gnu: facter: Update to 4.0.33.

[jackhill/guix/guix.git] / gnu / packages / algebra.scm

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 4df2e96..2fca9ec 100644 (file)
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -12,6 +12,7 @@
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
+;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -43,6 +44,7 @@
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages image)
   #:use-module (gnu packages java)
+  #:use-module (gnu packages llvm)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages multiprecision)
@@ -153,7 +155,7 @@ line applications.")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/fplll/fplll.git")
+                    (url "https://github.com/fplll/fplll")
                     (commit version)))
               (file-name (git-file-name name version))
               (sha256
@@ -203,7 +205,7 @@ the real span of the lattice.")
        ;; Github instead.
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/fplll/fpylll.git")
+             (url "https://github.com/fplll/fpylll")
              (commit (string-append version "dev"))))
        (file-name (git-file-name name version))
        (sha256
@@ -271,7 +273,7 @@ PARI is also available as a C library to allow for faster computations.")
 (define-public gp2c
   (package
    (name "gp2c")
-   (version "0.0.11pl3")
+   (version "0.0.11pl4")
    (source (origin
             (method url-fetch)
             (uri (string-append
@@ -279,7 +281,7 @@ PARI is also available as a C library to allow for faster computations.")
                   version ".tar.gz"))
             (sha256
               (base32
-                "0yymbrgyjw500hqgmkj5m4nmscd7c9rs9w2c96lxgrcyab8krhrm"))))
+                "1cnnh7diqc97q76q5pyhpbljbhc0sz8mlrbqgiwi0sjkgh8iqsj0"))))
    (build-system gnu-build-system)
    (native-inputs `(("perl" ,perl)))
    (inputs `(("pari-gp" ,pari-gp)))
@@ -349,7 +351,7 @@ precision.")
 (define-public giac
   (package
     (name "giac")
-    (version "1.5.0-87")
+    (version "1.6.0-7")
     (source
      (origin
        (method url-fetch)
@@ -361,7 +363,7 @@ precision.")
                            "~parisse/debian/dists/stable/main/source/"
                            "giac_" version ".tar.gz"))
        (sha256
-        (base32 "1d0h1yb7qvh9x7wwv9yrzmcp712f49w1iljkxp4y6g9pzsmg1mmv"))))
+        (base32 "1pvgp137zcl0rbhdn1j41xxfml7fp771a7x4ph8qrhhlx0hxzn3p"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)
@@ -401,7 +403,7 @@ precision.")
                (delete-file (string-append out "/bin/xcasnew"))
                #t))))))
     (inputs
-     ;;; TODO: Add libnauty.
+;;; TODO: Add libnauty.
      `(("fltk" ,fltk)
        ("glpk" ,glpk)
        ("gmp" ,gmp)
@@ -438,34 +440,43 @@ or text interfaces) or as a C++ library.")
 (define-public flint
   (package
    (name "flint")
-   (version "2.5.2")
-   (source (origin
-            (method url-fetch)
-            (uri (string-append
-                  "http://flintlib.org/flint-"
-                  version ".tar.gz"))
-            (sha256 (base32
-                     "11syazv1a8rrnac3wj3hnyhhflpqcmq02q8pqk2m6g2k6h0gxwfb"))
-            (patches (search-patches "flint-ldconfig.patch"))))
+   ;; When updating this package, change its licence to lgpl2.1+.
+   ;; https://github.com/wbhart/flint2/issues/812
+   (version "2.6.2")
+   (source
+    (origin
+      (method url-fetch)
+      (uri (string-append "http://flintlib.org/flint-" version ".tar.gz"))
+      (sha256
+       (base32 "1np1p8dx4g3jnlfr1sxmi1jdk2pb57crskm0ch2w2l1v7h8lb6sz"))))
    (build-system gnu-build-system)
+   (inputs
+    `(("ntl" ,ntl)))
    (propagated-inputs
     `(("gmp" ,gmp)
       ("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
    (arguments
-    `(#:parallel-tests? #f ; seems to be necessary on arm
+    `(#:parallel-tests? #f              ; seems to be necessary on arm
       #:phases
        (modify-phases %standard-phases
+         (add-before 'configure 'newer-c++
+           (lambda _
+             (substitute* "configure"
+               (("-ansi") ""))
+             #t))
          (replace 'configure
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out"))
                    (gmp (assoc-ref inputs "gmp"))
-                   (mpfr (assoc-ref inputs "mpfr")))
-               ;; do not pass "--enable-fast-install", which makes the
-               ;; homebrew configure process fail
+                   (mpfr (assoc-ref inputs "mpfr"))
+                   (ntl (assoc-ref inputs "ntl")))
+               ;; Do not pass "--enable-fast-install", which makes the
+               ;; homebrew configure process fail.
                (invoke "./configure"
                        (string-append "--prefix=" out)
                        (string-append "--with-gmp=" gmp)
-                       (string-append "--with-mpfr=" mpfr))
+                       (string-append "--with-mpfr=" mpfr)
+                       (string-append "--with-ntl=" ntl))
                #t))))))
    (synopsis "Fast library for number theory")
    (description
@@ -485,16 +496,16 @@ fast arithmetic.")
 (define-public arb
   (package
     (name "arb")
-    (version "2.17.0")
+    (version "2.18.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/fredrik-johansson/arb.git")
+                    (url "https://github.com/fredrik-johansson/arb")
                     (commit version)))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "05lpy3hkl5f8ik19aw40cqydrb932xaf2n8hbq9ib5dnk7f010p1"))))
+                "15fx3dcbzgwddw9p1nysmx0dbh058afv5m8cj5pdjkcmcl7kw7z9"))))
     (build-system gnu-build-system)
     (propagated-inputs
      `(("flint" ,flint)))               ; flint.h is included by arf.h
@@ -533,7 +544,7 @@ real and complex numbers, with automatic, rigorous error control.")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/fredrik-johansson/python-flint.git")
+                    (url "https://github.com/fredrik-johansson/python-flint")
                     (commit version)))
               (file-name (git-file-name name version))
               (sha256
@@ -609,7 +620,7 @@ matrices, and polynomials over the integers and over finite fields.")
 (define-public singular
   (package
    (name "singular")
-   (version "4.1.2p1")
+   (version "4.1.3p2")
    (source
     (origin
       (method url-fetch)
@@ -623,7 +634,7 @@ matrices, and polynomials over the integers and over finite fields.")
                         #\.) "-")
                       "/singular-" version ".tar.gz"))
              (sha256 (base32
-                      "0kvd55353fiqyq1msmi0kka66n5h0aqs7m3km60r01b1w2f8085m"))))
+                      "1524yrni7gh0hir5ckridq671q5s6avfjdsdyahj51kzdl3wcypf"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("doxygen" ,doxygen)
@@ -726,7 +737,7 @@ syntax is similar to that of C, so basic usage is familiar.  It also includes
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/extemporelang/kiss_fft.git")
+                    (url "https://github.com/extemporelang/kiss_fft")
                     (commit version)))
               (file-name (git-file-name name version))
               (sha256
@@ -832,7 +843,7 @@ cosine/ sine transforms or DCT/DST).")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/vkostyukov/la4j.git")
+                    (url "https://github.com/vkostyukov/la4j")
                     (commit version)))
               (file-name (string-append name "-" version "-checkout"))
               (sha256
@@ -946,6 +957,46 @@ minimization and curve fitting.  It is mature code, based on decades-old
 algorithms from the FORTRAN library MINPACK.")
     (license license:bsd-2)))
 
