diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 542 |
1 files changed, 351 insertions, 191 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 3bac086666..9a0f913c5a 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -12,7 +12,7 @@ ;;; Copyright © 2015 Fabian Harfert <[email protected]> ;;; Copyright © 2016 Roel Janssen <[email protected]> ;;; Copyright © 2016, 2018, 2020, 2021 Kei Kebreau <[email protected]> -;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès <[email protected]> +;;; Copyright © 2016-2022 Ludovic Courtès <[email protected]> ;;; Copyright © 2016 Leo Famulari <[email protected]> ;;; Copyright © 2016, 2017 Thomas Danckaert <[email protected]> ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <[email protected]> @@ -34,7 +34,7 @@ ;;; Copyright © 2019 Steve Sprang <[email protected]> ;;; Copyright © 2019 Robert Smith <[email protected]> ;;; Copyright © 2020 Jakub Kądziołka <[email protected]> -;;; Copyright © 2020, 2021 Felix Gruber <[email protected]> +;;; Copyright © 2020–2022 Felix Gruber <[email protected]> ;;; Copyright © 2020 R Veera Kumar <[email protected]> ;;; Copyright © 2020 Vincent Legoll <[email protected]> ;;; Copyright © 2020 Nicolò Balzarotti <[email protected]> @@ -79,7 +79,9 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system glib-or-gtk) #:use-module (guix build-system gnu) + #:use-module (guix build-system meson) #:use-module (guix build-system ocaml) + #:use-module (guix build-system perl) #:use-module (guix build-system python) #:use-module (guix build-system ruby) #:use-module (gnu packages algebra) @@ -95,6 +97,7 @@ #:use-module (gnu packages coq) #:use-module (gnu packages curl) #:use-module (gnu packages cyrus-sasl) + #:use-module (gnu packages datamash) #:use-module (gnu packages dbm) #:use-module (gnu packages documentation) #:use-module (gnu packages elf) @@ -270,7 +273,7 @@ interactive dialogs to guide them.") (arguments '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python" "LIBS= -lz -lpcre -lexpat"))) - (synopsis "A common interface to various earth observation data formats") + (synopsis "Common interface to various earth observation data formats") (description "The Common Data Access toolbox (CODA) provides a set of interfaces for reading remote sensing data from earth observation data files. It consists of @@ -316,7 +319,7 @@ triangulations.") (define-public python-cvxopt (package (name "python-cvxopt") - (version "1.2.3") + (version "1.2.7") (source (origin (method git-fetch) (uri (git-reference @@ -325,7 +328,7 @@ triangulations.") (file-name (git-file-name name version)) (sha256 (base32 - "1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b")))) + "114z34wwx1bsv4q6xj9p5q99dffgnj9s4i4arx10g191xq9q8i5y")))) (build-system python-build-system) (arguments `(#:phases @@ -354,9 +357,6 @@ extensive standard library and on the strengths of Python as a high-level programming language.") (license license:gpl3+))) -(define-public python2-cvxopt - (package-with-python2 python-cvxopt)) - (define-public units (package (name "units") @@ -576,6 +576,10 @@ 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.") + + ;; Linear algebra routines should benefit from SIMD optimizations. + (properties `((tunable? . #t))) + (license license:gpl3+))) ;; TODO: Merge back into the gsl package as a separate output. @@ -1011,6 +1015,67 @@ singular value problems.") (license (license:non-copyleft "file://LICENSE" "See LICENSE in the distribution.")))) +(define-public feedgnuplot + (package + (name "feedgnuplot") + (version "1.60") + (home-page "https://github.com/dkogan/feedgnuplot") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0403hwlian2s431m36qdzcczhvfjvh7128m64hmmwbbrgh0n7md7")))) + (build-system