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Merge pull request #297 from kerimoyle/final_tweaks
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Final tweaks
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@kerimoyle
kerimoyle authored Apr 17, 2020
2 parents baa1691 + 3083b14 commit e515834
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Showing 11 changed files with 121 additions and 106 deletions.
59 changes: 31 additions & 28 deletions src/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -117,33 +117,36 @@ def define_excluded_patterns():
'calvin_and_hobbes': ('https://www.gocomics.com/calvinandhobbes/%s', ''),
'cellml1to2': ('https://github.com/hsorby/cellml1to2%s', ''),
'cellml2namespace': ('http://www.cellml.org/cellml/2.0%s', None),
'cellml2spec_display': ('https://www.cellml.org/specifications/cellml_2.0%s', None),
'cellml2spec_display': ('https://cellml.org/specifications/cellml_2.0%s', None),
'cellsolver': ('https://github.com/hsorby/cellsolver%s', ''),
'cmake': ('https://cmake.org/%s', ''),
'doxygen': ('http://www.doxygen.nl/%s', ''),
'euler_method': ('https://en.wikipedia.org/wiki/Euler_method%s', ''),
'git': ('https://git-scm.com/%s', ''),
'github': ('https://github.com/%s', ''),
'google_styleguide': ('https://google.github.io/styleguide/cppguide.html/%s', ''),
'href_locator': ('https://www.w3.org/TR/2001/REC-xlink-20010627/#link-locators/%s', ''),
'libcellml': ('https://libcellml.org/%s', ''),
'libcellml_repo': ('https://github.com/cellml/libcellml.git%s', ''),
'libxml2': ('http://www.xmlsoft.org/%s', ''),

# These should be identical: one for links, one for full URL display
'mathml2': ('http://www.w3.org/TR/2003/REC-MathML2-20031021%s', ''),
'mathml2_display': ('http://www.w3.org/TR/2003/REC-MathML2-20031021%s', None),
'mathml2': ('https://www.w3.org/TR/MathML2%s', ''),
'mathml2_display': ('https://www.w3.org/TR/MathML2%s', None),

'mathml2help': ('https://www.w3.org/TR/MathML2/chapter4.html%s', ''),
'mathml2namespace': ('http://www.w3.org/1998/Math/MathML%s', None),

# This will get MathML added to the end so it becomes http://www.w3.org/1998/Math/MathML
# in the final display, to avoid trailing slashes.
'mathml2namespace': ('http://www.w3.org/1998/Math/%s', None),

'namespace_help': ('https://www.w3schools.com/xml/xml_namespaces.asp%s', ''),
'opencor': ('https://opencor.ws/%s', ''),
'pmr': ('https://models.physiomeproject.org/welcome/%s', ''),
'python': ('https://www.python.org/%s', ''),

# These should be identical: one for links, one for full URL display
'rfc2119': ('http://www.ietf.org/rfc/rfc2119.txt%s', ''),
'rfc2119_display': ('http://www.ietf.org/rfc/%s', None),
'rfc2119': ('https://www.ietf.org/rfc/rfc2119.txt%s', ''),
'rfc2119_display': ('https://www.ietf.org/rfc/%s', None),

'sphinx': ('http://sphinx-doc.org/%s', ''),
'swig': ('http://www.swig.org/%s', ''),
Expand All @@ -154,21 +157,21 @@ def define_excluded_patterns():
'unicode13_display': ('https://www.unicode.org/versions/Unicode13.0.0%s', None),

# These should be identical: one for links, one for full URL display
'xlink': ('http://www.w3.org/TR/2001/REC-xlink-20010627%s', ''),
'xlink_display': ('http://www.w3.org/TR/2001/REC-xlink-20010627%s', None),
'xlink': ('https://www.w3.org/TR/xlink11%s', ''),
'xlink_display': ('https://www.w3.org/TR/xlink11%s', None),

'xml_help': ('https://www.w3.org/XML/%s', ''),

# These should be identical: one for links, one for full URL display
'xml_1_1': ('http://www.w3.org/TR/xml11%s', ''),
'xml_1_1_display': ('http://www.w3.org/TR/xml11%s', None),
'xml_1_1': ('https://www.w3.org/TR/xml11%s', ''),
'xml_1_1_display': ('https://www.w3.org/TR/xml11%s', None),

