Fix warnings when building the docs.

docs/conf.py

@@ -91,7 +91,7 @@ def __isclassname(name):
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.coverage']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.mathjax']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/contributors/contributing.rst

@@ -26,7 +26,6 @@ Code repository organization
 GC3Pie code is hosted in a GitHub_ repository, which you can
 access online__ or using any Git_ client.
 
-.. _GitHub: https://github.com/
 .. __: http://github.com/uzh/gc3pie/
 
 We encourage anyone to fork the repository and contribute back
@@ -550,7 +549,7 @@ GC3Pie documentation is divided in three sections:
 * :ref:`Contributor Documentation`: detailed information on how to
   contribute to GC3Pie and get your code included in the main library.
 
-The :ref:`GC3Libs programming API` is the most relevant part of the
+The `GC3Libs programming API <gc3libs_>` is the most relevant part of the
 docs for developers contributing code and is generated automatically
 from the docstrings inside the modules. Automatic documentation in
 Sphinx is described under

docs/global.inc

@@ -20,6 +20,8 @@
 .. _GAMESS: http://www.msg.ameslab.gov/gamess/
 .. _GC3Pie: http://gc3pie.googlecode.com/
 .. _`GC3Pie mailing list`: mailto:gc3pie@googlegroups.com
+.. _Git: https://git-scm.org/
+.. _GitHub: https://github.com/
 .. _`Grid Engine`: http://gridengine.org/blog/2011/11/23/what-now/
 .. _`Torque`: http://www.adaptivecomputing.com/products/open-source/torque/
 .. _`PBSPro`: http://www.pbspro.org/

docs/programmers/api/gc3libs/authentication/ec2.rst

@@ -0,0 +1,10 @@
+.. Hey Emacs, this is -*- rst -*-
+
+   This file follows reStructuredText markup syntax; see
+   http://docutils.sf.net/rst.html for more information.
+
+
+`gc3libs.authentication.ec2`
+============================
+.. automodule:: gc3libs.authentication.ec2
+   :members:

docs/programmers/api/gc3libs/authentication/openstack.rst

@@ -0,0 +1,10 @@
+.. Hey Emacs, this is -*- rst -*-
+
+   This file follows reStructuredText markup syntax; see
+   http://docutils.sf.net/rst.html for more information.
+
+
+`gc3libs.authentication.openstack`
+==================================
+.. automodule:: gc3libs.authentication.openstack
+   :members:

docs/programmers/api/gc3libs/backends/ec2.rst

@@ -0,0 +1,10 @@
+.. Hey Emacs, this is -*- rst -*-
+
+   This file follows reStructuredText markup syntax; see
+   http://docutils.sf.net/rst.html for more information.
+
+
+`gc3libs.backends.ec2`
+======================
+.. automodule:: gc3libs.backends.ec2
+   :members:

docs/programmers/api/gc3libs/backends/openstack.rst

@@ -0,0 +1,10 @@
+.. Hey Emacs, this is -*- rst -*-
+
+   This file follows reStructuredText markup syntax; see
+   http://docutils.sf.net/rst.html for more information.
+
+
+`gc3libs.backends.openstack`
+============================
+.. automodule:: gc3libs.backends.openstack
+   :members:

docs/programmers/api/index.rst

@@ -22,11 +22,13 @@
    gc3libs/application/turbomole
    gc3libs/authentication
    gc3libs/authentication/ec2
+   gc3libs/authentication/openstack
    gc3libs/authentication/ssh
    gc3libs/backends
    gc3libs/backends/batch
    gc3libs/backends/ec2
    gc3libs/backends/lsf
+   gc3libs/backends/openstack
    gc3libs/backends/pbs
    gc3libs/backends/sge
    gc3libs/backends/shellcmd

docs/programmers/tutorials/index.rst

@@ -17,8 +17,9 @@
 Implementing scientific workflows with GC3Pie
 ---------------------------------------------
 
-This is the course material prepared for the `GC3Pie for programmers training`__,
-held at the University of Zurich on July 11-14, 2016.
+This is the course material prepared for the `"GC3Pie for Programmers"
+training`__, held at the University of Zurich for the first time on July
+11-14, 2016. (The slides presented here are revised at each course re-run.)
 
 .. __: http://www.s3it.uzh.ch/en/scienceit/support/training/gc3pie/programmers.html
 
@@ -27,65 +28,89 @@ in scientific computational workflows using Python and GC3Pie, and
 provide users with enough knowledge of the tools available in GC3Pie
 to extend and adapt the examples provided.
 
-`Introduction to the training <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part00.pdf>`_
+`Introduction to the training`__
 
   A presentation of the training material and outline of the course.
   Probably not much useful unless you're actually sitting in class.
 
-`Overview of GC3Pie use cases <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part01.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part00.pdf
+
+`Overview of GC3Pie use cases`__
 
   A quick overview of the kind of computational use cases that GC3Pie
   can easily solve.
 
-`GC3Pie basics <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part02.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part01.pdf
+
+`GC3Pie basics`__
 
   The basics needed to write simple GC3Pie scripts: the minimal
   session-based script scaffolding, and the properties and features of
   the `Application`:class: object.
 
-`Useful debugging commands <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part03.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part02.pdf
+
+`Useful debugging commands`__
 
   Recall a few GC3Pie utilities that are especially useful when
   debugging code.
 
