Merge remote-tracking branch 'origin/version-1.2.0' into master

Conflicts:
	gnu/packages/bioinformatics.scm

The python-pysam package fixed in master was kept instead of the update done
in the version-1.2.0 branch.

6 files changed, 156 insertions, 21 deletions

diff --git a/gnu/local.mk b/gnu/local.mk
index d4d10bc32b..217c05eab6 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1054,6 +1054,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/ghostscript-no-header-id.patch		\
   %D%/packages/patches/ghostscript-no-header-uuid.patch		\
   %D%/packages/patches/ghostscript-no-header-creationdate.patch \
+  %D%/packages/patches/glib-appinfo-watch.patch			\
   %D%/packages/patches/glib-tests-timer.patch			\
   %D%/packages/patches/glibc-CVE-2018-11236.patch		\
   %D%/packages/patches/glibc-CVE-2018-11237.patch		\
diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm
index 901222476a..43523e516d 100644
--- a/gnu/packages/glib.scm
+++ b/gnu/packages/glib.scm
@@ -181,6 +181,7 @@ shared NFS home directories.")
   (package
    (name "glib")
    (version "2.62.6")
+   (replacement glib-with-gio-patch)
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnome/sources/"
@@ -387,11 +388,20 @@ dynamic loading, and an object system.")
    (home-page "https://developer.gnome.org/glib/")
    (license license:lgpl2.1+)))
 
+(define glib-with-gio-patch
+  ;; GLib with a fix for <https://bugs.gnu.org/35594>.
+  ;; TODO: Fold into 'glib' above in the next rebuild cycle.
+  (package
+    (inherit glib)
+    (source (origin
+              (inherit (package-source glib))
+              (patches (cons (search-patch "glib-appinfo-watch.patch")
+                             (origin-patches (package-source glib))))))))
+
 (define-public glib-with-documentation
   ;; glib's doc must be built in a separate package since it requires gtk-doc,
   ;; which in turn depends on glib.
-  (package
-    (inherit glib)
+  (package/inherit glib
     (properties (alist-delete 'hidden? (package-properties glib)))
     (outputs (cons "doc" (package-outputs glib))) ; 20 MiB of GTK-Doc reference
     (native-inputs
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 4a7a15c378..6075df6afa 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -130,9 +130,9 @@
   ;; Latest version of Guix, which may or may not correspond to a release.
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
-  (let ((version "1.1.0")
-        (commit "5e7cf66fb35780f930ad0bc5fe21ac330df4411d")
-        (revision 32))
+  (let ((version "1.2.0rc1")
+        (commit "3ba6ffd0dd092ae879d014e4971989f231eaa56d")
+        (revision 1))
     (package
       (name "guix")
 
@@ -148,7 +148,7 @@
                       (commit commit)))
                 (sha256
                  (base32
-                  "15clfjp845gvl0p6qw0b1gdibqfq20zwzr6dbxvq8l9fgzj1kb6b"))
+                  "1wa67gdipmzqr400hp0cw5ih0rlfvj345h65rqbk9s4g3bkg38hm"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments
@@ -336,7 +336,13 @@ $(prefix)/etc/init.d\n")))
                             (let ((bash (assoc-ref inputs "bash")))
                               (substitute* (string-append out "/bin/guix")
                                 (("^#!.*/bash") (string-append "#! " bash "/bin/bash")))))
-                          #t))))))
+                          #t)))
+
+                    ;; The 'guix' executable has 'OUT/libexec/guix/guile' has
+                    ;; its shebang; that should remain unchanged, thus remove
+                    ;; the 'patch-shebangs' phase, which would otherwise
+                    ;; change it to 'GUILE/bin/guile'.
+                    (delete 'patch-shebangs))))
       (native-inputs `(("pkg-config" ,pkg-config)
 
