;;; 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>
;;;
;;; 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)
(license license:gpl3+)
(home-page "http://www.gnu.org/software/c-graph/")))
+(define-public coda
+ (package
+ (name "coda")
+ (version "2.17.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/stcorp/coda/releases/download/"
+ version "/coda-" version ".tar.gz"))
+ (sha256
+ (base32 "04b9l3wzcix0mnfq77mwnil6cbr8h2mki8myvy0lzn236qcwaq1h"))
+ (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")
(define-public gsl
(package
(name "gsl")
- (version "2.2.1")
+ (version "2.3")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/gsl/gsl-"
version ".tar.gz"))
(sha256
(base32
- "095hp01d8lkqdvv0p1k25kvbisgfdmvx1rzpyc2i8kl2n33kvlhk"))
+ "1yxdzqjwmi2aid650fa9zyr8llw069x7lm489wx9nnfdi6vh09an"))
(patches (search-patches "gsl-test-i686.patch"))))
(build-system gnu-build-system)
(arguments
(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),
"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
(define-public hdf4
(package
(name "hdf4")
- (version "4.2.11")
+ (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 "16yr50j845zlfx20skmw3y75ww77akk9gg0affjqkg66ih5r03mv"))
+ (base32 "020jh563sjyxsgml8l809d2i1d4ms9shivwj3gbm7n0ilxbll8id"))
(patches (search-patches "hdf4-architectures.patch"
"hdf4-reproducibility.patch"
"hdf4-shared-fortran.patch"))))
(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")
(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 "4.2.0")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://gnu/octave/octave-"
- version ".tar.xz"))
+ version ".tar.lz"))
(sha256
(base32
- "11day29k4yfvxh4101x5yf26ld992x5n6qvmhjjk6mzsd26fqayw"))))
+ "19vvliwxgip0af812vny5xy5r8kacyj7v62203mh4z2n3p14b78i"))))
(build-system gnu-build-system)
(inputs
`(("lapack" ,lapack)
("glu" ,glu)
("zlib" ,zlib)))
(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
(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")
- (version "16.04.2")
+ (version "16.12.0")
(source
(origin
(method url-fetch)
version "/" name "-" version ".tar.gz"))
(sha256
(base32
- "1fpqzk1921isiqrpgpf433ldq41924qs9sy99fl1zn5661b2l73n"))))
+ "01kas9viqabw5id6crbhz8ahjimmv78gqzizs5hgnj9kngrgrm1h"))))
(build-system gnu-build-system)
(inputs
`(("wxwidgets" ,wxwidgets)
(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 "7.400.2")
+ (version "7.600.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/arma/armadillo-"
version ".tar.xz"))
(sha256
(base32
- "0xmpnqhm9mwr1lssjyarj0cl8b4svbqv6z1xa1dxlwd2ly1srkg4"))))))
+ "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
(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)
@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")
+ ;; The source specifies no "and later" of GPL3.
+ (license license:gpl3))))
HCoop / jackhill / guix / guix.git / blobdiff