-`Customizing command-line processing <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part04.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part03.pdf
+
+`Customizing command-line processing`__
 
   How to set up command-line argument and option processing in
   GC3Pie's `SessionBasedScript`:class:
 
-`Application requirements <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part05.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part04.pdf
+
+`Application requirements`__
 
   How to specify running requirements for `Application`:class: tasks,
   e.g., how much memory is needed to run.
 
-`Application control and post-processing <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part06.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part05.pdf
+
+`Application control and post-processing`__
 
   How to check and react on the termination status of a GC3Pie
   Task/Application.
 
-`Introduction to workflows <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part07.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part06.pdf
+
+`Introduction to workflows`__
 
   A worked-out example of a many-step workflow.
 
-`Running tasks in a sequence <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part08.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part07.pdf
+
+`Running tasks in a sequence`__
 
   How to run tasks in sequence: basic usage of
   `SequentialTaskCollection`:class: and `StagedTaskCollection`:class:
 
-`Running tasks in parallel <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part09.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part08.pdf
+
+`Running tasks in parallel`__
 
   How to run independent tasks in parallel: the `ParallelTaskCollection`:class:
 
-`Automated construction of task dependency graphs <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part10.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part09.pdf
+
+`Automated construction of task dependency graphs`__
 
   How to use the `DependentTaskCollection`:class: for automated
   arrangement of tasks given their dependencies.
 
-`Dynamic and Unbounded Sequences of Tasks <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part11.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part10.pdf
+
+`Dynamic and Unbounded Sequences of Tasks`__
 
   How to construct `SequentialTaskCollection`:class: classes that
   change the sequence of tasks while being run.
 
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/workflows/part11.pdf
+
 
 A bottom-up introduction to programming with GC3Pie
 ---------------------------------------------------
@@ -103,57 +128,75 @@ already familiar with batch-computing and grid computing, as it
 provides an immediate map of the job submission and monitoring
 commands to GC3Pie equivalents.
 
-`Introduction to GC3Pie <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part01.pdf>`_
+`Introduction to GC3Pie`__
 
     Introduction to the software: what is GC3Pie, what is it for, and
     an overview of its features for writing high-throughput computing
     scripts.
 
-`Basic GC3Pie programming <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part03.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part01.pdf
+
+`Basic GC3Pie programming`__
 
     The `Application` class, the smallest building block of
     GC3Pie. Introduction to the concept of Job, states of an
     application and to the `Core` class.
 
-`Application requirements <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part04.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part03.pdf
+
+`Application requirements`__
 
     How to define extra requirements for an application, such as the
     minimum amount of memory it will use, the number of cores needed
     or the architecture of the CPUs.
 
-`Managing applications: the SessionBasedScript class <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part05.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part04.pdf
+
+`Managing applications: the SessionBasedScript class`__
 
     Introduction to the highest-level interface to build applications
     with GC3Pie, the `SessionBasedScript`. Information on how to
     create simple scripts that take care of the execution of your
     applications, from submission to getting back the final results.
 
-`The GC3Utils commands <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part06.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part05.pdf
+
+`The GC3Utils commands`__
 
     Low-level tools to aid debugging the scripts.
 
-`Introduction to Workflows with GC3Pie <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part08.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part06.pdf
+
+`Introduction to Workflows with GC3Pie`__
 
     Using a practical example (the :ref:`warholize tutorial`) we show
     how workflows are implemented with GC3Pie. The following slides
     will cover in more details the single steps needed to produce a
     complex workflow.
 
-`ParallelTaskCollection <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part09.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part08.pdf
+
+`ParallelTaskCollection`__
 
     Description of the `ParallelTaskCollection` class, used to run
     tasks in parallel.
 
-`StagedTaskCollection <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part10.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part09.pdf
+
+`StagedTaskCollection`__
 
     Description of the `StagedTaskCollection` class, used to run a
     sequence of a fixed number of jobs.
 
-`SequentialTaskCollection <https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part11.pdf>`_
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part10.pdf
+
+`SequentialTaskCollection`__
 
     Description of the `SequentialTaskCollection` class, used to run a
     sequence of jobs that can be altered during runtime.
 
+.. __: https://github.com/uzh/gc3pie/tree/master/docs/programmers/tutorials/bottom-up/part11.pdf
+
 
 .. _`Warholize Tutorial`:
 

docs/programmers/tutorials/workflows/recap.tex

@@ -112,7 +112,7 @@
   \frametitle{...and after the course?}
   \centering
 
-  All VMs to be deleted tomorrow morning. \\
+  All VMs to be deleted Monday morning. \\
   So, \textbf{copy all data you want to save} today!
 
   \+ 
@@ -126,10 +126,24 @@
 \end{frame}
 
 
+\begin{frame}
+  \frametitle{...and after the course?}
+
+  You're very welcome to keep asking questions!
+  \begin{itemize}
+  \item on the mailing-list: \\
+    \href{mailto:gc3pie@googlegroups.com}{gc3pie@googlegroups.com}
+  \item or through the forum web interface: {\small
+      \url{https://groups.google.com/d/forum/gc3pie}}
+  \item and on the GC3Pie chat room: \url{http://gitter.im/gc3pie/chat}
+  \end{itemize}
+\end{frame}
+
+
 \begin{frame}{}
   \begin{center}
     \Large Please provide your feedback \\ about this course: \\
-    \url{http://tinyurl.com/gc3pie-feedback-nov-2016}
+    \url{http://tinyurl.com/gc3pie-feedback-jan-2017}
   \end{center}
 \end{frame}