From bf95a142bbe8ab4ae6ccf87ad0df21cb56bbd3d3 Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Mon, 17 Jun 2019 12:12:31 +0200
Subject: gnu: gap: Update to 4.10.1.

* gnu/packages/algebra.scm (gap): Update to 4.10.1.
Install headers and library files by hand, since the make targets have
disappeared. Delete the special check phase, since the "make check" target
has appeared. Remove a package that is no longer recommended, and enable
two recommended packages with clarified licenses.
---
 gnu/packages/algebra.scm | 62 ++++++++++++++++++++++++++++++++++--------------
 1 file changed, 44 insertions(+), 18 deletions(-)

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 69163a43d9..20ecc71b81 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -928,7 +928,7 @@ xtensor provides:
 (define-public gap
   (package
     (name "gap")
-    (version "4.10.0")
+    (version "4.10.1")
     (source
      (origin
        (method url-fetch)
@@ -939,7 +939,7 @@ xtensor provides:
                            ".tar.bz2"))
        (sha256
         (base32
-         "1dmb8v4p7j1nnf7sx8sg54b49yln36bi9acwp7w1d3a1nxj17ird"))
+         "136s0zvhcw41fshj5zgsrjcy2kd58cdh2m3ddp5rdizi4rx54f10"))
        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
        (snippet
         '(begin
@@ -967,20 +967,20 @@ xtensor provides:
                    ;; Optional packages, searched for at start,
                    ;; and their depedencies.
                    "alnuth-3.1.0"
-                   "AutoDoc-2018.09.20"
                    "autpgrp-1.10"
                    "crisp-1.4.4"     ; bsd-2
-                   ; "ctbllib"       ; no explicit license, drop
+                   "ctbllib"       ; gpl3+ according to doc/chap0.txt
                    "FactInt-1.6.2"
                    "fga"
                    "irredsol-1.4"    ; bsd-2
-                   "laguna-3.9.0"
+                   "laguna-3.9.2"
                    "polenta-1.3.8"
                    "polycyclic-2.14"
                    "radiroot-2.8"
                    "resclasses-4.7.1"
                    "sophus-1.24"
-                   ; "tomlib-1.2.7"  ; no explicit license, drop
+                   "tomlib-1.2.7"  ; gpl2+, clarified in the git repository
+                                   ; and the next release
                    "utils-0.59"))))
            #t))))
     (build-system gnu-build-system)
@@ -988,7 +988,11 @@ xtensor provides:
      `(("gmp" ,gmp)
        ("zlib" ,zlib)))
     (arguments
-     `(#:phases
+     `(#:modules ((ice-9 ftw)
+                  (srfi srfi-26)
+                  (guix build gnu-build-system)
+                  (guix build utils))
+       #:phases
        (modify-phases %standard-phases
          (add-after 'build 'build-packages
            ;; Compile all packages that have not been deleted by the
@@ -1004,19 +1008,16 @@ xtensor provides:
              (with-directory-excursion "doc"
                (invoke "./make_doc"))
              #t))
-         (replace 'check
-           (lambda _
-             ;; "make check" is expected to appear in gap-4.10.1
-             (invoke "./gap" "tst/testinstall.g")
-             #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin"))
+                    (lib (string-append out "/lib"))
                     (prog (string-append bin "/gap"))
                     (prog-real (string-append bin "/.gap-real"))
                     (share (string-append out "/share/gap"))
-                    (include (string-append out "/include/gap")))
+                    (include (string-append out "/include/gap"))
+                    (include-hpc (string-append include "/hpc")))
                ;; Install only the gap binary; the gac compiler is left
                ;; for maybe later. "Wrap" it in a shell script that calls
                ;; the binary with the correct parameter.
@@ -1030,12 +1031,37 @@ xtensor provides:
                            prog-real
                            share)))
                (chmod prog #o755)
-               ;; Install the headers and the library, which are needed by
-               ;; Sage. The Makefile targets are available in gap-4.10.0,
-               ;; but planned to be removed in gap-4.10.1.
-               (invoke "make" "install-headers")
-               (invoke "make" "install-libgap")
+               ;; Install the headers, which are needed by Sage. The
+               ;; Makefile target "install-headers" was available in
+               ;; gap-4.10.0, but has been commented out in gap-4.10.1.
+               (mkdir-p include-hpc)
                (install-file "gen/config.h" include)
+               (let ((file-name-predicate-without-stat
+                       (lambda (regex)
+                         (cut (file-name-predicate regex) <> #f))))
+                 (with-directory-excursion "src"
+                   (for-each
+                     (cut install-file <> include)
+                     (scandir "."
+                              (file-name-predicate-without-stat ".*\\.h$"))))
+                 (with-directory-excursion "src/hpc"
+                   (for-each
+                     (cut install-file <> include-hpc)
+                     (scandir "."
+                              (file-name-predicate-without-stat ".*\\.h$")))))
+               ;; Install the library, which is needed by Sage. The
+               ;; Makefile target "install-libgap" was available in
+               ;; gap-4.10.0, but has been commented out in gap-4.10.1.
+               ;; Compared to the Makefile, which used libtool, the
+               ;; following approach of copying files and making symlinks
+               ;; is rather pedestrian. There is hope that some later
+               ;; version of gap reinstates and completes the install
+               ;; targets.
+               (invoke "make" "libgap.la")
+               (install-file "libgap.la" lib)
+               (install-file ".libs/libgap.so.0.0.0" lib)
+               (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so")) 
+               (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0"))
                ;; Install a certain number of files and directories to
                ;; SHARE, where the wrapped shell script expects them.
                ;; Remove information on the build directory from sysinfo.gap.
-- 
cgit v1.2.3


From f0fbb31d0175ec37f4c76addbfddf5a546361f6d Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Tue, 18 Jun 2019 10:38:57 +0200
Subject: gnu: Add givaro.

