Merge branch 'master' into staging

author: Marius Bakke <mbakke@fastmail.com> 2020-03-06 00:17:50 +0100
committer: Marius Bakke <mbakke@fastmail.com> 2020-03-06 00:17:50 +0100
commit: b6f946f039afad6cbc7027d52685072f7fbb8d35 (patch)
tree: 9dc33d1ef9d307f1e3ed8a825902ff69bbe288f9 /gnu/packages
parent: e32aea5472007507e62933b27a4db9a50810e5dc (diff)
parent: bc8b2ffdac3f55414629ace5b1a0db32e9656c0a (diff)
43 files changed, 607 insertions, 627 deletions
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index cbddb8c407..2406aa16b2 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -322,7 +322,7 @@ namespace ARDOUR { const char* revision = \"" version "\" ; }"))
        ("itstool" ,itstool)
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)))
-    (home-page "http://ardour.org")
+    (home-page "https://ardour.org")
     (synopsis "Digital audio workstation")
     (description
      "Ardour is a multi-channel digital audio workstation, allowing users to
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index f283f9eec3..15ab54dd8a 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -756,7 +756,7 @@ interfaces and processes.")
     (propagated-inputs
      `(("python-six" ,python-six)
        ("python-traceback2" ,python-traceback2)))
-    (home-page "http://pypi.python.org/pypi/unittest2")
+    (home-page "https://pypi.org/project/unittest2/")
     (synopsis "Python unit testing library")
     (description
      "Unittest2 is a replacement for the unittest module in the Python
@@ -1540,7 +1540,7 @@ the last py.test invocation.")
     (synopsis "Py.test plugin to test server connections locally")
     (description "Pytest-localserver is a plugin for the pytest testing
 framework which enables you to test server connections locally.")
-    (home-page "https://pypi.python.org/pypi/pytest-localserver")
+    (home-page "https://pypi.org/project/pytest-localserver/")
     (license license:expat)))
 
 (define-public python-pytest-xprocess
@@ -1994,7 +1994,7 @@ especially -cover-package.")
         (base32
          "0y8d0zwiqar51kxj8lzmkvwc3b8kazb04gk5zcb4nzg5k68zmhq5"))))
     (build-system python-build-system)
-    (home-page "http://pypi.python.org/pypi/discover/")
+    (home-page "https://pypi.org/project/discover/")
     (synopsis
      "Python test discovery for unittest")
     (description
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 3bdd406a47..2b3b5d7df6 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -147,7 +148,7 @@ powerful plugin architecture.")
      `(#:python ,python-2
        ;; No test suite
        #:tests? #f))
-    (home-page "http://dirac.cnrs-orleans.fr/DomainFinder")
+    (home-page "http://dirac.cnrs-orleans.fr/DomainFinder.html")
     (synopsis "Analysis of dynamical domains in proteins")
     (description "DomainFinder is an interactive program for the determination
 and characterization of dynamical domains in proteins.  It can infer dynamical
@@ -290,7 +291,7 @@ analogy is that InChI is the bar-code for chemistry and chemical structures.")
                ;; Show documentation as PDF
                (("PREFERENCES\\['documentation_style'\\] = 'html'")
                 "PREFERENCES['documentation_style'] = 'pdf'") ))))))
-    (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN/")
+    (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN.html")
     (synopsis "Analysis software for Molecular Dynamics trajectories")
     (description "nMOLDYN is an interactive analysis program for Molecular Dynamics
 simulations.  It is especially designed for the computation and decomposition of
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index b7438a323f..549d53dd7d 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -25,6 +25,7 @@
 ;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2019 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -410,7 +411,8 @@ compatible with bzip2 – both at file format and command line level.")
        #:phases (modify-phases %standard-phases
                   (delete 'configure))  ; no configure script
        #:make-flags (list (string-append "PREFIX=" %output))))
-    (home-page "http://compression.ca/pbzip2/")
+    (home-page (string-append "https://web.archive.org/web/20180412020219/"
+                              "http://compression.ca/pbzip2/"))
     (synopsis "Parallel bzip2 implementation")
     (description
      "Pbzip2 is a parallel implementation of the bzip2 block-sorting file
@@ -813,7 +815,7 @@ time for compression ratio.")
        ("lzo" ,lzo)
        ("xz" ,xz)
        ("zlib" ,zlib)))
-    (home-page "http://squashfs.sourceforge.net/")
+    (home-page "https://github.com/plougher/squashfs-tools")
     (synopsis "Tools to create and extract squashfs file systems")
     (description
      "Squashfs is a highly compressed read-only file system for Linux.  It uses
diff --git a/gnu/packages/coq.scm b/gnu/packages/coq.scm
index 3eba39e5d0..f883c2f690 100644
--- a/gnu/packages/coq.scm
+++ b/gnu/packages/coq.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Dan Frumin <dfrumin@cs.ru.nl>
 ;;; Copyright © 2020 Brett Gilio <brettg@gnu.org>
+;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -353,7 +354,7 @@ assistant.")
                      (string-append "COQLIB=" (assoc-ref outputs "out")
                                     "/lib/coq/")
                      "install"))))))
-    (home-page "https://math-comp.github.io/math-comp/")
+    (home-page "https://math-comp.github.io/")
     (synopsis "Mathematical Components for Coq")
     (description "Mathematical Components for Coq has its origins in the formal
 proof of the Four Colour Theorem.  Since then it has grown to cover many areas
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 8b32c3f0a9..dba9ec75f6 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -7,6 +7,7 @@
 ;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2019 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
 ;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
+;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -439,3 +440,47 @@ create fluid interpolations when animating position, scale, rotation, frames or
 other values of screen objects, by setting their values as the tween starting
 point and then, after each tween step, plugging back the result.")
     (license license:expat)))
+
+(define-public abseil-cpp
+  (package
+    (name "abseil-cpp")
+    (version "20200225")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/abseil/abseil-cpp.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0wb04pszzrl39ny1pz9jvvq8lbbm355dd60jspcyqfwxnk6njgd1"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON"
+                               "-DABSL_RUN_TESTS=ON"
+                               ;; Needed, else we get errors like:
+                               ;;
+                               ;; ld: CMakeFiles/absl_periodic_sampler_test.dir/internal/periodic_sampler_test.cc.o:
+                               ;;   undefined reference to symbol '_ZN7testing4Mock16UnregisterLockedEPNS_8internal25UntypedFunctionMockerBaseE'
+                               ;; ld: /gnu/store/bxapb1f1l8frjpbjckk3zdxhmcig3xzk-googletest-1.10.0/lib/libgmock.so:
+                               ;;   error adding symbols: DSO missing from command line
+                               ;; collect2: error: ld returned 1 exit status
+                               "-DCMAKE_EXE_LINKER_FLAGS=-lgtest -lpthread -lgmock")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'remove-gtest-check
+           ;; The CMakeLists fails to find our googletest for some reason, but
+           ;; it works nonetheless.
+           (lambda _
+             (substitute* "CMakeLists.txt"
+               (("check_target\\(gtest\\)") "")
+               (("check_target\\(gtest_main\\)") "")
+               (("check_target\\(gmock\\)") "")))))))
+    (native-inputs
+     `(("googletest" ,googletest)))
+    (home-page "https://abseil.io")
+    (synopsis "Augmented C++ standard library")
+    (description "Abseil is a collection of C++ library code designed to
+augment the C++ standard library.  The Abseil library code is collected from
+Google's C++ code base.")
+    (license license:asl2.0)))
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9e834415da..6c7c95dc68 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7180,13 +7180,13 @@ and coverage methods to tune the choice of threshold.")
 (define-public r-ggformula
   (package
     (name "r-ggformula")
-    (version "0.9.3")
+    (version "0.9.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggformula" version))
        (sha256
-        (base32 "1bpsfp9hx001r91pxfiwgxcn5vw5bl1gclb865wz6g9l0jqjfk2p"))))
+        (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggforce" ,r-ggforce)
@@ -7196,8 +7196,7 @@ and coverage methods to tune the choice of threshold.")
        ("r-mosaiccore" ,r-mosaiccore)
        ("r-rlang" ,r-rlang)
        ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-tidyr" ,r-tidyr)))
+       ("r-tibble" ,r-tibble)))
     (home-page "https://github.com/ProjectMOSAIC/ggformula/")
     (synopsis "Formula interface for the @code{r-ggplot2}")
     (description
@@ -8238,14 +8237,14 @@ Hothorn, Westfall, 2010, CRC Press).")
 (define-public r-emmeans
   (package
     (name "r-emmeans")
-    (version "1.4.4")
+    (version "1.4.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "emmeans" version))
        (sha256
         (base32
-         "0l1qj6x834fmcvqbj807p7yz7462df925vw91xvg50faqm19d41x"))))
+         "10fmvmd6q4zjr6b18hhc85mwrzv778qzj6lwl9kbs2fsfvsgw7mm"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-estimability" ,r-estimability)
@@ -11986,14 +11985,14 @@ users of rARPACK are advised to switch to the RSpectra package.")
 (define-public r-compositions
   (package
     (name "r-compositions")
-    (version "1.40-3")
+    (version "1.40-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "compositions" version))
        (sha256
         (base32
-         "103hbmibrf1n333pn4xpll1gqqsv4szms0n5gdq7zak31aar0bg4"))))
+         "0z40llyij3cc80ac1vzzrpykk6ysp89bn6dyyh40fbnc4anwx69a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bayesm" ,r-bayesm)
@@ -19403,14 +19402,14 @@ analysis and natural language processing.")
 (define-public r-spacyr
   (package
     (name "r-spacyr")
-    (version "1.2")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spacyr" version))
        (sha256
         (base32
-         "1xsiz6zx89vs6ykrkkp011d8fz4ksdgnf5nyaq5ynjr6zv865vks"))))
+         "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
     (properties `((upstream-name . "spacyr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20136,20 +20135,22 @@ Latent regression models and plausible value imputation are also supported.")
 (define-public r-erm
   (package
     (name "r-erm")
-    (version "1.0-0")
+    (version "1.0-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "eRm" version))
        (sha256
         (base32
-         "11p8j61arq1ih2qi33wf0442vcdbp3zvknzm5aknsifwl4mbzzly"))))
+         "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
     (properties `((upstream-name . "eRm")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-lattice" ,r-lattice)
+     `(("r-colorspace" ,r-colorspace)
+       ("r-lattice" ,r-lattice)
        ("r-mass" ,r-mass)
-       ("r-matrix" ,r-matrix)))
+       ("r-matrix" ,r-matrix)
+       ("r-psych" ,r-psych)))
     (native-inputs `(("gfortran" ,gfortran)))
     (home-page "https://cran.r-project.org/package=eRm")
     (synopsis "Extended Rasch modeling")
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 1788e0d6df..98f80db89f 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2284,13 +2284,13 @@ for ODBC.")
 (define-public python-pyodbc
   (package
     (name "python-pyodbc")
-    (version "4.0.27")
+    (version "4.0.30")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyodbc" version))
        (sha256
-        (base32 "1kd2i7hc1330cli72vawzby17c3039cqn1aba4i0zrjnpghjhmib"))
+        (base32 "0skjpraar6hcwsy82612bpj8nw016ncyvvq88j5syrikxgp5saw5"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system python-build-system)
     (inputs
diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index 0628017b9a..534b64ef95 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2015 Mathieu Lirzin <mthl@gnu.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2016, 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
@@ -210,14 +210,14 @@ scheme.")
 (define-public ddrescue
   (package
     (name "ddrescue")
-    (version "1.24")
+    (version "1.25")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "mirror://gnu/ddrescue/ddrescue-"
                           version ".tar.lz"))
       (sha256
-       (base32 "11qh0bbzf00mfb4yq35gnv5m260k4d7q9ixklry6bqvhvvp3ypab"))))
+       (base32 "0qqh38izl5ppap9a5izf3hijh94k65s3zbfkczd4b7x04syqwlyf"))))
     (build-system gnu-build-system)
     (home-page "https://www.gnu.org/software/ddrescue/ddrescue.html")
     (synopsis "Data recovery utility")
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 3e63847a87..0652ea15e6 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -248,7 +248,7 @@ with arguments to the field constructor.")
