Add transitional links for online gmxapi Python package reference.

* Update and clarify pythonreference stub for when Python package was
  not available.
* Note related Redmine reference.
* Remove `python-procedural` label, which had lost meaning and which
  could cause awkward repositioning for the pythonreference stub with
  no section heading to follow the label.

Refs #2985

Change-Id: If81ba6500ce078fe4fc94bf37285324ec5702b1b

diff --git a/docs/gmxapi/userguide-stub/pythonreference.rst b/docs/gmxapi/userguide-stub/pythonreference.rst
index 44803b891059aa1ad528983c7b6518c40bb7f18d..40fbf8f78af0d8c9401775db5debbed9694d3f4d 100644 (file)
--- a/docs/gmxapi/userguide-stub/pythonreference.rst
+++ b/docs/gmxapi/userguide-stub/pythonreference.rst
@@ -21,11 +21,14 @@ Package documentation is extracted from the ``gmxapi`` Python module and is also
 directly, using either ``pydoc`` from the command line or :py:func:`help` from within Python, such
 as during an interactive session.
 
-.. seealso:: :ref:`gmxapi_package_documentation`
-
 Refer to the Python source code itself for additional clarification.
 
-.. _python-procedural:
+.. seealso::
+
+    This copy of the documentation was built without
+    :doc:`installing the gmxapi package <../userguide/install>`,
+    and therefore lacks the full module reference.
+    Refer to :ref:`gmxapi_package_documentation` for instructions on building
+    complete documentation, or `view online <http://gmxapi.org/>`__.
 
-This copy of the documentation was built without the gmxapi package,
-and therefore lacks the full module reference.
+.. todo:: :issue:`2985` Replace reference URL with http://manual.gromacs.org/current/gmxapi/

diff --git a/docs/gmxapi/userguide/install.rst b/docs/gmxapi/userguide/install.rst
index bacc2d6d5003115640d437f6c1b99f7fa047ab4d..e76f60d788e011fa89e527489c160fdc9d9fd0aa 100644 (file)
--- a/docs/gmxapi/userguide/install.rst
+++ b/docs/gmxapi/userguide/install.rst
@@ -434,9 +434,11 @@ be accessed in the usual ways, using ``pydoc`` from the command line or
 ``help()`` in an interactive Python session.
 
 The complete documentation (which you are currently reading)
-can be browsed `online <http://manual.gromacs.org/current/gmxapi/>`__
+can be browsed `online <http://gmxapi.org/>`__
 or built from a copy of the GROMACS source repository.
 
+.. todo:: :issue:`2985` Replace reference URL with http://manual.gromacs.org/current/gmxapi/
+
 Documentation is built from a combination of Python module documentation and
 static content, and requires a local copy of the GROMACS source repository.
 

diff --git a/docs/gmxapi/userguide/pythonreference.rst b/docs/gmxapi/userguide/pythonreference.rst
index 0cb784907a14c928addb527ad20b25bc719ad304..b976fe0dfd2ba874304f093b047cbbce4e24e281 100644 (file)
--- a/docs/gmxapi/userguide/pythonreference.rst
+++ b/docs/gmxapi/userguide/pythonreference.rst
@@ -21,18 +21,16 @@ Package documentation is extracted from the ``gmxapi`` Python module and is also
 directly, using either ``pydoc`` from the command line or :py:func:`help` from within Python, such
 as during an interactive session.
 
-.. seealso:: :ref:`gmxapi_package_documentation`
-
 Refer to the Python source code itself for additional clarification.
 
+.. seealso:: :ref:`gmxapi_package_documentation`
+
 .. Configuration for doctest: automated syntax checking in documentation code snippets
 .. testsetup::
 
     import gmxapi as gmx
     from gmxapi.data import tpr_filename
 
-.. _python-procedural:
-
 gmxapi basic package
 =====================
 

diff --git a/docs/gmxapi/userguide/usage.rst b/docs/gmxapi/userguide/usage.rst
index 0d4b88c22d5cdd042c95e6852305a199b4e33768..78872801cbebe5beedb32ba52eec5e4abe186caa 100644 (file)
--- a/docs/gmxapi/userguide/usage.rst
+++ b/docs/gmxapi/userguide/usage.rst
@@ -13,7 +13,7 @@ of ``gmx`` to refer to the ``gmxapi`` Python package.
 
 For full documentation of the Python-level interface and API, use the ``pydoc``
 command line tool or the :py:func:`help` interactive Python function, or refer to
-the :ref:`procedural interface <python-procedural>` documentation.
+the :doc:`pythonreference`.
 
 Python does not wrap any command-line tool, so once installation is complete,
 there shouldn't be any additional configuration necessary, and any errors that