+(define-public symengine
+  (package
+    (name "symengine")
+    (version "0.6.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/symengine/symengine")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "129iv9maabmb42ylfdv0l0g94mcbf3y4q3np175008rcqdr8z6h1"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:configure-flags
+       ;; These are the suggested build options in the README.
+       '("-DCMAKE_BUILD_TYPE=Release"
+         "-DWITH_GMP=on"
+         "-DWITH_MPFR=on"
+         "-DWITH_MPC=on"
+         "-DINTEGER_CLASS=flint"
+         "-DWITH_LLVM=on"
+         "-DWITH_SYMENGINE_THREAD_SAFE=on"
+         "-DBUILD_SHARED_LIBS=on")))    ;also build libsymengine
+    (native-inputs
+     `(("llvm" ,llvm)))
+    (inputs
+     `(("flint" ,flint)
+       ("gmp" ,gmp)
+       ("mpc" ,mpc)
+       ("mpfr" ,mpfr)))
+    (home-page "https://github.com/symengine/symengine")
+    (synopsis "Fast symbolic manipulation library")
+    (description
+     "SymEngine is a standalone fast C++ symbolic manipulation library.
+Optional thin wrappers allow usage of the library from other languages.")
+    (license (list license:expat        ;SymEngine
+                   license:bsd-3))))    ;3rd party code
+
 (define-public eigen
   (package
     (name "eigen")
@@ -1033,7 +1084,7 @@ features, and more.")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/QuantStack/xtensor.git")
+                    (url "https://github.com/QuantStack/xtensor")
                     (commit version)))
               (sha256
                (base32
@@ -1314,14 +1365,15 @@ algebra, such as the row echelon form.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))))
+                "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))
+              (patches (search-patches "linbox-fix-pkgconfig.patch"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
        ("libtool" ,libtool)
        ("pkg-config" ,pkg-config)))
-    (inputs
+    (propagated-inputs
      `(("fflas-ffpack" ,fflas-ffpack)))
     (synopsis "C++ library for linear algebra over exact rings")
     (description