        ("python-setuptools-scm" ,python-setuptools-scm)))
     (propagated-inputs
      `(("python-pytest" ,python-pytest)))
-    (home-page "http://pytest-django.readthedocs.org/")
+    (home-page "https://pytest-django.readthedocs.org/")
     (synopsis "Django plugin for py.test")
     (description "Pytest-django is a plugin for py.test that provides a set of
 useful tools for testing Django applications and projects.")
diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 6f31a30747..6bdfd7a640 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -60,6 +60,7 @@
 ;;; Copyright © 2020 Paul Garlick <pgarlick@tourbillion-technology.com>
 ;;; Copyright © 2020 Robert Smith <robertsmith@posteo.net>
 ;;; Copyright © 2020 Evan Straw <evan.straw99@gmail.com>
+;;; Copyright © 2020 Masaya Tojo <masaya@tojo.tokyo>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -17258,10 +17259,10 @@ leader key in vim), and much more.")
       (license license:gpl3+))))
 
 (define-public emacs-tldr
-  (let ((commit "398b197c8d2238628b07e1b32d0f373876279f4c"))
+  (let ((commit "7203d1be3dcbf12131846ffe06601933fa874d74"))
     (package
       (name "emacs-tldr")
-      (version (git-version "0" "0" commit))
+      (version (git-version "0" "1" commit))
       (home-page "https://github.com/kuanyui/tldr.el")
       (source (origin
                 (method git-fetch)
@@ -17270,9 +17271,11 @@ leader key in vim), and much more.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "0iq7qlis6c6r2qkdpncrhh5vsihkhvy5x4y1y8cjb7zxkh62w33f"))
+                  "1bw6la463l2yfm7rp76ga4makfy4kpxgwi7ni5gxk31w11g26ryk"))
                 (file-name (git-file-name name version))))
       (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-request" ,emacs-request)))
       (synopsis "Simplified and community-driven man pages for Emacs")
       (description "@code{emacs-tldr} allows the user to access tldr pages
 from within emacs.  The @code{tldr} pages are a community effort to simplify
@@ -17844,25 +17847,26 @@ Later you can insert it into an Org buffer using the command
 (define-public emacs-amx
   (package
     (name "emacs-amx")
-    (version "3.2")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/DarwinAwardWinner/amx")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "0bb8y1dmzyqkrb4mg6zndcsxppby3glridv2aap2pv05gv8kx7mj"))))
+    (version "3.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/DarwinAwardWinner/amx")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0ikjzs119g57cwh2v3jmy63lggqc0ib99q5gsl93slkk4y2ihavw"))))
     (build-system emacs-build-system)
-    (propagated-inputs `(("emacs-s" ,emacs-s)))
+    (propagated-inputs
+     `(("emacs-s" ,emacs-s)))
     (home-page "https://github.com/DarwinAwardWinner/amx")
-    (synopsis "Alternative interface for M-x")
+    (synopsis "Alternative M-x interface for Emacs")
     (description "Amx is an alternative interface for M-x in Emacs.  It
 provides several enhancements over the ordinary
 @code{execute-extended-command}, such as prioritizing your most-used commands
 in the completion list and showing keyboard shortcuts, and it supports several
-completion systems for selecting commands, such as ido and ivy.")
+completion systems for selecting commands, such as Ido and Ivy.")
     (license license:gpl3+)))
 
 (define-public emacs-lorem-ipsum
@@ -21729,3 +21733,49 @@ supports generation of phonetic and numeric passwords.")
 Separated Value) files.  It follows the format as defined in RFC 4180 \"Common
 Format and MIME Type for CSV Files\" (@url{http://tools.ietf.org/html/rfc4180}).")
     (license license:gpl3+)))
+
+(define-public emacs-ddskk
+  ;; XXX: Upstream adds code names to their release tags, so version and code
+  ;; name below need to be updated together.
+  (let ((version "16.3")
+        (code-name "Kutomatsunai"))
+    (package
+      (name "emacs-ddskk")
+      (version version)
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/skk-dev/ddskk")
+               (commit (string-append "ddskk-" version "_" code-name))))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0ln4x8f35z5y3kf9m718g223bn3lzcmw40jfjg2j5yi24ydf1wm9"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:modules ((guix build gnu-build-system)
+                    (guix build utils)
+                    (guix build emacs-utils))
+         #:imported-modules (,@%gnu-build-system-modules
+                             (guix build emacs-utils))
+         #:test-target "test"
+         #:phases
+         (modify-phases %standard-phases
+           (replace 'configure
+             (lambda* (#:key outputs #:allow-other-keys)
+               (make-file-writable "SKK-MK")
+               (emacs-substitute-variables "SKK-MK"
+                 ("PREFIX" (assoc-ref outputs "out"))
+                 ("LISPDIR" '(expand-file-name "/share/emacs/site-lisp" PREFIX))
+                 ("SKK_PREFIX" "")
+                 ("SKK_INFODIR" '(expand-file-name "info" PREFIX)))
+               (for-each make-file-writable (find-files "./doc"))
+               #t)))))
+      (native-inputs
+       `(("emacs-minimal" ,emacs-minimal)))
+      (home-page "https://github.com/skk-dev/ddskk")
+      (synopsis "Simple Kana to Kanji conversion program")
+      (description
+       "Daredevil SKK is a version of @acronym{SKK, Simple Kana to Kanji
+conversion program}, a Japanese input method on Emacs.")
+      (license license:gpl2+))))
diff --git a/gnu/packages/enchant.scm b/gnu/packages/enchant.scm
index 25825997bb..ff4fc03363 100644
--- a/gnu/packages/enchant.scm
+++ b/gnu/packages/enchant.scm
@@ -36,7 +36,7 @@
 (define-public enchant
   (package
     (name "enchant")
-    (version "2.2.7")
+    (version "2.2.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/AbiWord/enchant/releases"
@@ -44,7 +44,7 @@
                                   version ".tar.gz"))
               (sha256
                (base32
-                "029smcna98hllgkm2gy94qa7qphxs4xaa8cdbg5kaaw16mhrf8hv"))))
+                "0m9m564qqwbssvvf7y3dlz1yxzqsjiqy1yd2zsmb3l0d7y2y5df7"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--disable-static"
diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm
index 8d39730a7b..d802feb1da 100644
--- a/gnu/packages/fontutils.scm
+++ b/gnu/packages/fontutils.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2019 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -45,6 +46,7 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gperf)
   #:use-module (gnu packages xorg)
+  #:use-module (gnu packages fribidi)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages sqlite)
@@ -678,7 +680,7 @@ files.  UFO is a file format that stores fonts source files.")
     (propagated-inputs
      `(("python2-fonttools" ,python2-fonttools)
        ("python2-ufolib" ,python2-ufolib)))
-    (home-page "https://pypi.python.org/pypi/defcon")
+    (home-page "https://pypi.org/project/defcon/")
     (synopsis "Flexible objects for representing @acronym{UFO, unified font object} data")
     (description
      "Defcon is a set of @acronym{UFO, unified font object} based objects
@@ -836,3 +838,37 @@ work well with other GTK+ desktop environments.")
 samples that show coverage of the font and are similar in appearance to
 Unicode Charts.  It was developed for use with DejaVu Fonts project.")
     (license license:gpl3+)))
+
+(define-public libraqm
+  (package
+    (name "libraqm")
+    (version "0.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/HOST-Oman/libraqm/"
+                           "releases/download/v" version "/"
+                           "raqm-" version ".tar.gz"))
+       (sha256
+        (base32 "0hgry3fj2y3qaq2fnmdgd93ixkk3ns5jds4vglkiv2jfvpn7b1g2"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags (list "--disable-static")))
+    (native-inputs
+     `(("gtk-doc" ,gtk-doc)
+       ("pkg-config" ,pkg-config)
+       ("python" ,python-wrapper)))
+    (inputs
+     `(("freetype" ,freetype)
+       ("fribidi" ,fribidi)
+       ("harfbuzz" ,harfbuzz)))
+    (home-page "https://github.com/HOST-Oman/libraqm")
+    (synopsis "Library for complex text layout")
+    (description
+     "Raqm is a small library that encapsulates the logic for complex text
+layout and provides a convenient API.
+
+It currently provides bidirectional text support (using FriBiDi),
+shaping (using HarfBuzz), and proper script itemization.  As a result, Raqm
+can support most writing systems covered by Unicode.")
+    (license license:expat)))
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index d6f8abebdd..322e309591 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -5941,7 +5941,7 @@ affect gameplay).")
   (package
     (inherit chocolate-doom)
     (name "crispy-doom")
-    (version "5.6.4")
+    (version "5.7.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -5949,7 +5949,7 @@ affect gameplay).")
                     (commit (string-append "crispy-doom-" version))))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "1ls4v2kpb7vi7xji5yqbmyc5lfkz497h1vvj9w86wkrw8k59hlg2"))))
+               (base32 "1gqivy4pxasy7phyznixsagylf9f70bk33b0knpfzzlks6cc6zzj"))))
     (native-inputs
      (append
       (package-native-inputs chocolate-doom)
diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm
index 29b9d34569..ead50bb1dc 100644
--- a/gnu/packages/gcc.scm
+++ b/gnu/packages/gcc.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014, 2015, 2016, 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Carlos Sánchez de La Lama <csanchezdll@gmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
@@ -509,14 +509,14 @@ It also includes runtime support libraries for these languages.")))
 (define-public gcc-8
   (package
     (inherit gcc-7)
-    (version "8.3.0")
+    (version "8.4.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/gcc/gcc-"
                                   version "/gcc-" version ".tar.xz"))
               (sha256
                (base32
-                "0b3xv411xhlnjmin2979nxcbnidgvzqdf4nbhix99x60dkzavfk4"))
+                "1m1d3gfix56w4aq8myazzfffkl8bqcrx4jhhapnjf7qfs596w2p3"))
               (patches (search-patches "gcc-8-strmov-store-file-names.patch"
                                        "gcc-5.0-libvtv-runpath.patch"))))))
 
diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm
index 72d5ea0bdd..c98d8c18f5 100644
--- a/gnu/packages/glib.scm
+++ b/gnu/packages/glib.scm
@@ -670,7 +670,7 @@ useful for C++.")
     (arguments
      `(#:tests? #f                      ;segfaults during tests
        #:configure-flags '("LIBS=-lcairo-gobject")))
-    (home-page "https://pypi.python.org/pypi/PyGObject")
+    (home-page "https://pypi.org/project/PyGObject/")
     (synopsis "Python bindings for GObject")
     (description
      "Python bindings for GLib, GObject, and GIO.")
@@ -898,16 +898,15 @@ programming language.  It also contains the utility
 (define-public appstream-glib
   (package
     (name "appstream-glib")
-    (version "0.7.16")
+    (version "0.7.17")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://people.freedesktop.org/~hughsient/"
                                   "appstream-glib/releases/"
                                   "appstream-glib-" version ".tar.xz"))
-              (patches (search-patches "appstream-glib-2020.patch"))
               (sha256
                (base32
-                "14jr1psx5kxywdprgbqn79w309yz8lrqlsq7288hfrf87gbr1wh4"))))
+                "0jg58m1p5xfrh8zkpqhhg00nqs727z5i1qy6sb0a3vyc98fyk9vw"))))
     (build-system meson-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 0cd39f9104..c802164188 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -3671,7 +3671,7 @@ libxml to ease remote use of the RESTful API.")
 (define-public libsoup
   (package
     (name "libsoup")
-    (version "2.68.3")
+    (version "2.68.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/libsoup/"
@@ -3679,7 +3679,7 @@ libxml to ease remote use of the RESTful API.")
