diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 179 |
1 files changed, 161 insertions, 18 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index d7ba5fca0a..4b33056d1e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -28,7 +28,7 @@ ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com> ;;; Copyright © 2018, 2020, 2021 Marius Bakke <marius@gnu.org> ;;; Copyright © 2018 Eric Brown <brown@fastmail.com> -;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> +;;; Copyright © 2018, 2021 Julien Lepiller <julien@lepiller.eu> ;;; Copyright © 2018 Amin Bandali <bandali@gnu.org> ;;; Copyright © 2019, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr> ;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com> @@ -75,6 +75,7 @@ #: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 ocaml) #:use-module (guix build-system python) #:use-module (guix build-system ruby) #:use-module (gnu packages algebra) @@ -86,11 +87,13 @@ #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) + #:use-module (gnu packages coq) #:use-module (gnu packages curl) #:use-module (gnu packages cyrus-sasl) #:use-module (gnu packages dbm) #:use-module (gnu packages documentation) #:use-module (gnu packages elf) + #:use-module (gnu packages emacs) #:use-module (gnu packages file) #:use-module (gnu packages flex) #:use-module (gnu packages fltk) @@ -120,6 +123,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages netpbm) + #:use-module (gnu packages ocaml) #:use-module (gnu packages onc-rpc) #:use-module (gnu packages pcre) #:use-module (gnu packages popt) @@ -248,6 +252,9 @@ programming languages.") (base32 "0zlbhg0lb6j60188c2xhcrvviskr079552icjldqhy1jhgmxghmm")))) (build-system cmake-build-system) + (arguments + `(#:configure-flags '("-DLINK_APPS_SHARED=ON" + "-DCMAKE_POSITION_INDEPENDENT_CODE=ON"))) (synopsis "Calculate convex hulls and related structures") (description "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi @@ -1234,7 +1241,8 @@ extremely large and complex data collections.") "https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) (define-public hdf5-1.10 - (package/inherit hdf5-1.8 + (package + (inherit hdf5-1.8) (version "1.10.7") (source (origin @@ -1253,7 +1261,8 @@ extremely large and complex data collections.") (patches (search-patches "hdf5-config-date.patch")))))) (define-public hdf5-1.12 - (package/inherit hdf5-1.8 + (package + (inherit hdf5-1.8) (version "1.12.0") (source (origin @@ -1751,21 +1760,16 @@ online as well as original implementations of various other algorithms.") (define-public ipopt (package (name "ipopt") - (version "3.12.12") + (version "3.13.4") (source (origin - (method url-fetch) - (uri (string-append - "https://www.coin-or.org/download/source/Ipopt/Ipopt-" - version".tgz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/coin-or/Ipopt") + (commit (string-append "releases/" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv")) - (modules '((guix build utils))) - (snippet - ;; Make sure we don't use the bundled software. - '(begin - (delete-file-recursively "ThirdParty") - #t)))) + "08gznhwhqv1x4baksz350ih8q16r5rd0k8vals6078m3h94khr4b")))) (build-system gnu-build-system) (arguments '(#:phases (modify-phases %standard-phases @@ -1785,7 +1789,8 @@ online as well as original implementations of various other algorithms.") after "\n"))) #t)))))) (native-inputs - `(("gfortran" ,gfortran))) + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) (inputs ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL. `(("lapack" ,lapack))) ;for both libblas and liblapack @@ -1795,6 +1800,35 @@ online as well as original implementations of various other algorithms.") "The Interior Point Optimizer (IPOPT) is a software package for large-scale nonlinear optimization. It provides C++, C, and Fortran interfaces.") + (license license:epl2.0))) + +(define-public cbc + (package + (name "cbc") + (version "2.10.5") + (source (origin + (method url-fetch) + (uri (string-append "https://www.coin-or.org/download/source/" + "Cbc/Cbc-" version ".tgz")) + (sha256 + (base32 + "0wk9vr6zc62gw71v7gnra5wxqlcljcgbhm5lasx236v791b986ns")) + (modules '((guix build utils))) + (snippet + ;; Make sure we don't use the bundled software. + '(delete-file-recursively "ThirdParty")))) + (build-system gnu-build-system) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (inputs + `(("openblas" ,openblas))) + (home-page "https://www.coin-or.org") + (synopsis "Branch-and-cut solver") + (description + "Cbc (Coin-or branch and cut) is a mixed integer linear programming +solver written in C++. It can be used as a library or as a standalone +executable.") (license license:epl1.0))) (define-public clp @@ -4617,7 +4651,7 @@ set.