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-rw-r--r--gnu/packages/maths.scm373
1 files changed, 243 insertions, 130 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index cc42ce7902..9a37b681e9 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020, 2023 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020, 2023, 2024 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
;;; Copyright © 2014-2022 Eric Bavier <bavier@posteo.net>
@@ -48,7 +48,7 @@
;;; Copyright © 2021, 2022 Paul A. Patience <paul@apatience.com>
;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
-;;; Copyright © 2021, 2023 Guillaume Le Vaillant <glv@posteo.net>
+;;; Copyright © 2021, 2023, 2024 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>
@@ -63,6 +63,8 @@
;;; Copyright © 2023 Jake Leporte <jakeleporte@outlook.com>
;;; Copyright © 2023 Camilo Q.S. (Distopico) <distopico@riseup.net>
;;; Copyright © 2023 David Elsing <david.elsing@posteo.net>
+;;; Copyright © 2024 Herman Rimm <herman@rimm.ee>
+;;; Copyright © 2024 Foundation Devices, Inc. <hello@foundation.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -305,6 +307,42 @@ programmatic functions.")
(home-page "http://www.isthe.com/chongo/tech/comp/calc/")
(license license:lgpl2.1)))
+(define-public chuffed
+ (package
+ (name "chuffed")
+ (version "0.13.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/chuffed/chuffed")
+ (commit version)))
+ (sha256
+ (base32 "1c28q166qh84q4i5wz77fqvw7kld3fmhd245sgdvyxcbjpi2wr0m"))))
+ (build-system cmake-build-system)
+ (synopsis "Lazy clause generation solver")
+ (arguments
+ (list
+ #:tests? #f ;no 'test' target
+ #:phases #~(modify-phases %standard-phases
+ (add-before 'build 'patch-msc
+ (lambda _
+ (let ((out #$output))
+ (substitute* "chuffed.msc"
+ ;; Replace fzn-chuffed and chuffed paths
+ ;; before build.
+ (("\\.\\./../..")
+ out)
+ (("\\.\\.")
+ (string-append out "/share/minizinc")))))))))
+ (description
+ "Chuffed is a state of the art lazy clause solver designed from the
+ground up with lazy clause generation in mind. Lazy clause generation
+is a hybrid approach to constraint solving that combines features of
+finite domain propagation and Boolean satisfiability.")
+ (home-page "https://github.com/chuffed/chuffed")
+ (license license:expat)))
+
(define-public coda
(package
(name "coda")
@@ -839,6 +877,58 @@ LP/MIP solver is included in the package.")
(base32
"040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))))
+(define-public python-libensemble
+ (package
+ (name "python-libensemble")
+ (version "1.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "libensemble" version))
+ (sha256
+ (base32 "0ckmr04z7ai9mar58si0wzyyy8dnq6g89pg57mzmfz5mkbg4fbsa"))))
+ (build-system pyproject-build-system)
+ (native-inputs (list ncurses
+ python-mock
+ python-mpi4py
+ python-pytest
+ python-pytest-cov
+ python-pytest-timeout))
+ (propagated-inputs (list python-numpy
+ python-psutil
+ python-pydantic-2
+ python-pyyaml
+ python-tomli))
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-psutil
+ (lambda _
+ (substitute* "setup.py"
+ (("psutil>=5.9.4") "psutil>=5.9.2"))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ ;; These files require MPI and call subprocesses.
+ (delete-file
+ "libensemble/tests/unit_tests/test_executor.py")
+ (delete-file
+ "libensemble/tests/unit_tests/test_executor_gpus.py")
+ (setenv "TERM" "xterm")
+ ;; A very bad way to skip another MPI test.
+ (substitute* "libensemble/tests/run-tests.sh"
+ (("export UNIT_TEST_MPI_SUBDIR=.*")
+ "export UNIT_TEST_MPI_SUBDIR=''"))
+ ;; Run only unit tests, regression tests require MPI.
