diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 156 |
1 files changed, 116 insertions, 40 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ab3b4458b2..fe9d59b69a 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -22,7 +22,7 @@ ;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Dave Love <me@fx@gnu.org> -;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org> +;;; Copyright © 2018, 2019 Jan Nieuwenhuizen <janneke@gnu.org> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com> ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com> @@ -31,6 +31,7 @@ ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> ;;; Copyright © 2018 Amin Bandali <bandali@gnu.org> ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr> +;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -100,6 +101,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages netpbm) + #:use-module (gnu packages onc-rpc) #:use-module (gnu packages pcre) #:use-module (gnu packages popt) #:use-module (gnu packages perl) @@ -246,7 +248,7 @@ triangulations.") (define-public python-cvxopt (package (name "python-cvxopt") - (version "1.2.1") + (version "1.2.3") (source (origin (method git-fetch) (uri (git-reference @@ -255,7 +257,7 @@ triangulations.") (file-name (git-file-name name version)) (sha256 (base32 - "05mnjil9palaa48xafdfh4f5pr4z7aqjr995rwl08qfyxs8y0crf")))) + "1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b")))) (build-system python-build-system) (arguments `(#:phases @@ -674,17 +676,18 @@ computations.") (define-public hdf4 (package (name "hdf4") - (version "4.2.13") + (version "4.2.14") (source (origin (method url-fetch) (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF" version "/src/hdf-" version ".tar.bz2")) (sha256 - (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm")) + (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l")) (patches (search-patches "hdf4-architectures.patch" "hdf4-reproducibility.patch" - "hdf4-shared-fortran.patch")))) + "hdf4-shared-fortran.patch" + "hdf4-tirpc.patch")))) (build-system gnu-build-system) (native-inputs `(("gfortran" ,gfortran) @@ -692,10 +695,14 @@ computations.") ("flex" ,flex))) (inputs `(("zlib" ,zlib) - ("libjpeg" ,libjpeg))) + ("libjpeg" ,libjpeg) + ("libtirpc" ,libtirpc))) (arguments `(#:parallel-tests? #f - #:configure-flags '("--enable-shared") + #:configure-flags (list "--enable-shared" + (string-append "CPPFLAGS=-I" + (assoc-ref %build-inputs "libtirpc") + "/include/tirpc")) #:phases (modify-phases %standard-phases ;; This is inspired by two of Debian's patches. @@ -1044,8 +1051,11 @@ implemented in C.") `(("gfortran" ,gfortran))) (inputs `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API + ;; XXX: These inputs are really dependencies of hdf4. ("zlib" ,zlib) ("libjpeg" ,libjpeg) + ("libtirpc" ,libtirpc) + ("gctp" ,gctp))) (arguments `( #:configure-flags '("--enable-install-include" "--enable-shared" @@ -1543,7 +1553,7 @@ script files.") ,@(package-inputs octave-cli))) (native-inputs `(("qttools" , qttools) ;for lrelease - ("texlive" ,texlive) ;for texi2dvi + ("texlive" ,(texlive-union (list texlive-epsf))) ; for texi2dvi ,@(package-native-inputs octave-cli))) (arguments (substitute-keyword-arguments (package-arguments octave-cli) @@ -1716,11 +1726,16 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") (version "2.16.0") (source (origin - (method url-fetch) - (uri (string-append "http://gmsh.info/src/gmsh-" - version "-source.tgz")) + (method git-fetch) + (uri (git-reference + (url "https://gitlab.onelab.info/gmsh/gmsh.git") + (commit + (string-append "gmsh_" + (string-map (lambda (x) (if (eq? x #\.) #\_ x)) + version))))) + (file-name (git-file-name name version)) (sha256 - (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8")) + (base32 "08rq4jajwmlpivnm9yifz2jhaivnz065lnk0h2zv773nwl9wf162")) (modules '((guix build utils))) (snippet ;; Remove non-free METIS code @@ -1746,7 +1761,7 