                        ;; Guile libraries are needed here for
diff --git a/gnu/packages/patches/glib-appinfo-watch.patch b/gnu/packages/patches/glib-appinfo-watch.patch
new file mode 100644
index 0000000000..638a5e0949
--- /dev/null
+++ b/gnu/packages/patches/glib-appinfo-watch.patch
@@ -0,0 +1,92 @@
+This patch lets GLib's GDesktopAppInfo API watch and notice changes
+to the Guix user and system profiles.  That way, the list of available
+applications shown by the desktop environment is immediately updated
+when the user runs "guix install", "guix remove", or "guix system
+reconfigure" (see <https://issues.guix.gnu.org/35594>).
+
+It does so by monitoring /var/guix/profiles (for changes to the system
+profile) and /var/guix/profiles/per-user/USER (for changes to the user
+profile) and crawling their share/applications sub-directory when
+changes happen.
+
+diff --git a/gio/gdesktopappinfo.c b/gio/gdesktopappinfo.c
+index f1e2fdd..095c110 100644
+--- a/gio/gdesktopappinfo.c
++++ b/gio/gdesktopappinfo.c
+@@ -148,6 +148,7 @@ typedef struct
+   gchar                      *alternatively_watching;
+   gboolean                    is_config;
+   gboolean                    is_setup;
++  gchar                      *guix_profile_watch_dir;
+   GFileMonitor               *monitor;
+   GHashTable                 *app_names;
+   GHashTable                 *mime_tweaks;
+@@ -180,6 +181,7 @@ desktop_file_dir_unref (DesktopFileDir *dir)
+     {
+       desktop_file_dir_reset (dir);
+       g_free (dir->path);
++      g_free (dir->guix_profile_watch_dir);
+       g_free (dir);
+     }
+ }
+@@ -204,6 +206,13 @@ desktop_file_dir_get_alternative_dir (DesktopFileDir *dir)
+ {
+   gchar *parent;
+ 
++  /* If DIR is a profile, watch the specified directory--e.g.,
++   * /var/guix/profiles/per-user/$USER/ for the user profile.  Do not watch
++   * ~/.guix-profile or /run/current-system/profile because GFileMonitor does
++   * not pass IN_DONT_FOLLOW and thus cannot notice any change.  */
++  if (dir->guix_profile_watch_dir != NULL)
++    return g_strdup (dir->guix_profile_watch_dir);
++
+   /* If the directory itself exists then we need no alternative. */
+   if (g_access (dir->path, R_OK | X_OK) == 0)
+     return NULL;
+@@ -249,11 +258,11 @@ desktop_file_dir_changed (GFileMonitor      *monitor,
+    *
+    * If this is a notification for a parent directory (because the
+    * desktop directory didn't exist) then we shouldn't fire the signal
+-   * unless something actually changed.
++   * unless something actually changed or it's in /var/guix/profiles.
+    */
+   g_mutex_lock (&desktop_file_dir_lock);
+ 
+-  if (dir->alternatively_watching)
++  if (dir->alternatively_watching && dir->guix_profile_watch_dir == NULL)
+     {
+       gchar *alternative_dir;
+ 
+@@ -1555,6 +1564,32 @@ desktop_file_dirs_lock (void)
+       for (i = 0; dirs[i]; i++)
+         g_ptr_array_add (desktop_file_dirs, desktop_file_dir_new (dirs[i]));
+ 
++      {
++        /* Monitor the system and user profile under /var/guix/profiles and
++         * treat modifications to them as if they were modifications to their
++         * /share sub-directory.  */
++        const gchar *user;
++        DesktopFileDir *system_profile_dir, *user_profile_dir;
++
++        system_profile_dir =
++          desktop_file_dir_new ("/var/guix/profiles/system/profile/share");
++        system_profile_dir->guix_profile_watch_dir = g_strdup ("/var/guix/profiles");
++        g_ptr_array_add (desktop_file_dirs, desktop_file_dir_ref (system_profile_dir));
++
++        user = g_get_user_name ();
++        if (user != NULL)
++          {
++            gchar *profile_dir, *user_data_dir;
++
++            profile_dir = g_build_filename ("/var/guix/profiles/per-user", user, NULL);
++            user_data_dir = g_build_filename (profile_dir, "guix-profile", "share", NULL);
++            user_profile_dir = desktop_file_dir_new (user_data_dir);
++            user_profile_dir->guix_profile_watch_dir = profile_dir;
++            g_ptr_array_add (desktop_file_dirs, desktop_file_dir_ref (user_profile_dir));
++            g_free (user_data_dir);
++          }
++      }
++
+       /* The list of directories will never change after this, unless
+        * g_get_user_config_dir() changes due to %G_TEST_OPTION_ISOLATE_DIRS. */
+       desktop_file_dirs_config_dir = user_config_dir;
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 6e1720376f..504d9a112a 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -26,7 +26,7 @@
 ;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
 ;;; Copyright © 2018, 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
-;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2018, 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2019 Vagrant Cascadian <vagrant@debian.org>
 ;;; Copyright © 2019 Brendan Tildesley <mail@brendan.scot>
 ;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
@@ -2893,21 +2893,30 @@ pretty printer and a tree visitor.")
     (name "python-flask-basicauth")
     (version "0.2.0")
     (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "Flask-BasicAuth" version))
-        (sha256
-          (base32
-            "1zq1spkjr4sjdnalpp8wl242kdqyk6fhbnhr8hi4r4f0km4bspnz"))))
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "Flask-BasicAuth" version))
+       (sha256
+        (base32
+         "1zq1spkjr4sjdnalpp8wl242kdqyk6fhbnhr8hi4r4f0km4bspnz"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'fix-imports
+                    (lambda _
+                      (substitute* '("docs/index.rst"
+                                     "docs/conf.py"
+                                     "flask_basicauth.py"
+                                     "test_basicauth.py")
+                        (("flask\\.ext\\.basicauth")
+                         "flask_basicauth"))
+                      #t)))))
     (propagated-inputs
      `(("python-flask" ,python-flask)))
-    (home-page
-      "https://github.com/jpvanhal/flask-basicauth")
-    (synopsis
-      "HTTP basic access authentication for Flask")
+    (home-page "https://github.com/jpvanhal/flask-basicauth")
+    (synopsis "HTTP basic access authentication for Flask")
     (description
-      "This package provides HTTP basic access authentication for Flask.")
+     "This package provides HTTP basic access authentication for Flask.")
     (license license:bsd-3)))
 
