diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 251 |
1 files changed, 137 insertions, 114 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index fde47bf488..68c811f74b 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -22,7 +22,7 @@ ;;; Copyright © 2017, 2019, 2022 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Dave Love <me@fx@gnu.org> -;;; Copyright © 2018, 2019, 2020, 2021 Jan (janneke) Nieuwenhuizen <janneke@gnu.org> +;;; Copyright © 2018, 2019, 2020, 2021, 2022 Jan (janneke) 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> @@ -50,6 +50,8 @@ ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me> ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net> ;;; Copyright © 2021 Pierre-Antoine Bouttier <pierre-antoine.bouttier@univ-grenoble-alpes.fr> +;;; Copyright © 2022 Zhu Zihao <all_but_last@163.com> +;;; Copyright © 2022 Sharlatan Hellseher <sharlatanus@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1091,6 +1093,31 @@ 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 giza + (package + (name "giza") + (version "1.3.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/danieljprice/giza") + (commit (string-append "v" version)))) + (sha256 + (base32 "1clklh3nzgwrwg80h3k5x65gdymbvcc84c44nql7m4bv9b8rqfsq")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (native-inputs + (list perl pkg-config)) + (inputs + (list cairo freetype gfortran)) + (home-page "https://danieljprice.github.io/giza/") + (synopsis "Scientific plotting library for C/Fortran") + (description + "Giza is a lightweight scientific plotting library built on top of +@code{cairo} that provides uniform output to multiple devices.") + (license license:gpl2+))) + (define-public gnuplot (package (name "gnuplot") @@ -2657,7 +2684,7 @@ can solve two kinds of problems: (define-public octave-cli (package (name "octave-cli") - (version "6.2.0") + (version "7.1.0") (source (origin (method url-fetch) @@ -2665,7 +2692,7 @@ can solve two kinds of problems: version ".tar.xz")) (sha256 (base32 - "06id09zspya24gshcwgp039cp35c06150mdlxysawgnbrhj16wkv")))) + "0wv26nsfi6cq80np6p4av4wfrvbaflca6szajf6c60mbpdg63m1z")))) (build-system gnu-build-system) (inputs `(("alsa-lib" ,alsa-lib) @@ -2926,23 +2953,21 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") (define-public gmsh (package (name "gmsh") - (version "4.9.5") + (version "4.10.5") (source (origin - (method git-fetch) - (uri (git-reference - (url "https://gitlab.onelab.info/gmsh/gmsh.git") - (commit - (string-append "gmsh_" - (string-replace-substring version "." "_"))))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0asd9p64ng5l2zk5glc33x3ynnvdpndlflg3q9mr0jxr7y9x0lrm")) - (modules '((guix build utils))) - (snippet - '(begin - (delete-file-recursively "contrib/metis") - #t)))) + (method git-fetch) + (uri (git-reference + (url "https://gitlab.onelab.info/gmsh/gmsh.git") + (commit + (string-append "gmsh_" + (string-replace-substring version "." "_"))))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08p39yjgf3lbnjg90skpmsq9n1a9pmwppdmy5s94dc6sq2nfr7xl")) + (modules '((guix build utils))) + (snippet + '(delete-file-recursively "contrib/metis")))) (build-system cmake-build-system) (propagated-inputs (list fltk @@ -2957,9 +2982,9 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") metis opencascade-occt)) (inputs - `(("fontconfig" ,fontconfig) - ("libxft" ,libxft) - ("python" ,python))) + (list fontconfig + libxft + python)) (arguments `(#:configure-flags `("-DENABLE_SYSTEM_CONTRIB:BOOL=ON" "-DENABLE_BUILD_SHARED:BOOL=ON" @@ -2987,8 +3012,7 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") "/lib/libgmsh.so"))) (substitute* "api/gmsh.py" (("find_library\\(\"gmsh\"\\)") - (simple-format #f "\"~a\"" libgmsh)))) - #t))))) + (simple-format #f "\"~a\"" libgmsh))))))))) (home-page "http://gmsh.info/") (synopsis "3D finite element grid generator") (description "Gmsh is a 3D finite element grid generator with a built-in @@ -5820,7 +5844,7 @@ as equations, scalars, vectors, and matrices.") (define-public z3 (package (name "z3") - (version "4.8.9") + (version "4.8.17") (home-page "https://github.com/Z3Prover/z3") (source (origin (method git-fetch) @@ -5829,54 +5853,51 @@ as equations, scalars, vectors, and matrices.") (file-name (git-file-name name version)) (sha256 (base32 - "1hnbzq10d23drd7ksm3c1n2611c3kd0q0yxgz8y78zaafwczvwxx")))) - (build-system gnu-build-system) + "1vvb09q7w7zd29qc4qjysrrhyylszm1wf6azkff004ixwn026b05")))) + (build-system cmake-build-system) (arguments - `(#:imported-modules ((guix build python-build-system) - ,@%gnu-build-system-modules) - #:modules (((guix build python-build-system) #:select (site-packages)) - (guix build gnu-build-system) - (guix build utils)) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'enable-bytecode-determinism - (lambda _ - (setenv "PYTHONHASHSEED" "0") - #t)) - (add-after 'unpack 'fix-compatability - ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only. - (lambda _ - (substitute* "src/util/mpz.cpp" - (("#include <immintrin.h>") "")) - #t)) - (add-before 'configure 'bootstrap - (lambda _ - (invoke "python" "scripts/mk_make.py"))) - ;; work around gnu-build-system's setting --enable-fast-install - ;; (z3's `configure' is a wrapper around the above python file, - ;; which fails when passed --enable-fast-install) - (replace 'configure - (lambda* (#:key inputs outputs #:allow-other-keys) - (invoke "./configure" - "--python" - (string-append "--prefix=" (assoc-ref outputs "out")) - (string-append "--pypkgdir=" (site-packages inputs outputs))))) - (add-after 'configure 'change-directory - (lambda _ - (chdir "build") - #t)) - (add-before 'check 'make-test-z3 - (lambda _ - ;; Build the test suite executable. - (invoke "make" "test-z3" "-j" - (number->string (parallel-job-count))))) - (replace 'check - (lambda _ - ;; Run all the tests that don't require arguments. - (invoke "./test-z3" "/a")))))) + (list + #:imported-modules `((guix build python-build-system) + ,@%cmake-build-system-modules) + #:modules '((guix build cmake-build-system) + (guix build utils) + ((guix build python-build-system) #:select (site-packages))) + #:configure-flags + #~(list "-DZ3_BUILD_PYTHON_BINDINGS=ON" + "-DZ3_LINK_TIME_OPTIMIZATION=ON" + (string-append + "-DCMAKE_INSTALL_PYTHON_PKG_DIR=" + #$output "/lib/python" + #$(version-major+minor (package-version python-wrapper)) + "/site-packages")) + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key parallel-build? tests? #:allow-other-keys) + (when tests? + (invoke "make" "test-z3" + (format #f "-j~a" + (if parallel-build? + (parallel-job-count) + 1))) + (invoke "./test-z3" "/a")))) + (add-after 'install 'compile-python-modules + (lambda _ + (setenv "PYTHONHASHSEED" "0") + + (invoke "python" "-m" "compileall" + "--invalidation-mode=unchecked-hash" + #$output))) + ;; This step is missing in the CMake build system, do it here. + (add-after 'compile-python-modules 'fix-z3-library-path + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((dest (string-append (site-packages inputs outputs) + "/z3/lib/libz3.so")) + (z3-lib (string-append #$output "/lib/libz3.so"))) + (mkdir-p (dirname dest)) + (symlink z3-lib dest))))))) (native-inputs - `(("which" ,which) - ("python" ,python-wrapper))) + (list which python-wrapper)) (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.") @@ -5886,6 +5907,7 @@ theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.") (package (inherit z3) (name "ocaml-z3") + (build-system gnu-build-system) (arguments `(#:imported-modules ((guix build python-build-system) ,@%gnu-build-system-modules) @@ -5947,7 +5969,8 @@ theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.") (version "2018.11.001") (source (origin (method url-fetch) - (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/" + (uri (string-append "https://elpa.mpcdf.mpg.de/software/" + "tarball-archive/Releases/" version "/elpa-" version ".tar.gz")) (sha256 (base32 @@ -6090,15 +6113,17 @@ reduction.") (define-public mcrl2 (package (name "mcrl2") - (version "202106.0") + (version "202206.0") (source (origin (method url-fetch) (uri (string-append "https://www.mcrl2.org/download/release/mcrl2-" version ".tar.gz")) + (patches (search-patches "mcrl2-fix-1687.patch" + "mcrl2-fix-counterexample.patch")) (sha256 (base32 - "1xgx3cd57vc7gbjic24j1q2za6j3ybz6nk4afvvpbwsf33xnlf4v")))) + "0alpck09pbvwk4axqmrvcjmsabsn20yayq5b3apq284n0hcbf01q")))) (inputs (list boost glu mesa qtbase-5)) (build-system cmake-build-system) @@ -7004,7 +7029,7 @@ management via the GIMPS project's Primenet server.") (define-public nauty (package (name "nauty") - (version "2.7r3") + (version "2.7r4") (source (origin (method url-fetch) @@ -7012,50 +7037,48 @@ management via the GIMPS project's Primenet server.") "https://pallini.di.uniroma1.it/" "nauty" (string-join (string-split version #\.) "") ".tar.gz")) (sha256 - (base32 "1hl81gpf3xjf809w04jczvilq1ixy9ch1qrax8a7lgx52svna1jg")))) + (base32 "19j8i10cgnqavphj0p7kq939azxckj9ayjpjr6sg76g2dxdch45q")))) (build-system gnu-build-system) (outputs '("out" "lib")) (arguments - `(#:test-target "checks" - #:configure-flags '("--enable-generic") ;prevent -march-native - #:phases - (modify-phases %standard-phases - ;; Default make target does not build all available - ;; executables. Create them now. - (add-after 'build 'build-extra-programs - (lambda _ - (for-each (lambda (target) (invoke "make" target)) - '("blisstog" "bliss2dre" "checks6" "sumlines")) - #t)) - ;; Upstream does not provide any install target. - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (lib-output (assoc-ref outputs "lib")) - (bin (string-append out "/bin")) - (doc (string-append out "/share/doc/nauty/")) - (include (string-append lib-output "/include/nauty")) - (lib (string-append lib-output "/lib/nauty"))) - (for-each (lambda (f) (install-file f bin)) - '("addedgeg" "amtog" "assembleg" "biplabg" "blisstog" - "bliss2dre" "catg" "checks6" "complg" "converseg" - "copyg" "countg" "cubhamg" "deledgeg" "delptg" - "directg" "dreadnaut" "dretodot" "dretog" "genbg" - "genbgL" "geng" "genquarticg" "genrang" "genspecialg" - "gentourng" "gentreeg" "hamheuristic" "labelg" - "linegraphg" "listg" "multig" "newedgeg" "pickg" - "planarg" "ranlabg" "shortg" "showg" "subdivideg" - "sumlines" "twohamg" "underlyingg" "vcolg" - "watercluster2" "NRswitchg")) - (for-each (lambda (f) (install-file f include)) - (find-files "." "\\.h$")) - (for-each (lambda (f) (install-file f lib)) - (find-files "." "\\.a$")) - (for-each (lambda (f) (install-file f doc)) - (append '("formats.txt" "README" "schreier.txt") - (find-files "." "\\.pdf$"))))))))) + (list + #:test-target "checks" + #:configure-flags #~(list "--enable-generic") ;prevent -march-native + #:phases + #~(modify-phases %standard-phases + ;; Default make target does not build all available + ;; executables. Create them now. + (add-after 'build 'build-extra-programs + (lambda _ + (for-each (lambda (target) (invoke "make" target)) + '("blisstog" "bliss2dre" "checks6" "sumlines")))) + ;; Upstream does not provide any install target. + (replace 'install + (lambda _ + (let* ((bin (string-append #$output "/bin")) + (doc (string-append #$output "/share/doc/nauty/")) + (include (string-append #$output:lib "/include/nauty")) + (lib (string-append #$output:lib "/lib/nauty"))) + (for-each (lambda (f) (install-file f bin)) + '("addedgeg" "amtog" "assembleg" "biplabg" "blisstog" + "bliss2dre" "catg" "checks6" "complg" "converseg" + "copyg" "countg" "cubhamg" "deledgeg" "delptg" + "directg" "dreadnaut" "dretodot" "dretog" "genbg" + "genbgL" "geng" "genquarticg" "genrang" "genspecialg" + "gentourng" "gentreeg" "hamheuristic" "labelg" + "linegraphg" "listg" "multig" "newedgeg" "pickg" + "planarg" "ranlabg" "shortg" "showg" "subdivideg" + "sumlines" "twohamg" "underlyingg" "vcolg" + "watercluster2" "NRswitchg")) + (for-each (lambda (f) (install-file f include)) + (find-files "." "\\.h$")) + (for-each (lambda (f) (install-file f lib)) + (find-files "." "\\.a$")) + (for-each (lambda (f) (install-file f doc)) + (append '("formats.txt" "README" "schreier.txt") + (find-files "." "\\.pdf$"))))))))) (inputs - (list gmp)) ;for sumlines + (list gmp)) ;for sumlines (home-page "https://pallini.di.uniroma1.it/") (synopsis "Library for graph automorphisms") (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of |