* gnu/packages/algebra.scm (givaro): New variable.
---
 gnu/packages/algebra.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 20ecc71b81..449ca7b189 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1094,3 +1094,43 @@ objects.")
     ;; means that the gpl2+ licence of GAP itself applies, but to be on the
     ;; safe side, we drop them for now.
     (license license:gpl2+)))
+
+(define-public givaro
+  (package
+    (name "givaro")
+    (version "4.1.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/linbox-team/givaro")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (propagated-inputs
+     `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'setenv
+           ;; Prevent the autogen.sh script to carry out the configure
+           ;; script, which has not yet been patched to replace /bin/sh.
+           (lambda _
+             (setenv "NOCONFIGURE" "yes")
+             #t)))))
+    (synopsis "Algebraic computations with exact rings and fields")
+    (description
+     "Givaro is a C++ library implementing the basic arithmetic of various
+algebraic objects: prime fields, extension fields, finite fields, finite
+rings, polynomials, algebraic numbers, arbitrary precision integers and
+rationals (C++ wrappers over gmp), fixed precision integers.  It also
+provides data-structures and templated classes for the manipulation of
+compound objects, such as vectors, matrices and univariate polynomials.")
+    (license license:cecill-b)
+    (home-page "https://github.com/linbox-team/givaro")))
-- 
cgit v1.2.3


From 4bf9cb405358ab21be0a6d8650c51567dd8da0f2 Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Tue, 18 Jun 2019 13:08:07 +0200
Subject: gnu: Add fflas-ffpack.

* gnu/packages/algebra.scm (fflas-ffpack): New variable.
---
 gnu/packages/algebra.scm | 51 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 449ca7b189..6b15df1e64 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -43,6 +43,7 @@
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
@@ -1134,3 +1135,53 @@ provides data-structures and templated classes for the manipulation of
 compound objects, such as vectors, matrices and univariate polynomials.")
     (license license:cecill-b)
     (home-page "https://github.com/linbox-team/givaro")))
+
+(define-public fflas-ffpack
+  (package
+    (name "fflas-ffpack")
+    (version "2.4.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/linbox-team/fflas-ffpack")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("openblas" ,openblas)))
+    (propagated-inputs
+     `(("givaro" ,givaro))) ; required according to the .pc file
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--with-blas-libs="
+                            (assoc-ref %build-inputs "openblas")
+                            "/lib/libopenblas.so"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'setenv
+           ;; Prevent the autogen.sh script to carry out the configure
+           ;; script, which has not yet been patched to replace /bin/sh.
+           (lambda _
+             (setenv "NOCONFIGURE" "yes")
+             #t)))))
+    (synopsis "C++ library for linear algebra over finite fields")
+    (description
+     "FFLAS-FFPACK is a C++ template library for basic linear algebra
+operations over a finite field.
+FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation
+of a subset of routines of the numerical BLAS; it also supports sparse
+matrix-vector products.
+FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK
+library to provide functionalities of higher level, using the kernel
+of a BLAS.  Additionally, it provides routines specific to exact linear
+algebra, such as the row echelon form.")
+    (license license:lgpl2.1+)
+    (home-page "https://linbox-team.github.io/fflas-ffpack/")))
-- 
cgit v1.2.3


From a612f86684c5b93b2587fcfcf5ce52c1d6f23996 Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Tue, 18 Jun 2019 15:06:12 +0200
Subject: gnu: Add linbox.

* gnu/packages/algebra.scm (linbox): New variable.
---
 gnu/packages/algebra.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 6b15df1e64..86c0a42758 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1185,3 +1185,41 @@ of a BLAS.  Additionally, it provides routines specific to exact linear
 algebra, such as the row echelon form.")
     (license license:lgpl2.1+)
     (home-page "https://linbox-team.github.io/fflas-ffpack/")))
+
+(define-public linbox
+  (package
+    (name "linbox")
+    (version "1.6.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/linbox-team/linbox")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("fflas-ffpack" ,fflas-ffpack)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'setenv
+           ;; Prevent the autogen.sh script to carry out the configure
+           ;; script, which has not yet been patched to replace /bin/sh.
+           (lambda _
+             (setenv "NOCONFIGURE" "yes")
+             #t)))))
+    (synopsis "C++ library for linear algebra over exact rings")
+    (description
+     "LinBox is a C++ template library for exact linear algebra computation
+with dense, sparse, and structured matrices over the integers and over
+finite fields.")
+    (license license:lgpl2.1+)
+    (home-page "https://linbox-team.github.io/linbox/")))
-- 
cgit v1.2.3


From 7c5f623192d4d316ce62270cbdb9daa7848c323d Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Wed, 19 Jun 2019 18:54:52 +0200
Subject: gnu: Add gf2x.

* gnu/packages/algebra.scm (gf2x): New variable.
---
 gnu/packages/algebra.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 86c0a42758..fefe712a33 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -93,6 +93,27 @@ multiplication routines such as Toom–Cook and the FFT.")
    (license license:lgpl3+)
    (home-page "http://mpfrcx.multiprecision.org/")))
 
+(define-public gf2x
+  (package
+   (name "gf2x")
+   (version "1.2")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://gforge.inria.fr/frs/download.php/file/36934/gf2x-"
+                  version ".tar.gz"))
+            (sha256
+             (base32
+              "0d6vh1mxskvv3bxl6byp7gxxw3zzpkldrxnyajhnl05m0gx7yhk1"))))
+   (build-system gnu-build-system)
+   (synopsis "Arithmetic of polynomials over binary finite fields")
+   (description
+    "The gf2x library provides arithmetic of polynomials over finite fields
+of characteristic 2.  It implements the multiplication, squaring and
+greatest common divisor operations.")
+   (license license:gpl3+)
+   (home-page "https://gforge.inria.fr/projects/gf2x/")))
+
 (define-public cm
   (package
    (name "cm")
-- 
cgit v1.2.3


From 37edfb0f1cdff251b1231d687041dfe6e7ea92e5 Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Wed, 19 Jun 2019 19:37:52 +0200
Subject: gnu: Add m4ri.

* gnu/packages/algebra.scm (m4ri): New variable.
---
 gnu/packages/algebra.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index fefe712a33..05733fa405 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1244,3 +1244,33 @@ with dense, sparse, and structured matrices over the integers and over
 finite fields.")
     (license license:lgpl2.1+)
     (home-page "https://linbox-team.github.io/linbox/")))
+
+(define-public m4ri
+  (package
+    (name "m4ri")
+    (version "20140914")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://bitbucket.org/malb/m4ri")
+                    (commit (string-append "release-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("libpng" ,libpng)))
+    (synopsis "Arithmetic of dense matrices over F_2")
+    (description "M4RI is a library for fast arithmetic with dense matrices
+over F2.  The name M4RI comes from the first implemented algorithm: The
+Method of the Four Russians inversion algorithm published by Gregory Bard.
+This algorithm in turn is named after the Method of the Four Russians
+multiplication algorithm.")
+    (license license:gpl2+)
+    (home-page "https://bitbucket.org/malb/m4ri/")))
-- 
cgit v1.2.3


From ab398380eb5b7b0f77c0895bfbb22232fcf5ace6 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Thu, 20 Jun 2019 09:20:29 +0200
Subject: gnu: Move ratpoints into a different module.

