Merge branch 'master' into core-updates-frozen

 Conflicts:
	gnu/packages/bioinformatics.scm
	gnu/packages/cmake.scm
	gnu/packages/curl.scm
	gnu/packages/emacs-xyz.scm
	gnu/packages/gpodder.scm
	gnu/packages/music.scm
	gnu/packages/patches/glibc-bootstrap-system.patch
	gnu/packages/python-xyz.scm
	gnu/packages/shells.scm
	gnu/packages/statistics.scm

1 files changed, 85 insertions, 6 deletions

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 767e31db93..2abacec8e7 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -52,6 +52,7 @@
 ;;; Copyright © 2021 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com>
 ;;; Copyright © 2021 Simon Streit <simon@netpanic.org>
+;;; Copyright © 2021 Alexandre Hannud Abdo <abdo@member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -88,11 +89,14 @@
   #:use-module (gnu packages dbm)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages flex)
+  #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages glib)
+  #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages jemalloc)
@@ -109,6 +113,7 @@
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages onc-rpc)
+  #:use-module (gnu packages pantheon)
   #:use-module (gnu packages parallel)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages perl)
@@ -130,6 +135,7 @@
   #:use-module (gnu packages ruby)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages ssh)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages tcl)
   #:use-module (gnu packages terminals)
@@ -148,6 +154,7 @@
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
+  #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
   #:use-module (guix build-system ruby)
@@ -3638,7 +3645,7 @@ the SQL language using a syntax that reflects the resulting query.")
 (define-public apache-arrow
   (package
     (name "apache-arrow")
-    (version "4.0.1")
+    (version "5.0.0")
     (source
      (origin
        (method git-fetch)
@@ -3648,7 +3655,7 @@ the SQL language using a syntax that reflects the resulting query.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1lcd9gdpwlrr92rm812a5p4l6zx0arwd0zj72a4ga699s1psz8yv"))))
+         "0275aayzy78nbxzbj93w5152sv5q2c7020ijxnf8b58v9qwfxzz0"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f
@@ -3770,13 +3777,34 @@ algorithm implementations.")
        (modify-phases %standard-phases
          (delete 'build) ; XXX the build is performed again during the install phase
          (add-after 'unpack 'enter-source-directory
-           (lambda _ (chdir "python") #t))
+           (lambda _ (chdir "python")))
          (add-after 'unpack 'make-git-checkout-writable
            (lambda _
-             (for-each make-file-writable (find-files "."))
-             #t)))))
+             (for-each make-file-writable (find-files "."))))
+         (add-before 'install 'patch-cmake-variables
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; Replace cmake locations with hardcoded guix links for the
+             ;; underlying C++ library and headers.  This is a pretty awful
+             ;; hack.
+             (substitute* "cmake_modules/FindParquet.cmake"
+               (("# Licensed to the Apache Software Foundation" m)
+                (string-append "set(PARQUET_INCLUDE_DIR \""
+                               (assoc-ref inputs "apache-arrow:include")
+                               "/share/include\")\n" m))
+               (("find_package_handle_standard_args" m)
+                (string-append "set(PARQUET_LIB_DIR \""
+                               (assoc-ref inputs "apache-arrow:lib")
+                               "/lib\")\n" m)))))
+         (add-before 'install 'patch-parquet-library
+           (lambda _
+             (substitute* "CMakeLists.txt"
+               (("parquet_shared") "parquet"))))
+         (add-before 'install 'set-PYARROW_WITH_PARQUET
+           (lambda _
+             (setenv "PYARROW_WITH_PARQUET" "1"))))))
     (propagated-inputs
-     `(("apache-arrow" ,apache-arrow "lib")
+     `(("apache-arrow:lib" ,apache-arrow "lib")
+       ("apache-arrow:include" ,apache-arrow "include")
        ("python-numpy" ,python-numpy)
        ("python-pandas" ,python-pandas)
        ("python-six" ,python-six)))
@@ -3968,3 +3996,54 @@ PostreSQL, SQLite, ODBC and MySQL.")
      "FreeTDS is an implementation of the Tabular DataStream protocol, used for
 connecting to MS SQL and Sybase servers over TCP/IP.")
     (license license:lgpl2.0+)))
+
+(define-public sequeler
+  (package
+    (name "sequeler")
+    (version "0.8.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Alecaddd/sequeler")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1q1vzc3likpiwfh6blkyiz0wr0aarj9xrm8gbi7m3p1wslkpah7c"))))
+    (build-system meson-build-system)
+    (arguments
+     '(#:glib-or-gtk? #t
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'skip-gtk-update-icon-cache
+           ;; Don't create 'icon-theme.cache'.
+           (lambda _
+             (substitute* "build-aux/meson_post_install.py"
+               (("gtk-update-icon-cache") "true")
+               (("update-desktop-database") "true"))
+             #t)))))
+    (native-inputs
+     `(;("appstream-glib" ,appstream-glib)  ; validation fails for lack of network
+       ("gettext-minimal" ,gettext-minimal)
+       ("glib:bin" ,glib "bin")             ; for glib-compile-resources
+       ("gtk+" ,gtk+ "bin")
+       ("pkg-config" ,pkg-config)
+       ("vala" ,vala)))
+    (inputs
+     `(("glib" ,glib)
+       ("granite" ,granite)
+       ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
+       ("gtk+" ,gtk+)
+       ("gtksourceview-3" ,gtksourceview-3)
+       ("libgda" ,libgda)
+       ("libgee" ,libgee)
+       ("libsecret" ,libsecret)
+       ("libssh2" ,libssh2)
+       ("libxml2" ,libxml2)))
+    (synopsis "Friendly SQL Client")
+    (description "Sequeler is a native Linux SQL client built in Vala and
+Gtk.  It allows you to connect to your local and remote databases, write SQL in
+a handy text editor with language recognition, and visualize SELECT results in
+a Gtk.Grid Widget.")
+    (home-page "https://github.com/Alecaddd/sequeler")
+    (license license:gpl2+)))