;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2014 John Darrington <jmd@gnu.org>
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
+;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
;;;
;;; This file is part of GNU Guix.
;;;
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages maths)
+ #:use-module (ice-9 regex)
#:use-module (gnu packages)
- #:use-module ((guix licenses)
- #:renamer (symbol-prefix-proc 'license:))
+ #:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix utils)
#:use-module (gnu packages python)
#:use-module (gnu packages readline)
#:use-module (gnu packages tcsh)
+ #:use-module (gnu packages tcl)
#:use-module (gnu packages texinfo)
#:use-module (gnu packages texlive)
#:use-module (gnu packages xml))
(license license:gpl3+)
(home-page "http://www.gnu.org/software/units/")))
+(define-public dionysus
+ (package
+ (name "dionysus")
+ (version "1.3.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://gnu/dionysus/dionysus-" version
+ ".tar.gz"))
+ (sha256
+ (base32
+ "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
+ (build-system gnu-build-system)
+ (inputs `(("tcl" ,tcl))) ;for 'tclsh'
+ (synopsis "Local search for universal constants and scientific values")
+ (description
+ "GNU Dionysus is a convenient system for quickly retrieving the values of
+mathematical constants used in science and engineering. Values can be
+searched using a simple command-line tool, choosing from three databases:
+universal constants, atomic numbers, and constants related to
+semiconductors.")
+ (license license:gpl3+)
+ (home-page "http://www.gnu.org/software/dionysus/")))
+
(define-public gsl
(package
(name "gsl")
(define-public pspp
(package
(name "pspp")
- (version "0.8.3")
+ (version "0.8.4")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "0vri2pzvmm38qaihfvwlry30f40lcnps4blg59ixic4q20ldxf5d"))))
+ "0b65q45x05ps95pph6glbg7ymdr638nfb0rk9x5x9qm5k073pk5z"))))
(build-system gnu-build-system)
(inputs
`(("cairo" ,cairo)
(synopsis "Statistical analysis")
(description
"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.")
+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
(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
+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
+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.
%standard-phases)))
(outputs '("out" "bin" "lib" "include"))
(home-page "http://www.hdfgroup.org")
- (synopsis "Management suite for extremely large and complex data")
+ (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
(define-public petsc-complex
(package (inherit petsc)
+ (location (source-properties->location (current-source-location)))
(name "petsc-complex")
(arguments
(substitute-keyword-arguments (package-arguments petsc)
(define-public maxima
(package
(name "maxima")
- (version "5.33.0")
+ (version "5.34.1")
(source
(origin
(method url-fetch)
version "-source/" name "-" version ".tar.gz"))
(sha256
(base32
- "13axm11xw0f3frx5b0qdidi7igkn1524fzz77s9rbpl2yy2nrbz2"))))
+ "1dw9vfzldpj7lv303xbw0wpyn6ra6i2yzwlrjbcx7j0jm5n43ji0"))))
(build-system gnu-build-system)
+ (inputs
+ `(("gcl" ,gcl)
+ ("gnuplot" ,gnuplot) ;for plots
+ ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
+ (native-inputs
+ `(("texinfo" ,texinfo)
+ ("perl" ,perl)))
(arguments
- `(#:phases (alist-cons-before
+ `(#:configure-flags
+ (list "--enable-gcl"
+ (string-append "--with-posix-shell="
+ (assoc-ref %build-inputs "bash")
+ "/bin/sh")
+ (string-append "--with-wish="
+ (assoc-ref %build-inputs "tk")
+ "/bin/wish"
+ (let ((v ,(package-version tk)))
+ (string-take v (string-index-right v #\.)))))
+ ;; By default Maxima attempts to write temporary files to
+ ;; '/tmp/nix-build-maxima-5.34.1', which doesn't exist. Work around
+ ;; that.
+ #:make-flags (list "TMPDIR=/tmp")
+ #:phases (alist-cons-before
'check 'pre-check
- (lambda _
+ (lambda _
(chmod "src/maxima" #o555))
- %standard-phases)))
- (inputs
- `(("gcl" ,gcl)))
- (native-inputs
- `(("texinfo" ,texinfo)
- ("perl" ,perl)))
+ ;; Make sure the doc and emacs files are found in the
+ ;; standard location. Also configure maxima to find gnuplot
+ ;; without having it on the PATH.
+ (alist-cons-after
+ 'install 'post-install
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ (let* ((gnuplot (assoc-ref inputs "gnuplot"))
+ (out (assoc-ref outputs "out"))
+ (datadir (string-append out "/share/maxima/" ,version)))
+ (with-directory-excursion out
+ (mkdir-p "share/emacs")
+ (mkdir-p "share/doc")
+ (symlink
+ (string-append datadir "/emacs/")
+ (string-append out "/share/emacs/site-lisp"))
+ (symlink
+ (string-append datadir "/doc/")
+ (string-append out "/share/doc/maxima"))
+ (with-atomic-file-replacement
+ (string-append datadir "/share/maxima-init.lisp")
+ (lambda (in out)
+ (format out "~a ~s~a~%"
+ "(setf $gnuplot_command "
+ (string-append gnuplot "/bin/gnuplot") ")")
+ (dump-port in out))))))
+ %standard-phases))))
(home-page "http://maxima.sourceforge.net")
(synopsis "Numeric and symbolic expression manipulation")
(description "Maxima is a system for the manipulation of symbolic and
;; version (which implicitly means gpl1+).
