Merge pull request #107 from tclose/restructured_text

Merging this PR as it doesn't change any content of the specification only the format

.gitignore

@@ -3,6 +3,7 @@
 *.blg
 *.log
 *.out
+*.swp
 *.pdf
 *.synctex.gz
 *.toc
@@ -11,3 +12,9 @@
 /.sass-cache
 /.pydevproject
 .DS_Store
+/docs/_build
+/.settings/
+/.cproject
+/build/
+/images/
+/_config.yml.orig

Makefile

@@ -0,0 +1,130 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/NineMLSpecification.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/NineMLSpecification.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/NineMLSpecification"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/NineMLSpecification"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	make -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."

README.rst

@@ -0,0 +1,61 @@
+
+NineML
+======
+
+Network Interchange for NEuroscience (NineML) is a simulator-independent
+language with the aim of providing an unambiguous description of neuronal
+network models for efficient model sharing and reusability
+(http://nineml.net).
+
+NineML emerged from a joint effort of experts in the fields of computational
+neuroscience, simulator development and simulator-independent language
+initiatives (NeuroML_, PyNN_), grouped in the
+`INCF Multiscale Modeling Task Force: https://www.incf.org/activities/our-programs/modeling/people`__.
+This effort was initiated and is still supported by the
+`Multiscale Modeling Program: https://www.incf.org/activities/our-programs/modeling`__,
+as part of the standardization effort of the `International Neuroinformatics Coordinating Facility (INCF)`_,
+but the project is now run as a `community project <http://nineml.net/committee>`__.
+
+
+How to build the source
+-----------------------
+
+The source is written in reStructured text and can be build using
+Sphinx (http://www.sphinx-doc.org/) using the provided Makefile
+(or the make.bat if on Windows). If you have ``pip`` setup you can install
+sphinx with 
+
+    $ pip install sphinx
+
+HTML
+^^^^
+
+To make the html docs use the command
+
+    $ make html
+
+PDF
+~~~
+
+To make the pdf you will also need a TeX distribution installed
+(see `MacTex <https://www.tug.org/mactex/>`__ on macOS or the ``texlive-full``
+package on Ubuntu/Debian). After that the PDF can be made with.
+
+    $ make latexpdf
+
+Related repositories
+--------------------
+
+In addition to this main NineML repository (http://github.com/INCF/nineml-spec),
+which only contains the specification document and XML schema, there are
+related repositories that are maintained by the NineML team
+(see http://nineml.net/committee).
+
+- lib9ML (http://github.com/INCF/nineml-python): A Python library for reading,
+  writing and manipulating NineML descriptions
+- NineMLCatalog (http://github.com/INCF/nineml-catalog): A collection of
+  example NineML models written in XML.
+
+.. _PyNN: http://neuralensemble.org/PyNN/
+.. _NeuroML: http://neuroml.org
+.. _International Neuroinformatics Coordinating Facility (INCF): http://www.incf.org