* gnu/packages/maths.scm (ratpoints): Move...
* gnu/packages/algebra.scm: ...here.
---
 gnu/packages/algebra.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 gnu/packages/maths.scm   | 41 -----------------------------------------
 2 files changed, 41 insertions(+), 41 deletions(-)

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 05733fa405..4dbf537af3 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1274,3 +1274,44 @@ This algorithm in turn is named after the Method of the Four Russians
 multiplication algorithm.")
     (license license:gpl2+)
     (home-page "https://bitbucket.org/malb/m4ri/")))
+
+(define-public ratpoints
+  (package
+    (name "ratpoints")
+    (version "2.1.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://www.mathe2.uni-bayreuth.de/stoll/programs/"
+                    "ratpoints-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4"))
+              (patches
+               ;; Taken from
+               ;; <https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/>
+               (search-patches "ratpoints-sturm_and_rp_private.patch"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:test-target "test"
+       #:make-flags
+       (list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)            ;no configure script
+         (add-before 'install 'create-install-directories
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (mkdir-p out)
+               (with-directory-excursion out
+                 (for-each (lambda (d) (mkdir-p d))
+                           '("bin" "include" "lib"))))
+             #t)))))
+    (inputs
+     `(("gmp" ,gmp)))
+    (home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/")
+    (synopsis "Find rational points on hyperelliptic curves")
+    (description "Ratpoints tries to find all rational points within
+a given height bound on a hyperelliptic curve in a very efficient way,
+by using an optimized quadratic sieve algorithm.")
+    (license license:gpl2+)))
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index fc57801354..6d8fb9cec5 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5003,44 +5003,3 @@ command-line tools, and an Application Programming Interface (API).
 This package provides the static libraries required to run programs
 compiled against the nauty library.")
     (license license:asl2.0)))
-
-(define-public ratpoints
-  (package
-    (name "ratpoints")
-    (version "2.1.3")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "http://www.mathe2.uni-bayreuth.de/stoll/programs/"
-                    "ratpoints-" version ".tar.gz"))
-              (sha256
-               (base32
-                "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4"))
-              (patches
-               ;; Taken from
-               ;; <https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/>
-               (search-patches "ratpoints-sturm_and_rp_private.patch"))))
-    (build-system gnu-build-system)
-    (arguments
-     `(#:test-target "test"
-       #:make-flags
-       (list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out")))
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'configure)            ;no configure script
-         (add-before 'install 'create-install-directories
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (mkdir-p out)
-               (with-directory-excursion out
-                 (for-each (lambda (d) (mkdir-p d))
-                           '("bin" "include" "lib"))))
-             #t)))))
-    (inputs
-     `(("gmp" ,gmp)))
-    (home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/")
-    (synopsis "Find rational points on hyperelliptic curves")
-    (description "Ratpoints tries to find all rational points within
-a given height bound on a hyperelliptic curve in a very efficient way,
-by using an optimized quadratic sieve algorithm.")
-    (license license:gpl2+)))
-- 
cgit v1.2.3


From 75a73bb024c840dc7a917a527915ff8d8d918af8 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Wed, 19 Jun 2019 07:57:57 +0200
Subject: gnu: Add symmetrica.

* gnu/packages/algebra.scm (symmetrica): New variable.
* gnu/packages/patches/symmetrica-bruch.patch:
* gnu/packages/patches/symmetrica-int32.patch:
* gnu/packages/patches/symmetrica-return_values.patch:
* gnu/packages/patches/symmetrica-sort_sum_rename.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add patches.
---
 gnu/local.mk                                       |   6 +-
 gnu/packages/algebra.scm                           |  60 ++++
 gnu/packages/patches/symmetrica-bruch.patch        |  38 +++
 gnu/packages/patches/symmetrica-int32.patch        |  37 +++
 .../patches/symmetrica-return_values.patch         |  14 +
 .../patches/symmetrica-sort_sum_rename.patch       | 340 +++++++++++++++++++++
 6 files changed, 494 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/symmetrica-bruch.patch
 create mode 100644 gnu/packages/patches/symmetrica-int32.patch
 create mode 100644 gnu/packages/patches/symmetrica-return_values.patch
 create mode 100644 gnu/packages/patches/symmetrica-sort_sum_rename.patch

