Merge branch 'staging' into 'core-updates'.

Conflicts:

	gnu/local.mk
	gnu/packages/cmake.scm
	gnu/packages/curl.scm
	gnu/packages/gl.scm
	gnu/packages/glib.scm
	gnu/packages/guile.scm
	gnu/packages/node.scm
	gnu/packages/openldap.scm
	gnu/packages/package-management.scm
	gnu/packages/python-xyz.scm
	gnu/packages/python.scm
	gnu/packages/tls.scm
	gnu/packages/vpn.scm
	gnu/packages/xorg.scm

1 files changed, 96 insertions, 25 deletions

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 125edbea40..4019c7efaf 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8,7 +8,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016, 2018, 2020 Kei Kebreau <kkebreau@posteo.net>
@@ -521,7 +521,7 @@ numbers.")
 (define-public sleef
   (package
     (name "sleef")
-    (version "3.4.1")
+    (version "3.5.1")
     (source
      (origin
        (method git-fetch)
@@ -530,7 +530,7 @@ numbers.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1gvf7cfvszmgjrsqivwmyy1jnp3hy80dmszxx827lhjz8yqq5019"))))
+        (base32 "1jybqrl2dvjxzg30xrhh847s375n2jr1pix644wi6hb5wh5mx3f7"))))
     (build-system cmake-build-system)
     (arguments
      '(#:configure-flags (list "-DCMAKE_BUILD_TYPE=Release"
@@ -565,7 +565,7 @@ It can utilize SIMD instructions that are available on modern processors.")
 (define-public glpk
   (package
     (name "glpk")
-    (version "4.65")
+    (version "5.0")
     (source
      (origin
       (method url-fetch)
@@ -573,12 +573,13 @@ It can utilize SIMD instructions that are available on modern processors.")
                           version ".tar.gz"))
       (sha256
        (base32
-        "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
+        "05bgxidxj8d9xdp82niy7cy36w181cxq7p8vc3y2ixshpgp1642a"))))
     (build-system gnu-build-system)
     (inputs
      `(("gmp" ,gmp)))
     (arguments
-     `(#:configure-flags '("--with-gmp")))
+     `(#:configure-flags '("--with-gmp"
+                           "--disable-static")))
     (home-page "https://www.gnu.org/software/glpk/")
     (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
     (description
@@ -589,6 +590,20 @@ translator for the language.  In addition to the C library, a stand-alone
 LP/MIP solver is included in the package.")
     (license license:gpl3+)))
 