;; At least one file (src/maxima.asd) says "version 2."
;; GPLv2 only is therefore the smallest subset.
- (license license:gpl2)))
+ (license license:gpl2)))
+
+(define-public atlas
+ (package
+ (name "atlas")
+ (version "3.10.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/math-atlas/atlas"
+ version ".tar.bz2"))
+ (sha256
+ (base32
+ "0bqh4bdnjdyww4mcpg6kn0x7338mfqbdgysn97dzrwwb26di7ars"))))
+ (build-system gnu-build-system)
+ (home-page "http://math-atlas.sourceforge.net/")
+ (inputs `(("gfortran" ,gfortran-4.8)
+ ("lapack-tar" ,(package-source lapack))))
+ (outputs '("out" "doc"))
+ (arguments
+ `(#:parallel-build? #f
+ #:parallel-tests? #f
+
+ ;; ATLAS tunes itself for the machine it is built on, as explained at
+ ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
+ ;; For this reason, we want users to build it locally instead of using
+ ;; substitutes.
+ #:substitutable? #f
+
+ #:modules ((srfi srfi-26)
+ (srfi srfi-1)
+ (guix build gnu-build-system)
+ (guix build utils))
+ #:configure-flags
+ `(;; Generate position independent code suitable for dynamic libraries
+ ;; and use WALL timer to get more accurate timing.
+ "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
+ ;; Set word width.
+ "-b"
+ ,,(if (string-match "64" (%current-system))
+ "64"
+ "32")
+ ;; Disable parallel build as it gives errors: atlas_pthread.h is
+ ;; needed to compile C files before it is generated.
+ "-Ss" "pmake" "make -j 1"
+ ;; Probe is failing for MIPS. We therefore define the system
+ ;; architecture explicitly by setting (-A) MACHINETYPE = 49
+ ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
+ ,,@(if (string-prefix? "mips" (%current-system))
+ (list "-A" "49" "-V" "1")
+ (list))
+ ;; Generate shared libraries.
+ "--shared"
+ ;; Build a full LAPACK library.
+ ,(string-append "--with-netlib-lapack-tarfile="
+ (assoc-ref %build-inputs "lapack-tar")))
+ #:phases
+ (alist-cons-after
+ 'install 'install-doc
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ (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" ".*"))))
+ (alist-cons-after
+ 'check 'check-pt
+ (lambda _ (zero? (system* "make" "ptcheck")))
+ ;; Fix files required to run configure.
+ (alist-cons-before
+ 'configure 'fix-/bin/sh
+ (lambda _
+ ;; Use `sh', not `/bin/sh'.
+ (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
+ (("/bin/sh")
+ "sh")))
+ ;; Fix /bin/sh in generated make files.
+ (alist-cons-after
+ 'configure 'fix-/bin/sh-in-generated-files
+ (lambda _
+ (substitute* (find-files "." "^[Mm]ake\\.inc.*")
+ (("/bin/sh")
+ "sh")))
+ ;; ATLAS configure program does not accepts the default flags
+ ;; passed by the 'gnu-build-system'.
+ (alist-replace
+ 'configure
+ (lambda* (#:key native-inputs inputs outputs
+ (configure-flags '())
+ #:allow-other-keys #:rest args)
+ (let* ((prefix (assoc-ref outputs "out"))
+ (bash (or (and=> (assoc-ref
+ (or native-inputs inputs) "bash")
+ (cut string-append <> "/bin/bash"))
+ "/bin/sh"))
+ (flags `(,(string-append "--prefix=" prefix)
+ ,@configure-flags))
+ (abs-srcdir (getcwd))
+ (srcdir (string-append "../" (basename abs-srcdir))))
+ (format #t "source directory: ~s (relative from build: ~s)~%"
+ abs-srcdir srcdir)
+ (mkdir "../build")
+ (chdir "../build")
+ (format #t "build directory: ~s~%" (getcwd))
+ (format #t "configure flags: ~s~%" flags)
+ (zero? (apply system* bash
+ (string-append srcdir "/configure")
+ flags))))
+ %standard-phases)))))))
+ (synopsis "Automatically Tuned Linear Algebra Software")
+ (description
+ "ATLAS is an automatically tuned linear algebra software library
+providing C and Fortran77 interfaces to a portably efficient BLAS
+implementation, as well as a few routines from LAPACK.
+
+Optimization occurs at build time. For this reason, the library is built on
+the machine where it is installed, without resorting to pre-built substitutes.
+
+Before building the library, CPU throttling should be disabled. This can be
+done in the BIOS, or, on GNU/Linux, with the following commands:
+
+cpufreq-selector -g performance -c 0
+...
+cpufreq-selector -g performance -c N-1
+
+where N is the number of cores of your CPU. Failure to do so will result in a
+library with poor performance.")
+ (license license:bsd-3)))
HCoop / jackhill / guix / guix.git / blobdiff