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/local.mk b/gnu/local.mk
index ac5f0e9dbf..336b5c89ed 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1282,6 +1282,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/sssd-curl-compat.patch			\
   %D%/packages/patches/steghide-fixes.patch			\
   %D%/packages/patches/streamlink-update-test.patch		\
+  %D%/packages/patches/stumpwm-fix-broken-read-one-line.patch	\
   %D%/packages/patches/superlu-dist-awpm-grid.patch		\
   %D%/packages/patches/superlu-dist-fix-mpi-deprecations.patch	\
   %D%/packages/patches/superlu-dist-scotchmetis.patch		\
@@ -1290,7 +1291,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/swig-guile-gc.patch			\
   %D%/packages/patches/swish-e-search.patch			\
   %D%/packages/patches/swish-e-format-security.patch		\
-  %D%/packages/patches/stumpwm-fix-broken-read-one-line.patch	\
+  %D%/packages/patches/symmetrica-bruch.patch			\
+  %D%/packages/patches/symmetrica-int32.patch			\
+  %D%/packages/patches/symmetrica-return_values.patch 		\
+  %D%/packages/patches/symmetrica-sort_sum_rename.patch 	\
   %D%/packages/patches/t1lib-CVE-2010-2642.patch		\
   %D%/packages/patches/t1lib-CVE-2011-0764.patch		\
   %D%/packages/patches/t1lib-CVE-2011-1552+.patch		\
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 4dbf537af3..eeaee61755 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1315,3 +1315,63 @@ multiplication algorithm.")
 a given height bound on a hyperelliptic curve in a very efficient way,
 by using an optimized quadratic sieve algorithm.")
     (license license:gpl2+)))
+
+(define-public symmetrica
+  (package
+    (name "symmetrica")
+    (version "2.0")
+    (source (origin
+              (method url-fetch/tarbomb)
+              (uri (let ((v (string-join (string-split version #\.) "_")))
+                     (string-append "http://www.algorithm.uni-bayreuth.de/"
+                                    "en/research/SYMMETRICA/"
+                                    "SYM" v "_tar.gz")))
+              (sha256
+               (base32
+                "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"))
+              ;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/>
+              (patches (search-patches "symmetrica-bruch.patch"
+                                       "symmetrica-int32.patch"
+                                       "symmetrica-return_values.patch"
+                                       "symmetrica-sort_sum_rename.patch"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ;no test
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-makefile
+           (lambda _
+             (substitute* "makefile"
+               (("cc -c") "gcc -c"))
+             #t))
+         (add-after 'fix-makefile 'turn-off-banner
+           (lambda _
+             (substitute* "de.c"
+               (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE")))
+             #t))
+         (delete 'configure)            ;no configure script
+         (replace 'install              ;no install target
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (lib (string-append out "/lib"))
+                    (inc (string-append out "/include/symmetrica"))
+                    (doc (string-append out "/share/doc/symmetrica-" ,version))
+                    (static "libsymmetrica.a"))
+               ;; Build static library.
+               (apply invoke "ar" "crs" static (find-files "." "\\.o$"))
+               (invoke "ranlib" static)
+               ;; Install static library and headers.
+               (for-each (lambda (f) (install-file f inc))
+                         (find-files "." "\\.h$"))
+               (install-file "libsymmetrica.a" lib)
+               ;; Install documentation.
+               (for-each (lambda (f) (install-file f doc))
+                         (find-files "." "\\.doc$"))
+               #t))))))
+    (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/")
+    (synopsis "Combinatoric C Library")
+    (description "Symmetrica is a library for combinatorics.  It has support
+for the representation theory of the symmetric group and related groups,
+combinatorics of tableaux, symmetric functions and polynomials, Schubert
+polynomials, and the representation theory of Hecke algebras of type A_n.")
+    (license license:public-domain)))
diff --git a/gnu/packages/patches/symmetrica-bruch.patch b/gnu/packages/patches/symmetrica-bruch.patch
new file mode 100644
index 0000000000..ae88b79206
--- /dev/null
+++ b/gnu/packages/patches/symmetrica-bruch.patch
@@ -0,0 +1,38 @@
+--- src/bruch.c	2007-12-06 11:30:00.000000000 -0500
++++ b/bruch.c	2013-10-22 08:37:43.000000000 -0400
+@@ -975,14 +975,16 @@
+     ggterg = ggt_i(S_B_UI(bruch),S_B_OI(bruch));
+ 
+     if (ggterg == S_B_UI(bruch)) {
++        INT tmp = S_B_OI(bruch);
+         freeself_bruch(bruch);
+-        M_I_I(S_B_OI(bruch) / ggterg,bruch);
++        M_I_I(tmp / ggterg,bruch);
+         goto ende;
+         }
+ 
+     if (-ggterg == S_B_UI(bruch)) {
++        INT tmp = S_B_OI(bruch);
+         freeself_bruch(bruch);
+-        M_I_I(- S_B_OI(bruch) / ggterg,bruch);
++        M_I_I(- tmp / ggterg,bruch);
+         goto ende;
+         }
+ 
+@@ -1032,12 +1034,14 @@
+ 
+     if (S_O_K(S_B_U(bruch)) == INTEGER)
+         if (S_B_UI(bruch) == 1) { 
++            INT tmp = S_B_OI(bruch);
+             freeself_bruch(bruch);
+-            M_I_I(S_B_OI(bruch),bruch); 
++            M_I_I(tmp,bruch); 
+             goto ende; }
+         else if (S_B_UI(bruch) == -1) { 
++            INT tmp = S_B_OI(bruch);
+             freeself_bruch(bruch);
+-            M_I_I( - S_B_OI(bruch),bruch); 
++            M_I_I( - tmp,bruch); 
+             goto ende; }
+     if (NEGP(S_B_O(bruch)) && NEGP(S_B_U(bruch)))
+         {