+(define-public glpk-4
+  (package
+    (inherit glpk)
+    (name "glpk")
+    (version "4.65")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (string-append "mirror://gnu/glpk/glpk-"
+                          version ".tar.gz"))
+      (sha256
+       (base32
+        "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))))
+
 (define-public 4ti2
   (package
     (name "4ti2")
@@ -1894,7 +1909,7 @@ can solve two kinds of problems:
 (define-public octave-cli
   (package
     (name "octave-cli")
-    (version "5.2.0")
+    (version "6.1.0")
     (source
      (origin
       (method url-fetch)
@@ -1902,7 +1917,7 @@ can solve two kinds of problems:
                           version ".tar.lz"))
       (sha256
        (base32
-        "1848dq6nxzal8gwjrcp6xhi5gq96w89nss9d9rz75q408gb3mbl6"))))
+        "0355s0pi8603ccs2j08zym3nalgalslxn83s37zq8nkrrkwxrjfk"))))
     (build-system gnu-build-system)
     (inputs
      `(("alsa-lib" ,alsa-lib)
@@ -2214,13 +2229,13 @@ ASCII text files using Gmsh's own scripting language.")
 (define-public veusz
   (package
     (name "veusz")
-    (version "3.2.1")
+    (version "3.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "veusz" version))
        (sha256
-        (base32 "00vmfpvyd6f33l5awlf02qdik3gmbhzyfizfwwbx7qnam2i9bbwy"))))
+        (base32 "1q7hi1qwwg4pgiz62isvv1pia85m13bspdpp1q3mrnwl11in0ag0"))))
     (build-system python-build-system)
     (arguments
      `(;; Tests will fail because they depend on optional packages like
@@ -2687,7 +2702,7 @@ bindings to almost all functions of SLEPc.")
 (define-public metamath
   (package
     (name "metamath")
-    (version "0.192")
+    (version "0.193")
     (source
      (origin
        (method git-fetch)
@@ -2696,7 +2711,7 @@ bindings to almost all functions of SLEPc.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1k31zw36h2b0w5r6sbn9qc0v4hj42vw53qlhf5l7q2h3p5qlzvic"))))
+        (base32 "1s9hyknfvhj86g3giayyf3dxzg23iij0rs7bdvj075v9qbyhqn9b"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -2978,18 +2993,21 @@ also provides threshold-based ILU factorization preconditioners.")
 (define-public superlu-dist
   (package
     (name "superlu-dist")
-    (version "6.2.0")
+    (version "6.4.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://portal.nersc.gov/project/sparse/superlu/"
-                           "superlu_dist_" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/xiaoyeli/superlu_dist")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1ynmwqajc9sc3my2hssa5k9s58ggvizqv9rdss0j7w99pbh5mnvw"))
+        (base32 "0fa29yr72p4yq5ln4rgfsawmi5935n4qcr5niz6864bjladz4lql"))
        (modules '((guix build utils)))
        (snippet
         ;; Replace the non-free implementation of MC64 with a stub
         '(begin
+           (make-file-writable "SRC/mc64ad_dist.c")
            (call-with-output-file "SRC/mc64ad_dist.c"
              (lambda (port)
                (display "
@@ -3067,14 +3085,14 @@ implemented in ANSI C, and MPI for communications.")
 (define-public scotch
   (package
     (name "scotch")
-    (version "6.0.6")
+    (version "6.1.0")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "https://gforge.inria.fr/frs/download.php/"
                           "latestfile/298/scotch_" version ".tar.gz"))
       (sha256
-       (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
+       (base32 "1184fcv4wa2df8szb5lan6pjh0raarr45pk8ilpvbz23naikzg53"))
       (patches (search-patches "scotch-build-parallelism.patch"
                                "scotch-integer-declarations.patch"))))
     (build-system gnu-build-system)
@@ -3122,7 +3140,7 @@ YACC = bison -pscotchyy -y -b y
                           "COMMON_PTHREAD"
                           "COMMON_RANDOM_FIXED_SEED"
                           "INTSIZE64"             ;use 'int64_t'
-                          ;; Prevents symbolc clashes with libesmumps
+                          ;; Prevents symbol clashes with libesmumps
                           "SCOTCH_RENAME"
                           ;; XXX: Causes invalid frees in superlu-dist tests
                           ;; "SCOTCH_PTHREAD"
@@ -3914,7 +3932,8 @@ Fresnel integrals, and similar related functions as well.")
                             " -DCMAKE_C_FLAGS_RELEASE=\"$(CFLAGS) $(CPPFLAGS)\""
                             " -DCMAKE_CXX_FLAGS_RELEASE=\"$(CXXFLAGS) $(CPPFLAGS)\""
                             " -DCMAKE_SKIP_RPATH=TRUE"
-                            " -DCMAKE_BUILD_TYPE=Release")
+                            " -DCMAKE_BUILD_TYPE=Release"
+                            " -DCMAKE_INSTALL_LIBDIR=lib")
              (string-append "INSTALL_LIB="
                             (assoc-ref %outputs "out") "/lib")
              (string-append "INSTALL_INCLUDE="
@@ -4195,7 +4214,7 @@ revised simplex and the branch-and-bound methods.")
 (define-public dealii
   (package
     (name "dealii")
-    (version "9.1.1")
+    (version "9.2.0")
     (source
      (origin
        (method url-fetch)
@@ -4203,7 +4222,7 @@ revised simplex and the branch-and-bound methods.")
                            "download/v" version "/dealii-" version ".tar.gz"))
        (sha256
         (base32
-         "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw"))
+         "0fm4xzrnb7dfn4415j24d8v3jkh0lssi86250x2f5wgi83xq4nnh"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
@@ -4538,7 +4557,7 @@ structured and unstructured grid problems.")))
 (define-public matio
   (package
     (name "matio")
-    (version "1.5.6")
+    (version "1.5.19")
     (source
      (origin
        (method url-fetch)
@@ -4546,7 +4565,7 @@ structured and unstructured grid problems.")))
                            "matio-" version ".tar.gz"))
        (sha256
         (base32
-         "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
+         "0vr8c1mz1k6mz0sgh6n3scl5c3a71iqmy5fnydrgq504icj4vym4"))))
     (build-system gnu-build-system)
     (inputs
      `(("zlib" ,zlib)
@@ -4982,6 +5001,58 @@ be fed to @command{tcalc} through the command line.")
   (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
   (license license:gpl3+)))
 
+(define-public tiny-bignum
+  (let ((commit "1d7a1f9b8e77316187a6b3eae8e68d60a6f9a4d4"))
+    (package
+     (name "tiny-bignum")
+     (version (git-version "0" "0" commit))
+     (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+              (url "https://github.com/kokke/tiny-bignum-c")
+              (commit commit)))
+        (file-name (git-file-name "tiny-bignum" commit))
+        (sha256
+         (base32 "0vj71qlhlaa7d92bfar1kwqv6582dqrby8x3kdw0yzh82k2023g6"))))
+     (build-system gnu-build-system)
+     (arguments
+      `(#:phases
+        (modify-phases %standard-phases
+          (delete 'configure)
+          (add-after 'unpack 'patch-tests
+            (lambda _
+              (substitute* "scripts/test_rand.py"
+                (("\t") "  ")
+                (("\" % (\\w+)" _ symbol) (string-append "\" % int(" symbol ")")))
+              #t))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "make" "test"))
+              #t))
+          (replace 'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((share (string-append (assoc-ref outputs "out") "/share"))
+                    (doc (string-append (assoc-ref outputs "out") "/doc")))
+                (mkdir-p share)
+                (install-file "bn.c" share)
+                (install-file "bn.h" share)
+                (mkdir-p doc)
+                (install-file "LICENSE" doc)
+                (install-file "README.md" doc))
+              #t)))))
+     (native-inputs
+      `(("python" ,python-wrapper)))
+     (home-page "https://github.com/kokke/tiny-bignum-c")
+     (synopsis "Small portable multiple-precision unsigned integer arithmetic in C")
+     (description
+      "This library provides portable Arbitrary-precision unsigned integer
+arithmetic in C, for calculating with large numbers.  Basic arithmetic (+, -,
+*, /, %) and bitwise operations (&, |, ^. <<, >>) plus increments, decrements
+and comparisons are supported.")
+     (license license:unlicense))))
+
 (define-public sundials
   (package
     (name "sundials")