diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 251 |
1 files changed, 186 insertions, 65 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index aa9c7478b7..96a1ecb043 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -28,6 +28,7 @@ ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com> ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2018 Eric Brown <brown@fastmail.com> +;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> ;;; ;;; This file is part of GNU Guix. ;;; @@ -286,13 +287,13 @@ programming language.") (define-public units (package (name "units") - (version "2.17") + (version "2.18") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/units/units-" version ".tar.gz")) (sha256 (base32 - "1n2xzpnxfn475zkd8rzs5gg58xszjbr4bdbgvk6hryzimvwwj0qz")))) + "0y26kj349i048y4z3xrk90bvciw2j6ds3rka7r7yn3183hirr5b4")))) (build-system gnu-build-system) (inputs `(("readline" ,readline) @@ -884,6 +885,25 @@ extremely large and complex data collections.") (license (license:x11-style "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) +(define-public hdf5-1.10 + (package (inherit hdf5) + (version "1.10.4") + (source + (origin + (method url-fetch) + (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/" + "hdf5-" (version-major+minor version) + "/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 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj")) + (patches (list (search-patch "hdf5-config-date.patch"))))))) + (define-public hdf-java (package (name "hdf-java") @@ -1393,9 +1413,9 @@ can solve two kinds of problems: ;; For a fully featured Octave, users are strongly recommended also to install ;; the following packages: less, ghostscript, gnuplot. -(define-public octave +(define-public octave-cli (package - (name "octave") + (name "octave-cli") (version "4.4.1") (source (origin @@ -1477,21 +1497,21 @@ Work may be performed both at the interactive command-line as well as via script files.") (license license:gpl3+))) -(define-public qtoctave - (package (inherit octave) - (name "qtoctave") +(define-public octave + (package (inherit octave-cli) + (name "octave") (source (origin - (inherit (package-source octave)))) + (inherit (package-source octave-cli)))) (inputs `(("qscintilla" ,qscintilla) ("qt" ,qtbase) - ,@(package-inputs octave))) + ,@(package-inputs octave-cli))) (native-inputs `(("qttools" , qttools) ;for lrelease ("texlive" ,texlive) ;for texi2dvi - ,@(package-native-inputs octave))) + ,@(package-native-inputs octave-cli))) (arguments - (substitute-keyword-arguments (package-arguments octave) + (substitute-keyword-arguments (package-arguments octave-cli) ((#:phases phases) `(modify-phases ,phases (add-before 'configure 'patch-qscintilla-library-name @@ -1505,6 +1525,9 @@ script files.") "qscintilla2_qt5")) #t)))))))) +(define-public qtoctave + (deprecated-package "qtoctave" octave)) + (define-public opencascade-oce (package (name "opencascade-oce") @@ -1635,7 +1658,7 @@ September 2004}") (define-public petsc (package (name "petsc") - (version "3.9.3") + (version "3.10.2") (source (origin (method url-fetch) @@ -1643,7 +1666,7 @@ September 2004}") (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" "petsc-lite-" version ".tar.gz")) (sha256 - (base32 "1fwkbwv4g7zf2lc8fw865xd0bl9anb6jaczfis5dff7h449gwa48")))) + (base32 "0bl64pydak3rblnjffi482r8bin4xim9sb37ksl2jkcxf0i0irsi")))) (outputs '("out" ;libraries and headers "examples")) ;~30MiB of examples (build-system gnu-build-system) @@ -1747,16 +1770,18 @@ scientific applications modeled by partial differential equations.") (name "petsc-openmpi") (inputs `(("hdf5" ,hdf5-parallel-openmpi) + ("hypre" ,hypre-openmpi) ("metis" ,metis) ("mumps" ,mumps-openmpi) ("openmpi" ,openmpi) ("scalapack" ,scalapack) - ("scotch" ,pt-scotch) + ("scotch" ,pt-scotch32) ,@(package-inputs petsc))) (arguments (substitute-keyword-arguments (package-arguments petsc) ((#:configure-flags cf) - ``("--with-mpiexec=mpirun" + ``("--with-hypre=1" + "--with-mpiexec=mpirun" "--with-metis=1" "--with-mumps=1" "--with-scalapack=1" @@ -1789,6 +1814,41 @@ scientific applications modeled by partial differential equations.") ,@(delete "--with-mpi=0" ,cf))))) (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) +(define-public python-petsc4py + (package + (name "python-petsc4py") + (version "3.10.