Modified logo image and added first version of a documentation page.

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_build/html/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 9f15259458fc24a92c6fe38b5de81602
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_sources/index.rst.txt

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+.. FabSim3 documentation master file, created by
+   sphinx-quickstart on Fri Jun  7 11:11:04 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+.. image:: ../logo.jpg
+
+An automation toolkit for complex simulation tasks
+===========================================================
+
+FabSim3 is a Python-based automation toolkit for scientific simulation and data
+processing workflows, licensed under the BSD 3-clause license. It is developed 
+as part of VECMA (http://www.vecma.eu).
+
+FabSim3 helps users to perform comples remote tasks from a local command-line,
+and to run applications while curating data and environment variables. It
+supports the execution of jobs, job arrays and dynamic workflows through
+schedulers such as SLURM, PBSPro, LoadLeveller and QCG. It stores
+machine-specific configurations in the repository, and applies it to all
+applications run on that machine. These configurations are updated by any
+contributor who feels that a fix or improvement is required.
+
+FabSim3 relies strongly on Fabric (http://www.fabfile.org, shown to work with
+versions 1.5.3 and 1.10.0) and PyYAML. It has been used to run simulation
+workflows on supercomputers such as ARCHER, SuperMUC, Carthesius, Eagle, as well
+as local clusters and desktops.
+
+FabSim3 is publicly available at: http://www.github.com/djgroen/FabSim The
+accompanying software paper can be found here:
+https://doi.org/10.1016/j.cpc.2016.05.020
+
+The public plugins for FabSim3 include:
+
+* FabMD, focused on molecular dynamics.
+* FabFlee, focused on agent-based modelling.
+* FabUQCampaign, focused on ocean modelling.
+* FabDummy, a dummy plugin used for testing the toolkit.
+
+
+Key reference documents
+=======================
+Here's a list of particularly useful reference documents for FabSim3.
+
+**Basic:**
+
+* Basic installation and testing instructions: https://github.com/djgroen/FabSim3/blob/master/INSTALL.md
+* Testing simple jobs with FabDummy: https://github.com/djgroen/FabDummy/blob/master/README.md
+* How to set up and use FabSim3 with the Singularity containerization environment: https://github.com/djgroen/FabSim3/blob/master/doc/FabSim3SingularityUsage.md
+
+**Intermediate:**
+
+* Do UQ with molecular dynamics using the FabMD plugin: https://github.com/UCL-CCS/FabMD/blob/master/doc/EasyVVUQ_FabMD_example.md
+* Do UQ with a coupled agent-based migration model using the FabFlee plugin: https://github.com/djgroen/FabFlee/blob/master/doc/Tutorial.md
+
+**Advanced:**
+
+* How to create your own plugin: https://github.com/djgroen/FabSim3/blob/master/doc/CreatePlugins.md
+* How to write automation scripts: https://github.com/djgroen/FabSim3/blob/master/doc/CreateAutomationScripts.md
+* How to use FabSim with QCG middleware: https://github.com/djgroen/FabSim3/blob/master/doc/FabSim%2BQCG.md
+
+Citing FabSim3
+==============
+
+Please find the BibTex reference below of our FabSim software paper in *Computer Physics Communications*::
+
+
+  @article{GROEN2016375,
+  title = "FabSim: Facilitating computational research through automation on large-scale and distributed e-infrastructures",
+  journal = "Computer Physics Communications",
+  volume = "207",
+  number = "Supplement C",
+  pages = "375 - 385",
+  year = "2016",
+  issn = "0010-4655",
+  doi = "https://doi.org/10.1016/j.cpc.2016.05.020",
+  url = "http://www.sciencedirect.com/science/article/pii/S0010465516301448",
+  author = "Derek Groen and Agastya P. Bhati and James Suter and James Hetherington and Stefan J. Zasada and Peter V. Coveney",
+  }
+
+
+
+.. toctree::
+   :maxdepth: 2
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`