                                   "libsoup-" version ".tar.xz"))
               (sha256
                (base32
-                "1yxs0ax4rq3g0lgkbv7mz497rqj16iyyizddyc13gzxh6n7b0jsk"))))
+                "151j5dc84gbl6a917pxvd0b372lw5za48n63lyv6llfc48lv2l1d"))))
     (build-system meson-build-system)
     (outputs '("out" "doc"))
     (arguments
@@ -5688,7 +5688,7 @@ wraps things up in a developer-friendly way.")
 (define-public libgee
   (package
     (name "libgee")
-    (version "0.20.2")
+    (version "0.20.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/libgee/"
@@ -5696,7 +5696,7 @@ wraps things up in a developer-friendly way.")
                                   "libgee-" version ".tar.xz"))
               (sha256
                (base32
-                "0g1mhl7nidg82v4cikkk8dakzc18hg7wv0dsf2pbyijzfm5mq0wy"))))
+                "1pm525wm11dhwz24m8bpcln9547lmrigl6cxf3qsbg4cr3pyvdfh"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
diff --git a/gnu/packages/gps.scm b/gnu/packages/gps.scm
index 8f23be05e6..ac8deddad5 100644
--- a/gnu/packages/gps.scm
+++ b/gnu/packages/gps.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
+;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -24,17 +25,23 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system scons)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages)
   #:use-module (gnu packages base)
-  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages docbook)
-  #:use-module (gnu packages image)
-  #:use-module (gnu packages xml)
+  #:use-module (gnu packages glib)
   #:use-module (gnu packages gtk)
+  #:use-module (gnu packages image)
+  #:use-module (gnu packages libusb)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages qt)
-  #:use-module (gnu packages sqlite))
+  #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages xml))
 
 (define-public gpsbabel
   (package
@@ -204,3 +211,84 @@ coordinates as well as partial support for adjustments in global coordinate syst
      "GPXSee is a Qt-based GPS log file viewer and analyzer that supports
 all common GPS log file formats.")
     (license license:gpl3)))
+
+(define-public gpsd
+  (package
+    (name "gpsd")
+    (version "3.19")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://download-mirror.savannah.gnu.org"
+                           "/releases/gpsd/gpsd-" version ".tar.gz"))
+       (sha256
+        (base32 "0faz2mvk82hi7ispxxih07lhpyz5dazs4gcknym9piiabga29p97"))))
+    (build-system scons-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("python" ,python)))
+    (inputs
+     `(("bluez" ,bluez)
+       ("dbus" ,dbus)
+       ("libcap" ,libcap)
+       ("libusb" ,libusb)
+       ("ncurses" ,ncurses)))
+    (arguments
+     `(#:scons-flags (list (string-append "prefix=" %output)
+                            ;; TODO: Install python bindings.
+                           "python=no")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((python3 (string-append (assoc-ref inputs "python")
+                                           "/bin/python3")))
+               (substitute* '("contrib/gpsData.py"
+                              "contrib/ntpshmviz"
+                              "contrib/skyview2svg"
+                              "contrib/webgps.py"
+                              "devtools/ais.py"
+                              "devtools/aivdmtable"
+                              "devtools/cycle_analyzer"
+                              "devtools/flocktest"
+                              "devtools/identify_failing_build_options.py"
+                              "devtools/regress-builder"
+                              "devtools/regressdiff"
+                              "devtools/sizes"
+                              "devtools/striplog"
+                              "devtools/tablegen.py"
+                              "devtools/test_json_validity.py"
+                              "devtools/uninstall_cleanup.py"
+                              "gegps"
+                              "gps/gps.py"
+                              "gpscat"
+                              "gpsfake"
+                              "gpsprof"
+                              "jsongen.py"
+                              "leapsecond.py"
+                              "maskaudit.py"
+                              "test_maidenhead.py"
+                              "test_misc.py"
+                              "test_xgps_deps.py"
+                              "ubxtool"
+                              "valgrind-audit.py"
+                              "xgps"
+                              "xgpsspeed"
+                              "zerk")
+                 (("/usr/bin/python") python3)
+                 (("/usr/bin/env python") python3)))
+             #t))
+         (add-after 'fix-paths 'fix-build
+           (lambda _
+             (substitute* "SConstruct"
+               (("'PATH'")
+                "'PATH','CPATH','LIBRARY_PATH'"))
+             #t)))))
+    (synopsis "GPS service daemon")
+    (description
+     "@code{gpsd} is a service daemon that monitors one or more GPSes or AIS
+receivers attached to a host computer through serial or USB ports, making all
+data on the location/course/velocity of the sensors available to be queried on
+TCP port 2947 of the host computer.")
+    (home-page "https://gpsd.gitlab.io/gpsd/")
+    (license license:bsd-2)))
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 63eb36fd7d..ab2bf1daf0 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -119,7 +119,7 @@ more.")
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("python-pytest" ,python-pytest)))
-    (home-page "http://pypi.python.org/pypi/python-igraph")
+    (home-page "https://pypi.org/project/python-igraph/")
     (synopsis "Python bindings for the igraph network analysis library")))
 
 (define-public r-igraph
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index 365fe1a113..c4f88caa88 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -308,7 +308,7 @@ structure and layout algorithms.")
        ("gtk+" ,gtk+)
        ("python-pycairo" ,python-pycairo)
        ("python-pygobject" ,python-pygobject)))
-    (home-page "https://pypi.python.org/pypi/xdot")
+    (home-page "https://pypi.org/project/xdot/")
     (synopsis "Interactive viewer for graphviz dot files")
     (description "Xdot is an interactive viewer for graphs written in
 @code{graphviz}’s dot language.  Internally, it uses the xdot output format as
diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index 292a2836cc..05b4a52d39 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -15,7 +15,7 @@
 ;;; Copyright © 2016 Patrick Hetu <patrick.hetu@auf.org>
 ;;; Copyright © 2016 ng0 <ng0@n0.is>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
@@ -1446,7 +1446,7 @@ and routines to assist in editing internationalized text.")
 (define-public girara
   (package
     (name "girara")
-    (version "0.3.3")
+    (version "0.3.4")
     (source
      (origin
        (method git-fetch)
@@ -1455,7 +1455,7 @@ and routines to assist in editing internationalized text.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0q0yfv2777s72p473lw0ll435n7vz4v204cmp9naq8am7a6i6avn"))))
+        (base32 "08rpw9hkaprm4r853xy1d35i2af1pji8c3mzzl01mmwmyr9p0x8k"))))
     (native-inputs `(("pkg-config" ,pkg-config)
                      ("check" ,check)
                      ("gettext" ,gettext-minimal)
diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm
index 1062456885..b71b0178d6 100644
--- a/gnu/packages/guile-xyz.scm
+++ b/gnu/packages/guile-xyz.scm
@@ -17,7 +17,7 @@
 ;;; Copyright © 2017 ng0 <ng0@n0.is>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
-;;; Copyright © 2018, 2019 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2018, 2019, 2020 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
 ;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2019 swedebugia <swedebugia@riseup.net>
@@ -80,8 +80,10 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages sdl)
+  #:use-module (gnu packages search)
   #:use-module (gnu packages slang)
   #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages swig)
   #:use-module (gnu packages tex)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tls)
@@ -3096,3 +3098,49 @@ currently a re-implementation of the lentes library for Clojure.  Lenses
 provide composable procedures, which can be used to focus, apply functions
 over, or update a value in arbitrary data structures.")
       (license license:gpl3+))))
+
+(define-public guile-xapian
+  (let ((commit "ede26b808188eb4d14c6b4181c933dfc09c0a22e")
+        (revision "0"))
+    (package
+      (name "guile-xapian")
+      (version (git-version "0" revision commit))
+      (home-page "https://git.systemreboot.net/guile-xapian")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference (url home-page)
+                             (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "07a9fmqi3pm6mbbpzi01mjwrqwnljs2rnc3603sq49dz4lf663gb"))))
+      (build-system gnu-build-system)
+      (arguments
+       '(#:make-flags '("GUILE_AUTO_COMPILE=0"))) ; to prevent guild warnings
+      (inputs
+       `(("guile" ,guile-2.2)
+         ("xapian" ,xapian)
+         ("zlib" ,zlib)))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("autoconf-archive" ,autoconf-archive)
+         ("automake" ,automake)
+         ("libtool" ,libtool)
+         ("pkg-config" ,pkg-config)
+         ("swig" ,swig)))
+      (synopsis "Guile bindings for Xapian")
+      (description "@code{guile-xapian} provides Guile bindings for Xapian, a
+search engine library.  Xapian is a highly adaptable toolkit which allows
+developers to easily add advanced indexing and search facilities to their own
+applications.  It has built-in support for several families of weighting
+models and also supports a rich set of boolean query operators.")
+      (license license:gpl2+))))
+
+(define-public guile3.0-xapian
+  (package
+    (inherit guile-xapian)
+    (name "guile3.0-xapian")
+    (inputs
+     `(("guile" ,guile-next)
+       ,@(alist-delete "guile" (package-inputs guile-xapian))))))
diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm
index c0766c06bd..12a8d6758f 100644
--- a/gnu/packages/ibus.scm
+++ b/gnu/packages/ibus.scm
@@ -59,7 +59,7 @@
 (define-public ibus
   (package
     (name "ibus")
-    (version "1.5.21")
+    (version "1.5.22")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/ibus/ibus/"
@@ -67,7 +67,7 @@
                                   version "/ibus-" version ".tar.gz"))
               (sha256
                (base32
-                "1fd2d1jqpp1nn74x04zcilhhab0zar82n0kg614rma6n43kfbhdd"))))
+                "0jmy2w01phpmqnjnfnak7nvfna57mpgfnl87jwc4iai8ijjynw41"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      `(#:tests? #f  ; tests fail because there's no connection to dbus
diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index a0b5776807..5229eeda06 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2353,6 +2353,12 @@ new Date();"))
                                   (string-join (string-split version #\.) "u")
                                   "-ga"))))
               (file-name (string-append name "-" version "-checkout"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Delete included gradle jar
+                  (delete-file-recursively "gradle/wrapper")
+                  #t))
               (sha256
                (base32
                 "0yg38mwpivswccv9n96k06x3iv82i4px1a9xg9l8dswzwmfj259f"))))
diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm
index 23afd138a3..2831d3d842 100644
--- a/gnu/packages/kodi.scm
+++ b/gnu/packages/kodi.scm
@@ -269,7 +269,7 @@ alternatives. In compilers, this can reduce the cascade of secondary errors.")
 (define-public kodi
   (package
     (name "kodi")
-    (version "18.4")
+    (version "18.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -278,7 +278,7 @@ alternatives. In compilers, this can reduce the cascade of secondary errors.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1m0295czxabdcqyqf5m94av9d88pzhnzjvyfs1q07xqq82h313p7"))
+                "0rwymipn5hljy5xrslzmrljmj6f9wb191wi7gjw20wl6sv44d0bk"))
               (patches (search-patches "kodi-skip-test-449.patch"
                                        "kodi-increase-test-timeout.patch"
                                        "kodi-set-libcurl-ssl-parameters.patch"))
diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index d45f0ede90..2de9b84a1b 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -3008,7 +3008,7 @@ is a library for creating graphical user interfaces.")
   (sbcl-package->cl-source-package sbcl-cl-cffi-gtk))
 
 (define-public sbcl-cl-webkit
-  (let ((commit "cd2a9008e0c152e54755e8a7f07b050fe36bab31"))
+  (let ((commit "79ad41996a1bd7fc8e53fe8d168e8f2030603b14"))
     (package
       (name "sbcl-cl-webkit")
       (version (git-version "2.4" "1" commit))
@@ -3016,12 +3016,12 @@ is a library for creating graphical user interfaces.")
