Merge remote-tracking branch 'origin/master' into core-updates

 Conflicts:
	gnu/local.mk
	gnu/packages/boost.scm
	gnu/packages/chez.scm
	gnu/packages/compression.scm
	gnu/packages/crates-io.scm
	gnu/packages/docbook.scm
	gnu/packages/engineering.scm
	gnu/packages/gcc.scm
	gnu/packages/gl.scm
	gnu/packages/gtk.scm
	gnu/packages/nettle.scm
	gnu/packages/python-check.scm
	gnu/packages/python-xyz.scm
	gnu/packages/radio.scm
	gnu/packages/rust.scm
	gnu/packages/sqlite.scm
	guix/build-system/node.scm

1 files changed, 173 insertions, 69 deletions

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 879af45dc7..1f96ed907e 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -12,7 +12,7 @@
 ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016, 2018, 2020 Kei Kebreau <kkebreau@posteo.net>
-;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2017, 2018, 2019, 2020 Paul Garlick <pgarlick@tourbillion-technology.com>
@@ -34,7 +34,7 @@
 ;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
 ;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
-;;; Copyright © 2020 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2020, 2021 Felix Gruber <felgru@posteo.net>
 ;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
@@ -43,6 +43,8 @@
 ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Martin Becze <mjbecze@riseup.net>
 ;;; Copyright © 2021 Gerd Heber <gerd.heber@gmail.com>
+;;; Copyright © 2021 Franck Pérignon <franck.perignon@univ-grenoble-alpes.fr>
+;;; Copyright © 2021 Philip McGrath <philip@philipmcgrath.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2292,7 +2294,8 @@ ASCII text files using Gmsh's own scripting language.")
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ;;("python-astropy" ,python-astropy) ;; FIXME: Package this.
-       ("qttools" ,qttools)))
+       ("qttools" ,qttools)
+       ("python-sip" ,python-sip-4)))
     (inputs
      `(("ghostscript" ,ghostscript) ;optional, for EPS/PS output
        ("python-dbus" ,python-dbus)
@@ -3249,6 +3252,63 @@ YACC = bison -pscotchyy -y -b y
     (synopsis
      "Programs and libraries for graph algorithms (32-bit integers)")))
 
+(define-public scotch-shared
+  (package (inherit scotch)
+    (name "scotch-shared")
+    (native-inputs
+     `(("gcc" ,gcc)
+       ("flex" ,flex)
+       ("bison" ,bison)))
+    (arguments
+     (substitute-keyword-arguments (package-arguments scotch)
+       ((#:phases scotch-shared-phases)
+        `(modify-phases ,scotch-shared-phases
+           (replace
+            'configure
+           (lambda _
+             ;; Otherwise, the RUNPATH will lack the final path component.
+             (setenv "RPATHFLAGS" (string-append "-Wl,-rpath="
+                                              (assoc-ref %outputs "out") "/lib"))
+            (call-with-output-file "Makefile.inc"
+              (lambda (port)
+                (format port "
+EXE =
+LIB = .so
+OBJ = .o
+MAKE = make
+AR = gcc
+ARFLAGS = -shared -o
+CAT = cat
+CCS = gcc
+CCP = mpicc
+CCD = gcc
+CPPFLAGS =~{ -D~a~}
+CFLAGS = -O2 -g -fPIC $(CPPFLAGS) $(RPATHFLAGS)
+CLIBFLAGS = -shared -fPIC
+LDFLAGS = -lz -lm -lrt -lpthread -Xlinker --no-as-needed
+CP = cp
+LEX = flex -Pscotchyy -olex.yy.c
+LN = ln
+MKDIR = mkdir
+MV = mv
+RANLIB = echo
+YACC = bison -pscotchyy -y -b y
+"
+                        '("COMMON_FILE_COMPRESS_GZ"
+                          "COMMON_PTHREAD"
+                          "COMMON_RANDOM_FIXED_SEED"
+                          "INTSIZE64"             ;use 'int64_t'
+                          ;; Prevents symbolc clashes with libesmumps
+                          "SCOTCH_RENAME"
+                          ;; XXX: Causes invalid frees in superlu-dist tests
+                          ;; "SCOTCH_PTHREAD"
+                          ;; "SCOTCH_PTHREAD_NUMBER=2"
+                          "restrict=__restrict"
+                          ))))#t))
+           (delete 'check)))))
+     (synopsis
+      "Programs and libraries for graph algorithms (shared libraries version)")))
+
 (define-public pt-scotch
   (package (inherit scotch)
     (name "pt-scotch")
@@ -3296,6 +3356,28 @@ YACC = bison -pscotchyy -y -b y
     (synopsis
      "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
 