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "petsc4py" version)) + (sha256 + (base32 + "0ch3g6dsvxl7qi984fcssv7cxfbif4bw04gkvxl2l1b8wrmvrm25")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'pre-build + (lambda _ + ;; Define path to PETSc installation. + (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) + #t)) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) + (inputs + `(("petsc" ,petsc-openmpi) + ("python-numpy" ,python-numpy))) + (home-page "https://bitbucket.org/petsc/petsc4py/") + (synopsis "Python bindings for PETSc") + (description "PETSc, the Portable, Extensible Toolkit for +Scientific Computation, is a suite of data structures and routines for +the scalable (parallel) solution of scientific applications modeled by +partial differential equations. It employs the MPI standard for all +message-passing communication. @code{petsc4py} provides Python +bindings to almost all functions of PETSc.") + (license license:bsd-3))) + (define-public python-kiwisolver (package (name "python-kiwisolver") @@ -1816,7 +1876,7 @@ savings are consistently > 5x.") (define-public slepc (package (name "slepc") - (version "3.9.2") + (version "3.10.1") (source (origin (method url-fetch) @@ -1824,7 +1884,7 @@ savings are consistently > 5x.") version ".tar.gz")) (sha256 (base32 - "0gmhdqac8zm3jx43h935z7bflazjnpvqxjv4jh5za2y1z2rqax94")))) + "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) @@ -1920,6 +1980,43 @@ arising after the discretization of partial differential equations.") ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi)))) (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)"))) +(define-public python-slepc4py + (package + (name "python-slepc4py") + (version "3.10.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "slepc4py" version)) + (sha256 + (base32 + "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'pre-build + (lambda _ + ;; Define path to PETSc installation. + (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) + ;; Define path to SLEPc installation. + (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc")) + #t)) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) + (inputs + `(("python-numpy" ,python-numpy) + ("python-petsc4py" ,python-petsc4py) + ("slepc" ,slepc-openmpi))) + (home-page "https://bitbucket.org/slepc/slepc4py/") + (synopsis "Python bindings for SLEPc") + (description "SLEPc, the Scalable Library for Eigenvalue Problem +Computations, is based on PETSc, the Portable, Extensible Toolkit for +Scientific Computation. It employs the MPI standard for all +message-passing communication. @code{slepc4py} provides Python +bindings to almost all functions of SLEPc.") + (license license:bsd-3))) + (define-public mumps (package (name "mumps") @@ -2110,16 +2207,14 @@ programming problems.") (define-public r-pracma (package (name "r-pracma") - (version "2.1.5") + (version "2.1.8") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "18cv7c2gvagbmggfbsy2xk9bpn47izd0qrmqnc3q7afvj6pr6nf9")))) + (base32 "0m8ladhrfyxwybblkcdgg4xv1mk5kibmwarpj2k0c2y34zzcix4z")))) (build-system r-build-system) - (propagated-inputs - `(("r-quadprog" ,r-quadprog))) - (home-page "https://cran.r-project.org/web/packages/pracma") + (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") (description "This package provides functions for numerical analysis and linear algebra, numerical optimization, differential equations, plus some @@ -2510,15 +2605,16 @@ YACC = bison -pscotchyy -y -b y (replace 'build (lambda _ - (and - (zero? (system* "make" - (format #f "-j~a" (parallel-job-count)) - "ptscotch" "ptesmumps")) - ;; Install the serial metis compatibility library - (zero? (system* "make" "-C" "libscotchmetis" "install"))))) - (replace - 'check - (lambda _ (zero? (system* "make" "ptcheck")))))))) + (invoke "make" (format #f "-j~a" (parallel-job-count)) + "ptscotch" "ptesmumps") + + ;; Install the serial metis compatibility library + (invoke "make" "-C" "libscotchmetis" "install"))) + (add-before 'check 'mpi-setup + ,%openmpi-setup) + (replace 'check + (lambda _ + (invoke "make" "ptcheck"))))))) (synopsis "Programs and libraries for graph algorithms (with MPI)"))) (define-public pt-scotch32 @@ -2532,15 +2628,15 @@ YACC = bison -pscotchyy -y -b y `(modify-phases ,scotch32-phases (replace 'build (lambda _ - (and - (zero? (system* "make" - (format #f "-j~a" (parallel-job-count)) - "ptscotch" "ptesmumps")) - ;; Install the serial metis compatibility library - (zero? (system* "make" "-C" "libscotchmetis" "install"))))) + (invoke "make" (format #f "-j~a" (parallel-job-count)) + "ptscotch" "ptesmumps") + ;; Install the serial metis compatibility library + (invoke "make" "-C" "libscotchmetis" "install"))) + (add-before 'check 'mpi-setup + ,%openmpi-setup) (replace 'check (lambda _ - (zero? (system* "make" "ptcheck")))))))) + (invoke "make" "ptcheck"))))))) (synopsis "Programs and libraries for graph algorithms (with MPI and 32-bit integers)"))) @@ -2659,7 +2755,7 @@ to BMP, JPEG or PNG image