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/jmercouris/cl-webkit")
+               (url "https://github.com/joachifm/cl-webkit")
                (commit commit)))
          (file-name (git-file-name "cl-webkit" version))
          (sha256
           (base32
-           "0f5lyn9i7xrn3g1bddga377mcbawkbxydijpg389q4n04gqj0vwf"))))
+           "1gxvmxmss5k79v2ccigx92q46zbydxh9r7plnnqh8na348pffgcs"))))
       (build-system asdf-build-system/sbcl)
       (inputs
        `(("cffi" ,sbcl-cffi)
@@ -3038,7 +3038,7 @@ is a library for creating graphical user interfaces.")
                  (("libwebkit2gtk" all)
                   (string-append
                    (assoc-ref inputs "webkitgtk") "/lib/" all))))))))
-      (home-page "https://github.com/jmercouris/cl-webkit")
+      (home-page "https://github.com/joachifm/cl-webkit")
       (synopsis "Binding to WebKitGTK+ for Common Lisp")
       (description
        "@command{cl-webkit} is a binding to WebKitGTK+ for Common Lisp,
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index cab84a520b..a990ffc45e 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -34,6 +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>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3405,16 +3406,18 @@ Fresnel integrals, and similar related functions as well.")
 (define-public suitesparse
   (package
     (name "suitesparse")
-    (version "4.5.5")
+    (version "5.7.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append
-             "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
-             version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/DrTimothyAldenDavis/SuiteSparse.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
+         "174p3l78kv9gaa0i5hflyai2ydwnjzh34k9938sl4aa3li0543s8"))
+       (patches (search-patches "suitesparse-mongoose-cmake.patch"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled metis source
@@ -3429,6 +3432,14 @@ Fresnel integrals, and similar related functions as well.")
              "BLAS=-lblas"
              "TBB=-ltbb"
              "MY_METIS_LIB=-lmetis"
+             ;; Flags for cmake (required to build GraphBLAS and Mongoose)
+             (string-append "CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX="
+                            (assoc-ref %outputs "out")
+                            " -DCMAKE_VERBOSE_MAKEFILE=ON"
+                            " -DCMAKE_C_FLAGS_RELEASE=\"$(CFLAGS) $(CPPFLAGS)\""
+                            " -DCMAKE_CXX_FLAGS_RELEASE=\"$(CXXFLAGS) $(CPPFLAGS)\""
+                            " -DCMAKE_SKIP_RPATH=TRUE"
+                            " -DCMAKE_BUILD_TYPE=Release")
              (string-append "INSTALL_LIB="
                             (assoc-ref %outputs "out") "/lib")
              (string-append "INSTALL_INCLUDE="
@@ -3441,6 +3452,9 @@ Fresnel integrals, and similar related functions as well.")
      `(("tbb" ,tbb)
        ("lapack" ,lapack)
        ("metis" ,metis)))
+    (native-inputs
+     `(("cmake" ,cmake)
+       ("m4" ,m4)))
     (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
     (synopsis "Suite of sparse matrix software")
     (description
diff --git a/gnu/packages/patches/appstream-glib-2020.patch b/gnu/packages/patches/appstream-glib-2020.patch
deleted file mode 100644
index ab8a4bbdee..0000000000
--- a/gnu/packages/patches/appstream-glib-2020.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-2020 is no longer the future.
-
-Taken from upstream:
-https://github.com/hughsie/appstream-glib/commit/953c8e529d7291e60a95e580967ed79ce2c9ccf0
-
-diff --git a/data/tests/broken.appdata.xml b/data/tests/broken.appdata.xml
-index f7a5386e..cf80f5b4 100644
---- a/data/tests/broken.appdata.xml
-+++ b/data/tests/broken.appdata.xml
-@@ -40,7 +40,7 @@
-         <p>This is a duplicate release on the same day!</p>
-       </description>
-     </release>
--    <release date="2020-01-01" version="0.6.2">
-+    <release date="2050-01-01" version="0.6.2">
-       <description>
-         <p>This is a release in the future!</p>
-       </description>
-diff --git a/libappstream-glib/as-app-validate.c b/libappstream-glib/as-app-validate.c
-index c1103ace..f50e4e41 100644
---- a/libappstream-glib/as-app-validate.c
-+++ b/libappstream-glib/as-app-validate.c
-@@ -864,7 +864,7 @@ as_app_validate_release (AsApp *app,
- 				     AS_PROBLEM_KIND_ATTRIBUTE_MISSING,
- 				     "<release> has no timestamp");
- 	}
--	if (timestamp > 20120101 && timestamp < 20251231) {
-+	if (timestamp > 20120101 && timestamp < 20351231) {
- 		ai_app_validate_add (helper,
- 				     AS_PROBLEM_KIND_ATTRIBUTE_INVALID,
- 				     "<release> timestamp should be a UNIX time");
diff --git a/gnu/packages/patches/ceph-boost-compat.patch b/gnu/packages/patches/ceph-boost-compat.patch
deleted file mode 100644
index b3df659d6b..0000000000
--- a/gnu/packages/patches/ceph-boost-compat.patch
+++ /dev/null
@@ -1,81 +0,0 @@
-Fix compatibility with Boost 1.70.
-
-Adapted for 14.2.5 from these upstream commits:
-https://github.com/ceph/ceph/commit/064f142746ae97f54865069cdacf5aae2b1b14f6
-https://github.com/ceph/ceph/commit/f1651b8c509d60787d10c4115e29fecfd2da237c
-
-diff --git a/src/rgw/rgw_asio_frontend.cc b/src/rgw/rgw_asio_frontend.cc
---- a/src/rgw/rgw_asio_frontend.cc
-+++ b/src/rgw/rgw_asio_frontend.cc
-@@ -83,7 +83,8 @@
- using SharedMutex = ceph::async::SharedMutex<boost::asio::io_context::executor_type>;
- 
- template <typename Stream>
--void handle_connection(RGWProcessEnv& env, Stream& stream,
-+void handle_connection(boost::asio::io_context& context,
-+		       RGWProcessEnv& env, Stream& stream,
-                        parse_buffer& buffer, bool is_ssl,
-                        SharedMutex& pause_mutex,
-                        rgw::dmclock::Scheduler *scheduler,
-@@ -160,7 +161,7 @@
-                                   rgw::io::add_conlen_controlling(
-                                     &real_client))));
-       RGWRestfulIO client(cct, &real_client_io);
--      auto y = optional_yield{socket.get_io_context(), yield};
-+      auto y = optional_yield{context, yield};
-       process_request(env.store, env.rest, &req, env.uri_prefix,
-                       *env.auth_registry, &client, env.olog, y, scheduler);
-     }
-@@ -604,7 +605,7 @@
-           return;
-         }
-         buffer->consume(bytes);
--        handle_connection(env, stream, *buffer, true, pause_mutex,
-+        handle_connection(context, env, stream, *buffer, true, pause_mutex,
-                           scheduler.get(), ec, yield);
-         if (!ec) {
-           // ssl shutdown (ignoring errors)
-@@ -622,7 +623,7 @@
-         auto c = connections.add(conn);
-         auto buffer = std::make_unique<parse_buffer>();
-         boost::system::error_code ec;
--        handle_connection(env, s, *buffer, false, pause_mutex,
-+        handle_connection(context, env, s, *buffer, false, pause_mutex,
-                           scheduler.get(), ec, yield);
-         s.shutdown(tcp::socket::shutdown_both, ec);
-       });
-diff --git a/src/rgw/rgw_dmclock_async_scheduler.h b/src/rgw/rgw_dmclock_async_scheduler.h
---- a/src/rgw/rgw_dmclock_async_scheduler.h
-+++ b/src/rgw/rgw_dmclock_async_scheduler.h
-@@ -82,7 +82,12 @@ class AsyncScheduler : public md_config_obs_t, public Scheduler {
-   using Completion = async::Completion<Signature, async::AsBase<Request>>;
- 
-   using Clock = ceph::coarse_real_clock;
-+#if BOOST_VERSION < 107000
-   using Timer = boost::asio::basic_waitable_timer<Clock>;
-+#else
-+  using Timer = boost::asio::basic_waitable_timer<Clock,
-+        boost::asio::wait_traits<Clock>, executor_type>;
-+#endif
-   Timer timer; //< timer for the next scheduled request
- 
-   CephContext *const cct;
-diff --git a/src/rgw/rgw_reshard.h b/src/rgw/rgw_reshard.h
---- a/src/rgw/rgw_reshard.h
-+++ b/src/rgw/rgw_reshard.h
-@@ -183,7 +183,14 @@ class RGWReshardWait {
-   ceph::condition_variable cond;
- 
-   struct Waiter : boost::intrusive::list_base_hook<> {
--    boost::asio::basic_waitable_timer<Clock> timer;
-+#if BOOST_VERSION < 107000
-+    using Timer = boost::asio::basic_waitable_timer<Clock>;
-+#else
-+    using Executor = boost::asio::io_context::executor_type;
-+    using Timer = boost::asio::basic_waitable_timer<Clock,
-+          boost::asio::wait_traits<Clock>, Executor>;
-+#endif
-+    Timer timer;
-     explicit Waiter(boost::asio::io_context& ioc) : timer(ioc) {}
-   };
-   boost::intrusive::list<Waiter> waiters;
diff --git a/gnu/packages/patches/ceph-volume-respect-PATH.patch b/gnu/packages/patches/ceph-volume-respect-PATH.patch
deleted file mode 100644
index 08a9a15ddd..0000000000
--- a/gnu/packages/patches/ceph-volume-respect-PATH.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-Look for required tools in $PATH instead of just a handful locations.
-
-diff --git a/src/ceph-volume/ceph_volume/util/system.py b/src/ceph-volume/ceph_volume/util/system.py
-index b637f023a4..14516e1c65 100644
---- a/src/ceph-volume/ceph_volume/util/system.py
-+++ b/src/ceph-volume/ceph_volume/util/system.py
-@@ -33,14 +33,7 @@ def generate_uuid():
- 
- def which(executable):
-     """find the location of an executable"""
--    locations = (
--        '/usr/local/bin',
--        '/bin',
--        '/usr/bin',
--        '/usr/local/sbin',
--        '/usr/sbin',
--        '/sbin',
--    )
-+    locations = os.getenv('PATH').split(':')
- 
-     for location in locations:
-         executable_path = os.path.join(location, executable)
diff --git a/gnu/packages/patches/libgit2-avoid-python.patch b/gnu/packages/patches/libgit2-avoid-python.patch
deleted file mode 100644
index b2e5141563..0000000000
--- a/gnu/packages/patches/libgit2-avoid-python.patch
+++ /dev/null
@@ -1,322 +0,0 @@
-This provides a Guile reimplementation of clar's "generate.py".
-It makes it possible for us to remove Python from libgit2's build-time
-dependencies.
-libgit2 is used in order to fetch a lot of sources for guix packages.
-Both Python2 and Python3 builds acted up in the past.
-Hence this patch which makes the number of libgit2 dependencies very
-small.
-The reimplementation tries to keep as close as possible to the original
-in both structure and runtime effect.  Some things are thus overly
-convoluted just to make them the same as in the original.
-
-Both implementations basically do:
-
-grep -r 'test_.*__.*' . > clar.suite
-
-It is important that the directory traversal order of the original and
-the reimplementation stay the same.
-
-diff -ruN orig/libgit2-0.27.7/tests/CMakeLists.txt libgit2-0.27.7/tests/CMakeLists.txt
---- orig/libgit2-0.27.7/tests/CMakeLists.txt	1970-01-01 01:00:00.000000000 +0100
-+++ libgit2-0.27.7/tests/CMakeLists.txt	2019-03-04 11:13:06.640118979 +0100
-@@ -1,10 +1,3 @@
--FIND_PACKAGE(PythonInterp)
--
--IF(NOT PYTHONINTERP_FOUND)
--  MESSAGE(FATAL_ERROR "Could not find a python interpeter, which is needed to build the tests. "
--    "Make sure python is available, or pass -DBUILD_CLAR=OFF to skip building the tests")
--ENDIF()
--
- SET(CLAR_FIXTURES "${CMAKE_CURRENT_SOURCE_DIR}/resources/")
- SET(CLAR_PATH "${CMAKE_CURRENT_SOURCE_DIR}")
- ADD_DEFINITIONS(-DCLAR_FIXTURE_PATH=\"${CLAR_FIXTURES}\")
-@@ -21,7 +14,7 @@
- 
- ADD_CUSTOM_COMMAND(
- 	OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/clar.suite
--	COMMAND ${PYTHON_EXECUTABLE} generate.py -o "${CMAKE_CURRENT_BINARY_DIR}" -f -xonline -xstress -xperf .