diff --git a/gnu/packages/patches/symmetrica-int32.patch b/gnu/packages/patches/symmetrica-int32.patch
new file mode 100644
index 0000000000..b64f27d51e
--- /dev/null
+++ b/gnu/packages/patches/symmetrica-int32.patch
@@ -0,0 +1,37 @@
+diff -ru src/def.h c/def.h
+--- src/def.h	2007-12-06 17:30:56.000000000 +0100
++++ c/def.h	2013-10-19 18:42:55.118745730 +0200
+@@ -2,14 +2,9 @@
+ /* INT should always be 4 byte */
+ #ifndef DEF_H
+ 
+-
+-#ifdef __alpha
+-typedef  int INT;
+-typedef unsigned  int  UINT;
+-#else /* __alpha */
+-typedef long INT;
+-typedef unsigned long UINT;
+-#endif /* __alpha */
++#include <stdint.h>
++typedef int32_t INT;
++typedef uint32_t UINT;
+ 
+ #include <stdio.h>
+ #include <memory.h>
+@@ -65,10 +60,13 @@
+ 
+ 
+ /* definitionen fuer object.c */
+-typedef INT OBJECTKIND;   /* 4 byte */
++/* NOTE: partition code assumes that there is no unused space in the
++ * object struct when an INT is stored. This requires both OBJECTKIND
++ * and OBJECTSELF to have a size equal to a machine word. */
++typedef intptr_t OBJECTKIND;
+ 
+ typedef union {
+-	INT ob_INT;
++	intptr_t ob_INT;
+ 	INT * ob_INTpointer;
+ 	char *ob_charpointer;
+ 	struct bruch *ob_bruch;
diff --git a/gnu/packages/patches/symmetrica-return_values.patch b/gnu/packages/patches/symmetrica-return_values.patch
new file mode 100644
index 0000000000..e09c389337
--- /dev/null
+++ b/gnu/packages/patches/symmetrica-return_values.patch
@@ -0,0 +1,14 @@
+diff -ru src/part.c b/part.c
+--- src/part.c	Thu May 14 06:01:00 2009 -0400
++++ b/part.c 	Thu May 14 06:01:00 2009 -0400
+@@ -1767,8 +1767,8 @@
+ /* to compute number of partitions */
+ {
+     INT erg = OK;
+-    if (ni<0) return;
+-    if (not EMPTYP(S_V_I(vec,ni))) return;
++    if (ni<0) return 0;
++    if (not EMPTYP(S_V_I(vec,ni))) return 0;
+     else if (ni<=1) M_I_I(1,S_V_I(vec,ni));
+     else {
+     
diff --git a/gnu/packages/patches/symmetrica-sort_sum_rename.patch b/gnu/packages/patches/symmetrica-sort_sum_rename.patch
new file mode 100644
index 0000000000..2d9a2dae06
--- /dev/null
+++ b/gnu/packages/patches/symmetrica-sort_sum_rename.patch
@@ -0,0 +1,340 @@
+diff -r 5cd656a07aa5 src/bar.c
+--- a/bar.c	Thu May 14 06:01:00 2009 -0400
++++ b/bar.c	Thu May 14 07:38:17 2009 -0400
+@@ -237,7 +237,7 @@
+     g = callocobject();
+     e = S_V_I(a,0L);
+     f = S_V_I(a,1L);
+-    erg += sum(f,g);
++    erg += sym_sum(f,g);
+     j=0L;
+     for (i=0L;i<S_V_LI(e);i++)
+         j += S_V_II(e,i)*(i+1L);
+@@ -427,7 +427,7 @@
+     for (i=0L;i<S_V_LI(b);i++)
+         erg += kranztypus_to_matrix(S_V_I(c,i),S_V_I(b,i));
+     erg += freeall(c);
+-    erg += sort(b); /* AK 130592 */
++    erg += sym_sort(b); /* AK 130592 */
+     ENDR("makevectorof_class_bar");
+ }
+ 
+@@ -615,7 +615,7 @@
+     c = callocobject();
+     d = callocobject();
+     erg += lehmercode_bar(a,c);
+-    erg += sum(S_V_I(c,1L),b);
++    erg += sym_sum(S_V_I(c,1L),b);
+     for(i=0L;i<S_P_LI(a);i++)
+         {
+         if (S_V_II(S_V_I(c,0L),i) == 1L)
+diff -r 5cd656a07aa5 src/def.h
+--- a/def.h	Thu May 14 06:01:00 2009 -0400
++++ b/def.h	Thu May 14 07:38:17 2009 -0400
+@@ -3105,7 +3105,7 @@
+ extern INT so_character ();
+ extern INT so_dimension ();
+ extern OBJECTKIND s_o_k();
+-extern INT sort();
++extern INT sym_sort();
+ extern INT sort_rows_tableaux_apply();
+ extern INT sort_vector();
+ extern OBJECTSELF s_o_s();
+@@ -3271,7 +3271,7 @@
+ extern INT sub_part_part();
+ extern INT substitute_one_matrix ();
+ extern INT substitute_one_monopoly ();
+-extern INT sum();
++extern INT sym_sum();
+ extern INT sum_integervector();
+ extern INT sum_matrix();
+ extern INT sum_vector();
+diff -r 5cd656a07aa5 src/di.c
+--- a/di.c	Thu May 14 06:01:00 2009 -0400
++++ b/di.c	Thu May 14 07:38:17 2009 -0400
+@@ -1355,7 +1355,7 @@
+ 				m_il_nv(0L,weight_watcher);
+ 				m_il_nv(0L,perm_vec);
+ 				copy(S_V_I(FP,0L),fix);
+-				sort(fix);
++				sym_sort(fix);
+ 
+ 				get_perm(hweight,p,b,S_I_I(n),S_I_I(m),0L,
+ 						 perm_vec,weight_watcher,fix);
+@@ -1502,7 +1502,7 @@
+ 	if(ind == m)
+ 	{
+ 		mult_perm_fix(p,fix,hfix);
+-		sort(hfix);
++		sym_sort(hfix);
+ 		if(!hfix_in_ww(hfix,ww))
+ 		{
+ 			inc(ww);
+diff -r 5cd656a07aa5 src/ga.c
+--- a/ga.c	Thu May 14 06:01:00 2009 -0400
++++ b/ga.c	Thu May 14 07:38:17 2009 -0400
+@@ -632,7 +632,7 @@
+     else if (what == 0L)
+         erg += vertikal_sum(S_V_L(a),c);
+     erg += copy(a,d);
+-    erg += sort(d);
++    erg += sym_sort(d);
+     erg += m_il_p(S_V_II(d,S_V_LI(d)-1L),e); /* identitaet */
+     for (i=0L,k=0L,j=S_V_LI(d);i<S_P_LI(e);i++)
+         if (i+1L == S_V_II(d,k) )
+@@ -722,7 +722,7 @@
+ 
+     j=0L;
+     erg += append(h,g,h2); 
+-    erg += sort(h2);
++    erg += sym_sort(h2);
+     for (i=0L;i<S_V_LI(g);i++)
+         {
+         erg += m_i_i(S_V_II(g,i),S_P_I(a,j));
+diff -r 5cd656a07aa5 src/galois.c
+--- a/galois.c	Thu May 14 06:01:00 2009 -0400
++++ b/galois.c	Thu May 14 07:38:17 2009 -0400
+@@ -758,7 +758,7 @@
+ 		}
+         }
+     FREEALL2(v,nv);
+-    sort(res);
++    sym_sort(res);
+     }
+     S3R(k,phg_c,phg_d,"all_points_phg_store",res);
+     ENDR("all_points");
+diff -r 5cd656a07aa5 src/macro.h
+--- a/macro.h	Thu May 14 06:01:00 2009 -0400
++++ b/macro.h	Thu May 14 07:38:17 2009 -0400
+@@ -1,6 +1,8 @@
+ /* file: macro.h symmetrica source code */
+ #ifndef MACRO_H
+ 
++#include "string.h"
++
+ #ifdef SYMMAGMA
+ #define SYM_MALLOC(a) mem_malloc(a)
+ #else
+ #define C_O_K(a,b) ((a)->ob_kind = (OBJECTKIND)(b))
+--- a/nc.c	Thu May 14 06:01:00 2009 -0400
++++ b/nc.c	Thu May 14 07:38:17 2009 -0400
+@@ -204,7 +204,7 @@
+     erg += mult(S_NC_C(a),S_NC_C(b),d);
+     erg += m_gl_co(S_NC_GL(a),e);
+     erg += mult_apply(e,d);
+-    erg += sum(d,e);
++    erg += sym_sum(d,e);
+     erg += m_gl_go(S_NC_GL(a),d);