formats.") (define-public maxima (package (name "maxima") - (version "5.42.0") + (version "5.42.1") (source (origin (method url-fetch) @@ -2667,7 +2763,7 @@ to BMP, JPEG or PNG image formats.") version "-source/" name "-" version ".tar.gz")) (sha256 (base32 - "0d5pdihvcbwb7r4i4qs5qqgsz46hxlq33qj8is053llrgn9ylpyn")) + "1ka0xf70a55ndgmyrq7p5xxbd78pq7bfkqhgxsivaqdw6gn5lmcg")) (patches (search-patches "maxima-defsystem-mkdir.patch")))) (build-system gnu-build-system) (inputs @@ -2699,6 +2795,18 @@ to BMP, JPEG or PNG image formats.") (lambda _ (chmod "src/maxima" #o555) #t)) + (replace 'check + (lambda _ + ;; This is derived from the testing code in the "debian/rules" file + ;; of Debian's Maxima package. + ;; If Maxima can successfully run this, the binary to be installed + ;; should be fine. + (zero? + (system + (string-append "./maxima-local " + "--lisp=gcl " + "--batch-string=\"run_testsuite();\" " + "| grep -q \"No unexpected errors found\""))))) ;; 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. @@ -2746,18 +2854,17 @@ point numbers.") (define-public wxmaxima (package (name "wxmaxima") - (version "18.02.0") + (version "18.11.4") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/andrejv/" name "/archive" - "/Version-" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/wxMaxima-developers/wxmaxima.git") + (commit (string-append "Version-" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj")) - (patches - (search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch")))) + "1sz8n9v23q442l7yjj67pjh0dk78rl4cbcc3j8m1bm88anlfxl9r")))) (build-system cmake-build-system) (native-inputs `(("gettext" ,gettext-minimal))) @@ -3294,7 +3401,7 @@ Failure to do so will result in a library with poor performance.") (define-public glm (package (name "glm") - (version "0.9.9.2") + (version "0.9.9.3") (source (origin (method url-fetch) @@ -3302,7 +3409,7 @@ Failure to do so will result in a library with poor performance.") version "/glm-" version ".zip")) (sha256 (base32 - "1m2gws1d7l6h4mdn0ap74pfnm3vva3kk8rybdqd5x4lksd1mk6r0")))) + "0yqk5r3qh60d4r2iab5q7wq0fryn8p3pz6s28y1i7amqj1aqavj9")))) (build-system cmake-build-system) (native-inputs `(("unzip" ,unzip))) @@ -3476,7 +3583,7 @@ in finite element programs.") `(("unzip" ,unzip))) (inputs `(("hdf5" ,hdf5) - ("octave" ,octave) + ("octave" ,octave-cli) ("python" ,python-2) ; print syntax ;; ("python2-numpy" ,python2-numpy) ; only required for the tests ("zlib" ,zlib))) @@ -3846,15 +3953,15 @@ as equations, scalars, vectors, and matrices.") (define-public z3 (package (name "z3") - (version "4.5.0") + (version "4.8.1") + (home-page "https://github.com/Z3Prover/z3") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/Z3Prover/z3/archive/z3-" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference (url home-page) + (commit (string-append "z3-" version)))) (sha256 (base32 - "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf")))) + "1vr57bwx40sd5riijyrhy70i2wnv9xrdihf6y5zdz56yq88rl48f")))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -3883,43 +3990,57 @@ as equations, scalars, vectors, and matrices.") (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") + (version "1.1.2") (source (origin (method url-fetch) (uri (string-append "http://cubicle.lri.fr/cubicle-" version ".tar.gz")) (sha256 (base32 - "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h")))) + "10kk80jdmpdvql88sdjsh7vqzlpaphd8vip2lp47aarxjkwjlz1q")))) (build-system gnu-build-system) (native-inputs - `(("ocaml" ,ocaml) + `(("automake" ,automake) + ("ocaml" ,ocaml) ("which" ,(@@ (gnu packages base) which)))) (propagated-inputs - `(("z3" ,z3))) + `(("ocaml-num" ,ocaml-num) + ("z3" ,z3))) (arguments `(#:configure-flags (list "--with-z3") + #:make-flags (list "QUIET=") #:tests? #f #:phases (modify-phases %standard-phases (add-before 'configure 'configure-for-release (lambda _ (substitute* "Makefile.in" - (("SVNREV=") "#SVNREV=")))) + (("SVNREV=") "#SVNREV=")) + #t)) (add-before 'configure 'fix-/bin/sh (lambda _ (substitute* "configure" - (("/bin/sh") (which "sh"))))) + (("-/bin/sh") (string-append "-" (which "sh")))) + #t)) (add-before 'configure 'fix-smt-z3wrapper.ml (lambda _ (substitute* "Makefile.in" - (("\\\\n") ""))))))) + (("\\\\n") "")) + #t)) + (add-before 'configure 'fix-ocaml-num + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "Makefile.in" + (("= \\$\\(FUNCTORYLIB\\)") + (string-append "= -I " + (assoc-ref inputs "ocaml-num") + "/lib/ocaml/site-lib" + " $(FUNCTORYLIB)"))) + #t))))) (home-page "http://cubicle.lri.fr/") (synopsis "Model checker for array-based systems") (description "Cubicle is a model checker for verifying safety properties |