;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2013, 2014 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
+;;; Copyright © 2014 John Darrington <jmd@gnu.org>
+;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
;;;
;;; This file is part of GNU Guix.
;;;
#:renamer (symbol-prefix-proc 'license:))
#:use-module (guix packages)
#:use-module (guix download)
+ #:use-module (guix utils)
+ #:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
+ #:use-module (gnu packages algebra)
+ #:use-module (gnu packages bison)
+ #:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
- #:use-module ((gnu packages gettext)
- #:renamer (symbol-prefix-proc 'gnu:))
+ #:use-module (gnu packages curl)
+ #:use-module (gnu packages elf)
+ #:use-module (gnu packages flex)
+ #:use-module (gnu packages fltk)
+ #:use-module (gnu packages fontutils)
+ #:use-module (gnu packages gettext)
+ #:use-module (gnu packages gcc)
+ #:use-module (gnu packages gd)
+ #:use-module (gnu packages ghostscript)
+ #:use-module (gnu packages gtk)
+ #:use-module (gnu packages less)
+ #:use-module (gnu packages xorg)
+ #:use-module (gnu packages gl)
+ #:use-module (gnu packages multiprecision)
+ #:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages python)
#:use-module (gnu packages readline)
+ #:use-module (gnu packages tcsh)
+ #:use-module (gnu packages texinfo)
+ #:use-module (gnu packages texlive)
#:use-module (gnu packages xml))
(define-public units
(package
(name "units")
- (version "2.01")
+ (version "2.11")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/units/units-" version
".tar.gz"))
(sha256 (base32
- "1wl8kaxgk4l5jgc1f71mx1rwa6ib84krjmzyzn2f987z1g3i52qk"))))
+ "1gjs3wc212aaiq4r76hx9nl1h3fa39n0ljwl9420d6ixl3rdmdjk"))))
(build-system gnu-build-system)
(synopsis "Conversion between thousands of scales")
(description
- "GNU Units converts quantities expressed in various systems of
-measurement to their equivalents in other systems of measurement. Like
-many similar programs, it can handle multiplicative scale changes. It can
-also handle nonlinear conversions such as Fahrenheit to Celsius or wire
-gauge, and it can convert from and to sums of units, such as converting
-between meters and feet plus inches.
-
-Beyond simple unit conversions, GNU Units can be used as a general-purpose
-scientific calculator that keeps track of units in its calculations. You
-can form arbitrary complex mathematical expressions of dimensions including
-sums, products, quotients, powers, and even roots of dimensions. Thus you
-can ensure accuracy and dimensional consistency when working with long
-expressions that involve many different units that may combine in complex
-ways.
-
-The units are defined in an external data file. You can use the extensive
-data file that comes with this program, or you can provide your own data
-file to suit your needs. You can also use your own data file to supplement
-the standard data file.")
+ "GNU Units converts numeric quantities between units of measure. It
+can handle scale changes through adaptive usage of standard scale prefixes
+(micro-, kilo-, etc.). It can also handle nonlinear conversions such as
+Fahrenheit to Celsius. Its interpreter is powerful enough to be used
+effectively as a scientific calculator.")
(license license:gpl3+)
(home-page "http://www.gnu.org/software/units/")))
(define-public gsl
(package
(name "gsl")
- (version "1.15")
+ (version "1.16")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "18qf6jzz1r3mzb5qynywv4xx3z9g61hgkbpkdrhbgqh2g7jhgfc5"))))
+ "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))))
(build-system gnu-build-system)
(arguments
- `(#:phases
+ `(#:parallel-tests? #f
+ #:phases
(alist-replace
'configure
(lambda* (#:key target system outputs #:allow-other-keys #:rest args)
(home-page "http://www.gnu.org/software/gsl/")
(synopsis "Numerical library for C and C++")
(description
- "The GNU Scientific Library (GSL) is a numerical library for C
-and C++ programmers. It is free software under the GNU General
-Public License.
+ "The GNU Scientific Library is a library for numerical analysis in C
+and C++. It includes a wide range of mathematical routines, with over 1000
+functions in total. Subject areas covered by the library include:
+differential equations, linear algebra, Fast Fourier Transforms and random
+numbers.")
+ (license license:gpl3+)))
-The library provides a wide range of mathematical routines such
-as random number generators, special functions and least-squares
-fitting. There are over 1000 functions in total with an
-extensive test suite.")