+(define-public pt-scotch-shared
+  (package (inherit scotch-shared)
+    (name "pt-scotch-shared")
+    (propagated-inputs
+     `(("openmpi" ,openmpi)))           ;Headers include MPI headers
+    (arguments
+     (substitute-keyword-arguments (package-arguments scotch-shared)
+       ((#:phases scotch-shared-phases)
+        `(modify-phases ,scotch-shared-phases
+           (replace
+            'build
+            (lambda _
+              (invoke "make" (format #f "-j~a" (parallel-job-count))
+                      "ptscotch" "ptesmumps")
+
+              ;; Install the serial metis compatibility library
+              (invoke "make" "-C" "libscotchmetis" "install")))
+           (add-before 'check 'mpi-setup
+             ,%openmpi-setup)))))
+    (synopsis "Graph algorithms (shared libraries version, with MPI)")))
+
+
 (define-public metis
   (package
     (name "metis")
@@ -3308,6 +3390,9 @@ YACC = bison -pscotchyy -y -b y
        (sha256
         (base32
          "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
+    (properties
+     `((release-monitoring-url
+        . "http://glaros.dtc.umn.edu/gkhome/metis/metis/download")))
     (build-system cmake-build-system)
     (inputs
      `(("blas" ,openblas)))
@@ -3745,52 +3830,94 @@ parts of it.")
     (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
     (license license:bsd-3)))
 
-(define* (make-blis implementation #:optional substitutable?)
-  "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
-source tree for a list of implementations.)
-
-SUBSTITUTABLE? determines whether the package is made available as a
-substitute.
-
-Currently the specialization must be selected at configure-time, but work is
-underway to allow BLIS to select the right optimized kernels at run time:
-<https://github.com/flame/blis/issues/129>."
+(define-public blis
   (package
-    (name (if (string=? implementation "reference")
-              "blis"
-              (string-append "blis-" implementation)))
-    (version "0.2.2")
+    (name "blis")
+    (version "0.8.1")
     (home-page "https://github.com/flame/blis")
     (source (origin
               (method git-fetch)
               (uri (git-reference (url home-page) (commit version)))
               (sha256
                (base32
-                "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
+                "05ifil6jj9424sr8kmircl8k4bmxnl3y12a79vwj1kxxva5gz50g"))
               (file-name (git-file-name "blis" version))))
+    (native-inputs
+     `(("python" ,python)
+       ("perl" ,perl)))
     (build-system gnu-build-system)
     (arguments
-     `(#:test-target "test"
-
-       #:substitutable? ,substitutable?
-
-       #:phases (modify-phases %standard-phases
-                  (replace 'configure
-                    (lambda* (#:key outputs #:allow-other-keys)
-                      ;; This is a home-made 'configure' script.
-                      (let ((out (assoc-ref outputs "out")))
-                        (invoke "./configure" "-p" out
-                                "-d" "opt"
-                                "--disable-static"
-                                "--enable-shared"
-                                "--enable-threading=openmp"
-
-                                ,implementation))))
-                  (add-before 'check 'show-test-output
-                    (lambda _
-                      ;; By default "make check" is silent.  Make it verbose.
-                      (system "tail -F output.testsuite &")
-                      #t)))))
+     `(#:modules
+       ((guix build gnu-build-system)
+        (guix build utils)
+        (srfi srfi-1))
+        #:test-target "test"
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs
+                           target
+                           system
+                           (configure-flags '())
+                           #:allow-other-keys)
+             ;; This is a home-made 'configure' script.
+             (let* ((out (assoc-ref outputs "out"))
+                     ;; Guix-specific support for choosing the configuration
+                     ;; via #:configure-flags: see below for details.
+                    (config-flag-prefix "--blis-config=")
+                    (maybe-config-flag (find
+                                        (lambda (s)
+                                          (string-prefix? config-flag-prefix s))
+                                        configure-flags))
+                    (configure-flags (if maybe-config-flag
+                                         (delete maybe-config-flag
+                                                 configure-flags)
+                                         configure-flags))
+                    ;; Select the "configuration" to build.
+                    ;; The "generic" configuration is non-optimized but
+                    ;; portable (no assembly).
+                    ;; The "x86_64" configuration family includes
+                    ;; sub-configurations for all supported
+                    ;; x86_64 microarchitectures.
+                    ;; BLIS currently lacks runtime hardware detection
+                    ;; for other architectures: see
+                    ;; <https://github.com/flame/blis/commit/c534da6>.
+                    ;; Conservatively, we stick to "generic" on armhf,
+                    ;; aarch64, and ppc64le for now. (But perhaps
+                    ;; "power9", "cortexa9", and "cortexa57" might be
+                    ;; general enough to use?)
+                    ;; Another approach would be to use the "auto"
+                    ;; configuration and make this package
+                    ;; non-substitutable.
+                    ;; The build is fairly intensive, though.
+                    (blis-config
+                     (cond
+                      (maybe-config-flag
+                       (substring maybe-config-flag
+                                  (string-length config-flag-prefix)))
+                      ((string-prefix? "x86_64" (or target system))
+                       "x86_64")
+                      (else
+                       "generic")))
+                    (configure-args
+                     `("-p" ,out
+                       "-d" "opt"
+                       "--disable-static"
+                       "--enable-shared"
+                       "--enable-threading=openmp"
+                       "--enable-verbose-make"
+                       ,@configure-flags
+                       ,blis-config)))
+               (format #t "configure args: ~s~%" configure-args)
+               (apply invoke
+                      "./configure"
+                      configure-args)
+               #t)))
+         (add-before 'check 'show-test-output
+           (lambda _
+             ;; By default "make check" is silent.  Make it verbose.
+             (system "tail -F output.testsuite &")
+             #t)))))
     (synopsis "High-performance basic linear algebra (BLAS) routines")
     (description
      "BLIS is a portable software framework for instantiating high-performance
@@ -3802,35 +3929,12 @@ it also includes a BLAS compatibility layer which gives application developers
 access to BLIS implementations via traditional BLAS routine calls.")
     (license license:bsd-3)))
 