perl-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'check 'adjust-tests + (lambda _ + (substitute* "t/plots.t" + ;; XXX: The vnlog tests uses 'echo' with escaped strings, + ;; but does not enable escape interpretation. + (("echo -n ") + "echo -ne ")))) + (add-after 'install 'install-documentation + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (doc (string-append out "/share/doc/feedgnuplot"))) + (mkdir-p doc) + (invoke "pod2html" "--title=feedgnuplot" "bin/feedgnuplot" + "--outfile" (string-append doc "/feedgnuplot.html"))))) + (add-after 'install 'wrap + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (gnuplot (search-input-file inputs "/bin/gnuplot")) + ;; XXX: We need List::MoreUtils as well as its supporting + ;; (propagated) modules; for now just refer to labels. + (modules '("perl-list-moreutils" "perl-exporter-tiny")) + (PERL5LIB (string-join + (map (lambda (input) + (string-append (assoc-ref inputs input) + "/lib/perl5/site_perl")) + modules) + ":"))) + (wrap-program (string-append out "/bin/feedgnuplot") + `("PERL5LIB" ":" suffix (,PERL5LIB)) + `("PATH" ":" suffix (,(dirname gnuplot)))))))))) + (inputs + (list gnuplot perl-list-moreutils vnlog)) + (native-inputs + ;; For tests. + (list perl-ipc-run perl-string-shellquote)) + (synopsis "Pipe-oriented plotting tool") + (description + "@command{feedgnuplot} is a tool to plot realtime and stored data +from the command line, using @command{gnuplot}. It can read data from +a pipe or file, make a variety of transformations, and render the result +in the terminal or with an external viewer.") + (license license:gpl1+))) ;any version + (define-public gnuplot (package (name "gnuplot") @@ -2369,7 +2434,7 @@ satisfiability checking (SAT).") (define-public ceres (package (name "ceres-solver") - (version "1.14.0") + (version "2.0.0") (home-page "http://ceres-solver.org/") (source (origin (method url-fetch) @@ -2377,7 +2442,7 @@ satisfiability checking (SAT).") version ".tar.gz")) (sha256 (base32 - "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27")))) + "00vng9vnmdb1qga01m0why90m0041w7bn6kxa2h4m26aflfqla8h")))) (build-system cmake-build-system) (arguments ;; TODO: Build HTML user documentation and install separately. @@ -2396,11 +2461,11 @@ satisfiability checking (SAT).") (propagated-inputs (list glog)) ;for #include <glog/glog.h> (inputs - `(("eigen" ,eigen) - ("blas" ,openblas) - ("lapack" ,lapack) - ("suitesparse" ,suitesparse) - ("gflags" ,gflags))) + (list eigen + openblas + lapack + suitesparse + gflags)) (synopsis "C++ library for solving large optimization problems") (description "Ceres Solver is a C++ library for modeling and solving large, @@ -2411,7 +2476,56 @@ can solve two kinds of problems: @item non-linear least squares problems with bounds constraints; @item general unconstrained optimization problems. @end enumerate\n") - (license license:bsd-3))) + (license license:bsd-3) + + ;; Mark as tunable to take advantage of SIMD code in Eigen. + (properties `((tunable? . #t))))) + +(define-public ceres-solver-benchmarks + (package + (inherit ceres) + (name "ceres-solver-benchmarks") + (arguments + '(#:modules ((ice-9 popen) + (ice-9 rdelim) + (guix build utils) + (guix build cmake-build-system)) + + #:phases (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (define flags + (string-tokenize + (read-line (open-pipe* OPEN_READ + "pkg-config" "eigen3" + "--cflags")))) + + (define (compile-file top-dir) + (lambda (file) + (let ((source (string-append file ".cc"))) + (format #t "building '~a'...