 (define-public python-flask-htpasswd
diff --git a/gnu/services/base.scm b/gnu/services/base.scm
index 416bc02a96..e6341e3cd9 100644
--- a/gnu/services/base.scm
+++ b/gnu/services/base.scm
@@ -106,6 +106,12 @@
             agetty-service-type
 
             mingetty-configuration
+            mingetty-configuration-tty
+            mingetty-configuration-auto-login
+            mingetty-configuration-login-program
+            mingetty-configuration-login-pause?
+            mingetty-configuration-clear-on-logout?
+            mingetty-configuration-mingetty
             mingetty-configuration?
             mingetty-service
             mingetty-service-type
@@ -285,8 +291,19 @@ This service must be the root of the service dependency graph so that its
 (define (file-system->shepherd-service-name file-system)
   "Return the symbol that denotes the service mounting and unmounting
 FILE-SYSTEM."
-  (symbol-append 'file-system-
-                 (string->symbol (file-system-mount-point file-system))))
+  (define valid-characters
+    ;; Valid store characters; see 'checkStoreName' in the daemon.
+    (string->char-set
+     "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz+-._?="))
+
+  (define mount-point
+    (string-map (lambda (chr)
+                  (if (char-set-contains? valid-characters chr)
+                      chr
+                      #\-))
+                (file-system-mount-point file-system)))
+
+  (symbol-append 'file-system- (string->symbol mount-point)))
 
 (define (mapped-device->shepherd-service-name md)
   "Return the symbol that denotes the shepherd service of MD, a <mapped-device>."