Doc updates/indexing.

doc/admin_guide.txt, doc/customizing.txt, doc/features.txt,
  doc/installation.txt, doc/mysql.txt, doc/postgresql.txt: adding
  index entries

doc/customizing.txt: reference schema changes later in document in
   addition to wiki.

website/www/contents.txt: make wiki url https:.... Remove
   indices/tables as they don't show up in web interface. Put
   docs/announcement.txt into hidden toctree to silence warning from
   sphinx. Announcement.txt is referenced from index.txt so can't
   silence by adding to conf.py exclude_patern.

website/www/index.txt: mention security and other improvements in jinja2
    templates.

website/www/conf.py: get rid of all warning by using exclude_patterns
   to ignore docs that aren't included. Remove exclude_trees using
   exclude_pattern instead. Make html_add_permalinks value acceptable
   so no warning reported.

website/www/_static/style.css, website/www/_templtes/layout.html:
   add prev/next/index links for all doc pages.

Author: rouilj

doc/admin_guide.txt

@@ -289,6 +289,8 @@ reinstall the older version of the sofware using the same install command::
     python setup.py install
 
 
+.. index:: database; convert from one database backend to another
+
 Migrating Backends
 ------------------
 
@@ -338,6 +340,8 @@ moved using the above steps) then you'll need to:
    machine, and
 6. start the tracker web and email frontends on the new machine.
 
+.. index::
+   pair: roundup; migrate from other bugtracker software
 
 Migrating From Other Software
 -----------------------------
@@ -364,6 +368,8 @@ directory containing files with the following format:
   The ``<N>`` value is ``int(<id> / 1000)``.
 
 
+.. index:: pair: roundup-admin; managing users
+
 Adding A User From The Command-Line
 -----------------------------------
 

doc/customizing.txt

@@ -68,7 +68,9 @@ schema`_.  Some configuration is also performed using permissions - see the
 automatically register through the email interface, you must grant the
 "Anonymous" Role the "Email Access" Permission.
 
-.. index:: configuration; sections
+.. index::
+   single: config.ini; sections
+   see: configuration; config.ini
 
 The following is taken from the `Python Library Reference`__ (July 18, 2018)
 section "ConfigParser -- Configuration file parser":
@@ -236,6 +238,16 @@ Section **rdbms**
  addition settings needed by RDBMs like SQLite, Postgresql and
  MySQL backends.
 
+ .. index::
+    single: postgres; select backend in config.ini 
+    single: mysql; select backend in config.ini
+    single: sqlite; select backend in config.ini
+    single: anydbm; select backend in config.ini
+    see: database; postgres
+    see: database; mysql
+    see: database; sqlite
+    see: database; anydbm
+
  backend -- set to value by init
   The database backend such as anydbm, sqlite, mysql or postgres.
 
@@ -263,6 +275,9 @@ Section **rdbms**
   Name of the group to use in the MySQL defaults file. Only used in
   MySQL connections.
 
+ .. index::
+    single: sqlite; lock timeout
+
  sqlite_timeout -- ``30``
   Number of seconds to wait when the SQLite database is locked.
   Used only for SQLite.
@@ -487,6 +502,11 @@ Section **nosy**
   download page for the file.
 
 
+.. index:: single: roundup-admin; config.ini update
+           single: roundup-admin; config.ini create
+           single: config.ini; create
+           single: config.ini; update
+
 You may generate a new default config file using the ``roundup-admin
 genconfig`` command. You can generate a new config file merging in
 existing settings using the ``roundup-admin updateconfig`` command.
@@ -523,7 +543,7 @@ applied to the extension config files, so if you instead have::
 
 then the above ``db.config.detectors['QA_RECIPIENTS']`` will still work.
 
-.. index:: schema
+.. index:: ! schema
 
 Tracker Schema
 ==============
@@ -995,12 +1015,15 @@ property, or sorting will result in random ordering.
 Examples of adding to your schema
 ---------------------------------
 
-The `Roundup wiki`_ has examples of
-how schemas can be customised to add new functionality.
+Some examples are in the :ref:`CustomExamples` section below.
+
+Also the `Roundup wiki`_ has additional examples of how schemas can be
+customised to add new functionality.
 
