diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 273 |
1 files changed, 183 insertions, 90 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 1bf049fc4c..c3c2191a94 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2013, 2014, 2015, 2016 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 Eric Bavier <bavier@member.fsf.org> +;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch> ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org> ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> @@ -18,6 +18,7 @@ ;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com> ;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net> ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com> +;;; Copyright © 2017 Theodoros Foradis <theodoros.for@openmailbox.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -316,7 +317,7 @@ the OCaml language.") (define-public glpk (package (name "glpk") - (version "4.62") + (version "4.63") (source (origin (method url-fetch) @@ -324,7 +325,7 @@ the OCaml language.") version ".tar.gz")) (sha256 (base32 - "0w7s3869ybwyq9a4490dikpib1qp3jnn5nqz1vvwqy1qz3ilnvh9")))) + "1xp7nclmp8inp20968bvvfcwmz3mz03sbm0v3yjz8aqwlpqjfkci")))) (build-system gnu-build-system) (inputs `(("gmp" ,gmp))) @@ -437,7 +438,7 @@ large scale eigenvalue problems.") version ".tgz")) (sha256 (base32 - "0yavf6m9l78pwlnk5g61cg8x28mr30j0g8gkai0jrdqfjjmf3whs")))) + "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign")))) (build-system cmake-build-system) (home-page "http://www.netlib.org/lapack/") (inputs `(("fortran" ,gfortran) @@ -560,18 +561,17 @@ computations.") (define-public hdf4 (package (name "hdf4") - (version "4.2.12") + (version "4.2.13") (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")) + (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm")) (patches (search-patches "hdf4-architectures.patch" "hdf4-reproducibility.patch" "hdf4-shared-fortran.patch")))) - (build-system gnu-build-system) (native-inputs `(("gfortran" ,gfortran) @@ -585,6 +585,14 @@ computations.") #:configure-flags '("--enable-shared") #:phases (modify-phases %standard-phases + ;; This is inspired by two of Debian's patches. + (add-before 'configure 'add-more-aarch64-support + (lambda _ + (substitute* '("mfhdf/ncgen/ncgen.l" + "mfhdf/ncgen/ncgenyy.c" + "mfhdf/libsrc/netcdf.h.in") + (("AIX5L64") "__aarch64__")) + #t)) (add-before 'configure 'patchbuild (lambda _ (substitute* @@ -596,7 +604,8 @@ computations.") -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\\)") ""))))))) +-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")) + #t))))) (home-page "https://www.hdfgroup.org/products/hdf4/") (synopsis "Library and multi-object file format for storing and managing data") @@ -1216,7 +1225,7 @@ September 2004}") (define-public petsc (package (name "petsc") - (version "3.7.2") + (version "3.7.6") (source (origin (method url-fetch) @@ -1224,7 +1233,7 @@ September 2004}") (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" "petsc-lite-" version ".tar.gz")) (sha256 - (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d")))) + (base32 "1y3f5jjq0v5b62i3sabp4kp5mgfyp3vnk0dxhwkrhpypax77nzxh")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2) @@ -1247,6 +1256,10 @@ September 2004}") (assoc-ref %build-inputs "superlu") "/include") ,(string-append "--with-superlu-lib=" (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) + #:make-flags + ;; Honor (parallel-job-count) for build. Do not use --with-make-np, + ;; whose value is dumped to $out/lib/petsc/conf/petscvariables. + (list (format #f "MAKE_NP=~a" (parallel-job-count))) #:phases (modify-phases %standard-phases (replace 'configure @@ -1261,13 +1274,17 @@ September 2004}") (format #t "configure flags: ~s~%" flags) (zero? (apply system* "./configure" flags))))) (add-after 'configure 'clean-local-references - (lambda* (#:key inputs outputs #:allow-other-keys) + (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (substitute* (find-files "." "^petsc(conf|machineinfo).h$") ;; Prevent build directory from leaking into compiled code (((getcwd)) out) ;; Scrub timestamp for reproducibility ((".