Initial commit of reST version of the CellML 1.1 Specification, initi…

…ally obtained from https://github.com/A1kmm/cellml-core-spec/tree/normative in docbook format and converted to reST using pandoc. A basic sphinx project has also been added.

Makefile

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+# 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
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+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 "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@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/CellMLSpecifications.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/CellMLSpecifications.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/CellMLSpecifications"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/CellMLSpecifications"
+	@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."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+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.md

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+cellml-spec-sphinx-test
+=======================
+
+This repository will be used by the CellML editors to test out the use of reST and sphinx with github and readthedocs in developing the CellML 1.2 specification. The content was initially obtained from https://github.com/A1kmm/cellml-core-spec/tree/normative, using pandoc to convert the docbook XML to reST format (``for f in *.xml; do pandoc -f docbook -o `basename $f .xml`.rst $f; done``). This was incorporated into a basic sphinx project.
+
+If things work correctly, changes in this repository will be reflected over at: https://cellml-specifications-sphinx-testing.readthedocs.org/.

source/abstract.rst

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+   This document is an unofficial working draft. The below describes
+   the intended status of the specification, and not its current status.
+
+   This document specifies version 1.2 of `CellML <http://www.cellml.org/>`_,
+   an `XML <http://www.w3.org/XML/>`_-based language for
+   describing and exchanging mathematical models.
+
+   This is the *normative* specification of CellML. It is intended to
+   provide the minimum amount of information needed to describe CellML.
+   An |informative-specification|_ is available which is annotated with
+   much more explanatory material.
+
+.. |informative-specification| replace:: *informative* specification
+.. _informative-specification: http://www.cellml.org/
+
+.. todo::
+
+   Provide a 'proper' URL for the informative version of the specification.

source/component-element-item.rst

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+The ``component`` element information item
+==========================================
+
+``component`` element information items (referred to in this specification
+as ``component`` elements) are element information items in the CellML
+namespace with local name ``component``, and which appear as a child of a
+``model`` element.
+
+Specific information items
+--------------------------
+
+1. Every ``component`` element MUST contain a ``name`` attribute in the empty
+   namespace. The value of the ``name`` attribute MUST be a valid CellML
+   identifier. The value of the ``name`` attribute MUST NOT be identical to
+   the ``name`` attribute on any other ``component`` element or ``import component``
+   element in the CellML infoset.
+
+2. A ``component`` element MAY contain zero or more specific information
+   item children, each of which MUST be of one of the following types:
+
+   a. A ``units`` element;
+
+   b. A ``variable`` element; or
+
+   c. An element information item in the MathML namespace, and with
+      local name ``math``, which MUST be the top-level of a content MathML
+      tree, as described in `MathML 2.0 <http://www.w3.org/TR/2003/REC-MathML2-20031021/>`_.

source/component-ref-element-item.rst

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+The ``component_ref`` element information item
+===============================================
+
+``component_ref`` element information items (referred to in this
+specification as ``component_ref`` elements) are element information items
+in the CellML namespace with local name equal to ``component_ref``.
+
+Specific information items
+--------------------------
+
+1. Every ``component_ref`` element MUST contain an attribute information
+   item in the empty namespace and with local name ``component``. The value
+   of this attribute MUST be a valid CellML identifier, and MUST match
+   the ``name`` attribute on a ``component`` element or an ``import
+   component`` element in the CellML infoset.
+
+2. Every ``component_ref`` element MAY in turn contain zero or more
+   ``component_ref`` element children.
+
+3. In addition, ``component_ref`` elements which are children of ``group``
+   elements MUST contain at least one ``component_ref`` element child.