+ (invoke "bash" "libensemble/tests/run-tests.sh" "-u")))))))
+ (home-page "https://github.com/Libensemble/libensemble")
+ (synopsis "Toolkit for dynamic ensembles of calculations")
+ (description "@code{libensemble} is a complete toolkit for dynamic
+ensembles of calculations. It connects @code{deciders} to experiments or
+simulations.")
+ (license license:bsd-3)))
+
(define-public linasm
(package
(name "linasm")
@@ -2614,73 +2704,77 @@ and quadratic objectives using the Simplex algorithm.")
(license license:epl1.0)))
(define-public gecode
- (package
- (name "gecode")
- (version "6.2.0")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/Gecode/gecode")
- (commit (string-append "release-" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0b1cq0c810j1xr2x9y9996p894571sdxng5h74py17c6nr8c6dmk"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- ;; delete generated sources
- (for-each delete-file
- '("gecode/kernel/var-imp.hpp"
- "gecode/kernel/var-type.hpp"))))))
- (outputs '("out" "examples"))
- (build-system gnu-build-system)
- (arguments
- `(#:configure-flags
- (list (string-append "GLDFLAGS=-Wl,-rpath="
- (assoc-ref %outputs "out")
- "/lib")
- "--enable-examples=no")
- #:modules ((guix build gnu-build-system)
- (guix build utils)
- (ice-9 rdelim)
- (ice-9 popen))
- #:phases
- (modify-phases %standard-phases
- (add-after 'build 'build-examples
- (lambda* (#:key outputs #:allow-other-keys)
- (invoke "make" "compileexamples")))
- ;; The Makefile disrespects GLDFLAGS for some reason, so we have to
- ;; patch it ourselves... *sigh*
- (add-after 'install 'fix-rpath
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((libdir (string-append (assoc-ref outputs "out") "/lib")))
- (for-each
- (lambda (file)
- (let* ((pipe (open-pipe* OPEN_READ "patchelf"
- "--print-rpath" file))
- (line (read-line pipe)))
- (and (zero? (close-pipe pipe))
- (invoke "patchelf" "--set-rpath"
- (string-append libdir ":" line)
- file))))
- (find-files libdir ".*\\.so$")))))
- (add-after 'install 'install-examples
- (lambda* (#:key outputs #:allow-other-keys)
- (invoke "make" "installexamples"
- (string-append "bindir=" (assoc-ref outputs "examples")
- "/bin"))))
- ;; Tests depend on installed libraries.
- (delete 'check)
- (add-after 'fix-rpath 'check
- (assoc-ref %standard-phases 'check)))))
- (native-inputs
- (list patchelf perl sed))
- (home-page "https://www.gecode.org")
- (synopsis "Toolkit for developing constraint-based systems")
- (description "Gecode is a C++ toolkit for developing constraint-based
+ ;; The current release is not compatible with minizinc anymore.
+ ;; Use a commit that has been tested with minizinc.
+ (let ((commit "2d20e88cae176584b6e09d909aca3eb72ae76829")
+ (revision "2"))
+ (package
+ (name "gecode")
+ (version (git-version "6.2.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Gecode/gecode")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0hf7hd7m5p26xwn8f561f0gn2a6q33xz818jg3ivmvp2ysmmmm4r"))
+ (modules '((guix build utils)))
+ (snippet '(begin
+ ;; delete generated sources
+ (for-each delete-file
+ '("gecode/kernel/var-imp.hpp"
+ "gecode/kernel/var-type.hpp"))))))
+ (outputs '("out" "examples"))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:configure-flags #~(list (string-append "GLDFLAGS=-Wl,-rpath="
+ #$output "/lib")
+ "--enable-examples=no")
+ #:modules '((guix build gnu-build-system)
+ (guix build utils)
+ (ice-9 rdelim)
+ (ice-9 popen))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'build 'build-examples
+ (lambda _
+ (invoke "make" "compileexamples")))
+ ;; The Makefile disrespects GLDFLAGS for some reason,
+ ;; so we have to patch it ourselves.