-+	COMMAND guile generate.scm -o "${CMAKE_CURRENT_BINARY_DIR}" -f -x online -x stress -x perf .
- 	DEPENDS ${SRC_TEST}
- 	WORKING_DIRECTORY ${CLAR_PATH}
- )
-diff -ruN orig/libgit2-0.27.7/tests/generate.scm libgit2-0.27.7/tests/generate.scm
---- orig/libgit2-0.27.7/tests/generate.scm	1970-01-01 01:00:00.000000000 +0100
-+++ libgit2-0.27.7/tests/generate.scm	2019-03-04 12:18:00.688040975 +0100
-@@ -0,0 +1,277 @@
-+;; -*- geiser-scheme-implementation: guile -*-
-+
-+;;; Implementation: Danny Milosavljevic <dannym@scratchpost.org>
-+;;; Based on: Implementation in Python by Vicent Marti.
-+;;; License: ISC, like the original generate.py in clar.
-+
-+(use-modules (ice-9 ftw))
-+(use-modules (ice-9 regex))
-+(use-modules (ice-9 getopt-long))
-+(use-modules (ice-9 rdelim))
-+(use-modules (ice-9 match))
-+(use-modules (ice-9 textual-ports))
-+(use-modules (srfi srfi-1))
-+
-+(define (render-callback cb)
-+  (if cb
-+      (string-append "    { \"" (assoc-ref cb "short-name") "\", &"
-+                     (assoc-ref cb "symbol") " }")
-+      "    { NULL, NULL }"))
-+
-+(define (replace needle replacement haystack)
-+  "Replace all occurences of NEEDLE in HAYSTACK by REPLACEMENT.
-+NEEDLE is a regular expression."
-+  (regexp-substitute/global #f needle haystack 'pre replacement 'post))
-+
-+(define (skip-comments* text)
-+  (call-with-input-string
-+   text
-+   (lambda (port)
-+     (let loop ((result '())
-+                (section #f))
-+       (define (consume-char)
-+         (cons (read-char port) result))
-+       (define (skip-char)
-+         (read-char port)
-+         result)
-+       (match section
-+        (#f
-+         (match (peek-char port)
-+          (#\/ (loop (consume-char) 'almost-in-block-comment))
-+          (#\" (loop (consume-char) 'in-string-literal))
-+          (#\' (loop (consume-char) 'in-character-literal))
-+          ((? eof-object?) result)
-+          (_ (loop (consume-char) section))))
-+        ('almost-in-block-comment
-+         (match (peek-char port)
-+          (#\* (loop (consume-char) 'in-block-comment))
-+          (#\/ (loop (consume-char) 'in-line-comment))
-+          ((? eof-object?) result)
-+          (_ (loop (consume-char) #f))))
-+        ('in-line-comment
-+         (match (peek-char port)
-+          (#\newline (loop (consume-char) #f))
-+          ((? eof-object?) result)
-+          (_ (loop (skip-char) section))))
-+        ('in-block-comment
-+         (match (peek-char port)
-+           (#\* (loop (skip-char) 'almost-out-of-block-comment))
-+           ((? eof-object?) result)
-+           (_ (loop (skip-char) section))))
-+        ('almost-out-of-block-comment
-+         (match (peek-char port)
-+           (#\/ (loop (cons (read-char port) (cons #\* result)) #f))
-+           (#\* (loop (skip-char) 'almost-out-of-block-comment))
-+           ((? eof-object?) result)
-+           (_ (loop (skip-char) 'in-block-comment))))
-+        ('in-string-literal
-+         (match (peek-char port)
-+           (#\\ (loop (consume-char) 'in-string-literal-escape))
-+           (#\" (loop (consume-char) #f))
-+           ((? eof-object?) result)
-+           (_ (loop (consume-char) section))))
-+        ('in-string-literal-escape
-+         (match (peek-char port)
-+           ((? eof-object?) result)
-+           (_ (loop (consume-char) 'in-string-literal))))
-+        ('in-character-literal
-+         (match (peek-char port)
-+           (#\\ (loop (consume-char) 'in-character-literal-escape))
-+           (#\' (loop (consume-char) #f))
-+           ((? eof-object?) result)
-+           (_ (loop (consume-char) section))))
-+        ('in-character-literal-escape
-+         (match (peek-char port)
-+           ((? eof-object?) result)
-+           (_ (loop (consume-char) 'in-character-literal)))))))))
-+
-+(define (skip-comments text)
-+  (list->string (reverse (skip-comments* text))))
-+
-+(define (maybe-only items)
-+  (match items
-+   ((a) a)
-+   (_ #f)))
-+
-+(define (Module name path excludes)
-+  (let* ((clean-name (replace "_" "::" name))
-+         (enabled (not (any (lambda (exclude)
-+                              (string-prefix? exclude clean-name))
-+                            excludes))))
-+    (define (parse contents)
-+      (define (cons-match match prev)
-+        (cons
-+         `(("declaration" . ,(match:substring match 1))
-+           ("symbol" . ,(match:substring match 2))
-+           ("short-name" . ,(match:substring match 3)))
-+         prev))
-+      (let* ((contents (skip-comments contents))
-+             (entries (fold-matches (make-regexp
-+                                     (string-append "^(void\\s+(test_"
-+                                                    name
-+                                                    "__(\\w+))\\s*\\(\\s*void\\s*\\))\\s*\\{")
-+                                     regexp/newline)
-+                                    contents
-+                                    '()
-+                                    cons-match))
-+             (entries (reverse entries))
-+             (callbacks (filter (lambda (entry)
-+                                   (match (assoc-ref entry "short-name")
-+                                    ("initialize" #f)
-+                                    ("cleanup" #f)
-+                                    (_ #t)))
-+                                entries)))
-+        (if (> (length callbacks) 0)
-+            `(("name" . ,name)
-+              ("enabled" . ,(if enabled "1" "0"))
-+              ("clean-name" . ,clean-name)
-+              ("initialize" . ,(maybe-only (filter-map (lambda (entry)
-+                                                      (match (assoc-ref entry "short-name")
-+                                                       ("initialize" entry)
-+                                                       (_ #f)))
-+                                                     entries)))
-+              ("cleanup" . ,(maybe-only (filter-map (lambda (entry)
-+                                                   (match (assoc-ref entry "short-name")
-+                                                    ("cleanup" entry)
-+                                                    (_ #f)))
-+                                                  entries)))
-+              ("callbacks" . ,callbacks))
-+            #f)))
-+
-+    (define (refresh path)
-+      (and (file-exists? path)
-+           (parse (call-with-input-file path get-string-all))))
-+    (refresh path)))
-+
-+(define (generate-TestSuite path output excludes)
-+    (define (load)
-+        (define enter? (const #t))
-+        (define (leaf file stat result)
-+          (let* ((module-root (string-drop (dirname file)
-+                                           (string-length path)))
-+                 (module-root (filter-map (match-lambda
-+                                           ("" #f)
-+                                           (a a))
-+                                          (string-split module-root #\/))))
-+            (define (make-module path)
-+              (let* ((name (string-join (append module-root (list (string-drop-right (basename path) (string-length ".c")))) "_"))
-+                     (name (replace "-" "_" name)))
-+                (Module name path excludes)))
-+            (if (string-suffix? ".c" file)
-+                (let ((module (make-module file)))
-+                  (if module
-+                      (cons module result)
-+                      result))
-+                result)))
-+        (define (down dir stat result)
-+          result)
-+        (define (up file state result)
-+          result)
-+        (define skip (const #f))
-+        (file-system-fold enter? leaf down up skip error '() path))
-+
-+    (define (CallbacksTemplate module)
-+      (string-append "static const struct clar_func _clar_cb_"
-+                     (assoc-ref module "name") "[] = {\n"
-+                     (string-join (map render-callback
-+                                       (assoc-ref module "callbacks"))
-+                                  ",\n")
-+                     "\n};\n"))
-+
-+    (define (DeclarationTemplate module)
-+      (string-append (string-join (map (lambda (cb)
-+                                         (string-append "extern "
-+                                                        (assoc-ref cb "declaration")
-+                                                        ";"))
-+                                       (assoc-ref module "callbacks"))
-+                                  "\n")
-+                     "\n"
-+                     (if (assoc-ref module "initialize")
-+                         (string-append "extern " (assoc-ref (assoc-ref module "initialize") "declaration") ";\n")
-+                         "")
-+                     (if (assoc-ref module "cleanup")
-+                         (string-append "extern " (assoc-ref (assoc-ref module "cleanup") "declaration") ";\n")
-+                         "")))
-+
-+    (define (InfoTemplate module)
-+      (string-append "
-+    {
-+        \"" (assoc-ref module "clean-name") "\",
-+    " (render-callback (assoc-ref module "initialize")) ",
-+    " (render-callback (assoc-ref module "cleanup")) ",
-+        _clar_cb_" (assoc-ref module "name") ", "
-+        (number->string (length (assoc-ref module "callbacks")))
-+        ", " (assoc-ref module "enabled") "
-+    }"))
-+
-+    (define (Write data)
-+      (define (name< module-a module-b)
-+        (string<? (assoc-ref module-a "name")
-+                  (assoc-ref module-b "name")))
-+      (define modules (sort (load) name<))
-+
-+      (define (suite-count)
-+        (length modules))
-+
-+      (define (callback-count)
-+        (fold + 0 (map (lambda (entry)
-+                         (length (assoc-ref entry "callbacks")))
-+                         modules)))
-+
-+      (define (display-x value)
-+        (display value data))
-+
-+      (for-each (compose display-x DeclarationTemplate) modules)
-+      (for-each (compose display-x CallbacksTemplate) modules)
-+
-+      (display-x "static struct clar_suite _clar_suites[] = {")
-+      (display-x (string-join (map InfoTemplate modules) ","))
-+      (display-x "\n};\n")
-+
-+      (let ((suite-count-str (number->string (suite-count)))
-+            (callback-count-str (number->string (callback-count))))
-+        (display-x "static const size_t _clar_suite_count = ")
-+        (display-x suite-count-str)
-+        (display-x ";\n")
-+
-+        (display-x "static const size_t _clar_callback_count = ")
-+        (display-x callback-count-str)
-+        (display-x ";\n")
-+
-+        (display (string-append "Written `clar.suite` ("
-+                                callback-count-str
-+                                " tests in "
-+                                suite-count-str
-+                                " suites)"))
-+        (newline))
-+      #t)
-+
-+    (call-with-output-file (string-append output "/clar.suite") Write))
-+
-+;;; main
-+
-+(define (main)
-+  (define option-spec
-+    '((force (single-char #\f) (value #f))
-+      (exclude (single-char #\x) (value #t))
-+      (output (single-char #\o) (value #t))
-+      (help  (single-char #\h) (value #f))))
-+
-+  (define options (getopt-long (command-line) option-spec #:stop-at-first-non-option #t))
-+  (define args (reverse (option-ref options '() '())))
-+  (when (> (length args) 1)
-+    (display "More than one path given\n")
-+    (exit 1))
-+
-+  (if (< (length args) 1)
-+      (set! args '(".")))
