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.

1 files changed, 92 insertions, 0 deletions

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;