~%" file) + (apply invoke "c++" "-fopenmp" "-O2" "-g" "-DNDEBUG" + source "-lceres" "-lbenchmark" "-lglog" + "-pthread" + "-o" (string-append bin "/" file) + "-I" top-dir flags)))) + + (mkdir-p bin) + (with-directory-excursion "internal/ceres" + (for-each (compile-file "..") + '("schur_eliminator_benchmark" + "small_blas_gemm_benchmark" + "small_blas_gemv_benchmark")) + (with-directory-excursion "autodiff_benchmarks" + ((compile-file "../..") "autodiff_benchmarks")))))) + (delete 'check) + (delete 'install)))) + (inputs (modify-inputs (package-inputs ceres) + (prepend googlebenchmark ceres))) + (synopsis "Benchmarks of the Ceres optimization problem solver"))) ;; For a fully featured Octave, users are strongly recommended also to install ;; the following packages: less, ghostscript, gnuplot. @@ -4859,7 +4973,7 @@ Failure to do so will result in a library with poor performance.") (define-public cglm (package (name "cglm") - (version "0.8.2") + (version "0.8.4") (source (origin (method git-fetch) @@ -4868,11 +4982,10 @@ Failure to do so will result in a library with poor performance.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1lcfl9ph4bnl3hckpx4hzwh8r4llnw94ik75igc5qy38wk468gmk")))) - (build-system cmake-build-system) + (base32 "0zgckh56vcdar3a4n51r84wrizyd2ssqal4nsvxd4qdjm0rvb4h0")))) + (build-system meson-build-system) (arguments - `(#:configure-flags - (list "-DCGLM_USE_TEST=ON"))) + `(#:configure-flags '("-Dbuild_tests=true"))) (home-page "https://github.com/recp/cglm") (synopsis "Mathematics C library for graphics programming") (description @@ -5155,14 +5268,16 @@ A unique design feature of Trilinos is its focus on packages.") (define-public dealii (package (name "dealii") - (version "9.3.1") + (version "9.3.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/dealii/dealii/releases/" "download/v" version "/dealii-" version ".tar.gz")) (sha256 - (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6")) + (base32 "1s0kawnljg24jj6nibwrif5gxdgg2daqfylhqqpl1lvmzmmxfhak")) + (patches (search-patches "dealii-fix-compiliation-with-boost-1.78.patch" + "dealii-fix-sundials.patch")) (modules '((guix build utils))) (snippet '(begin @@ -5173,16 +5288,14 @@ A unique design feature of Trilinos is its focus on packages.") (outputs '("out" "doc")) (native-inputs ;; Required to build the documentation. - `(("dot" ,graphviz) - ("doxygen" ,doxygen) - ("perl" ,perl))) + (list graphviz doxygen perl)) (inputs - `(("arpack" ,arpack-ng) - ("blas" ,openblas) - ("gfortran" ,gfortran) - ("lapack" ,lapack) - ("muparser" ,muparser) - ("zlib" ,zlib))) + (list arpack-ng + openblas + gfortran + lapack + muparser + zlib)) (propagated-inputs ;; Some scripts are installed into share/deal.II/scripts that require ;; perl and python, but they are not executable (and some are missing the @@ -5676,15 +5789,14 @@ Longest Commons Subsequence of a set of strings.") (define-public jacal (package (name "jacal") - (version "1c4") + (version "1c7") (source (origin (method url-fetch) (uri (string-append "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-" version ".zip")) - (sha256 (base32 - "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q")) - (patches (search-patches "jacal-fix-texinfo.patch")))) + (sha256 + (base32 "06a5sx9ikd62bpnd898g3yk818b020b1a27mk7dbfla2zizib4xz")))) (build-system gnu-build-system) (arguments `(#:phases @@ -5710,7 +5822,7 @@ Longest Commons Subsequence of a set of strings.") (chmod wrapper #o555)))) (replace 'configure (lambda* (#:key outputs #:allow-other-keys) - (invoke "./configure" + (invoke "sh" "configure" (string-append "--prefix=" (assoc-ref outputs "out")))))))) (inputs (list scm)) @@ -6249,7 +6361,7 @@ linear algebra primitives specifically targeting graph analytics.") (define-public dune-common (package (name "dune-common") - (version "2.7.0") + (version "2.7.1") (source (origin (method url-fetch) @@ -6257,14 +6369,18 @@ linear algebra primitives