+(define-public glpk
+ (package
+ (name "glpk")
+ (version "4.54")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://gnu/glpk/glpk-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "18gr2anv8gyps6j9f22k7li6w07glvww666sdqblvlq2hh3whwmb"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("gmp" ,gmp)))
+ (arguments
+ `(#:configure-flags '("--with-gmp")))
+ (home-page "http://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),
+mixed integer programming (MIP), and other related problems. It supports the
+GNU MathProg modeling language, a subset of the AMPL language, and features a
+translator for the language. In addition to the C library, a stand-alone
+LP/MIP solver is included in the package.")
(license license:gpl3+)))
(define-public pspp
(package
(name "pspp")
- (version "0.8.0a")
+ (version "0.8.2")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "1pgkb3z8b4wk4gymnafclhkrqq7n05wq83mra3v53jdl6bnllmyq"))))
+ "1w7h3dglgx0jlq1wb605b8pgfsk2vr1q2q2rj7bsajh9ihbcsixr"))))
(build-system gnu-build-system)
(inputs
- `(("gettext" ,gnu:gettext)
+ `(("cairo" ,cairo)
+ ("fontconfig" ,fontconfig)
+ ("gettext" ,gnu-gettext)
("gsl" ,gsl)
("libxml2" ,libxml2)
+ ("pango" ,pango)
("readline" ,readline)
+ ("gtk" ,gtk+-2)
+ ("gtksourceview" ,gtksourceview)
("zlib" ,zlib)))
(native-inputs
`(("perl" ,perl)
("pkg-config" ,pkg-config)))
- (arguments
- `(#:configure-flags
- `("--without-cairo" ; FIXME: tests currently fail for lack of font
- "--without-gui"))) ; FIXME: package missing dependencies
(home-page "http://www.gnu.org/software/pspp/")
(synopsis "Statistical analysis")
(description
- "PSPP is a program for statistical analysis of sampled data. It is a
-free replacement for the proprietary program SPSS, and appears very similar
-to it.
+ "GNU PSPP is a statistical analysis program. It can perform
+descriptive statistics, T-tests, linear regression and non-parametric tests.
+It features both a graphical interface as well as command-line input. PSPP is
+designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data can
+be imported from spreadsheets, text files and database sources and it can be
+output in text, PostScript, PDF or HTML.")
+ (license license:gpl3+)))
+
+(define-public lapack
+ (package
+ (name "lapack")
+ (version "3.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://www.netlib.org/lapack/lapack-"
+ version ".tgz"))
+ (sha256
+ (base32
+ "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))
+ (build-system cmake-build-system)
+ (home-page "http://www.netlib.org/lapack/")
+ (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath
+ (inputs `(("fortran" ,gfortran-4.8)
+ ("python" ,python-2)))
+ (arguments
+ `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES")
+ #: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)))
+ (synopsis "Library for numerical linear algebra")
+ (description
+ "LAPACK is a Fortran 90 library for solving the most commonly occurring
+problems in numerical linear algebra.")
+ (license (license:bsd-style "file://LICENSE"
+ "See LICENSE in the distribution."))))
+
+(define-public gnuplot
+ (package
+ (name "gnuplot")
+ (version "4.6.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
+ version "/gnuplot-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1xd7gqdhlk7k1p9yyqf9vkk811nadc7m4si0q3nb6cpv4pxglpyz"))))
+ (build-system gnu-build-system)
+ (inputs `(("readline" ,readline)
+ ("cairo" ,cairo)
+ ("pango" ,pango)
+ ("gd" ,gd)))
+ (native-inputs `(("texlive" ,texlive)
+ ("pkg-config" ,pkg-config)))
+ (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"))))
+
+(define-public hdf5
+ (package
+ (name "hdf5")
+ (version "1.8.12")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-"
+ version ".tar.bz2"))
+ (sha256
+ (base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (alist-cons-before
+ 'configure 'patch-configure
+ (lambda _
+ (substitute* "configure"
+ (("/bin/mv") "mv")))
+ %standard-phases)))
+ (outputs '("out" "bin" "lib" "include"))
+ (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
+extremely large and complex data collections.")
+ (license (license:x11-style
+ "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
+
-PSPP can perform descriptive statistics, T-tests, anova, linear and logistic
-regression, cluster analysis, factor analysis, non-parametric tests and
-more. Its backend is designed to perform its analyses as fast as possible,
-regardless of the size of the input data. You can use PSPP with its
-graphical interface or the more traditional syntax commands.")
+;; For a fully featured Octave, users are strongly recommended also to install
+;; the following packages: texinfo, less, ghostscript, gnuplot.