 .. _Roundup wiki:
    https://wiki.roundup-tracker.org/
 
+.. index:: !detectors
 
 Detectors - adding behaviour to your tracker
 ============================================
@@ -1017,6 +1040,8 @@ have some installed by default - have a look. You can write new
 detectors or modify the existing ones. The existing detectors installed
 for you are:
 
+.. index:: detectors; installed
+
 **nosyreaction.py**
   This provides the automatic nosy list maintenance and email sending.
   The nosy reactor (``nosyreaction``) fires when new messages are added
@@ -1045,6 +1070,8 @@ interface for detectors.
 __ design.html
 
 
+.. index:: detectors; writing api
+
 Detector API
 ------------
 
@@ -1082,6 +1109,7 @@ values of properties that were changed.
 For a ``retire()`` or ``restore()`` operation, ``itemid`` is the id of
 the retired or restored item and ``olddata`` is None.
 
+.. index:: detectors; additional
 
 Additional Detectors Ready For Use
 ----------------------------------
@@ -1612,6 +1640,9 @@ Put together, these settings appear in the tracker's ``schema.py`` file::
     #   db.security.addPermissionToRole('Anonymous', 'Create', cl)
     #   db.security.addPermissionToRole('Anonymous', 'Edit', cl)
 
+.. index::
+   single: roundup-admin; class permissions
+
 You can use ``roundup-admin security`` to verify the permissions
 defined in the schema. It also verifies that properties specified in
 permissions are valid for the class. This helps detect typos that can
@@ -3755,6 +3786,7 @@ should be changed to include actual character set name::
 
 The charset is also sent in the http header.
 
+.. _CustomExamples:
 
 Examples
 ========
@@ -3783,6 +3815,8 @@ Schema changes are automatically applied to the database on the next
 tracker access (note that roundup-server would need to be restarted as it
 caches the schema).
 
+.. index:: schema; example changes
+
 1. Modify the ``schema.py``::
 
     issue = IssueClass(db, "issue", 
@@ -4282,6 +4316,8 @@ be able to give a summary of the total time spent on a particular issue.
 
     db.security.addPermissionToRole('User', 'Edit', 'timelog')
 
+.. index:: schema; example changes
+
 2. Link to the new class from your issue class (again, in
    ``schema.py``)::
 

doc/features.txt

@@ -4,7 +4,7 @@ Roundup Features
 
 Roundup is a simple-to-use and -install issue-tracking system with
 web, e-mail and command-line interfaces. It is based on the winning design
-from Ka-Ping Yee in the Software Carpentry "Track" design competition.
+from Ka-Ping Yee in the :index:`Software Carpentry` "Track" design competition.
 
 *simple to install*
  - installation (including web interface) takes about 30 minutes

doc/installation.txt

@@ -331,6 +331,7 @@ installation. That is, it has the configuration files, defines a user database
 and the basic HTML interface to that. It's a completely clean slate for you to
 create your tracker on.
 
+.. index:: database; choosing your backend
 
 Choosing Your Backend
 ---------------------
@@ -396,6 +397,7 @@ You may need to give the web server user permission to access the tracker home
 - see the `UNIX environment steps`_ for information. You may also need to
 configure your system in some way - see `platform-specific notes`_.
 
+.. index:: pair: web interface; cgi
 
 Web Server cgi-bin
 ~~~~~~~~~~~~~~~~~~
@@ -489,6 +491,7 @@ Now loading the (sub-)domain in a browser should load the tracker web
 interface. If you get a "500" error then enable the "cgitb" lines in the
 stub to get some debugging information.
 
+.. index:: pair: web interface; stand alone server
 
 Stand-alone Web Server
 ~~~~~~~~~~~~~~~~~~~~~~
@@ -508,6 +511,8 @@ To make the server run in the background, use the "-d" option, specifying the
 name of a file to write the server process id (pid) to.
 
 
+.. index:: pair: web interface; Zope
+
 Zope Product - ZRoundup
 ~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -518,6 +523,9 @@ code tree lib/python/Products.
 When you next (re)start up Zope, you will be able to add a ZRoundup object
 that interfaces to your new tracker.
 