specifically targeting graph analytics.") version "/dune-common-" version ".tar.gz")) (sha256 (base32 - "140q1zh44cr5yrjwg4b5ga803rkqv55vk30l2cqm29aklj1wb0rw")))) + "0sidwdkyrrqjkqhpvrlc991pzi5xzlvxk91s2n7qk3widwy7fch2")))) (build-system cmake-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'build 'build-tests - (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags)))))) + (lambda* (#:key make-flags parallel-build? #:allow-other-keys) + (apply invoke "make" "build_tests" + `(,@(if parallel-build? + `("-j" ,(number->string (parallel-job-count))) + '()) + ,@make-flags))))))) (inputs (list gmp metis openblas python superlu)) (native-inputs @@ -6282,7 +6398,7 @@ Differences} (FD).") (define-public dune-geometry (package (name "dune-geometry") - (version "2.7.0") + (version "2.7.1") (source (origin (method url-fetch) @@ -6290,14 +6406,18 @@ Differences} (FD).") version "/dune-geometry-" version ".tar.gz")) (sha256 (base32 - "1cicvlwbyyw76npicnblxckyvhbfn3ip8isydiv3hlrlz8zcg5nr")))) + "068mh3fd110xl27rwxqlqy4d9cpqw2vqm2pzfrripiaqscb3byfy")))) (build-system cmake-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'build 'build-tests - (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags)))))) + (lambda* (#:key make-flags parallel-build? #:allow-other-keys) + (apply invoke "make" "build_tests" + `(,@(if parallel-build? + `("-j" ,(number->string (parallel-job-count))) + '()) + ,@make-flags))))))) (inputs (list dune-common ;; Optional @@ -6319,7 +6439,7 @@ This package contains the basic DUNE geometry classes.") (define-public dune-uggrid (package (name "dune-uggrid") - (version "2.7.0") + (version "2.7.1") (source (origin (method git-fetch) @@ -6329,14 +6449,18 @@ This package contains the basic DUNE geometry classes.") (file-name (git-file-name name version)) (sha256 (base32 - "192miqgmfj6jwk969gydzpbv9ki7jg5nky3ydnrwa2nq29b5xkh0")))) + "11qz52g9d5k96fqik2lyi80xryw174rnny074pj70ardl6zzz83p")))) (build-system cmake-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'build 'build-tests - (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags)))))) + (lambda* (#:key make-flags parallel-build? #:allow-other-keys) + (apply invoke "make" "build_tests" + `(,@(if parallel-build? + `("-j" ,(number->string (parallel-job-count))) + '()) + ,@make-flags))))))) (inputs (list dune-common)) (native-inputs @@ -6355,7 +6479,7 @@ This package contains the DUNE UG grid classes.") (define-public dune-grid (package (name "dune-grid") - (version "2.7.0") + (version "2.7.1") (source (origin (method url-fetch) @@ -6363,14 +6487,18 @@ This package contains the DUNE UG grid classes.") version "/dune-grid-" version ".tar.gz")) (sha256 (base32 - "17fjz30qazjgl11sryyxnw9klai4yz1ji4bs68013xcxc5hdv27s")))) + "15iws03hkbmr4a4rqqb0rriz1m8szl96wdr7gw0jmrcnlzbdbbx5")))) (build-system cmake-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'build 'build-tests - (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags)))))) + (lambda* (#:key make-flags parallel-build? #:allow-other-keys) + (apply invoke "make" "build_tests" + `(,@(if parallel-build? + `("-j" ,(number->string (parallel-job-count))) + '()) + ,@make-flags))))))) (inputs (list dune-common dune-geometry @@ -6397,7 +6525,7 @@ This package contains the basic DUNE grid classes.") (define-public dune-istl (package (name "dune-istl") - (version "2.7.0") + (version "2.7.1") (source (origin (method url-fetch) @@ -6405,8 +6533,7 @@ This package contains the basic DUNE grid classes.") version "/dune-istl-" version ".tar.gz")) (sha256 (base32 - "0gl3wgz5rs6sb4m83440ny45sbx7z7lnbi3gx6r9nm3rvy5j33f9")) - (patches (search-patches "dune-istl-2.7-fix-non-mpi-tests.patch")))) + "1cy69s1266hvnh8blznlvvkrf8i2g640rc3mf7kp872wgvdz4nb9")))) (build-system