Merge branch 'staging' into core-updates

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

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 9518940..a31ac8d 100644 (file)
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -8,6 +8,7 @@
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017, 2019 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -201,6 +202,7 @@ the real span of the lattice.")
        (uri (git-reference
              (url "https://github.com/fplll/fpylll.git")
              (commit (string-append version "dev"))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
          "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w"))))
@@ -224,7 +226,7 @@ the real span of the lattice.")
 (define-public pari-gp
   (package
     (name "pari-gp")
-    (version "2.11.1")
+    (version "2.11.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -232,12 +234,11 @@ the real span of the lattice.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "1jfax92jpydjd02fwl30r6b8kfzqqd6sm4yx94gidyz9lqjb7a94"))))
+                "0fck8ssmirl8fy7s4mspgrxjs5sag76xbshqlqzkcl3kqyrk4raa"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("texlive" ,(texlive-union
-                    (list texlive-fonts-amsfonts
-                          texlive-latex-amsfonts)))))
+                    (list texlive-amsfonts)))))
     (inputs `(("gmp" ,gmp)
               ("libx11" ,libx11)
               ("perl" ,perl)
@@ -267,7 +268,7 @@ PARI is also available as a C library to allow for faster computations.")
 (define-public gp2c
   (package
    (name "gp2c")
-   (version "0.0.11pl1")
+   (version "0.0.11pl2")
    (source (origin
             (method url-fetch)
             (uri (string-append
@@ -275,7 +276,7 @@ PARI is also available as a C library to allow for faster computations.")
                   version ".tar.gz"))
             (sha256
               (base32
-                "1c6f6vmncw032kfzrfyr8bynw6yd3faxpy2285r009fmr0zxfs5s"))))
+                "0wqsf05wgkqvmmsx7jinvzdqav6rl56sr8haibgs31nzz4x9xz9g"))))
    (build-system gnu-build-system)
    (native-inputs `(("perl" ,perl)))
    (inputs `(("pari-gp" ,pari-gp)))
@@ -298,6 +299,20 @@ GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
    (license license:gpl2)
    (home-page "https://pari.math.u-bordeaux.fr/")))
 
+(define fplll-4-cmh
+  (package
+    (inherit fplll)
+    (name "fplll")
+    (version "4.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
+             version ".tar.gz"))
+       (sha256
+        (base32 "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))))
+
 (define-public cmh
   (package
    (name "cmh")
@@ -316,7 +331,7 @@ GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
        ("mpfr" ,mpfr)
        ("mpc" ,mpc)
        ("mpfrcx" ,mpfrcx)
-       ("fplll" ,fplll)
+       ("fplll" ,fplll-4-cmh)
        ("pari-gp"  ,pari-gp)))
    (synopsis "Igusa class polynomial computations")
    (description
@@ -331,7 +346,7 @@ precision.")
 (define-public giac
   (package
     (name "giac")
-    (version "1.5.0-57")
+    (version "1.5.0-85")
     (source (origin
               (method url-fetch)
               ;; "~parisse/giac" is not used because the maintainer regularly
@@ -343,7 +358,7 @@ precision.")
                                   "source/giac_" version ".tar.gz"))
               (sha256
                (base32
-                "08c93knsisbk9dkyyrignw0wvqbr1sa5czlvk5l307ahxbbmqncf"))))
+                "03icgrfhb1xiy95cqmfgmcb1lw3775mr2ybnzandmyn44iycs6rh"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)
@@ -470,7 +485,7 @@ fast arithmetic.")
 (define-public arb
   (package
     (name "arb")
-    (version "2.16.0")
+    (version "2.17.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -479,7 +494,7 @@ fast arithmetic.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0478671wfwy3gl26sbxh1jq1ih36z4k72waa8y2y2lvn649gb7cd"))))
+                "05lpy3hkl5f8ik19aw40cqydrb932xaf2n8hbq9ib5dnk7f010p1"))))
     (build-system gnu-build-system)
     (propagated-inputs
      `(("flint" ,flint)))               ; flint.h is included by arf.h
@@ -495,8 +510,8 @@ fast arithmetic.")
                    (flint (assoc-ref inputs "flint"))
                    (gmp (assoc-ref inputs "gmp"))
                    (mpfr (assoc-ref inputs "mpfr")))
-               ;; do not pass "--enable-fast-install", which makes the
-               ;; homebrew configure process fail
+               ;; Do not pass "--enable-fast-install", which makes the
+               ;; homebrew configure process fail.
                (invoke "./configure"
                        (string-append "--prefix=" out)
                        (string-append "--with-flint=" flint)
@@ -509,7 +524,7 @@ arithmetic.  It supports efficient high-precision computation with
 polynomials, power series, matrices and special functions over the
 real and complex numbers, with automatic, rigorous error control.")
     (license license:lgpl2.1+)
-    (home-page "http://fredrikj.net/arb/")))
+    (home-page "http://arblib.org")))
 
