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-rw-r--r--gnu/packages/maths.scm542
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 <fhmgufs@web.de>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2018, 2020, 2021 Kei Kebreau <kkebreau@posteo.net>
-;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016-2022 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
@@ -34,7 +34,7 @@
;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
-;;; Copyright © 2020, 2021 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2020–2022 Felix Gruber <felgru@posteo.net>
;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
@@ -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
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