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/LLNL/hypre") + (url "https://github.com/hypre-space/hypre") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -4722,7 +4756,8 @@ set.") (copy-recursively (string-append base "-html") (string-append docdir "/" base))) '("usr-manual" "ref-manual"))))))))) - (home-page "http://www.llnl.gov/casc/hypre/") + (home-page "https://computing.llnl.gov/projects\ +/hypre-scalable-linear-solvers-multigrid-methods") (synopsis "Library of solvers and preconditioners for linear equations") (description "HYPRE is a software library of high performance preconditioners and @@ -6284,3 +6319,111 @@ interval arithmetic, plotting.") "Numdiff compares files line by line and field by field, ignoring small numeric differences and differences in numeric formats.") (license license:gpl3+))) + +(define-public why3 + (package + (name "why3") + (version "1.3.1") + (source (origin + (method url-fetch) + (uri (string-append "https://gforge.inria.fr/frs/download.php/file" + "/38291/why3-" version ".tar.gz")) + (sha256 + (base32 + "16zcrc60zz2j3gd3ww93z2z9x2jkxb3kr57y8i5rcgmacy7mw3bv")))) + (build-system ocaml-build-system) + (native-inputs + `(("coq" ,coq) + ("ocaml" ,ocaml) + ("which" ,which))) + (propagated-inputs + `(("camlzip" ,camlzip) + ("ocaml-graph" ,ocaml-graph) + ("ocaml-menhir" ,ocaml-menhir) + ("ocaml-num" ,ocaml-num) + ("ocaml-zarith" ,ocaml-zarith))) + (inputs + `(("coq-flocq" ,coq-flocq) + ("emacs-minimal" ,emacs-minimal) + ("zlib" ,zlib))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'configure 'fix-configure + (lambda _ + (setenv "CONFIG_SHELL" (which "sh")) + (substitute* "configure" + ;; find ocaml-num in the correct directory + (("\\$DIR/nums.cma") "$DIR/../nums.cma") + (("\\$DIR/num.cmi") "$DIR/../num.cmi")) + #t)) + (add-after 'configure 'fix-makefile + (lambda _ + (substitute* "Makefile" + ;; find ocaml-num in the correct directory + (("site-lib/num") "site-lib")) + #t)) + (add-after 'install 'install-lib + (lambda _ + (invoke "make" "byte") + (invoke "make" "install-lib") + #t))))) + (home-page "http://why3.lri.fr") + (synopsis "Deductive program verification") + (description "Why3 provides a language for specification and programming, +called WhyML, and relies on external theorem provers, both automated and +interactive, to discharge verification conditions. Why3 comes with a standard +library of logical theories (integer and real arithmetic, Boolean operations, +sets and maps, etc.) and basic programming data structures (arrays, queues, +hash tables, etc.). A user can write WhyML programs directly and get +correct-by-construction OCaml programs through an automated extraction +mechanism. WhyML is also used as an intermediate language for the verification +of C, Java, or Ada programs.") + (license license:lgpl2.1))) + +(define-public frama-c + (package + (name "frama-c") + (version "22.0") + (source (origin + (method url-fetch) + (uri (string-append "http://frama-c.com/download/frama-c-" + version "-Titanium.tar.gz")) + (sha256 + (base32 + "1mq1fijka95ydrla486yr4w6wdl9l7vmp512s1q00b0p6lmfwmkh")))) + (build-system ocaml-build-system) + (arguments + `(#:tests? #f; no test target in Makefile + #:phases + (modify-phases %standard-phases + (add-before 'configure 'export-shell + (lambda* (#:key inputs #:allow-other-keys) + (setenv "CONFIG_SHELL" (string-append (assoc-ref inputs "bash") + "/bin/sh")) + #t))))) + (inputs + `(("gmp" ,gmp))) + (propagated-inputs + `(("ocaml-biniou" ,ocaml-biniou) + ("ocaml-easy-format" ,ocaml-easy-format) + ("ocaml-graph" ,ocaml-graph) + ("ocaml-yojson" ,ocaml-yojson) + ("ocaml-zarith" ,ocaml-zarith) + ("why3" ,why3))) + (native-search-paths + (list (search-path-specification + (variable "FRAMAC_SHARE") + (files '("share/frama-c")) + (separator #f)) + (search-path-specification + (variable "FRAMAC_LIB") + (files '("lib/frama-c")) + (separator #f)))) + (home-page "http://frama-c.com") + (synopsis "C source code analysis platform") + (description "Frama-C is an extensible and collaborative platform dedicated +to source-code analysis of C software. The Frama-C analyzers assist you in +various source-code-related activities, from the navigation through unfamiliar +projects up to the certification of critical software.") + (license license:lgpl2.1+))) |