-+
-+  (let* ((path (car args))
-+         (output (option-ref options 'output path))
-+         (excluded (filter-map (match-lambda
-+                                (('exclude . value) value)
-+                                (_ #f))
-+                               options)))
-+    (generate-TestSuite path output excluded)))
-+
-+(main)
diff --git a/gnu/packages/patches/suitesparse-mongoose-cmake.patch b/gnu/packages/patches/suitesparse-mongoose-cmake.patch
new file mode 100644
index 0000000000..e5062f9aaa
--- /dev/null
+++ b/gnu/packages/patches/suitesparse-mongoose-cmake.patch
@@ -0,0 +1,27 @@
+Fix required by suitesparse to build Mongoose
+
+The CMakeLists.txt of Mongoose assumes that SuiteSparse_config has been
+installed into the suitesparse source directory, which is not the case
+for us, as we are building suitesparse out-of-tree.
+
+SuiteSparse_config can instead be found in the ${CMAKE_INSTALL_PREFIX}
+directory.
+
+diff --git a/Mongoose/CMakeLists.txt b/Mongoose/CMakeLists.txt
+index 7e134ab..76fa9e2 100644
+--- a/Mongoose/CMakeLists.txt
++++ b/Mongoose/CMakeLists.txt
+@@ -148,10 +148,10 @@ set(CMAKE_CXX_STANDARD 11)
+ #set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+ # determine which SuiteSparse_config to use
+-if (EXISTS ${PROJECT_SOURCE_DIR}/../SuiteSparse_config)
+-    message(STATUS "External ../SuiteSparse_config" ${BoldBlue} " found" ${ColourReset} ".")
++if (EXISTS ${CMAKE_INSTALL_PREFIX})
++    message(STATUS "External SuiteSparse_config" ${BoldBlue} " found" ${ColourReset} ".")
+     set ( SUITESPARSE_CONFIG_DIR ${PROJECT_SOURCE_DIR}/../SuiteSparse_config )
+-    link_directories ( ${PROJECT_SOURCE_DIR}/../lib )
++    link_directories ( ${CMAKE_INSTALL_PREFIX}/lib )
+     message ( STATUS "Note: ../SuiteSparse_config must be compiled before compiling Mongoose" )
+     set ( SUITESPARSE_CONFIG_LIBRARY suitesparseconfig )
+ else ()
diff --git a/gnu/packages/patchutils.scm b/gnu/packages/patchutils.scm
index e32e6c7b12..e01ebe72ec 100644
--- a/gnu/packages/patchutils.scm
+++ b/gnu/packages/patchutils.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2018 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015, 2018 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Christopher Baines <mail@cbaines.net>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -247,7 +247,7 @@ GiB).")
 (define-public meld
   (package
     (name "meld")
-    (version "3.20.1")
+    (version "3.20.2")
     (source
      (origin
        (method url-fetch)
@@ -255,7 +255,7 @@ GiB).")
                            (version-major+minor version)
                            "/meld-" version ".tar.xz"))
        (sha256
-        (base32 "0jdj7kd6vj1mdc16gvrj1kar88b2j5875ajq18fx7cbc9ny46j55"))))
+        (base32 "0a0x156zr3w2yg0rnhwy39giy3xnfm6sqcfa4xcw4i6ahvwqa2dc"))))
     (build-system python-build-system)
     (native-inputs
      `(("intltool" ,intltool)
diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index c065e97da5..5a536141f5 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -226,7 +226,7 @@ When present, Poppler is able to correctly render CJK and Cyrillic text.")
        ("python-pyqt" ,python-pyqt)
        ("poppler-qt5" ,poppler-qt5)
        ("qtbase" ,qtbase)))
-    (home-page "https://pypi.python.org/pypi/python-poppler-qt5")
+    (home-page "https://pypi.org/project/python-poppler-qt5/")
     (synopsis "Python bindings for Poppler-Qt5")
     (description
      "This package provides Python bindings for the Qt5 interface of the
@@ -392,7 +392,7 @@ using libspectre.")
 (define-public zathura-djvu
   (package
     (name "zathura-djvu")
-    (version "0.2.8")
+    (version "0.2.9")
     (source (origin
               (method url-fetch)
               (uri
@@ -400,7 +400,7 @@ using libspectre.")
                               version ".tar.xz"))
               (sha256
                (base32
-                "0axkv1crdxn0z44whaqp2ibkdqcykhjnxk7qzms0dp1b67an9rnh"))))
+                "0062n236414db7q7pnn3ccg5111ghxj3407pn9ri08skxskgirln"))))
     (native-inputs `(("pkg-config" ,pkg-config)))
     (inputs
      `(("djvulibre" ,djvulibre)
@@ -472,7 +472,7 @@ by using the @code{mupdf} rendering library.")
 (define-public zathura-pdf-poppler
   (package
     (name "zathura-pdf-poppler")
-    (version "0.2.9")
+    (version "0.3.0")
     (source (origin
               (method url-fetch)
               (uri
@@ -480,7 +480,7 @@ by using the @code{mupdf} rendering library.")
                               version ".tar.xz"))
               (sha256
                (base32
-                "1p4jcny0jniygns78mcf0nlm298dszh49qpmjmackrm6dq8hc25y"))))
+                "1vfl4vkyy3rf39r1sqaa7y8113bgkh2bkfq3nn2inis9mrykmk6m"))))
     (native-inputs `(("pkg-config" ,pkg-config)))
     (inputs
      `(("poppler" ,poppler)
@@ -508,7 +508,7 @@ by using the poppler rendering engine.")
 (define-public zathura
   (package
     (name "zathura")
-    (version "0.4.3")
+    (version "0.4.5")
     (source (origin
               (method url-fetch)
               (uri
@@ -516,7 +516,7 @@ by using the poppler rendering engine.")
                               version ".tar.xz"))
               (sha256
                (base32
-                "0hgx5x09i6d0z45llzdmh4l348fxh1y102sb1w76f2fp4r21j4ky"))))
+                "0b3nrcvykkpv2vm99kijnic2gpfzva520bsjlihaxandzfm9ff8c"))))
     (native-inputs `(("pkg-config" ,pkg-config)
                      ("gettext" ,gettext-minimal)
                      ("glib:bin" ,glib "bin")
@@ -1270,13 +1270,13 @@ manipulating PDF documents from the command line.  It supports
 (define-public weasyprint
   (package
     (name "weasyprint")
-    (version "50")
+    (version "51")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "WeasyPrint" version))
        (sha256
-        (base32 "0invs96zvmcr6wh5klj52jrcnr9qg150v9wpmbhcsf3vv1d1hbcw"))
+        (base32 "0skdzwq7cd715dnnds6abx0k0xmmnmsqp0vb1r1w20sg7abp3sdk"))
        (patches (search-patches "weasyprint-library-paths.patch"))))
     (build-system python-build-system)
     (arguments
@@ -1304,11 +1304,11 @@ manipulating PDF documents from the command line.  It supports
            (lambda _
              (substitute* "setup.cfg"
                ;; flake8 and isort syntax checks fail, which is not our
-               ;; business
+               ;; business.
                (("addopts = --flake8 --isort") ""))))
          (replace 'check
            (lambda _
-             ;; run pytest, excluding one failing test
+             ;; Run pytest, excluding one failing test.
              (invoke "pytest" "-k" "not test_flex_column_wrap_reverse"))))))
     (inputs
      `(("fontconfig" ,fontconfig)
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index ac75616657..08d75525be 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -972,7 +972,7 @@ object to help create WSGI responses.")
         (base32
          "1ksbc726av9xacml6jhcfyn828hlhb9xlddpx6fcvnlvmpmpvhk9"))))
     (build-system python-build-system)
-    (home-page "https://pypi.python.org/pypi/zope.event")
+    (home-page "https://pypi.org/project/zope.event/")
     (synopsis "Event publishing system for Python")
     (description "Zope.event provides an event publishing API, intended for
 use by applications which are unaware of any subscribers to their events.  It
@@ -1021,10 +1021,10 @@ conforming to a given API or contract.")
          "0zwxaaa66sqxg5k7zcrvs0fbg9ym1njnxnr28dfmchzhwjvwnfzl"))))
     (build-system python-build-system)
     (arguments
-     '(#:tests? #f)) ; circular dependency with zope.testrunner
+     '(#:tests? #f))                ; circular dependency with zope.testrunner
     (propagated-inputs
      `(("python-zope-interface" ,python-zope-interface)))
-    (home-page "http://cheeseshop.python.org/pypi/zope.exceptions")
+    (home-page "https://pypi.org/project/zope.exceptions/")
     (synopsis "Zope exceptions")
     (description "Zope.exceptions provides general-purpose exception types
 that have uses outside of the Zope framework.")
@@ -1051,7 +1051,7 @@ that have uses outside of the Zope framework.")
            (for-each delete-file (find-files "." "(\\.pyc|~)$"))
            #t))))
     (build-system python-build-system)
-    (home-page "https://pypi.python.org/pypi/zope.testing")
+    (home-page "https://pypi.org/project/zope.testing/")
     (synopsis "Zope testing helpers")
     (description "Zope.testing provides a number of testing utilities for HTML
 forms, HTTP servers, regular expressions, and more.")
@@ -1082,7 +1082,7 @@ forms, HTTP servers, regular expressions, and more.")
        ("unzip" ,unzip)))
     (propagated-inputs
      `(("python-zope-interface" ,python-zope-interface)))
-    (home-page "https://pypi.python.org/pypi/zope.testrunner")
+    (home-page "https://pypi.org/project/zope.testrunner/")
     (synopsis "Zope testrunner script")
     (description "Zope.testrunner provides a script for running Python
 tests.")
@@ -1109,7 +1109,7 @@ tests.")
         (base32
          "1rslyph0klk58dmjjy4j0jxy21k03azksixc3x2xhqbkv97cmzml"))))
     (build-system python-build-system)
-    (home-page "https://pypi.python.org/pypi/zope.i18nmessageid")
+    (home-page "https://pypi.org/project/zope.i18nmessageid/")
     (synopsis "Message identifiers for internationalization")
     (description "Zope.i18nmessageid provides facilities for declaring
 internationalized messages within program source text.")
@@ -1140,7 +1140,7 @@ internationalized messages within program source text.")
      `(("python-zope-testing" ,python-zope-testing)
        ("python-coverage" ,python-coverage)
        ("python-nose" ,python-nose)))
-    (home-page "https://pypi.python.org/pypi/zope.schema")
+    (home-page "https://pypi.org/project/zope.schema/")
     (synopsis "Zope data schemas")
     (description "Zope.scheme provides extensions to zope.interface for
 defining data schemas.")
@@ -1165,7 +1165,7 @@ defining data schemas.")
     (propagated-inputs
      `(("python-zope-i18nmessageid" ,python-zope-i18nmessageid)
        ("python-zope-schema" ,python-zope-schema)))
-    (home-page "https://pypi.python.org/pypi/zope.configuration")
+    (home-page "https://pypi.org/project/zope.configuration/")
     (synopsis "Zope Configuration Markup Language")
     (description "Zope.configuration implements ZCML, the Zope Configuration
 Markup Language.")
@@ -1190,7 +1190,7 @@ Markup Language.")
      '(#:tests? #f)) ; FIXME: Tests can't find zope.interface.
     (propagated-inputs
      `(("python-zope-interface" ,python-zope-interface)))
-    (home-page "https://pypi.python.org/pypi/zope.proxy")
+    (home-page "https://pypi.org/project/zope.proxy/")
     (synopsis "Generic, transparent proxies")
     (description "Zope.proxy provides generic, transparent proxies for Python.
 Proxies are special objects which serve as mostly-transparent wrappers around
@@ -1219,7 +1219,7 @@ brokering, etc.) for which the proxy is responsible.")
     (propagated-inputs
      `(("python-zope-proxy" ,python-zope-proxy)
        ("python-zope-schema" ,python-zope-schema)))
-    (home-page "https://pypi.python.org/pypi/zope.location/")
+    (home-page "https://pypi.org/project/zope.location/")
     (synopsis "Zope location library")
     (description "Zope.location implements the concept of \"locations\" in
 Zope3, which are are special objects that have a structural location.")