-(define-public blis
-  ;; This is the "reference" implementation, which is the non-optimized but
-  ;; portable variant (no assembly).
-  (make-blis "reference" #t))
+(define-public blis-sandybridge (deprecated-package "blis-sandybridge" blis))
+(define-public blis-haswell (deprecated-package "blis-haswell" blis))
+(define-public blis-knl (deprecated-package "blis-knl" blis))
 
 (define ignorance blis)
 
-(define-syntax-rule (blis/x86_64 processor)
-  "Expand to a package specialized for PROCESSOR."
-  (package
-    (inherit (make-blis processor))
-    (supported-systems '("x86_64-linux"))))
-
-(define-public blis-sandybridge
-  ;; BLIS specialized for Sandy Bridge processors (launched 2011):
-  ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
-  (blis/x86_64 "sandybridge"))
-
-(define-public blis-haswell
-  ;; BLIS specialized for Haswell processors (launched 2013):
-  ;; <http://ark.intel.com/products/codename/42174/Haswell>.
-  (blis/x86_64 "haswell"))
-
-(define-public blis-knl
-  ;; BLIS specialized for Knights Landing processor (launched 2016):
-  ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
-  (blis/x86_64 "knl"))
-
-
 (define-public openlibm
   (package
     (name "openlibm")
@@ -3911,7 +4015,7 @@ Fresnel integrals, and similar related functions as well.")
 (define-public suitesparse
   (package
     (name "suitesparse")
-    (version "5.8.1")
+    (version "5.9.0")
     (source
      (origin
        (method git-fetch)
@@ -3921,7 +4025,7 @@ Fresnel integrals, and similar related functions as well.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0qjlyfxs8s48rs63c2fzspisgq1kk4bwkgnhmh125hgkdhrq2w1c"))
+         "1zhkix58afw92s7p291prljdm3yi0pjg1kbi3lczdb8rb14jkz5n"))
        (patches (search-patches "suitesparse-mongoose-cmake.patch"))
        (modules '((guix build utils)))
        (snippet
@@ -3931,9 +4035,9 @@ Fresnel integrals, and similar related functions as well.")
            #t))))
     (build-system gnu-build-system)
     (arguments
-     '(#:tests? #f  ;no "check" target
+     `(#:tests? #f  ;no "check" target
        #:make-flags
-       (list "CC=gcc"
+       (list (string-append "CC=" ,(cc-for-target))
              "TBB=-ltbb"
              "MY_METIS_LIB=-lmetis"
              ;; Flags for cmake (required to build GraphBLAS and Mongoose)