+     erg += div(e,d,c);
+     erg += freeall(e);
+@@ -617,7 +617,7 @@
+         erg += mult_nc_kranz(c,a,e);
+         erg += mult(S_V_I(e,1L),f,c);
+         erg += div(c,g,c);
+-        erg += sum(c,S_V_I(S_NC_C(b),S_I_I(d)));
++        erg += sym_sum(c,S_V_I(S_NC_C(b),S_I_I(d)));
+     }
+     erg += freeall(c); 
+     erg += freeall(d); 
+@@ -712,7 +712,7 @@
+     for(j = 0L; j<S_V_LI(c);j++) {
+         kranztypus_to_matrix(S_V_I(c,j),S_V_I(a,j)); 
+     }
+-    sort(a);
++    sym_sort(a);
+     freeall(f); freeall(h); freeall(c);
+     return OK;
+ }
+@@ -739,7 +739,7 @@
+         kranztypus_to_matrix(S_V_I(c,j),S_V_I(h,j)); 
+         }
+     
+-    sort(h); 
++    sym_sort(h); 
+     m_l_v(S_V_L(h),a);
+     for(j = 0L; j<S_V_LI(c);j++) {
+         typusorder(S_V_I(h,j), zb, za, S_V_I(a,j), f);
+@@ -789,7 +789,7 @@
+         erg += kranztypus_to_matrix(S_V_I(c,j),S_V_I(h,j)); 
+     }
+     
+-    erg += sort(h);
++    erg += sym_sort(h);
+     erg += typusorder(S_V_I(h,S_I_I(i)), zb, za, a, f);
+     erg += freeall(f); 
+     erg += freeall(c); 
+diff -r 5cd656a07aa5 src/nu.c
+--- a/nu.c	Thu May 14 06:01:00 2009 -0400
++++ b/nu.c	Thu May 14 07:38:17 2009 -0400
+@@ -531,13 +531,13 @@
+     ENDR("add");
+ }
+ 
+-INT sort(a) OP a;
++INT sym_sort(a) OP a;
+ /* sortiert das object in aufsteigender reihenfolge AK 270787 */
+ /* AK 160986 */ /* AK 280689 V1.0 */ /* AK 050390 V1.1 */
+ /* AK 070891 V1.3 */
+ {
+     INT erg = OK;
+-    EOP("sort(1)",a);
++    EOP("sym_sort(1)",a);
+ 
+     switch(S_O_K(a))
+     {
+@@ -547,9 +547,9 @@
+         erg += sort_vector(a);break;
+ #endif /* VECTORTRUE */
+     default:
+-        erg += WTO("sort",a); break;
++        erg += WTO("sym_sort",a); break;
+     };
+-    ENDR("sort");
++    ENDR("sym_sort");
+ }
+ 
+ INT length(a,d) OP a,d;
+@@ -641,7 +641,7 @@
+     ENDR("content");
+ }
+ 
+-INT sum(a,res) OP a,res;
++INT sym_sum(a,res) OP a,res;
+ /* AK 280689 V1.0 */ /* AK 050390 V1.1 */ /* AK 120391 V1.2 */
+ /* AK 140891 V1.3 */
+ /* AK 170298 V2.0 */
+@@ -649,7 +649,7 @@
+     INT erg = OK;
+     COP("sum(1)",a);
+     COP("sum(2)",res);
+-    CE2(a,res,sum);
++    CE2(a,res,sym_sum);
+ 
+     switch(S_O_K(a))
+     {
+@@ -680,7 +680,7 @@
+         erg += WTO("sum",a); break;
+     };
+ 
+-    ENDR("sum");
++    ENDR("sym_sum");
+ }
+ 
+ 
+diff -r 5cd656a07aa5 src/part.c
+--- a/part.c	Thu May 14 06:01:00 2009 -0400
++++ b/part.c	Thu May 14 07:38:17 2009 -0400
+@@ -347,7 +347,7 @@
+     if (a == b) { /* a := a+a */
+         if (S_PA_K(a) == VECTOR) {
+             erg += append_apply_vector(S_PA_S(a),S_PA_S(b));
+-            erg += sort(S_PA_S(a));
++            erg += sym_sort(S_PA_S(a));
+             goto endr_ende;
+         }
+         else if (S_PA_K(a) == EXPONENT) {
+@@ -406,7 +406,7 @@
+             k=S_PA_LI(b)-1;
+ /*
+             erg += append_apply_vector(S_PA_S(a),S_PA_S(b));
+-            erg += sort(S_PA_S(a));
++            erg += sym_sort(S_PA_S(a));
+ */
+             inc_vector_co(S_PA_S(a),S_PA_LI(b));
+             for (j=S_PA_LI(a)-1;j>=0;j--)
+diff -r 5cd656a07aa5 src/perm.c
+--- a/perm.c	Thu May 14 06:01:00 2009 -0400
++++ b/perm.c	Thu May 14 07:38:17 2009 -0400
+@@ -833,9 +833,9 @@
+     /* s = Anzahl der spalten */
+         
+     s = S_V_LI(S_V_I(a,0L));
+-    sum(S_V_I(a,0L),summe);/* composition ist vector */
++    sym_sum(S_V_I(a,0L),summe);/* composition ist vector */
+     z = S_I_I(summe);
+-    FREEALL(summe); 
++    FREEALL(summe);
+     m_ilih_nm(s,z,b); 
+     C_O_K(b,KRANZTYPUS);
+     for (i=0L;i<s;i++)
+@@ -1114,7 +1114,7 @@
+         erg += kranztypus_to_matrix(S_V_I(c,i),S_V_I(h,i)); 
+     }
+     
+-    erg += sort(h);
++    erg += sym_sort(h);
+ 
+     erg += chartafel(b,ct);
+ 
+@@ -1926,7 +1926,7 @@
+     OP c;
+     c = CALLOCOBJECT();
+     erg += lehmercode_permutation(a,c); /*result is a vector */
+-    erg += sum(c,b); 
++    erg += sym_sum(c,b); 
+     FREEALL(c);
+     }
+     ENDR("numberof_inversionen");
+@@ -2364,7 +2364,7 @@
+     COP("rz_lehmercode(2)",b);
+ 
+     zw = callocobject();
+-    erg += sum(lc,zw); 
++    erg += sym_sum(lc,zw); 
+     if (NULLP(zw)) 
+         {
+         erg += m_il_integervector((INT)0,b);
+diff -r 5cd656a07aa5 src/rest.c
+--- a/rest.c	Thu May 14 06:01:00 2009 -0400
++++ b/rest.c	Thu May 14 07:38:17 2009 -0400
+@@ -3998,7 +3998,7 @@
+                 oj = j;
+                 }
+         }
+-    erg += sum(c,b);
++    erg += sym_sum(c,b);
+ eee:
+     erg += freeall(c);
+     ENDR("charge_word");
+diff -r 5cd656a07aa5 src/ta.c
+--- a/ta.c	Thu May 14 06:01:00 2009 -0400
++++ b/ta.c	Thu May 14 07:38:17 2009 -0400
+@@ -1596,7 +1596,7 @@
+     {
+     OP d,e;
+     e = CALLOCOBJECT();
+-    erg += sum(content,e); /* AK 271098 */
++    erg += sym_sum(content,e); /* AK 271098 */
+     d = CALLOCOBJECT();
+     erg += weight(shape,d);
+     if (NEQ(d,e))
+@@ -1821,7 +1821,7 @@
+     CE3(matrix, column_index, row_index,matrix_twoword);
+     c = callocobject();
+     erg += zeilen_summe(matrix,c);
+-    erg += sum(c,c);
++    erg += sym_sum(c,c);
+     erg += m_l_v(c,column_index);
+     erg += m_l_v(c,row_index);
+     for(i=0,l=0;i<S_M_HI(matrix);i++)
+diff -r 5cd656a07aa5 src/zyk.c
+--- a/zyk.c	Thu May 14 06:01:00 2009 -0400
++++ b/zyk.c	Thu May 14 07:38:17 2009 -0400
+@@ -804,7 +804,7 @@
+     zykeltypvec = CALLOCOBJECT();
+     ak_order = CALLOCOBJECT();
+ 
+-    sum(numztvec,ak_order); /* AK 060295 */
++    sym_sum(numztvec,ak_order); /* AK 060295 */
+ 
+ 
+ 
+@@ -1176,7 +1176,7 @@
+     erg += m_i_i(0,c);
+     while (z!=NULL)
+         {
+-        erg += sum(S_PO_S(z),e);
++        erg += sym_sum(S_PO_S(z),e);
+         erg += hoch(b,e,e);
+         erg += mult_apply(S_PO_K(z),e);
+         erg += add_apply(e,c);
-- 
cgit v1.2.3