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF" "-DENABLE_BUILD_SHARED:BOOL=ON" "-DENABLE_BUILD_DYNAMIC:BOOL=ON"))) - (home-page "http://www.geuz.org/gmsh/") + (home-page "http://gmsh.info/") (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 @@ -1760,18 +1775,20 @@ ASCII text files using Gmsh's own scripting language.") (define-public maxflow (package (name "maxflow") - (version "3.04") + ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’, + ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’. + (version "3.0.5") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/gerddie/maxflow.git") - (commit "42401fa54823d16b9da47716f04e5d9ef1605875"))) - (file-name (string-append name "-" version "-checkout")) + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb")))) (build-system cmake-build-system) - (home-page "http://pub.ist.ac.at/~vnk/software.html") + (home-page "https://pub.ist.ac.at/~vnk/software.html") (synopsis "Library implementing Maxflow algorithm") (description "An implementation of the maxflow algorithm described in @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for @@ -2967,7 +2984,7 @@ point numbers.") (define-public wxmaxima (package (name "wxmaxima") - (version "19.05.7") + (version "19.09.0") (source (origin (method git-fetch) @@ -2976,8 +2993,7 @@ point numbers.") (commit (string-append "Version-" version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "0zaz71fh156b9inrxf86scnix247al5pl9v18cxhjxcm0lanqxdp")))) + (base32 "195j6j8z0jd6xg3a63ywbrbsc6dany795m3fb95nbx1vq0bqqvvn")))) (build-system cmake-build-system) (native-inputs `(("gettext" ,gettext-minimal))) @@ -3090,8 +3106,12 @@ parts of it.") (define-public openblas (package + ;; TODO: Incorporate 'openblas/fixed-num-threads' changes on the next + ;; rebuild cycle. + (replacement openblas/fixed-num-threads) + (name "openblas") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) @@ -3100,7 +3120,7 @@ parts of it.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "062kg4ny1ywz7k5grpb4pbf0hba0w6manbajwkmv4f477a31sxpl")))) + "1r2g9zzwq5dm8vjd19pxwggfvfzy56cvkmpmp5d014qr3svgmsap")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -3160,7 +3180,7 @@ parts of it.") (license license:bsd-3))) (define-public openblas-ilp64 - (package (inherit openblas) + (package/inherit openblas (name "openblas-ilp64") (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux")) (arguments @@ -3171,6 +3191,24 @@ parts of it.") (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)") (license license:bsd-3))) +(define openblas/fixed-num-threads + ;; TODO: Move that to 'openblas' proper on the next rebuild cycle. + (package + (inherit openblas) + (version (match (string-split (package-version openblas) #\.) + ((numbers ... (= string-length len)) + (string-join (append numbers + (list (make-string len #\a))) + ".")))) + (arguments + (substitute-keyword-arguments (package-arguments openblas) + ((#:make-flags flags ''()) + ;; This is the maximum number of threads OpenBLAS will ever use (that + ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS + ;; is used.) If we don't set it, the makefile sets it to the number + ;; of cores of the build machine, which is obviously wrong. + `(cons "NUM_THREADS=128" ,flags)))))) + (define* (make-blis implementation #:optional substitutable?) "Return a BLIS package with the given IMPLEMENTATION (see config/ in the source tree for a list of implementations.) @@ -3516,15 +3554,15 @@ Failure to do so will result in a library with poor performance.") (define-public glm (package (name "glm") - (version "0.9.9.5") + (version "0.9.9.6") (source (origin (method url-fetch) (uri (string-append "https://github.com/g-truc/glm/releases/download/" version "/glm-" version ".zip")) (sha256 - (base32 - "1vmg7hb4xvsa77zpbwiw6lqc7pyaj56dihx6xriny5b9rrh4iqsg")))) + (base32 "1l0pi1qi37mk6s0yrkrw07lspv4gcqnr9ryg3521hrl77ff37dwx")) + (patches (search-patches "glm-restore-install-target.patch")))) (build-system