# These should be identical: one for links, one for full URL display
'xml_infoset': ('http://www.w3.org/TR/2004/REC-xml-infoset-20040204/%s', ''),
'xml_infoset_display': ('https://www.w3.org/TR/xml-infoset%s', None),
'xml_infoset': ('https://www.w3.org/TR/2004/REC-xml-infoset-20040204/%s', ''),
'xml_infoset_display': ('https://www.w3.org/TR/2004/REC-xml-infoset-20040204%s', None),

'xml_namespace_1_1': ('https://www.w3.org/TR/2006/REC-xml-names11-20060816%s', ''),
'xml_namespace_1_1_display': ('https://www.w3.org/TR/2006/REC-xml-names11-20060816%s', None),
'xml_namespace_1_1': ('https://www.w3.org/TR/xml-names11%s', ''),
'xml_namespace_1_1_display': ('https://www.w3.org/TR/xml-names11%s', None),

}

Expand All @@ -189,9 +192,9 @@ def define_excluded_patterns():
# built documents.
#
# The short X.Y version.
version = '2.0.0-rc1'
version = '2.0'
# The full version, including alpha/beta/rc tags.
release = '2.0.0-rc1'
release = '2.0'
if unofficial:
version += '-unofficial'
release += '-unofficial'
Expand All @@ -204,7 +207,7 @@ def define_excluded_patterns():
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
today_fmt = '%d %B %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
Expand Down Expand Up @@ -297,7 +300,7 @@ def define_excluded_patterns():

# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
html_last_updated_fmt = '%d %B %Y'

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
Expand Down Expand Up @@ -356,21 +359,21 @@ def define_excluded_patterns():

# Additional stuff for the LaTeX preamble.
'preamble': r'''
% Preamble set from Sphinx configuration
\usepackage[titles]{tocloft}
\usepackage{textgreek}
\usepackage{amssymb}
% Stop cross-references from showing up in italics
\protected\def\sphinxcrossref#1{#1}
'''
% Preamble set from Sphinx configuration
\usepackage[titles]{tocloft}
\usepackage{textgreek}
\usepackage{amssymb}
% Stop cross-references from showing up in italics
\protected\def\sphinxcrossref#1{#1}
'''
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
('index', '{0}.tex'.format(tex_document_name()), u'CellML Specification',
('index', '{0}.tex'.format(tex_document_name()), u'CellML Normative Specification',
u'CellML 2.0 Editors and Contributors', 'manual'),
]

Expand Down
3 changes: 2 additions & 1 deletion src/normative_only_index.rst
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Expand Up @@ -13,7 +13,8 @@ It is intended primarily for the developers of software tools which directly con

Users of CellML models may prefer the informative version of the CellML Specification, which is available at :cellml2spec_display:`/`.

A PDF version of the normative specification is available at :cellml2spec_display:`/specification.pdf`.
The official version of the CellML Normative Specification is available at :cellml2spec_display:`/cellml_2_0_normative_specification.pdf`.


.. include:: reference/acknowledgements.inc

Expand Down
4 changes: 2 additions & 2 deletions src/reference/acknowledgements.inc
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Expand Up @@ -19,8 +19,8 @@ Peter J. Hunter,
Gary R. Mirams, and
Maxwell L. Neal.

The authors also wish to acknowledge the significant contribution of the (discontinued) draft CellML 1.2 specification, much of the text of which was incorporated into this specification, although the semantics have changed considerably.
The CellML 1.2 specification was itself the result of a collaborative effort by a number of researchers during 2008-2011\:
The authors also wish to acknowledge the significant contribution of the (discontinued) CellML 1.2 draft specification, much of the text of which was incorporated into this specification, although the semantics have changed considerably.
The CellML 1.2 draft specification was itself the result of a collaborative effort by a number of researchers during 2008-2011\:

Andrew K. Miller (who wrote the text reused here),
Randall Britten,
Expand Down
25 changes: 12 additions & 13 deletions src/reference/sectionA_definitions.inc
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Expand Up @@ -40,7 +40,7 @@ The namespace :cellml2namespace:`#`.
.. _specA_mathml_namespace:

**MathML namespace:**
The namespace :mathml2namespace:`/`.
The namespace :mathml2namespace:`MathML`.

.. _specA_cellml_information_item:

Expand Down Expand Up @@ -119,7 +119,7 @@ Specific information items

#. A document type declaration information item;

#. An unparsed entity information item;
#. An unparsed entity information item; or

#. A notational information item.