+ (add-after 'install 'fix-rpath
+ (lambda _
+ (let ((libdir (string-append #$output "/lib")))
+ (for-each (lambda (file)
+ (let* ((pipe (open-pipe* OPEN_READ
+ "patchelf"
+ "--print-rpath" file))
+ (line (read-line pipe)))
+ (and (zero? (close-pipe pipe))
+ (invoke "patchelf" "--set-rpath"
+ (string-append libdir
+ ":" line)
+ file))))
+ (find-files libdir ".*\\.so$")))))
+ (add-after 'install 'install-examples
+ (lambda _
+ (invoke "make" "installexamples"
+ (string-append "bindir="
+ #$output "/bin"))))
+ ;; Tests depend on installed libraries.
+ (delete 'check)
+ (add-after 'fix-rpath 'check
+ (assoc-ref %standard-phases
+ 'check)))))
+ (native-inputs (list patchelf perl sed))
+ (home-page "https://www.gecode.org")
+ (synopsis "Toolkit for developing constraint-based systems")
+ (description
+ "Gecode is a C++ toolkit for developing constraint-based
systems and applications. It provides a modular and extensible solver.")
- (license license:expat)))
+ (license license:expat))))
(define-public libfixmath
(let ((commit "1416c9979635c69f344d3c1de84b3246001a6540")
@@ -4028,9 +4122,9 @@ book.")
(lambda (file)
(member file (cons* "." ".." targets)))
(scandir ".")))
- (substitute* "libmzn.cmake"
- (("include\\(cmake/targets/(.*)\\)" all target)
- (if (member target targets) all "")))))
+ (substitute* "libmzn.cmake"
+ (("include\\(cmake/targets/(.*)\\)" all target)
+ (if (member target targets) all "")))))
(with-directory-excursion "include/minizinc/solvers/MIP"
(for-each delete-file
(remove
@@ -4061,17 +4155,19 @@ book.")
#t))))
(build-system cmake-build-system)
(arguments
- `(#:tests? #f ; no ‘check’ target
- #:modules ((guix build cmake-build-system)
- (guix build utils)
- (srfi srfi-1))
+ (list
+ #:tests? #f ; no ‘check’ target
+ #:modules '((guix build cmake-build-system)
+ (guix build utils)
+ (srfi srfi-1))
#:phases
- (modify-phases %standard-phases
+ #~(modify-phases %standard-phases
(add-after 'install 'install-solver-configs
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((gecode (assoc-ref inputs "gecode"))
- (pkgdatadir (string-append (assoc-ref outputs "out")
- "/share/minizinc")))
+ (lambda _
+ (let ((chuffed #$(this-package-input "chuffed"))
+ (gecode #$(this-package-input "gecode"))
+ (pkgdatadir (string-append #$output
+ "/share/minizinc")))
(call-with-output-file (string-append pkgdatadir
"/Preferences.json")
(lambda (port)
@@ -4086,7 +4182,9 @@ book.")
port)
(newline port)))
- (mkdir-p (string-append pkgdatadir "/solvers"))
+ (copy-recursively
+ (string-append chuffed "/share/minizinc/solvers")
+ (string-append pkgdatadir "/solvers"))
(call-with-output-file (string-append pkgdatadir
"/solvers/gecode.msc")
(lambda (port)
@@ -4113,7 +4211,7 @@ book.")
(native-inputs
(list bison flex))
(inputs
- (list cbc gecode zlib))
+ (list cbc chuffed gecode zlib))
(home-page "https://www.minizinc.org")
(synopsis "High-level constraint modeling language")
(description "MiniZinc is a high-level modeling language for constraint
@@ -4915,7 +5013,7 @@ point numbers.")
(define-public wxmaxima
(package
(name "wxmaxima")
- (version "23.11.0")
+ (version "24.02.2")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -4924,7 +5022,7 @@ point numbers.")