 (define-public python-flint
   (package
@@ -668,15 +683,23 @@ binary.")
              (uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
              (sha256
               (base32
-               "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))))
+               "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))
+             (patches (search-patches "bc-fix-cross-compilation.patch"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("ed" ,ed)
+     `(("automake" ,automake)
+       ("autoconf" ,autoconf)
+       ("ed" ,ed)
        ("flex" ,flex)
        ("texinfo" ,texinfo)))
     (arguments
      '(#:configure-flags
-       (list "--with-readline")))
+       (list "--with-readline")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'autogen
+           (lambda _
+             (invoke "autoreconf" "-vif"))))))
     (home-page "https://www.gnu.org/software/bc/")
     (synopsis "Arbitrary precision numeric processing language")
     (description
@@ -974,7 +997,7 @@ features, and more.")
 (define-public xtensor
   (package
     (name "xtensor")
-    (version "0.20.5")
+    (version "0.20.10")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -982,7 +1005,7 @@ features, and more.")
                     (commit version)))
               (sha256
                (base32
-                "0kkc4ar7p2d94jnclmrh46dwv7ldy9lx630vm9gci3pp4hnhbj9f"))
+                "1fmv2hpx610xwhxrndfsfvlbqfyk4l3gi5q5d7pa9m82kblxjj9l"))
               (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (native-inputs
@@ -992,7 +1015,7 @@ features, and more.")
      `(#:configure-flags
        '("-DBUILD_TESTS=ON")
        #:test-target "xtest"))
-    (home-page "http://quantstack.net/xtensor")
+    (home-page "https://quantstack.net/xtensor")
     (synopsis "C++ tensors with broadcasting and lazy computing")
     (description "xtensor is a C++ library meant for numerical analysis with
 multi-dimensional array expressions.
@@ -1008,7 +1031,7 @@ xtensor provides:
 (define-public gap
   (package
     (name "gap")
-    (version "4.10.1")
+    (version "4.10.2")
     (source
      (origin
        (method url-fetch)
@@ -1018,8 +1041,7 @@ xtensor provides:
                            version
                            ".tar.bz2"))
        (sha256
-        (base32
-         "136s0zvhcw41fshj5zgsrjcy2kd58cdh2m3ddp5rdizi4rx54f10"))
+        (base32 "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"))
        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
        (snippet
         '(begin
@@ -1423,7 +1445,7 @@ of M4RI from F_2 to F_{2^e}.")
 (define-public eclib
   (package
     (name "eclib")
-    (version "20190226")
+    (version "20190909")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1432,7 +1454,7 @@ of M4RI from F_2 to F_{2^e}.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1910np1xzyjzszay24xn4b81qhpsvhp5aix9vdpknplni2mq8kwb"))))
+                "1gw27lqc3f525n8qdcmr2nyn16y9g10z9f6dnmckyyxcdzvhq35n"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)