cmake-build-system) (arguments `(#:phases @@ -6424,8 +6551,12 @@ This package contains the basic DUNE grid classes.") ":")) #t))) (add-after 'build 'build-tests - (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags)))))) + (lambda* (#:key make-flags parallel-build? #:allow-other-keys) + (apply invoke "make" "build_tests" + `(,@(if parallel-build? + `("-j" ,(number->string (parallel-job-count))) + '()) + ,@make-flags))))))) (inputs (list dune-common ;; Optional @@ -6455,7 +6586,7 @@ aggregation-based algebraic multigrid.") (define-public dune-localfunctions (package (name "dune-localfunctions") - (version "2.7.0") + (version "2.7.1") (source (origin (method url-fetch) @@ -6463,7 +6594,7 @@ aggregation-based algebraic multigrid.") version "/dune-localfunctions-" version ".tar.gz")) (sha256 (base32 - "1yih59h6vngii696bx1c2vil02lriij4kz0nc583mjn9kiaqxfqd")))) + "031i42anrhi0ngpvp42rdjbkic7v3008fwild9xg7flffwvnpshg")))) (build-system cmake-build-system) (arguments `(#:phases @@ -6481,8 +6612,12 @@ aggregation-based algebraic multigrid.") ":")) #t))) (add-after 'build 'build-tests - (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags)))))) + (lambda* (#:key make-flags parallel-build? #:allow-other-keys) + (apply invoke "make" "build_tests" + `(,@(if parallel-build? + `("-j" ,(number->string (parallel-job-count))) + '()) + ,@make-flags))))))) (inputs (list dune-common dune-geometry @@ -6507,97 +6642,111 @@ assemble global function spaces on finite-element grids.") (license license:gpl2))) (define-public dune-alugrid - (package - (name "dune-alugrid") - (version "2.7.0-git-81d35682") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://gitlab.dune-project.org/extensions/dune-alugrid.git") - (commit "81d356827c84454b971937db02c02b90bbcd7fe5"))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0z54lwfp53prcrs94k8gwh047l9z642jll3l56xlyfr69z0b2zz1")))) - (build-system cmake-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-include - (lambda _ - (substitute* "dune/alugrid/test/test-alugrid.cc" - (("doc/grids/gridfactory/testgrids") - "doc/dune-grid/grids/gridfactory/testgrids")) - #t)) - (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")) - (apply invoke "make" "build_tests" make-flags)))))) - (inputs - (list dune-common - dune-geometry - dune-grid - ;; Optional - metis - openblas - python - superlu - gmp - zlib)) - (native-inputs - (list gfortran pkg-config)) - (home-page "https://dune-project.org/") - (synopsis "Distributed and Unified Numerics Environment") - (description "ALUGrid is an adaptive, loadbalancing, unstructured + ;; This was the last commit on the releases/2.7 branch as of 2021-12-17, + ;; unfortunately there was no tag for any 2.7 release. + (let ((commit "51bde29a2dfa7cfac4fb73d40ffd42b9c1eb1d3d")) + (package + (name "dune-alugrid") + (version (git-version "2.7.1" "0" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.dune-project.org/extensions/dune-alugrid.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0z16wg6llzxs7vjg2yilg31vwnkz8k050j6bspg3blbym0razy15")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-include + (lambda _ + (substitute* "dune/alugrid/test/test-alugrid.cc" + (("doc/grids/gridfactory/testgrids") + "doc/dune-grid/grids/gridfactory/testgrids")) + #t)) + (add-after 'build 'build-tests + (lambda* (#:key make-flags parallel-build? #:allow-other-keys) + (setenv "CPLUS_INCLUDE_PATH" + (string-append (assoc-ref inputs "dune-grid") "/share")) + (apply invoke "make" "build_tests" + `(,@(if parallel-build? + `("-j" ,(number->string (parallel-job-count))) + '()) + ,@make-flags))))))) + (inputs + (list dune-common + dune-geometry + dune-grid + ;; Optional + metis + openblas + python + superlu + gmp + zlib)) + (native-inputs + (list gfortran pkg-config)) + (home-page "https://dune-project.org/") + (synopsis "Distributed and Unified Numerics Environment") + (description "ALUGrid is an adaptive, loadbalancing, unstructured implementation of the DUNE grid interface supporting either simplices or cubes.") - (license license:gpl2+))) + (license license:gpl2+)))) (define-public dune-subgrid - (package - (name "dune-subgrid") - (version "2.7.0-git-2103a363") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid") - (commit "2103a363f32e8d7b60e66eee7ddecf969f6cf762"))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1wsjlypd3835c3arqjkw836cxx5q67zy447wa65q634lf6f6v9ia")))) - (build-system cmake-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'build 'build-tests - (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags)))))) - (inputs - (list dune-common - dune-geometry - dune-grid - ;; Optional - metis - openblas - gmp)) - (native-inputs - (list gfortran pkg-config)) - (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php") - (synopsis "Distributed and Unified Numerics Environment") - (description "The dune-subgrid module marks elements of + ;; This was the last commit on the releases/2.7 branch as of 2021-12-17. + ;; Unfortunately the dune-subgrid repository contains no release tags. + (let ((commit "45d1ee9f3f711e209695deee97912f4954f7f280")) + (package + (name "dune-subgrid") + (version (git-version "2.7.1" "0" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xjf7865wil7kzym608kv3nc3ff3m3nlqich4k9wjyvy3lz6panh")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-tests + (lambda* (#:key make-flags parallel-build? #:allow-other-keys) + (apply invoke "make" "build_tests" + `(,@(if parallel-build? + `("-j" ,(number->string (parallel-job-count))) + '()) + ,@make-flags))))))) + (inputs + (list dune-common + dune-geometry + dune-grid + ;; Optional + metis + openblas + gmp)) + (native-inputs + (list gfortran pkg-config)) + (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php") + (synopsis "Distributed and Unified Numerics Environment") + (description "The dune-subgrid module marks elements of another hierarchical dune grid. The set of marked elements can then be accessed as a hierarchical dune grid in its own right. Dune-Subgrid provides the full grid interface including adaptive mesh refinement.") - (license license:gpl2+))) + (license license:gpl2+)))) (define-public dune-typetree (package (name "dune-typetree") - (version "2.7.0") + (version "2.7.1") (source (origin (method git-fetch) @@ -6607,14 +6756,18 @@ provides the full grid interface including adaptive mesh refinement.") (file-name (git-file-name name version)) (sha256 (base32 - "1rhv25yg0q1hw50c8wlfqhgwrjl4mh62zq9v14ilwgzbfgxmpiy7")))) + "1kx9k8i7pdw6l6ny6nq85v5p1nd6yxldzaj8k3nizaz3q1j407pv")))) (build-system cmake-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'build 'build-tests - (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags)))))) + (lambda* (#:key make-flags parallel-build? #:allow-other-keys) + (apply invoke "make" "build_tests" + `(,@(if parallel-build? + `("-j" ,(number->string (parallel-job-count))) + '()) + ,@make-flags))))))) (inputs (list dune-common ;; Optional @@ -6635,7 +6788,7 @@ operating on statically typed trees of objects.") (define-public dune-functions (package (name "dune-functions") - (version "2.7.0") + (version "2.7.1") (source (origin (method git-fetch) @@ -6645,7 +6798,7 @@ operating on statically typed trees of objects.") (file-name (git-file-name name version)) (sha256 (base32 - "1na4gcih0kin37ksj2xj07ds04v7zx53pjdhm1hzy55jjfqdjk8h")))) + "04dhr4asnl38bf1gp8hrk31maav33m7q71lhl2n5yk1q1x6i77nw")))) (build-system cmake-build-system) (arguments `(#:phases @@ -6657,8 +6810,12 @@ operating on statically typed trees of objects.") "--exclude-regex gridviewfunctionspacebasistest") #t)) (add-after 'build 'build-tests - (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags)))))) + (lambda* (#:key make-flags parallel-build? #:allow-other-keys) + (apply invoke "make" "build_tests" + `(,@(if parallel-build? + `("-j" ,(number->string (parallel-job-count))) + '()) + ,@make-flags))))))) (inputs (list dune-common dune-istl @@ -6682,44 +6839,47 @@ implemented as callable objects, and bases of finite element spaces.") (license (list license:lgpl3+ license:gpl2)))) (define-public dune-pdelab - (package - (name "dune-pdelab") - (version "2.7.0-git-476fe437") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://gitlab.dune-project.org/pdelab/dune-pdelab") - (commit "476fe43763fa6f459c5e4658e2a2b4b5582db834"))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0cs36piqzn6rq0j2ih3ab3q3q9yg199wk72k5qi86pkzh7i7fdn1")))) - (build-system cmake-build-system) - (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled - (inputs - (list dune-common - dune-istl - dune-localfunctions - dune-geometry - dune-grid - dune-typetree - dune-functions - ;; Optional - openblas - eigen - metis - python - superlu - gmp)) - (native-inputs - (list gfortran pkg-config)) - (home-page "https://dune-project.org/") - (synopsis "Differential equations solver toolbox") - (description "PDELab is a partial differential equations solver toolbox + ;; This was the last commit on the releases/2.7 branch as of 2021-12-17, + ;; unfortunately there was no tag for any 2.7 release. + (let ((commit "09aef74d95661d18a7789d2f517ae77797eec738")) + (package + (name "dune-pdelab") + (version (git-version "2.7.1" "0" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.dune-project.org/pdelab/dune-pdelab") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0nv69ayr4gln9m1s94z9zkrxqi8nzar3z6awnvgqz595nmjf82ac")))) + (build-system cmake-build-system) + (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled + (inputs + (list dune-common + dune-istl + dune-localfunctions + dune-geometry + dune-grid + dune-typetree + dune-functions + ;; Optional + openblas + eigen + metis + python + superlu + gmp)) + (native-inputs + (list gfortran pkg-config)) + (home-page "https://dune-project.org/") + (synopsis "Differential equations solver toolbox") + (description "PDELab is a partial differential equations solver toolbox built on top of DUNE, the Distributed and Unified Numerics Environment.") - ;; Either GPL version 2 with "runtime exception" or LGPLv3+. - (license (list license:lgpl3+ license:gpl2)))) + ;; Either GPL version 2 with "runtime exception" or LGPLv3+. + (license (list license:lgpl3+ license:gpl2))))) (define add-openmpi-to-dune-package (let ((dune-package? @@ -6729,8 +6889,8 @@ built on top of DUNE, the Distributed and Unified Numerics Environment.") (if (dune-package? p) (package (inherit p) (name (string-append (package-name p) "-openmpi")) - (inputs `(,@(package-inputs p) - ("openmpi" ,openmpi))) + (inputs (modify-inputs (package-inputs p) + (append openmpi))) (arguments (substitute-keyword-arguments (package-arguments p) ((#:phases phases '%standard-phases) @@ -7195,14 +7355,14 @@ of C, Java, or Ada programs.") (define-public frama-c (package (name "frama-c") - (version "23.1") + (version "24.0") (source (origin (method url-fetch) (uri (string-append "http://frama-c.com/download/frama-c-" - version "-Vanadium.tar.gz")) + version "-Chromium.tar.gz")) (sha256 (base32 - "1rgkq9sg436smw005ag0j6y3xryhjn18a07m5wjfrfp0s1438nnj")))) + "0x1xgip50jdz1phsb9rzwf2ra8lshn1hmd9g967xia402wrg3sjf")))) (build-system ocaml-build-system) (arguments `(#:tests? #f; no test target in Makefile |