@@ -1253,7 +1253,7 @@ Zope3, which are are special objects that have a structural location.")
        ("python-zope-location" ,python-zope-location)
        ("python-zope-testrunner" ,python-zope-testrunner)
        ("python-zope-testing" ,python-zope-testing)))
-    (home-page "https://pypi.python.org/pypi/zope.security")
+    (home-page "https://pypi.org/project/zope.security/")
     (synopsis "Zope security framework")
     (description "Zope.security provides a generic mechanism to implement
 security policies on Python objects.")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ed599cd5d5..bc5ff3d2d8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -475,14 +475,14 @@ NetCDF files can also be read and modified.  Python-HDF4 is a fork of
 (define-public python-h5py
   (package
     (name "python-h5py")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
       (method url-fetch)
       (uri (pypi-uri "h5py" version))
       (sha256
        (base32
-        "0mdr6wrq02ac93m1aqx9kad0ppfzmm4imlxqgyy1x4l7hmdcc9p6"))))
+        "0baipzv8n93m0dq0riyi8rfhzrjrfrfh8zqhszzp1j2xjac2fhc4"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ; no test target
@@ -504,10 +504,11 @@ NetCDF files can also be read and modified.  Python-HDF4 is a fork of
      `(("python-six" ,python-six)
        ("python-numpy" ,python-numpy)))
     (inputs
-     `(("hdf5" ,hdf5)))
+     `(("hdf5" ,hdf5-1.10)))
     (native-inputs
      `(("python-cython" ,python-cython)
-       ("python-pkgconfig" ,python-pkgconfig)))
+       ("python-pkgconfig" ,python-pkgconfig)
+       ("pkg-config" ,pkg-config)))
     (home-page "https://www.h5py.org/")
     (synopsis "Read and write HDF5 files from Python")
     (description
@@ -748,7 +749,7 @@ other machines, such as over the network.")
     ;; One could bootstrap with an internal untested setuptools.
     (arguments
      `(#:tests? #f))
-    (home-page "https://pypi.python.org/pypi/setuptools")
+    (home-page "https://pypi.org/project/setuptools/")
     (synopsis
      "Library designed to facilitate packaging Python projects")
     (description
@@ -1111,7 +1112,7 @@ from the Python interpreter, or as a small part of a larger application.")
     (native-inputs
      `(("python-py" ,python-py)
        ("python-pytest" ,python-pytest-bootstrap)))
-    (home-page "https://pypi.python.org/pypi/six/")
+    (home-page "https://pypi.org/project/six/")
     (synopsis "Python 2 and 3 compatibility utilities")
     (description
      "Six is a Python 2 and 3 compatibility library.  It provides utility
@@ -1282,7 +1283,7 @@ Python 3.3+.")
     (arguments `(#:python ,python-2
                  #:tests? #f))                    ; invalid command "test"
     ;; Currently no offical homepage.
-    (home-page "https://pypi.python.org/pypi/dogtail/")
+    (home-page "https://pypi.org/project/dogtail/")
     (synopsis "GUI test tool and automation framework written in Python")
     (description
      "Dogtail is a GUI test tool and automation framework written in Python.
@@ -1393,7 +1394,7 @@ bug tracker.")
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2))
-    (home-page "https://pypi.python.org/pypi/enum/")
+    (home-page "https://pypi.org/project/enum/")
     (synopsis "Robust enumerated type support in Python")
     (description
      "This provides a module for robust enumerations in Python.  It has
@@ -1414,7 +1415,7 @@ compatibility.")
        (base32
         "1cgm5ng2gcfrkrm3hc22brl6chdmv67b9zvva9sfs7gn7dwc9n4a"))))
     (build-system python-build-system)
-    (home-page "https://pypi.python.org/pypi/enum34")
+    (home-page "https://pypi.org/project/enum34/")
     (synopsis "Backported Python 3.4 Enum")
     (description
      "Enum34 is the new Python stdlib enum module available in Python 3.4
@@ -1757,7 +1758,7 @@ code introspection, and logging.")
     (build-system python-build-system)
     (arguments
      `(#:tests? #f))
-    (home-page "http://docs.openstack.org/developer/pbr/")
+    (home-page "https://docs.openstack.org/pbr/latest/")
     (synopsis "Minimal build of python-pbr used for bootstrapping")
     (description
      "Used only for bootstrapping python2-pbr, you should not need this.")
@@ -2158,7 +2159,7 @@ cutting and pasting that code over and over.")
               (base32
                "1s6cp2lv4m0f00hjckjz8p6m7d3n3v16jvg353llf5ia1iqsnsib"))))
     (build-system python-build-system)
-    (home-page "https://pypi.python.org/pypi/Unidecode")
+    (home-page "https://pypi.org/project/Unidecode/")
     (synopsis "ASCII transliterations of Unicode text")
     (description
      "Unidecode provides ASCII transliterations of Unicode text.  Unidecode is
@@ -2337,7 +2338,7 @@ environments and back.")
     (build-system python-build-system)
     (inputs
      `(("libyaml" ,libyaml)))
-    (home-page "http://pyyaml.org/wiki/PyYAML")
+    (home-page "https://pyyaml.org")
     (synopsis "YAML parser and emitter for Python")
     (description
      "PyYAML is a YAML parser and emitter for Python.  PyYAML features a
@@ -3829,7 +3830,7 @@ that client code uses to construct the grammar directly in Python code.")
      `(("python-sphinx" ,python-sphinx)))
     (native-inputs
      `(("python-nose" ,python-nose)))
-    (home-page "https://pypi.python.org/pypi/numpydoc")
+    (home-page "https://pypi.org/project/numpydoc/")
     (synopsis
      "Numpy's Sphinx extensions")
     (description
@@ -4779,7 +4780,7 @@ PNG, PostScript, PDF, and SVG file output.")
        (sha256
         (base32 "0308djallnh00v112y5b7nadl657ysmkp6vc8xn51d6yzc9zm7n3"))))
     (build-system python-build-system)
-    (home-page "https://pypi.python.org/pypi/decorator/")
+    (home-page "https://pypi.org/project/decorator/")
     (synopsis "Python module to simplify usage of decorators")
     (description
       "The aim of the decorator module is to simplify the usage of decorators
@@ -4808,7 +4809,7 @@ etc.  The core of this module is a decorator factory.")
     (arguments '(#:tests? #f))
     (native-inputs
      `(("python-nose" ,python-nose)))
-    (home-page "https://pypi.python.org/pypi/drmaa")
+    (home-page "https://pypi.org/project/drmaa/")
     (synopsis "Python bindings for the DRMAA library")
     (description
       "A Python package for Distributed Resource Management (DRM) job
@@ -5023,7 +5024,7 @@ them as the version argument or in a SCM managed file.")
     (propagated-inputs
      `(("python-scandir" ,python-scandir)
        ("python-six" ,python-six)))
-    (home-page "https://pypi.python.org/pypi/pathlib2/")
+    (home-page "https://pypi.org/project/pathlib2/")
     (synopsis "Object-oriented file system paths")
     (description "The goal of pathlib2 is to provide a backport of the
 standard @code{pathlib} module which tracks the standard library module, so
@@ -6930,7 +6931,7 @@ from an XML-based format.")
     (description "This package provides a Python library to parse, manipulate
 or create documents in LilyPond format.  A command line program ly is also
 provided that can be used to do various manipulations with LilyPond files.")
-    (home-page "https://pypi.python.org/pypi/python-ly")
+    (home-page "https://pypi.org/project/python-ly/")
     (license license:gpl2+)))
 
 (define-public python-appdirs
@@ -7035,7 +7036,7 @@ should be stored on various operating systems.")
     (description "MessagePack is a fast, compact binary serialization format,
 suitable for similar data to JSON.  This package provides CPython bindings for
 reading and writing MessagePack data.")
-    (home-page "https://pypi.python.org/pypi/msgpack/")
+    (home-page "https://pypi.org/project/msgpack/")
     (license license:asl2.0)))
 
 ;; This msgpack library's name changed from "python-msgpack" to "msgpack" with
@@ -7528,7 +7529,7 @@ a hash value.")
     (arguments
      ;; There are no tests.
      `(#:tests? #f))
-    (home-page "https://pypi.python.org/pypi/termcolor")
+    (home-page "https://pypi.org/project/termcolor/")
     (synopsis "ANSII Color formatting for terminal output")
     (description
      "This package provides ANSII Color formatting for output in terminals.")
@@ -8782,7 +8783,7 @@ for the module to work under Python 3.3.")
    (synopsis "Colored terminal text rendering for Python")
    (description "Colorama is a Python library for rendering colored terminal
 text.")
-   (home-page "https://pypi.python.org/pypi/colorama")
+   (home-page "https://pypi.org/project/colorama/")
    (license license:bsd-3)))
 
 (define-public python2-colorama
@@ -8830,7 +8831,7 @@ library as well as on the command line.")
    (synopsis "Plugin and hook calling mechanism for Python")
    (description "Pluggy is an extraction of the plugin manager as used by
 Pytest but stripped of Pytest specific details.")
-   (home-page "https://pypi.python.org/pypi/pluggy")
+   (home-page "https://pypi.org/project/pluggy/")
    (license license:expat)))
 
 (define-public python2-pluggy
@@ -9535,7 +9536,7 @@ anymore.")
     (propagated-inputs
      `(("python2-scandir" ,python2-scandir)
        ("python2-six" ,python2-six)))
-    (home-page "https://pypi.python.org/pypi/pathlib2/")
+    (home-page "https://pypi.org/project/pathlib2/")
     (synopsis "Object-oriented file system paths - backport of standard
 pathlib module")
     (description "The goal of pathlib2 is to provide a backport of standard
@@ -12328,7 +12329,7 @@ projects.")
 (define-public python-invoke
   (package
     (name "python-invoke")
-    (home-page "http://www.pyinvoke.org/")
+    (home-page "https://www.pyinvoke.org/")
     (version "1.3.0")
     (source (origin
               (method url-fetch)
@@ -13486,7 +13487,7 @@ which adds support for zone identifiers to IPv6 addresses.")
        (base32
         "192pclzs2y0yaywqkrlvd0x73740q310kvqvm6jldhi619mq59wi"))))
     (build-system python-build-system)
-    (home-page "https://pypi.python.org/pypi/rfc3987")
+    (home-page "https://pypi.org/project/rfc3987/")
     (synopsis "Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)")
     (description "@code{rfc3987} provides routines for parsing and
 validation of URIs (see RFC 3986) and IRIs (see RFC 3987).")
@@ -15735,23 +15736,126 @@ infrastructure at import time, runtime, or statically (using the included pycc
 tool).")
     (license license:bsd-3)))
 
+(define-public python-numcodecs
+  (package
+    (name "python-numcodecs")
+    (version "0.6.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "numcodecs" version))
+       (sha256
+        (base32
+         "0kbfr8pl3x9glsypbq8hzim003f16ml1b1cvgrh4w1sdvgal6j7g"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-msgpack" ,python-msgpack)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-setuptools-scm" ,python-setuptools-scm)))
+    (home-page "https://github.com/zarr-developers/numcodecs")
+    (synopsis "Buffer compression and transformation codecs")
+    (description
+     "This Python package provides buffer compression and transformation
+codecs for use in data storage and communication applications.")
+    (license license:expat)))
+
+(define-public python-asciitree
+  (package
+    (name "python-asciitree")
+    (version "0.3.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "asciitree" version))
+       (sha256
+        (base32
+         "0vhgri2m2xlnibhz4xwn4hpbc7xacisxjqrk6k5kyppq96vbk92a"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/mbr/asciitree")
+    (synopsis "Draws ASCII trees")
+    (description "This package draws tree structures using characters.")