+.. index:: ! triple: web interface; apache; mod_wsgi
+   ! single:  wsgi; apache
+
 Apache HTTP Server with mod_wsgi
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -676,6 +684,8 @@ To run as a background process
 2. Then, run ``sudo /etc/mod_wsgi-express-80/apachectl start``
 3. To stop, run ``sudo /etc/mod_wsgi-express-80/apachectl stop``
 
+.. index:: triple: web interface; apache; mod_python (depricated)
+
 Apache HTTP Server with mod_python
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -812,6 +822,9 @@ serving with SSL.
 WSGI Variations
 ~~~~~~~~~~~~~~~
 
+.. index:: triple: web interface; apache; mod_wsgi
+   single: wsgi; apache
+
 Apache Alternate
 ^^^^^^^^^^^^^^^^
 
@@ -914,6 +927,9 @@ One last change is needed. In the tracker's config.ini change the db
 parameter in the [main] section to be /home/roundup-foo/db. This will
 put the files and messages in the db directory for the user.
 
+.. index:: pair: web interface; gunicorn
+   single: wsgi; gunicorn
+
 Gunicorn Installation
 ^^^^^^^^^^^^^^^^^^^^^
 
@@ -943,6 +959,9 @@ Assuming the proxy forwards /tracker, run gunicorn as::
 this runs roundup at port 8917 on the loopback interface. You should
 configure the reverse proxy to talk to 127.0.0.1 at port 8917.
 
+.. index:: pair: web interface; uWSGI
+   single: wsgi; uWSGI
+
 uWSGI Installation
 ^^^^^^^^^^^^^^^^^^
 

doc/mysql.txt

@@ -1,3 +1,5 @@
+.. index:: mysql; debugging notes
+
 =============
 MySQL Backend
 =============

doc/postgresql.txt

@@ -1,3 +1,5 @@
+.. index:: postgres; debugging notes
+
 ==========================
 PostgreSQL/psycopg Backend
 ==========================

website/www/_static/style.css

@@ -21,6 +21,7 @@ body > .content
   margin: 0;
 }
 body > .header > #searchbox { position: absolute; right: 1em; top: 1em;}
+body > .content > #subnav    { position: absolute; right: 1.5em; top: 5em;}
 
 /* style */
 

website/www/_templates/layout.html

@@ -84,6 +84,18 @@
       <script type="text/javascript" src="http://www.ohloh.net/p/488/widgets/project_users_logo.js"></script>
     </div>
     <div class="content">
+	<div id="subnav">
+        {%- if prev %}
+           <a title="{{ prev.title|striptags }}" href="{{ prev.link|e }}">
+	     Prev</a>
+        {%- endif %}
+	{%- if next %}
+           <a title="{{ next.title|striptags }}" href="{{ next.link|e }}">
+	     Next</a>
+	{%- endif %}
+        <a title="{{ _('Index') }}" href="{{ pathto('genindex') }}">
+	  Index</a>
+	</div>
        {% block body %} {% endblock %}
     </div>
 {%- block footer %}

website/www/conf.py

@@ -67,11 +67,11 @@
 #today_fmt = '%B %d, %Y'
 
 # List of documents that shouldn't be included in the build.
-#unused_docs = []
-
-# List of directories, relative to source directory, that shouldn't be searched
-# for source files.
-exclude_trees = ['.build']
+exclude_patterns = ['docs/index.txt',
+                    'docs/whatsnew-0.7.txt',
+                    'docs/whatsnew-0.8.txt',
+                    'docs/security.txt',
+                    '_tmp']
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 #default_role = None
@@ -137,7 +137,7 @@
 # template names.
 #html_additional_pages = {}
 
-html_add_permalinks = False
+html_add_permalinks = ''
 
 # If false, no module index is generated.
 #html_use_modindex = True

website/www/contents.txt

@@ -15,13 +15,11 @@ Contents:
    docs
    Issues <https://issues.roundup-tracker.org>
    contact
-   Wiki <http://wiki.roundup-tracker.org>
+   Wiki <https://wiki.roundup-tracker.org>
    code
 
-Indices and tables
-==================
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+.. toctree::
+   :hidden:
 
+   docs/announcement