+(define-public octave
+ (package
+ (name "octave")
+ (version "3.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://gnu/octave/octave-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0ks9pr154syw0vb3jn6xsnrkkrbvf9y7i7gaxa28rz6ngxbxvq9l"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("lapack" ,lapack)
+ ("readline" ,readline)
+ ("glpk" ,glpk)
+ ("curl" ,curl)
+ ("pcre" ,pcre)
+ ("fltk" ,fltk)
+ ("fontconfig" ,fontconfig)
+ ("freetype" ,freetype)
+ ("hdf5-lib" ,hdf5 "lib")
+ ("hdf5-include" ,hdf5 "include")
+ ("libxft" ,libxft)
+ ("mesa" ,mesa)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("gfortran" ,gfortran-4.8)
+ ("pkg-config" ,pkg-config)
+ ("perl" ,perl)
+ ;; The following inputs are not actually used in the build process. However, the
+ ;; ./configure gratuitously tests for their existence and assumes that programs not
+ ;; present at build time are also not, and can never be, available at run time!
+ ;; If these inputs are therefore not present, support for them will be built out.
+ ;; However, Octave 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"))))
+ (home-page "http://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 non-linear
+applications and it provides great support for visualizing results. Work may
+be performed both at the interactive command-line as well as via script
+files.")
(license license:gpl3+)))
+
+(define-public gmsh
+ (package
+ (name "gmsh")
+ (version "2.8.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-"
+ version "-source.tgz"))
+ (sha256
+ (base32 "0jv2yvk28w86rx5mvjkb0w12ff2jxih7axnpvznpd295lg5jg7hr"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Remove non-free METIS code
+ '(delete-file-recursively "contrib/Metis"))))
+ (build-system cmake-build-system)
+ (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath
+ (propagated-inputs
+ `(("fltk" ,fltk)
+ ("gfortran" ,gfortran-4.8)
+ ("gmp" ,gmp)
+ ("hdf5-lib" ,hdf5 "lib")
+ ("hdf5-include" ,hdf5 "include")
+ ("lapack" ,lapack)
+ ("mesa" ,mesa)
+ ("libx11" ,libx11)
+ ("libxext" ,libxext)))
+ (arguments
+ `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
+ "-DENABLE_BUILD_SHARED:BOOL=ON"
+ "-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
+CAD engine and post-processor. Its design goal is to provide a fast, light
+and user-friendly meshing tool with parametric input and advanced
+visualization capabilities. Gmsh is built around four modules: geometry,
+mesh, solver and post-processing. The specification of any input to these
+modules is done either interactively using the graphical user interface or in
+ASCII text files using Gmsh's own scripting language.")
+ (license license:gpl2+)))
+
+(define-public petsc
+ (package
+ (name "petsc")
+ (version "3.4.4")
+ (source
+ (origin
+ (method url-fetch)
+ ;; The *-lite-* tarball does not contain the *large* documentation
+ (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
+ "petsc-lite-" version ".tar.gz"))
+ (sha256
+ (base32 "0v5dg6dhdjpi5ianvd4mm6hsvxzv1bsxwnh9f9myag0a0d9xk9iv"))
+ (patches
+ (list (search-patch "petsc-fix-threadcomm.patch")))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("python" ,python-2)
+ ("perl" ,perl)))
+ (inputs
+ `(("gfortran" ,gfortran-4.8)
+ ("lapack" ,lapack)
+ ("superlu" ,superlu)
+ ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
+ ;; leaving out opengl, as configuration seems to only be for mac
+ ))
+ (arguments
+ `(#:test-target "test"
+ #:parallel-build? #f
+ #:configure-flags
+ `("--with-mpi=0"
+ "--with-openmp=1"
+ "--with-superlu=1"
+ ,(string-append "--with-superlu-include="
+ (assoc-ref %build-inputs "superlu") "/include")
+ ,(string-append "--with-superlu-lib="
+ (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
+ #:phases
+ (alist-replace
+ 'configure
+ ;; PETSc's configure script is actually a python script, so we can't
+ ;; run it with bash.
+ (lambda* (#:key outputs (configure-flags '())
+ #:allow-other-keys)
+ (let* ((prefix (assoc-ref outputs "out"))
+ (flags `(,(string-append "--prefix=" prefix)
+ ,@configure-flags)))
+ (format #t "build directory: ~s~%" (getcwd))
+ (format #t "configure flags: ~s~%" flags)
+ (zero? (apply system* "./configure" flags))))
+ (alist-cons-after
+ 'install 'clean-local-references
+ ;; Try to keep installed files from leaking build directory names.
