Add issue numbers

doc/internal/architecture.rst

@@ -29,6 +29,8 @@ The module registry also sends some signals when modules get added or removed, w
 
     Possible future directions: allow packages to provide a list of packages (for the palette), but to provide modules lazily. This would make packages that dynamically generate modules a lot faster, because they would only need to generate all the modules upfront (or at all).
 
+    :issue:`1117`
+
 ..  _concept-packagemngr:
 
 Package manager
@@ -42,6 +44,8 @@ The :class:`~vistrails.core.packagemanager.PackageManager` contains the list of
 
     If this is kept, it should be fixed to use an actual full graph at the package manager level, since multiple packages might depend on the same library and the current logic will fail to see that.
 
+    :issue:`959`
+
 ..  _concept-application:
 
 Application
@@ -104,6 +108,8 @@ When a pipeline is executed, structured information from each module is appended
 
     This provenance information should be made available to modules so they can reuse a past context exactly.
 
+    :issue:`548`
+
 ..  _concept-api:
 
 High-level API

doc/internal/conf.py

@@ -34,6 +34,7 @@
     'sphinx.ext.todo',
     'sphinx.ext.coverage',
     'sphinx.ext.ifconfig',
+    'sphinx_issues',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -295,3 +296,6 @@
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {'https://docs.python.org/': None}
+
+# sphinx-issues link
+issues_uri = 'https://github.com/VisTrails/VisTrails/issues/{issue}'

doc/internal/packages.rst

@@ -53,6 +53,8 @@ The ``my_codepath.init`` (if separate, else ``my_codepath``) module is can conta
 
     Right now, ``contextMenuName()`` only allows package creator to display a one-element context menu.
 
+    :issue:`1115`
+
 ..  autoclass:: vistrails.core.modules.package.Package
     :members:
 

doc/internal/requirements.txt

@@ -0,0 +1 @@
+sphinx-issues

doc/internal/upgrades.rst

@@ -18,6 +18,10 @@ The controller triggers the upgrade of a version when it gets selected. Since ea
 
     There are currently some issues with how the controller keeps these unflushed upgrades.
 
+    :issue:`907`
+
 ..  todo::
 
     Upgrades should be triggered when necessary during diff, query, subworkflow update, parameter exploration.
+
+    :issue:`695,1054,1071,1087`