From 1de48e8f8afec23847458c533d2fae0d69d8942a Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Thu, 20 Jun 2019 11:03:37 +0200
Subject: gnu: fplll: Update to 5.2.1.

* gnu/packages/algebra.scm (fplll): Update to 5.2.1.
[source]: Use Github tagged release: the original tarball no longer exists.
[native-inputs]: Add Autoconf and al.
[homepage]: Update it, the previous one no longer exists.
[description]: Expound description.
---
 gnu/packages/algebra.scm | 62 ++++++++++++++++++++++++++++++++++--------------
 1 file changed, 44 insertions(+), 18 deletions(-)

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index eeaee61755..8d7c9709d1 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -144,24 +144,50 @@ line applications.")
 
 (define-public fplll
   (package
-   (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"))))
-   (build-system gnu-build-system)
-   (inputs `(("gmp" ,gmp)
-             ("mpfr" ,mpfr)))
-   (synopsis "Library for LLL-reduction of euclidean lattices")
-   (description
-    "fplll LLL-reduces euclidean lattices.  Since version 3, it can also
-solve the shortest vector problem.")
-   (license license:lgpl2.1+)
-   (home-page "http://perso.ens-lyon.fr/damien.stehle/fplll/")))
+    (name "fplll")
+    (version "5.2.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/fplll/fplll.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "015qmrd7nfaysbv1hbwiprz9g6hnww1y1z1xw8f43ysb7k1b5nbg"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (inputs
+     `(("gmp" ,gmp)
+       ("mpfr" ,mpfr)))
+    (home-page "https://github.com/fplll/fplll")
+    (synopsis "Library for LLL-reduction of euclidean lattices")
+    (description
+     "fplll contains implementations of several lattice algorithms.
+The implementation relies on floating-point orthogonalization, and LLL
+is central to the code, hence the name.
+
+It includes implementations of floating-point LLL reduction
+algorithms, offering different speed/guarantees ratios.  It contains
+a @emph{wrapper} choosing the estimated best sequence of variants in
+order to provide a guaranteed output as fast as possible.  In the case
+of the wrapper, the succession of variants is oblivious to the user.
+
+It includes an implementation of the BKZ reduction algorithm,
+including the BKZ-2.0 improvements (extreme enumeration
+pruning, pre-processing of blocks, early termination).  Additionally,
+Slide reduction and self dual BKZ are supported.
+
+It also includes a floating-point implementation of the
+Kannan-Fincke-Pohst algorithm that finds a shortest non-zero lattice
+vector.  For the same task, the GaussSieve algorithm is also available
+in fplll.  Finally, it contains a variant of the enumeration algorithm
+that computes a lattice vector closest to a given vector belonging to
+the real span of the lattice.")
+    (license license:lgpl2.1+)))
 
 (define-public pari-gp
   (package
-- 
cgit v1.2.3


From 25cbaa9e705a4d8cde39b5a83c4c54114db45984 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Thu, 20 Jun 2019 11:07:12 +0200
Subject: gnu: Add python-fpylll.

* gnu/packages/algebra.scm (python-fpylll): New variable.
---
 gnu/packages/algebra.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 8d7c9709d1..22d458d36d 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -189,6 +189,38 @@ that computes a lattice vector closest to a given vector belonging to
 the real span of the lattice.")
     (license license:lgpl2.1+)))
 
+(define-public python-fpylll
+  (package
+    (name "python-fpylll")
+    (version "0.4.1")
+    (source
+     (origin
+       ;; Pypi contains and older release, so we use a tagged release from
+       ;; Github instead.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/fplll/fpylll.git")
+             (commit (string-append version "dev"))))
+       (sha256
+        (base32
+         "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w"))))
+    (build-system python-build-system)
+    (inputs
+     `(("fplll" ,fplll)
+       ("gmp" ,gmp)
+       ("mpfr" ,mpfr)
+       ("pari-gp" ,pari-gp)))
+    (propagated-inputs
+     `(("cysignals" ,python-cysignals)
+       ("cython" ,python-cython)
+       ("flake8" ,python-flake8)
+       ("numpy" ,python-numpy)
+       ("pytest" ,python-pytest)))
+    (home-page "https://github.com/fplll/fpylll")
+    (synopsis "Python interface for fplll")
+    (description "fpylll is a Python wrapper for fplll.")
+    (license license:gpl2+)))
+
 (define-public pari-gp
   (package
     (name "pari-gp")
-- 
cgit v1.2.3


From 6cbedbd2f25f7e4da057d226e0fa2ac21e2577b1 Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Thu, 20 Jun 2019 11:15:37 +0200
Subject: gnu: Add m4rie.

