-in
(define-public mumps
(package
(name "mumps")
- (version "5.0.1")
+ (version "5.0.2")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "1820jfp3mbl7n85765v5mp6p0gzqpgr4d2lrnhwj4gl7cwp5ndah"))
+ "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp"))
(patches (search-patches "mumps-build-parallelism.patch"))))
(build-system gnu-build-system)
(inputs
,@%gnu-build-system-modules)
#:phases
(modify-phases %standard-phases
- (replace
- 'configure
+ (replace 'configure
(lambda* (#:key inputs #:allow-other-keys)
(call-with-output-file "Makefile.inc"
(lambda (port)
`((,ptscotch
"-lptesmumps -lptscotch -lptscotcherr "
"-Dptscotch")))))))))
- (replace
- 'build
+ (replace 'build
;; 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))))))
- (replace
- 'check
+ (replace 'check
;; Run the simple test drivers, which read test input from stdin:
;; from the "real" input for the single- and double-precision
;; testers, and from the "cmplx" input for complex-precision
(zero? (close-pipe tester)))))
'("s" "d" "c" "z")
'("real" "real" "cmplx" "cmplx")))))
- (replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (copy-recursively "lib" (string-append out "/lib"))
- (copy-recursively "include" (string-append out "/include"))
- (when (file-exists? "libseq/libmpiseq.a")
- (copy-file "libseq/libmpiseq.a"
- (string-append out "/lib/libmpiseq.a")))))))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (libdir (string-append out "/lib")))
+ (copy-recursively "lib" libdir)
+ (copy-recursively "include" (string-append out "/include"))
+ (when (file-exists? "libseq/libmpiseq.a")
+ (install-file "libseq/libmpiseq.a" libdir))
+ #t))))))
(home-page "http://mumps.enseeiht.fr")
(synopsis "Multifrontal sparse direct solver")
(description
(define-public maxima
(package
(name "maxima")
- (version "5.36.1")
+ (version "5.39.0")
(source
(origin
(method url-fetch)
version "-source/" name "-" version ".tar.gz"))
(sha256
(base32
- "0x1rk659sn3cq0n5c90848ilzr1gb1wf0072fl6jhkdq00qgh2s0"))
+ "1cvignn5y6qzrby6qb885yc8zdcdqdr1d50vcvc3gapw2f0gk3zm"))
(patches (search-patches "maxima-defsystem-mkdir.patch"))))
(build-system gnu-build-system)
(inputs
("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
(native-inputs
`(("texinfo" ,texinfo)
- ("perl" ,perl)))
+ ("perl" ,perl)
+ ("python" ,python)))
(arguments
`(#:configure-flags
(list "--enable-gcl"
(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")
(source
(origin
(define-public armadillo
(package
(name "armadillo")
- (version "6.700.7")
+ (version "7.600.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/arma/armadillo-"
- version ".tar.gz"))
+ version ".tar.xz"))
(sha256
(base32
- "0xbidcxrvbq33xf7iysg2nic2ai9a043psl33kiv6ifkk7p8hcra"))))
+ "0bac9y46m61zxinj51l82w06v01ra9vw7a9j6rrwdjhznkkdb437"))))
(build-system cmake-build-system)
(arguments `(#:tests? #f)) ;no test target
(inputs
(define-public armadillo-for-rcpparmadillo
(package (inherit armadillo)
- (version "6.700.6")
+ (version "7.600.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/arma/armadillo-"
- version ".tar.gz"))
+ version ".tar.xz"))
(sha256
(base32
- "1cdpjxb0fz5f28y5qrqgpw53s7qi8s2v3al9lfdldqxngb21vpx8"))))))
+ "1dxgfd2r9lbh24nszvqm2lag439s0srxaf1l86f6ww6waqm5r8zk"))))))
(define-public muparser
;; When switching download sites, muparser re-issued a 2.2.5 release with a
(define-public openblas
(package
(name "openblas")
- (version "0.2.15")
+ (version "0.2.19")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1k5f6vjlk54qlplk5m7xkbaw6g2y7dl50lwwdv6xsbcsgsbxfcpy"))))
+ "071zqnmnxhh0c9phzyn3f198yxa0hjxda7016azdbq2056sm70w7"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ;no "check" target
have a good libm for the Julia programming language that worked consistently
across compilers and operating systems, and in 32-bit and 64-bit
environments.")