Expand All @@ -129,7 +129,7 @@ Specific information items

.. marker_cellml_information_sets_2

.. _specA_semantic_equivalence:


Non-specific information items
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand All @@ -138,25 +138,24 @@ Non-specific information items

#. A comment information item;

#. A namespace information item;
#. A namespace information item; or

#. A character information item.

2. An element information item in the :ref:`CellML namespace<specA_cellml_namespace>` MUST NOT contain any character information items, except for whitespace characters.
2. An element information item in the :ref:`CellML namespace<specA_cellml_namespace>` MUST NOT contain any character information items, except for :ref:`whitespace characters<specA_whitespace_character>`.

.. marker_cellml_information_sets_3

.. _specA_semantic_equivalence:

3. Two :ref:`CellML infosets<specA_cellml_infoset>` SHALL be deemed semantically equivalent if one can be transformed into the other by making zero or more of the following changes:

#. Adding, removing, and/or modifying comment information items.

#. Changing (inserting, removing, and/or modifying) one or more namespace information items, and/or modifying the prefix of one or more information items, without changing the namespace that any information item is in.

#. The following paragraph applies to character information items which are the direct child of an element information item in the :ref:`CellML namespace<specA_cellml_namespace>`, or in the :ref:`MathML namespace<specA_mathml_namespace>`:

Inserting or removing character information items that consist entirely of :ref:`whitespace characters<specA_whitespace_character>`,
changing the number of whitespace characters in such an information item,
or changing the number of whitespace characters at the beginning or end of any character information item.
inserting or removing character information items that consist entirely of :ref:`whitespace characters<specA_whitespace_character>`, changing the number of whitespace characters in such an information item, or changing the number of whitespace characters at the beginning or end of any character information item.

.. marker_cellml_information_sets_4

Expand All @@ -165,7 +164,7 @@ Use of namespaces

#. Element information items in a :ref:`CellML infoset<specA_cellml_infoset>` MUST belong to one of the following namespaces, unless explicitly indicated otherwise:

#. The :ref:`CellML namespace<specA_cellml_namespace>`;
#. The :ref:`CellML namespace<specA_cellml_namespace>`; or

#. The :ref:`MathML namespace<specA_mathml_namespace>`.

Expand All @@ -175,7 +174,7 @@ XML ID Attributes
~~~~~~~~~~~~~~~~~

#. Any element information item in the :ref:`CellML namespace<specA_cellml_namespace>` MAY contain an attribute with local name :code:`id.`
This attribute SHALL be treated as having attribute type ID, as defined in :xml_1_1:`section 3.3.1 <#sec-attribute-types>` of :xml_1_1:`XML 1.1 <>` [:ref:`5<ref_xml_1_1>`].
This attribute SHALL be treated as having attribute type ID, as defined in :xml_1_1:`Section 3.3.1 <#sec-attribute-types>` of :xml_1_1:`XML 1.1 <>` [:ref:`5<ref_xml_1_1>`].

.. marker_cellml_information_sets_end
.. marker_data_formats_start
Expand Down Expand Up @@ -211,7 +210,7 @@ The following data representation formats are defined for use in this specificat

.. container:: issue-data-repr-int-sign

2. MAY begin with a single Basic Latin plus character :unicode:`002B` or a Basic Latin hyphen-minus character :unicode:`002D` as the sign indicator.
2. MAY begin with a single Basic Latin plus character :unicode:`002B` or a single Basic Latin hyphen-minus character :unicode:`002D` as the sign indicator.

.. container:: issue-data-repr-int-euro-num

Expand All @@ -229,7 +228,7 @@ The following data representation formats are defined for use in this specificat

.. container:: issue-data-repr-basic-real-sign

2. MAY begin with a single Basic Latin plus character :unicode:`002B` or a Basic Latin hyphen-minus character :unicode:`002D` as the sign indicator.
2. MAY begin with a single Basic Latin plus character :unicode:`002B` or a single Basic Latin hyphen-minus character :unicode:`002D` as the sign indicator.

.. container:: issue-data-repr-basic-real-decimal

Expand Down
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