* gnu/packages/algebra.scm (m4rie): New variable.
---
 gnu/packages/algebra.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 22d458d36d..c1cbaca311 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1433,3 +1433,30 @@ for the representation theory of the symmetric group and related groups,
 combinatorics of tableaux, symmetric functions and polynomials, Schubert
 polynomials, and the representation theory of Hecke algebras of type A_n.")
     (license license:public-domain)))
+
+(define-public m4rie
+  (package
+    (name "m4rie")
+    (version "20150908")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://bitbucket.org/malb/m4rie")
+                    (commit (string-append "release-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (inputs
+     `(("m4ri" ,m4ri)))
+    (synopsis "Arithmetic of dense matrices over F_{2^e}")
+    (description "M4RI is a library for fast arithmetic with dense matrices
+over finite fields of characteristic 2.  So it extends the functionality
+of M4RI from F_2 to F_{2^e}.")
+    (license license:gpl2+)
+    (home-page "https://bitbucket.org/malb/m4rie/")))
-- 
cgit v1.2.3


From 66c67e7ba1b468dc3874fb9c84997992b7737181 Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Thu, 20 Jun 2019 11:45:04 +0200
Subject: gnu: Add eclib.

* gnu/packages/algebra.scm (eclib): New variable.
---
 gnu/packages/algebra.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index c1cbaca311..810e9ce12a 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1460,3 +1460,33 @@ over finite fields of characteristic 2.  So it extends the functionality
 of M4RI from F_2 to F_{2^e}.")
     (license license:gpl2+)
     (home-page "https://bitbucket.org/malb/m4rie/")))
+
+(define-public eclib
+  (package
+    (name "eclib")
+    (version "20190226")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/JohnCremona/eclib/")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1910np1xzyjzszay24xn4b81qhpsvhp5aix9vdpknplni2mq8kwb"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (inputs
+     `(("gmp" ,gmp)
+       ("ntl" ,ntl)
+       ("pari-gp" ,pari-gp)))
+    (synopsis "Ranks of elliptic curves and modular symbols")
+    (description "The eclib package includes mwrank (for 2-descent on
+elliptic curves over Q) and modular symbol code; it has been written by
+John Cremona to compute his elliptic curve database.")
+    (license license:gpl2+)
+    (home-page (string-append "http://homepages.warwick.ac.uk/staff/"
+                              "J.E.Cremona/mwrank/index.html"))))
-- 
cgit v1.2.3


From 197ebc36be1dd44f90bcfbbaddda8632cdeff3d2 Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Thu, 20 Jun 2019 12:15:07 +0200
Subject: gnu: Add lrcalc.

* gnu/packages/algebra.scm (lrcalc): New variable.
---
 gnu/packages/algebra.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 810e9ce12a..1b401f8e5b 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1490,3 +1490,39 @@ John Cremona to compute his elliptic curve database.")
     (license license:gpl2+)
     (home-page (string-append "http://homepages.warwick.ac.uk/staff/"
                               "J.E.Cremona/mwrank/index.html"))))
+
+(define-public lrcalc
+  (package
+    (name "lrcalc")
+    (version "1.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://bitbucket.org/asbuch/lrcalc")
+                    (commit (string-append "lrcalc-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'fix-permission
+           (lambda _
+             (chmod "lrcalc.maple.src" #o644)
+             #t)))))
+    (synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
+    (description "The Littlewood-Richardson Calculator (lrcalc) is a
+program designed to compute Littlewood-Richardson coefficients.  It computes
+single Littlewood-Richardson coefficients, products of Schur functions, or
+skew Schur functions.  In addition it computes products in the small quantum
+cohomology ring of a Grassmann variety.  The software package also includes
+a program that performs fast computation of the more general multiplicative
+structure constants of Schubert polynomials.")
+    (license license:gpl2+)
+    (home-page "http://sites.math.rutgers.edu/~asbuch/lrcalc/")))
-- 
cgit v1.2.3


From eacf29835dac41240fc63e080572998cd5982775 Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Thu, 20 Jun 2019 17:36:39 +0200
Subject: gnu: Add iml.

* gnu/packages/algebra.scm (iml): New variable.
---
 gnu/packages/algebra.scm | 56 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

(limited to 'gnu/packages/algebra.scm')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 1b401f8e5b..561347ad98 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1526,3 +1526,59 @@ a program that performs fast computation of the more general multiplicative
 structure constants of Schubert polynomials.")
     (license license:gpl2+)
     (home-page "http://sites.math.rutgers.edu/~asbuch/lrcalc/")))
+
+(define-public iml
+  (package
+    (name "iml")
+    (version "1.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-"
+                           version ".tar.bz2"))
+       (sha256
+        (base32
+         "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("gmp", gmp)
+       ("cblas" ,openblas))) ; or any other BLAS library; the documentation
+                             ; mentions ATLAS in particular
+    (arguments
+     `(#:configure-flags
+       (list
+        (string-append "--with-gmp-include="
+                       (assoc-ref %build-inputs "gmp") "/include")
+        (string-append "--with-gmp-lib="
+                       (assoc-ref %build-inputs "gmp") "/lib")
+        "--with-cblas=-lopenblas"
+        (string-append "--with-cblas-include="
+                       (assoc-ref %build-inputs "cblas") "/include")
+        (string-append "--with-cblas-lib="
+                       (assoc-ref %build-inputs "cblas") "/lib"))))
+    (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html")
+    (synopsis
+     "Solver for systems of linear equations over the integers")
+    (description
+     "IML is a C library implementing algorithms for computing exact
+solutions to dense systems of linear equations over the integers.
+Currently, IML provides the following functionality:
+
+@itemize
+@item Nonsingular rational system solving:
+compute the unique rational solution X to the system AX=B, where A and B
+are integer matrices, A nonsingular.
+@item Compute the right nullspace or kernel of an integer matrix.
+@item Certified linear system solving:
+compute a minimal denominator solution x to a system Ax=b, where b is an
+integer vector and A is an integer matrix with arbitrary shape and
+rank profile.
+@end itemize
+
+In addition, IML provides some low level routines for a variety of mod p
+matrix operations: computing the row-echelon form, determinant, rank
+profile, and inverse of a mod p matrix. These mod p routines are not
+general purpose; they require that p satisfy some preconditions based on
+the dimension of the input matrix (usually p should be prime and should be
+no more than about 20 bits long).")
+    (license license:bsd-3)))
-- 
cgit v1.2.3