+ ;; Each architecture has its own make target, and there is none for mips.
+ (supported-systems (delete "mips64el-linux" %supported-systems))
;; See LICENSE.md for details.
(license (list license:expat
license:isc
(base32
"15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
(build-system gnu-build-system)
- (native-inputs `(("gettext" ,gnu-gettext)))
+ (native-inputs `(("gettext" ,gettext-minimal)))
(inputs `(("libx11" ,libx11)
("zlib" ,zlib)
("libpng" ,libpng)
;; Custom install because docs/Makefile doesn't honor ${docdir}.
(let* ((doc (assoc-ref outputs "doc"))
(docdir (string-append doc "/share/doc/hypre-" ,version)))
- (mkdir-p docdir)
(with-directory-excursion "docs"
(for-each (lambda (base)
(install-file (string-append base ".pdf") docdir)
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")
+ (source
+ (origin (method url-fetch)
+ (uri (string-append "https://github.com/VcDevel/Vc/releases/"
+ "download/" version "/Vc-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1rh6dhqar3y07n4xqyml0sa0v48qv3ch9dc3yc2in855hlh4vnqi"))))
+ (build-system cmake-build-system)
+ (arguments
+ '(#:configure-flags
+ '("-DBUILD_TESTING=ON")))
+ (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
+vectorization of C++ code. Its types enable explicitly stating data-parallel
+operations on multiple values. The parallelism is therefore added via the type
+system. Vc has an intuitive API and provides portability between different
+compilers and compiler versions as well as portability between different vector
+instruction sets. Thus, an application written with Vc can be compiled for:
+@enumerate
+@item AVX and AVX2
+@item SSE2 upto SSE4.2 or SSE4a
+@item Scalar
+@item MIC
+@item NEON (in development)
+@item NVIDIA GPUs / CUDA (in development)
+@end enumerate\n")
+ (home-page "https://github.com/VcDevel/Vc")
+ (license license:bsd-3)))
+
+(define-public reducelcs
+ ;; This is the last commit which is available upstream, no
+ ;; release happened since 2010.
+ (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
+ (revision "1"))
+ (package
+ (name "reducelcs")
+ (version (string-append "1.0-" revision "." (string-take commit 7)))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/gdv/Reduce-Expand-for-LCS")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("openlibm" ,openlibm)))
+ (arguments
+ `(#:tests? #f ; no tests
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; No configure script exists.
+ (replace 'install ; No install phase exists.
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (install-file "Approximation" bin)
+ (install-file "CollectResults" bin)
+ (install-file "GenerateInstances" bin)
+ #t))))))
+ (synopsis "Approximate Longest Commons Subsequence computation tool")
+ (description
+ "@code{reduceLCS} is an implementation of the Reduce-Expand
+algorithm for LCS. It is a fast program to compute the approximate
+Longest Commons Subsequence of a set of strings.")
+ (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
+ (license license:gpl3+))))
+
+(define-public jacal
+ (package
+ (name "jacal")
+ (version "1c4")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
+ version ".zip"))
+ (sha256 (base32
+ "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
+ (patches (search-patches "jacal-fix-texinfo.patch"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'build 'pre-build
+ ;; Don't use upstream's script - it really doesn't fit into
+ ;; Guix's functional paradigm.
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* "Makefile"
+ (("^install: install-script") "install: "))))
+ (add-after 'install 'post-install
+ ;; Instead, we provide our own simplified script.
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((wrapper (string-append (assoc-ref outputs "out")
+ "/bin/jacal")))
+ (format (open wrapper (logior O_WRONLY O_CREAT))
+ (string-append "#!~a\nexec ~a/bin/scm -ip1 "
+ "-e '(slib:load \"~a/lib/jacal/math\") "
+ "(math)' \"$@\"\n")
+ (which "bash")
+ (assoc-ref inputs "scm")
+ (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")))))))))
+ (inputs `(("scm" ,scm)))
+ (native-inputs `(("unzip" ,unzip)
+ ("texinfo" ,texinfo)))
+ (synopsis "Symbolic mathematics system")
+ (description "GNU JACAL is an interactive symbolic mathematics program based on
+Scheme. It manipulate and simplify a range of mathematical expressions such
+as equations, scalars, vectors, and matrices.")
+ (home-page "http://www.gnu.org/software/jacal")
+ (license license:gpl3+)))
+
HCoop / jackhill / guix / guix.git / blobdiff