*Libraries compiled on.*") "")) + (substitute* (find-files "." "petscvariables") + ;; Do not expose build machine characteristics, set to defaults. + (("MAKE_NP = [:digit:]+") "MAKE_NP = 2") + (("NPMAX = [:digit:]+") "NPMAX = 2")) #t))) (add-after 'install 'clean-install ;; Try to keep installed files from leaking build directory names. @@ -1342,16 +1359,15 @@ scientific applications modeled by partial differential equations.") (define-public slepc (package (name "slepc") - (version "3.7.1") + (version "3.7.4") (source (origin (method url-fetch) - (uri (string-append "http://slepc.upv.es/download/download.php?" - "filename=slepc-" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (string-append "http://slepc.upv.es/download/distrib/slepc-" + version ".tar.gz")) (sha256 (base32 - "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7")))) + "12pbl8yd6r8k9xjlr1qw25rs0k1acgic7hw1s6l6bhiv9s285drg")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) @@ -1365,6 +1381,8 @@ scientific applications modeled by partial differential equations.") #:configure-flags `(,(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))) #:phases (modify-phases %standard-phases (replace 'configure @@ -1626,12 +1644,12 @@ programming problems.") (define-public r-pracma (package (name "r-pracma") - (version "2.0.4") + (version "2.0.7") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "1z3i90mkzwvp9di17caf4934z2xlb2imm3hwxllcrbwvmnmhrwyc")))) + (base32 "0hxa0rbbp54j0c05qj7vfwhqfdmiz5ax8vhqxd09g33x7c0hqbc5")))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog))) @@ -1850,7 +1868,7 @@ implemented in ANSI C, and MPI for communications.") (build-system gnu-build-system) (inputs `(("zlib" ,zlib) - ("flex" ,flex-2.6.1) ; A bug in flex prevents building with flex-2.6.3. + ("flex" ,flex) ("bison" ,bison))) (arguments `(#:phases @@ -2075,8 +2093,7 @@ to BMP, JPEG or PNG image formats.") (patches (search-patches "maxima-defsystem-mkdir.patch")))) (build-system gnu-build-system) (inputs - `(("gcc" ,gcc) - ("gcl" ,gcl) + `(("gcl" ,gcl) ("gnuplot" ,gnuplot) ;for plots ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima' (native-inputs @@ -2100,13 +2117,6 @@ to BMP, JPEG or PNG image formats.") #:make-flags (list "TMPDIR=/tmp") #:phases (modify-phases %standard-phases - (add-before 'configure 'set-gcc-path - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "lisp-utils/defsystem.lisp" - (("\\(defparameter \\*c-compiler\\* \"gcc\"\\)") - (string-append "(defparameter *c-compiler* \"" - (assoc-ref inputs "gcc") "/bin/gcc\")"))) - #t)) (add-before 'check 'pre-check (lambda _ (chmod "src/maxima" #o555) @@ -2118,7 +2128,9 @@ to BMP, JPEG or PNG image formats.") (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))) + (datadir (string-append out "/share/maxima/" ,version)) + (binutils (string-append (assoc-ref inputs "binutils") + "/bin"))) (with-directory-excursion out (mkdir-p "share/emacs") (mkdir-p "share/doc") @@ -2134,7 +2146,11 @@ to BMP, JPEG or PNG image formats.") (format out "~a ~s~a~%" "(setf $gnuplot_command " (string-append gnuplot "/bin/gnuplot") ")") - (dump-port in out))))) + (dump-port in out)))) + ;; Ensure that Maxima will have access to the GNU binutils + ;; components at runtime. + (wrap-program (string-append out "/bin/maxima") + `("PATH" prefix (,binutils)))) #t))))) (home-page "http://maxima.sourceforge.net") (synopsis "Numeric and symbolic expression manipulation") @@ -2152,7 +2168,7 @@ point numbers.") (define-public wxmaxima (package (name "wxmaxima") - (version "17.05.0") + (version "17.05.1") (source (origin (method url-fetch) @@ -2161,7 +2177,7 @@ point numbers.