cmake-build-system) (native-inputs `(("unzip" ,unzip))) @@ -3609,7 +3647,7 @@ revised simplex and the branch-and-bound methods.") (define-public dealii (package (name "dealii") - (version "9.0.1") + (version "9.1.1") (source (origin (method url-fetch) @@ -3617,8 +3655,7 @@ revised simplex and the branch-and-bound methods.") "download/v" version "/dealii-" version ".tar.gz")) (sha256 (base32 - "0r7f8rhl3xr94imd372plizdcbqk0a70w73lwc3vw912dxk0sbyz")) - (patches (search-patches "dealii-mpi-deprecations.patch")) + "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw")) (modules '((guix build utils))) (snippet ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost @@ -3827,8 +3864,8 @@ set.") `(("doc++" ,doc++) ("netpbm" ,netpbm) ("perl" ,perl) ; needed to run 'ppmquant' during tests - ("texlive" ,(texlive-union (list texlive-generic-xypic - texlive-fonts-xypic + ("texlive" ,(texlive-union (list texlive-xypic + texlive-cm texlive-latex-hyperref texlive-bibtex))) ("ghostscript" ,ghostscript))) @@ -4080,7 +4117,7 @@ as equations, scalars, vectors, and matrices.") (define-public z3 (package (name "z3") - (version "4.8.4") + (version "4.8.6") (home-page "https://github.com/Z3Prover/z3") (source (origin (method git-fetch) @@ -4089,7 +4126,7 @@ as equations, scalars, vectors, and matrices.") (file-name (git-file-name name version)) (sha256 (base32 - "014igqm5vwswz0yhz0cdxsj3a6dh7i79hvhgc3jmmmz3z0xm1gyn")))) + "1sywcqj5y8yp28m4cdvzsgw74kd6zr1s3y1x17ky8pr9prvpvl6x")))) (build-system gnu-build-system) (arguments `(#:phases @@ -4280,7 +4317,7 @@ reduction.") (define-public mcrl2 (package (name "mcrl2") - (version "201707.1.15162") + (version "201908.0") (source (origin (method url-fetch) (uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-" @@ -4288,9 +4325,7 @@ reduction.") ".tar.gz")) (sha256 (base32 - "1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f")))) - (native-inputs - `(("subversion" ,subversion))) + "1i4xgl2d5fgiz1mwi50cyfkrrcpm8nxfayfjgmhq7chs58wlhfsz")))) (inputs `(("boost" ,boost) ("glu" ,glu) @@ -4308,6 +4343,15 @@ analysed.") (home-page "https://mcrl2.org") (license license:boost1.0))) +(define-public mcrl2-minimal + (package + (inherit mcrl2) + (name "mcrl2-minimal") + (inputs + `(("boost" ,boost))) + (arguments + '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF"))))) + (define-public r-subplex (package (name "r-subplex") @@ -4832,8 +4876,7 @@ assemble global function spaces on finite-element grids.") (add-after 'build 'build-tests (lambda* (#:key inputs make-flags #:allow-other-keys) (setenv "CPLUS_INCLUDE_PATH" - (string-append (assoc-ref inputs "dune-grid") "/share:" - (getenv "CPLUS_INCLUDE_PATH"))) + (string-append (assoc-ref inputs "dune-grid") "/share")) (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) @@ -5136,3 +5179,36 @@ algorithm, a parametric integer programming solver, and primitives for termination analysis via the automatic synthesis of linear ranking functions.") (license license:gpl3+))) + +(define-public speedcrunch + (package + (name "speedcrunch") + (version "0.12.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://bitbucket.org/heldercorreia/speedcrunch.git") + (commit (string-append "release-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk")))) + (build-system cmake-build-system) + (inputs `(("qtbase" ,qtbase))) + (native-inputs `(("qttools" ,qttools))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir-to-src + (lambda _ (chdir "src") #t))))) + (synopsis "High-precision scientific calculator") + (description + "SpeedCrunch is a high-precision scientific calculator. It features a +syntax-highlighted scrollable display and is designed to be fully used via +keyboard. Some distinctive features are auto-completion of functions and +variables, a formula book, and quick insertion of constants from various +fields of knowledge.") + (home-page "http://speedcrunch.org/") + (license license:gpl2+))) + |