(file-name (git-file-name name version))
(sha256
(base32
- "0xj91wfkm19avwmpcfwgzdkcqjwfpkl3glhkpn4advsqc6sx3ra0"))))
+ "1k2fbhyg7xrbk6ivfns6sq68rrbcl5dn84s64viv6iavk3ws033v"))))
(build-system cmake-build-system)
(native-inputs (list gettext-minimal))
(inputs (list bash-minimal
@@ -4993,7 +5091,9 @@ full text searching.")
(base32
"15zkvjbdxiiazhvh0g6y0ig9pgc4rvwnzplmnkx9dffz4xfn69w1"))))
(build-system cmake-build-system)
- (arguments `(#:tests? #f)) ; no test target
+ (arguments
+ `(#:tests? #f ; no test target
+ #:configure-flags '("-DOPENBLAS_PROVIDES_LAPACK=ON")))
(inputs
(list openblas arpack-ng))
(home-page "https://arma.sourceforge.net/")
@@ -9386,7 +9486,7 @@ numeric differences and differences in numeric formats.")
(define-public why3
(package
(name "why3")
- (version "1.6.0")
+ (version "1.7.2")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -9395,38 +9495,49 @@ numeric differences and differences in numeric formats.")
(file-name (git-file-name name version))
(sha256
(base32
- "0k3y98xzhrl44vwzq2m6k4nrllrwp3ll69lc2gfl8d77w0wg7gkp"))))
+ "0fq8wg8ji2v2ssz1d681glmk8glps1irnmdlhqfklaggx01hlf4p"))))
(build-system ocaml-build-system)
- (native-inputs
- (list autoconf automake coq ocaml which))
- (propagated-inputs
- (list camlzip ocaml-graph ocaml-menhir ocaml-num ocaml-zarith))
- (inputs
- (list coq-flocq emacs-minimal zlib))
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-before 'configure 'bootstrap
- (lambda _
- (invoke "./autogen.sh")
- (setenv "CONFIG_SHELL" (which "sh"))
- (substitute* "configure"
- (("#! /bin/sh") (string-append "#!" (which "sh")))
- ;; find ocaml-num in the correct directory
- (("\\$DIR/nums.cma") "$DIR/num.cma")
- (("\\$DIR/num.cmi") "$DIR/core/num.cmi"))
- #t))
- (add-after 'configure 'fix-makefile
- (lambda _
- (substitute* "Makefile"
- ;; find ocaml-num in the correct directory
- (("site-lib/num") "site-lib"))
- #t))
- (add-after 'install 'install-lib
- (lambda _
- (invoke "make" "byte")
- (invoke "make" "install-lib")
- #t)))))
+ (list #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'configure 'bootstrap
+ (lambda _
+ (invoke "./autogen.sh")
+ (setenv "CONFIG_SHELL" (which "sh"))
+ (substitute* "configure"
+ (("#! /bin/sh") (string-append "#!" (which "sh")))
+ ;; find ocaml-num in the correct directory
+ (("\\$DIR/nums.cma") "$DIR/num.cma")
+ (("\\$DIR/num.cmi") "$DIR/core/num.cmi"))))
+ (add-after 'configure 'fix-makefile
+ (lambda _
+ (substitute* "Makefile"
+ ;; find ocaml-num in the correct directory
+ (("site-lib/num") "site-lib"))))
+ (add-after 'install 'install-lib
+ (lambda _
+ (invoke "make" "byte")
+ (invoke "make" "install-lib"))))))
+ (native-inputs (list autoconf
+ automake
+ coq
+ ocaml
+ ocaml-findlib
+ which))
+ (propagated-inputs (list camlzip
+ lablgtk3
+ ocaml-graph
+ ocaml-lablgtk3-sourceview3
+ ocaml-menhir
+ ocaml-ppx-deriving
+ ocaml-ppx-sexp-conv
+ ocaml-num
+ ocaml-re
+ ocaml-sexplib
+ ocaml-zarith))
+ (inputs (list coq-flocq
+ emacs-minimal
+ zlib))
(home-page "https://why3.lri.fr")
(synopsis "Deductive program verification")
(description "Why3 provides a language for specification and programming,
@@ -9443,14 +9554,14 @@ of C, Java, or Ada programs.")