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (fortran (assoc-ref inputs "gfortran")))
+ (substitute* (map (lambda (file)
+ (string-append out "/" file))
+ '("conf/petscvariables"
+ "conf/PETScConfig.cmake"
+ "include/petscconf.h"
+ "include/petscmachineinfo.h"))
+ (((getcwd)) out))
+ ;; Make compiler references point to the store
+ (substitute* (string-append out "/conf/petscvariables")
+ (("= g(cc|\\+\\+|fortran)" _ suffix)
+ (string-append "= " fortran "/bin/g" suffix)))
+ ;; PETSc installs some build logs, which aren't necessary.
+ (for-each (lambda (file)
+ (delete-file (string-append out "/" file)))
+ '("conf/configure.log"
+ "conf/make.log"
+ "conf/test.log"
+ "conf/RDict.db"
+ ;; Once installed, should uninstall with Guix
+ "conf/uninstall.py"))))
+ %standard-phases))))
+ (home-page "http://www.mcs.anl.gov/petsc")
+ (synopsis "Library to solve ODEs and algebraic equations")
+ (description "PETSc, pronounced PET-see (the S is silent), is a suite of
+data structures and routines for the scalable (parallel) solution of
+scientific applications modeled by partial differential equations.")
+ (license (license:bsd-style
+ "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
+
+(define-public petsc-complex
+ (package (inherit petsc)
+ (name "petsc-complex")
+ (arguments
+ (substitute-keyword-arguments (package-arguments petsc)
+ ((#:configure-flags cf)
+ `(cons "--with-scalar-type=complex" ,cf))))
+ (description
+ (string-append (package-description petsc)
+ " Complex scalar type version."))))
+
+(define-public superlu
+ (package
+ (name "superlu")
+ (version "4.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
+ "superlu_" version ".tar.gz"))
+ (sha256
+ (base32 "10b785s9s4x0m9q7ihap09275pq4km3k2hk76jiwdfdr5qr2168n"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("tcsh" ,tcsh)))
+ (inputs
+ `(("lapack" ,lapack)
+ ("gfortran" ,gfortran-4.8)))
+ (arguments
+ `(#:parallel-build? #f
+ #:tests? #f ;tests are run as part of `make all`
+ #:phases
+ (alist-replace
+ 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (call-with-output-file "make.inc"
+ (lambda (port)
+ (format port "
+PLAT =
+SuperLUroot = ~a
+SUPERLULIB = ~a/lib/libsuperlu.a
+TMGLIB = libtmglib.a
+BLASDEF = -DUSE_VENDOR_BLAS
+BLASLIB = -L~a/lib -lblas
+LIBS = $(SUPERLULIB) $(BLASLIB)
+ARCH = ar
+ARCHFLAGS = cr
+RANLIB = ranlib
+CC = gcc
+PIC = -fPIC
+CFLAGS = -O3 -DPRNTlevel=0 $(PIC)
+NOOPTS = -O0 $(PIC)
+FORTRAN = gfortran
+FFLAGS = -O2 $(PIC)
+LOADER = $(CC)
+CDEFS = -DAdd_"
+ (getcwd)
+ (assoc-ref outputs "out")
+ (assoc-ref inputs "lapack")))))
+ (alist-cons-before
+ 'build 'create-install-directories
+ (lambda* (#:key outputs #:allow-other-keys)
+ (for-each
+ (lambda (dir)
+ (mkdir-p (string-append (assoc-ref outputs "out")
+ "/" dir)))
+ '("lib" "include")))
+ (alist-replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Library is placed in lib during the build phase. Copy over
+ ;; headers to include.
+ (let* ((out (assoc-ref outputs "out"))
+ (incdir (string-append out "/include")))
+ (for-each (lambda (file)
+ (let ((base (basename file)))
+ (format #t "installing `~a' to `~a'~%"
+ base incdir)
+ (copy-file file
+ (string-append incdir "/" base))))
+ (find-files "SRC" ".*\\.h$"))))
+ %standard-phases)))))
+ (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
+ (synopsis "Supernodal direct solver for sparse linear systems")
+ (description
+ "SuperLU is a general purpose library for the direct solution of large,
+sparse, nonsymmetric systems of linear equations on high performance machines.
+The library is written in C and is callable from either C or Fortran. The
+library routines perform an LU decomposition with partial pivoting and
+triangular system solves through forward and back substitution. The library
+also provides threshold-based ILU factorization preconditioners.")
+ (license license:bsd-3)))
HCoop / jackhill / guix / guix.git / blobdiff