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1bsyd7r12xm2crpizb9iyyki3j0mbazzzwbsh871m06dv2wk97gq")))) + "0dv0cy0cf46v0cbw32izscpkdmpxg1qhwq1f4cz46kkqd8k4yfbj")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) @@ -2175,31 +2191,30 @@ point numbers.") ("gtk+" ,gtk+) ("shared-mime-info" ,shared-mime-info))) (arguments - `(#:phases (modify-phases %standard-phases - (add-before - 'configure 'autoconf - (lambda _ - (zero? (system* "./bootstrap")))) - (add-after - 'install 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - (wrap-program (string-append (assoc-ref outputs "out") - "/bin/wxmaxima") - `("PATH" ":" prefix - (,(string-append (assoc-ref inputs "maxima") - "/bin"))) - ;; For GtkFileChooserDialog. - `("GSETTINGS_SCHEMA_DIR" = - (,(string-append (assoc-ref inputs "gtk+") - "/share/glib-2.0/schemas"))) - `("XDG_DATA_DIRS" ":" prefix - (;; Needed by gdk-pixbuf to know supported icon formats. - ,(string-append - (assoc-ref inputs "shared-mime-info") "/share") - ;; The default icon theme of GTK+. - ,(string-append - (assoc-ref inputs "adwaita-icon-theme") "/share")))) - #t))))) + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'autoconf + (lambda _ + (zero? (system* "sh" "bootstrap")))) + (add-after 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (wrap-program (string-append (assoc-ref outputs "out") + "/bin/wxmaxima") + `("PATH" ":" prefix + (,(string-append (assoc-ref inputs "maxima") + "/bin"))) + ;; For GtkFileChooserDialog. + `("GSETTINGS_SCHEMA_DIR" = + (,(string-append (assoc-ref inputs "gtk+") + "/share/glib-2.0/schemas"))) + `("XDG_DATA_DIRS" ":" prefix + (;; Needed by gdk-pixbuf to know supported icon formats. + ,(string-append + (assoc-ref inputs "shared-mime-info") "/share") + ;; The default icon theme of GTK+. + ,(string-append + (assoc-ref inputs "adwaita-icon-theme") "/share")))) + #t))))) (home-page "https://andrejv.github.io/wxmaxima/") (synopsis "Graphical user interface for the Maxima computer algebra system") (description @@ -2417,7 +2432,7 @@ Fresnel integrals, and similar related functions as well.") (define-public suitesparse (package (name "suitesparse") - (version "4.4.3") + (version "4.5.5") (source (origin (method url-fetch) @@ -2426,33 +2441,31 @@ Fresnel integrals, and similar related functions as well.") version ".tar.gz")) (sha256 (base32 - "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5")))) + "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr")) + (modules '((guix build utils))) + (snippet + ;; Remove bundled metis source + '(delete-file-recursively "metis-5.1.0")))) (build-system gnu-build-system) (arguments - '(#:parallel-build? #f ;cholmod build fails otherwise - #:tests? #f ;no "check" target + '(#:tests? #f ;no "check" target #:make-flags (list "CC=gcc" "BLAS=-lblas" "TBB=-ltbb" - "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used + "MY_METIS_LIB=-lmetis" (string-append "INSTALL_LIB=" (assoc-ref %outputs "out") "/lib") (string-append "INSTALL_INCLUDE=" - (assoc-ref %outputs "out") "/include")) + (assoc-ref %outputs "out") "/include") + "library") #:phases - (alist-cons-before - 'install 'prepare-out - ;; README.txt states that the target directories must exist prior to - ;; running "make install". - (lambda _ - (mkdir-p (string-append (assoc-ref %outputs "out") "/lib")) - (mkdir-p (string-append (assoc-ref %outputs "out") "/include"))) - ;; no configure script - (alist-delete 'configure %standard-phases)))) + (modify-phases %standard-phases + (delete 'configure)))) ;no configure script (inputs `(("tbb" ,tbb) - ("lapack" ,lapack))) + ("lapack" ,lapack) + ("metis" ,metis))) (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html") (synopsis "Suite of sparse matrix software") (description @@ -2688,7 +2701,7 @@ revised simplex and the branch-and-bound methods.") (define-public dealii (package (name "dealii") - (version "8.4.1") + (version "8.5.0") (source (origin (method url-fetch) @@ -2696,7 +2709,7 @@ revised simplex and the branch-and-bound methods.") "download/v" version "/dealii-" version ".tar.gz")) (sha256 (base32 - "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800")) + "0yfpy4zh8j7hmqakw17zdlmvfdcmhwgs66wcb716plc4y7v3z4g6")) (modules '((guix build utils))) (snippet ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost @@ -2715,21 +2728,10 @@ revised simplex and the branch-and-bound methods.") ("suitesparse" ,suitesparse))) ;for UMFPACK (arguments `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease - #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure - #:phases (modify-phases %standard-phases - (add-after - 'install 'hint-example-prefix - ;; Set Cmake hints in examples so that they can find this - ;; deal.II when configuring. - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref %outputs "out")) - (exmpl (string-append out "/share/doc" - "/dealii/examples"))) - (substitute* (find-files exmpl "CMakeLists.txt") - (("([[:space:]]*HINTS.*)\n" _ line) - (string-append line " $ENV{HOME}/.guix-profile " - out "\n"))) - #t)))))) + #:configure-flags + ;; Work around a bug in libsuitesparseconfig linking + ;; see https://github.com/dealii/dealii/issues/4745 + '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON"))) (home-page "https://www.dealii.org") (synopsis "Finite element library") (description @@ -3069,6 +3071,8 @@ instruction sets. Thus, an application written with Vc can be compiled for: @item NVIDIA GPUs / CUDA (in development) @end enumerate\n") (home-page "https://github.com/VcDevel/Vc") + ;; "No support_???.cpp file exists for this architecture." + (supported-systems '("x86_64-linux" "i686-linux")) (license license:bsd-3))) (define-public reducelcs @@ -3163,3 +3167,92 @@ as equations, scalars, vectors, and matrices.") (home-page "https://www.gnu.org/software/jacal/") (license license:gpl3+))) +(define-public z3 + (package + (name "z3") + (version "4.5.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/Z3Prover/z3/archive/z3-" + version ".tar.gz")) + (sha256 + (base32 + "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DBUILD_PYTHON_BINDINGS=true" + "-DINSTALL_PYTHON_BINDINGS=true" + (string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR=" + %output + "/lib/python2.7/site-packages") + (string-append "-DCMAKE_INSTALL_LIBDIR=" + %output + "/lib")) + + #:phases + (modify-phases %standard-phases + (add-before 'configure 'bootstrap + (lambda _ + (zero? + (system* "python" "contrib/cmake/bootstrap.py" "create")))) + (add-before 'check 'make-test-z3 + (lambda _ + ;; Build the test suite executable. + (zero? (system* "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"))))))) + (native-inputs + `(("python" ,python-2))) + (synopsis "Theorem prover") + (description "Z3 is a theorem prover and @dfn{satisfiability modulo +theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.") + (home-page "https://github.com/Z3Prover/z3") + (license license:expat))) + +(define-public cubicle + (package + (name "cubicle") + (version "1.1.1") + (source (origin + (method url-fetch) + (uri (string-append "http://cubicle.lri.fr/cubicle-" + version ".tar.gz")) + (sha256 + (base32 + "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h")))) + (build-system gnu-build-system) + (native-inputs + `(("ocaml" ,ocaml) + ("which" ,(@@ (gnu packages base) which)))) + (propagated-inputs + `(("z3" ,z3))) + (arguments + `(#:configure-flags (list "--with-z3") + #:tests? #f + #:phases + (modify-phases %standard-phases + (add-before 'configure 'configure-for-release + (lambda _ + (substitute* "Makefile.in" + (("SVNREV=") "#SVNREV=")))) + (add-before 'configure 'fix-/bin/sh + (lambda _ + (substitute* "configure" + (("/bin/sh") (which "sh"))))) + (add-before 'configure 'fix-smt-z3wrapper.ml + (lambda _ + (substitute* "Makefile.in" + (("\\\\n") ""))))))) + (home-page "http://cubicle.lri.fr/") + (synopsis "Model checker for array-based systems") + (description "Cubicle is an open source model checker for verifying safety +properties of array-based systems. This is a syntactically restricted class of +parametrized transition systems with states represented as arrays indexed by an +arbitrary number of processes. Cache coherence protocols and mutual exclusion +algorithms are typical examples of such systems.") + (license license:asl2.0))) |