(define-public frama-c
(package
(name "frama-c")
- (version "27.1")
+ (version "28.1")
(source (origin
(method url-fetch)
- (uri (string-append "http://frama-c.com/download/frama-c-"
- version "-Cobalt.tar.gz"))
+ (uri (string-append "https://frama-c.com/download/frama-c-"
+ version "-Nickel.tar.gz"))
(sha256
(base32
- "1lirkvhf5m53d33l0aw5jzc1fyzkwx5fkgh9g71732d52r55f4sv"))))
+ "14zmwghwhcryvri7k91vc1yampvxvhg36vwjxf64d8kx7dsbq802"))))
(build-system dune-build-system)
(arguments
`(#:phases
@@ -9473,6 +9584,7 @@ of C, Java, or Ada programs.")
ocaml-ppx-deriving-yojson
ocaml-ppx-deriving-yaml
ocaml-ppx-import
+ ocaml-unionfind
why3))
(native-inputs (list dune-site time ocaml-menhir ocaml-graph))
(native-search-paths
@@ -9722,6 +9834,8 @@ computation is supported via MPI.")
(sha256
(base32
"08nyfli3x7gd396ffd1a8zn9fj3gm6a8yw0ggm547c09sp2rgvl7"))
+ (patches (search-patches "scilab-better-compiler-detection.patch"
+ "scilab-tbx_build_help.patch"))
(modules '((guix build utils)
(ice-9 ftw)))
(snippet
@@ -9766,9 +9880,9 @@ computation is supported via MPI.")
"compile"
"config.guess"
"config.sub"
- "ltmain.sh"
"depcomp"
"install-sh"
+ "ltmain.sh"
"missing"))
(delete-file-recursively "modules/dynamic_link/src/scripts/m4")
(for-each delete-file
@@ -9792,6 +9906,7 @@ computation is supported via MPI.")
(inputs (list `(,pcre "bin")
`(,pcre "out")
arpack-ng
+ bash-minimal
curl
fftw
gettext-minimal
@@ -9849,10 +9964,8 @@ computation is supported via MPI.")
(add-after 'unpack 'set-version
(lambda _
(substitute* "modules/core/includes/version.h.in"
- (("scilab-branch-main") ; version
- (string-append
- "scilab-"
- #$(version-major+minor (package-version this-package)))))))
+ (("branch-[a-z0-9\\.]*") ; version
+ #$(version-major+minor (package-version this-package))))))
(add-after 'unpack 'restrain-to-scilab-cli
(lambda _
;; Install only scilab-cli.desktop
@@ -9883,13 +9996,13 @@ computation is supported via MPI.")
(add-after 'bootstrap 'bootstrap-dynamic_link-scripts
(lambda _
(with-directory-excursion "modules/dynamic_link/src/scripts"
- ((assoc-ref %standard-phases 'bootstrap)))))
+ ((assoc-ref %standard-phases 'bootstrap))
+ (substitute* "compilerDetection.sh"
+ (("PATHTOCONFIGURE=.*")
+ "PATHTOCONFIGURE=${BASH_SOURCE[0]%/*}/\n")
+ (("PROGNAME.*") "\n")))))
(add-before 'build 'pre-build
(lambda* (#:key inputs #:allow-other-keys)
- ;; Fix scilab script.
- (substitute* "bin/scilab"
- (("/bin/ls")
- (search-input-file inputs "bin/ls")))
;; Fix core.start.
(substitute* "modules/core/etc/core.start"
(("'SCI/modules")
generated by cgit v1.2.3 (git 2.25.4) at 2024-05-20 12:37:54 +0000