+    (license license:expat)))
+
+(define-public python-zarr
+  (package
+    (name "python-zarr")
+    (version "2.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "zarr" version))
+       (sha256
+        (base32
+         "026n3sjzjv2gmwx6y72b8ij0hk42bc8zdbvfj5gdqzd4i6wj3ajk"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'disable-service-tests
+           (lambda _
+             (setenv "ZARR_TEST_ABS" "0")
+             (setenv "ZARR_TEST_MONGO" "0")
+             (setenv "ZARR_TEST_REDIS" "0")
+             #t))
+         (replace 'check
+           (lambda _
+             (invoke "pytest" "-vv" "-k" "not lmdb")
+             #t)))))
+    (propagated-inputs
+     `(("python-asciitree" ,python-asciitree)
+       ("python-fasteners" ,python-fasteners)
+       ("python-numcodecs" ,python-numcodecs)
+       ("python-numpy" ,python-numpy)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-setuptools-scm" ,python-setuptools-scm)))
+    (home-page "https://github.com/zarr-developers/zarr-python")
+    (synopsis "Chunked, compressed, N-dimensional arrays for Python")
+    (description
+     "This package provides an implementation of chunked, compressed,
+N-dimensional arrays for Python.")
+    (license license:expat)))
+
 (define-public python-anndata
   (package
     (name "python-anndata")
-    (version "0.6.18")
+    (version "0.7.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "anndata" version))
        (sha256
         (base32
-         "03x83yjaccbqszj7x4fwwmpil0ai59yx64d1zmf2691za3j03w73"))))
+         "0rnfbpr55j1a1bi2kd4mz444741hrn74kz90h5rnjr59jmpfnh09"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'delete-inconvenient-tests
+           (lambda _
+             ;; This test depends on python-scikit-learn.
+             (delete-file "anndata/tests/test_inplace_subset.py")
+             #t))
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (invoke "pytest" "-vv"))))))
     (propagated-inputs
      `(("python-h5py" ,python-h5py)
+       ("python-importlib-metadata" ,python-importlib-metadata)
        ("python-natsort" ,python-natsort)
+       ("python-numcodecs" ,python-numcodecs)
+       ("python-packaging" ,python-packaging)
        ("python-pandas" ,python-pandas)
-       ("python-scipy" ,python-scipy)))
+       ("python-scipy" ,python-scipy)
+       ("python-zarr" ,python-zarr)))
+    (native-inputs
+     `(("python-joblib" ,python-joblib)
+       ("python-pytest" ,python-pytest)
+       ("python-setuptools-scm" ,python-setuptools-scm)))
     (home-page "https://github.com/theislab/anndata")
     (synopsis "Annotated data for data analysis pipelines")
     (description "Anndata is a package for simple (functional) high-level APIs
diff --git a/gnu/packages/regex.scm b/gnu/packages/regex.scm
index ef0d5d854b..5654104bcf 100644
--- a/gnu/packages/regex.scm
+++ b/gnu/packages/regex.scm
@@ -30,7 +30,7 @@
 (define-public re2
    (package
      (name "re2")
-     (version "2020-01-01")
+     (version "2020-03-03")
      (home-page "https://github.com/google/re2")
      (source (origin
                (method git-fetch)
@@ -38,7 +38,7 @@
                (file-name (git-file-name name version))
                (sha256
                 (base32
-                 "0gcli7y2ax3karx7m1q1r9qm49danaxbgxslywjwmya5nmr7x3p4"))))
+                 "0f1fncvg41dg9k06jiqbd7k51ljihk7rjb0kvxkbrlvgbzlpb860"))))
      (build-system gnu-build-system)
      (arguments
       `(#:modules ((guix build gnu-build-system)
diff --git a/gnu/packages/scsi.scm b/gnu/packages/scsi.scm
index f8c5d5ef60..803f49931e 100644
--- a/gnu/packages/scsi.scm
+++ b/gnu/packages/scsi.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Chris Marusich <cmmarusich@gmail.com>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,14 +27,14 @@
 (define-public sg3-utils
   (package
     (name "sg3-utils")
-    (version "1.44")
+    (version "1.45")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://sg.danny.cz/sg/p/sg3_utils-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "01avlgrbxlij8spish4i69ji1m49biz4mbayzzc2qx0hcl8ar56a"))))
+                "1vmjb17y33a73sv7jg8fzs6bhr7yh2k9sba81sjiyf1pvi3vbnn7"))))
     (build-system gnu-build-system)
     (home-page "http://sg.danny.cz/sg/sg3_utils.html")
     (synopsis "SCSI device utilities")
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b083ed02bd..81956c85e2 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -504,14 +504,14 @@ code for possible problems.")
 (define-public r-foreign
   (package
     (name "r-foreign")
-    (version "0.8-75")
+    (version "0.8-76")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreign" version))
        (sha256
         (base32
-         "0g4mi101srjbl17ydb2hl3854m3xj0llj6861lfr30sp08nkqavl"))))
+         "1z6x2x1z12wnv0z4p74d91r5wfaq30sdz4ynwx0lncz1q45mhbh5"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/foreign")
     (synopsis "Read data stored by other statistics software")
@@ -590,13 +590,13 @@ and operations on them using LAPACK and SuiteSparse.")
 (define-public r-nlme
   (package
     (name "r-nlme")
-    (version "3.1-144")
+    (version "3.1-145")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nlme" version))
        (sha256
-        (base32 "1gqyq53fdq23wsi3f4n9vg4mn5i0v18zam5lnzlpg581xifx2779"))))
+        (base32 "1i9a3afdmn2ziks0imz0j09ay9n0zb9mhrymy9mg97vvlz5diwrh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -933,13 +933,13 @@ in which the whole-plots or split-plots or both can be freely exchangeable.")
 (define-public r-plyr
   (package
     (name "r-plyr")
-    (version "1.8.5")
+    (version "1.8.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "plyr" version))
        (sha256
-        (base32 "0x4mbb3rgv1ayxqidw0p9i10khbg51fz5r62vw4il8d7licqq07a"))))
+        (base32 "11sjjdn146w95s1vsfmmgdls082cbnm1slv98xvyjhsl2mpx4mga"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
     (home-page "http://had.co.nz/plyr")
diff --git a/gnu/packages/storage.scm b/gnu/packages/storage.scm
index 1691939d7f..376a801fe2 100644
--- a/gnu/packages/storage.scm
+++ b/gnu/packages/storage.scm
@@ -53,18 +53,16 @@
 (define-public ceph
   (package
     (name "ceph")
-    (version "14.2.7")
+    (version "14.2.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.ceph.com/tarballs/ceph-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0qiqhm6hvz299q54k3i4crnb5dhpq6xnn2yqih9pxn9van0dq1ln"))
+                "0p7pjycqhxqg1mmix8ykx3xqq01d560p54iiidxps0rcvwfkyyki"))
               (patches
-               (search-patches "ceph-boost-compat.patch"
-                               "ceph-volume-respect-PATH.patch"
-                               "ceph-disable-cpu-optimizations.patch"))
+               (search-patches "ceph-disable-cpu-optimizations.patch"))
               (modules '((guix build utils)))
               (snippet
                '(begin
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index a8cb4cc347..514dfe7ab7 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -15,7 +15,7 @@
 ;;; Copyright © 2017 Vasile Dumitrascu <va511e@yahoo.com>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 André <eu@euandre.org>
-;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017, 2018, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org>
@@ -534,7 +534,7 @@ everything from small to very large projects with speed and efficiency.")
 (define-public libgit2
   (package
     (name "libgit2")
-    (version "0.28.4")
+    (version "0.99.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -543,21 +543,37 @@ everything from small to very large projects with speed and efficiency.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "171b25aym4q88bidc4c76y4l6jmdwifm3q9zjqsll0wjhlkycfy1"))
-              (patches (search-patches "libgit2-avoid-python.patch"
-                                       "libgit2-mtime-0.patch"))
+                "0qxzv49ip378g1n7hrbifb9c6pys2kj1hnxcafmbb94gj3pgd9kg"))
+              (patches (search-patches "libgit2-mtime-0.patch"))
 
-              ;; Remove bundled software.
+              ;; Remove bundled software.  Keep "http-parser" because it
+              ;; contains patches that are not available in the system version.
               (snippet '(begin
-                          (delete-file-recursively "deps")
+                          (with-directory-excursion "deps"
+                            (for-each (lambda (dir)
+                                        (delete-file-recursively dir))
+                                      (lset-difference equal?
+                                                       (scandir ".")
+                                                       '("." ".." "http-parser"))))
                           #t))
-              (modules '((guix build utils)))))
+              (modules '((guix build utils)
+                         (srfi srfi-1)
+                         (ice-9 ftw)))))
     (build-system cmake-build-system)
     (outputs '("out" "debug"))
     (arguments
-     `(#:configure-flags '("-DUSE_SHA1DC=ON") ; SHA-1 collision detection
+     `(#:configure-flags '("-DUSE_NTLMCLIENT=OFF" ;TODO: package this
+                           "-DREGEX_BACKEND=pcre2")
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'fix-pcre2-reference
+           (lambda _
+             ;; Use PCRE2 with 8-bit character support, as there is no "libpcre2.pc".
+             ;; See <https://github.com/libgit2/libgit2/issues/5438>.
+             (substitute* "src/CMakeLists.txt"
+               (("\"libpcre2\"")
+                "\"libpcre2-8\""))
+             #t))
          (add-after 'unpack 'fix-hardcoded-paths
            (lambda _
              (substitute* "tests/repo/init.c"
@@ -574,14 +590,14 @@ everything from small to very large projects with speed and efficiency.")
          (replace 'check
            (lambda _ (invoke "./libgit2_clar" "-v" "-Q"))))))
     (inputs
-     `(("libssh2" ,libssh2)
-       ("http-parser" ,http-parser)))
+     `(("libssh2" ,libssh2)))
     (native-inputs
-     `(("guile" ,guile-2.2)
-       ("pkg-config" ,pkg-config)))
+     `(("pkg-config" ,pkg-config)
+       ("python" ,python)))
     (propagated-inputs
-     ;; These two libraries are in 'Requires.private' in libgit2.pc.
+     ;; These libraries are in 'Requires.private' in libgit2.pc.
      `(("openssl" ,openssl)
+       ("pcre2" ,pcre2)
        ("zlib" ,zlib)))
     (home-page "https://libgit2.github.com/")
     (synopsis "Library providing Git core methods")
diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm
index f9ef1cb44b..1474b6623d 100644
--- a/gnu/packages/webkit.scm
+++ b/gnu/packages/webkit.scm
@@ -93,14 +93,14 @@ backend which implements them.")
 (define-public wpebackend-fdo
   (package
     (name "wpebackend-fdo")
-    (version "1.4.1")
+    (version "1.4.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://wpewebkit.org/releases/"
                                   "wpebackend-fdo-" version ".tar.xz"))
               (sha256
                (base32
-                "1799vf6wc78z15l39sfh39l5rrvlqpi29ynjm0324rpsrfvs0jb2"))))
+                "07wd736d4nhd2vpxnjzv9pb8firvbn11jmdbnhpkhjxbxa1k86pw"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f))                    ;no tests
diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index d79af78db2..8193975555 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -267,14 +267,14 @@ commands would.")
 (define-public i3-wm
   (package
     (name "i3-wm")
-    (version "4.17.1")
+    (version "4.18")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://i3wm.org/downloads/i3-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "0iazv2i2rgmakzh95pgj6iapyzn7bdpcbcd35a79mhlml4ry33qy"))))
+                "0dv5g8ycfmijxfjyw8hzsxaf80v09lb73zh7x2vszy78h3amifqz"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
author	Marius Bakke <mbakke@fastmail.com>	2020-03-06 00:17:50 +0100
committer	Marius Bakke <mbakke@fastmail.com>	2020-03-06 00:17:50 +0100
commit	b6f946f039afad6cbc7027d52685072f7fbb8d35 (patch)
tree	9dc33d1ef9d307f1e3ed8a825902ff69bbe288f9 /gnu/packages
parent	e32aea5472007507e62933b27a4db9a50810e5dc (diff)
parent	bc8b2ffdac3f55414629ace5b1a0db32e9656c0a (diff)