Fixed some errors in documentation generation

docs/developerguide/conf.py

@@ -17,6 +17,7 @@ import sys, os
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath('.'))
+sys.path.append(os.path.abspath('../sphinx'))
 
 # -- General configuration -----------------------------------------------------
 
@@ -25,7 +26,7 @@ sys.path.insert(0, os.path.abspath('.'))
 
 # 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/autonumber', '../sphinx/numsec']
+extensions = ['autonumber', 'numsec']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/usersguide/application.rst

@@ -63,8 +63,8 @@ install both the drivers and toolkit.
 
 4. (Optional) If you plan to use the CPU platform, it is recommended that you
 install FFTW, available from http://www.fftw.org.  When configuring it, be sure
-to specify single precision and multiple threads (the :code:`--enable-float`
-and :code:`--enable-threads` options).  OpenMM will still work without FFTW,
+to specify single precision and multiple threads (the |--|\ :code:`enable-float`
+and |--|\ :code:`enable-threads` options).  OpenMM will still work without FFTW,
 but the performance of particle mesh Ewald (PME) will be much worse.
 
 5. Launch the Terminal application.  Change to the OpenMM directory by typing
@@ -127,7 +127,7 @@ Installing on Linux
 
 2. Make sure you have Python 2.6 or higher (earlier versions will not work) and
 a C++ compiler (typically gcc or clang) installed on your computer.  You can
-check what version of Python is installed by typing :code:`python --version`
+check what version of Python is installed by typing :code:`python` |--|\ :code:`version`
 into a console window.
 
 3. (Optional) If you want to run OpenMM on a GPU, install CUDA and/or OpenCL.
@@ -142,8 +142,8 @@ into a console window.
 install FFTW.  It is probably available through your system’s package manager
 such as :code:`yum` or :code:`apt-get`\ .  Alternatively, you can download
 it from http://www.fftw.org.  When configuring it, be sure to specify single
-precision and multiple threads (the :code:`--enable-float` and :code
-:`--enable-threads` options).  OpenMM will still work without FFTW, but the
+precision and multiple threads (the |--|\ :code:`enable-float` and
+|--|\ :code:`enable-threads` options).  OpenMM will still work without FFTW, but the
 performance of particle mesh Ewald (PME) will be much worse.
 
 5. In a console window, change to the OpenMM directory by typing

docs/usersguide/autonumber.py

-from docutils.parsers.rst import roles
-from docutils.nodes import Text, reference, section
-from sphinx.roles import XRefRole
-    
-class autonumber(Text):
-    pass
-    
-class autonumber_ref(reference):
-    pass
-
-def autonumber_role(name, rawtext, text, lineno, inliner, options={}, content=[]):
-    return ([autonumber(text)], [])
-
-def doctree_resolved(app, doctree, docname):
-    index = {};
-    refTable = {}
-    if app.config.autonumber_by_chapter:
-        # Record the number of each chapter
-        
-        env = app.builder.env
-        sectionNumbers = {}
-        for doc in env.toc_secnumbers:
-            sections = env.toc_secnumbers[doc]
-            for sectionId in sections:
-                sectionNumbers[sectionId[1:]] = sections[sectionId]
-        lastChapter = -1
-    
-    # Assign numbers to all the autonumbered objects.
-    
-    for node in doctree.traverse(autonumber):
-        category = node.astext().split(',')[0]
-        if category in index:
-            nextNumber = index[category]+1
-        else:
-            nextNumber = 1
-        if app.config.autonumber_by_chapter:
-            parent = node.parent
-            chapter = None
-            while chapter is None:
-                if isinstance(parent, section):
-                    chapter = parent
-                parent = parent.parent
-            chapter = sectionNumbers[chapter.attributes['ids'][0]][0]
-            if chapter != lastChapter:
-                index = {}
-            newNode = Text('%s %d-%d' % (category, chapter, nextNumber))
-            lastChapter = chapter
-        else:
-            newNode = Text('%s %d' % (category, nextNumber))            
-        index[category] = nextNumber
-        refTable[node.astext()] = newNode
-        node.parent.replace(node, newNode)
-    
-    # Replace references with the name of the referenced object
-    
-    for ref_info in doctree.traverse(autonumber_ref):
-        target = ref_info['reftarget']
-        if target not in refTable:
-            raise ValueError('Unknown target for autonumber reference: '+target)
-        ref_info.replace_self(Text(refTable[target].astext()))
-
-def setup(app):
-    app.add_config_value('autonumber_by_chapter', True, False)
-    roles.register_local_role('autonumber', autonumber_role)
-    app.add_node(autonumber)
-    app.add_node(autonumber_ref)
-    app.add_role('numref', XRefRole(nodeclass=autonumber_ref))
-    app.connect('doctree-resolved', doctree_resolved)
-
-

docs/usersguide/caption.py

-from docutils.parsers.rst import Directive
-from docutils.nodes import compound, raw
-
-class CaptionDirective(Directive):
-    
-    has_content = True
-
-    def run(self):
-        latexPrefix = raw('', '{\\centering', format='latex')
-        latexSuffix = raw('', '\\par}\\bigskip', format='latex')
-        text = '\n'.join(self.content)
-        content_node = compound(rawsource=text)
-        self.state.nested_parse(self.content, self.content_offset, content_node)
-        content_node.attributes['classes'].append('caption')
-        return [latexPrefix, content_node, latexSuffix]
-
-def setup(app):
-    app.add_directive('caption', CaptionDirective)

docs/usersguide/conf.py

@@ -17,6 +17,7 @@ import sys, os
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath('.'))
+sys.path.append(os.path.abspath('../sphinx'))
 
 # -- General configuration -----------------------------------------------------
 
@@ -25,7 +26,7 @@ sys.path.insert(0, os.path.abspath('.'))
 
 # 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.pngmath', 'sphinx.ext.mathjax', 'sphinxcontrib.bibtex', '../sphinx/autonumber', '../sphinx/samepage', '../sphinx/caption', '../sphinx/numsec']
+extensions = ['sphinx.ext.pngmath', 'sphinx.ext.mathjax', 'sphinxcontrib.bibtex', 'autonumber', 'samepage', 'caption', 'numsec']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/usersguide/header.rst

@@ -3,3 +3,5 @@
 
     <style> .code {font-family:monospace;} </style>
     <style> .caption {text-align:center;} </style>
+
+.. |--| replace:: :option:`--`

docs/usersguide/library.rst

@@ -2490,7 +2490,7 @@ Make sure you have Python 2.6 or later installed.  For Python installation
 packages and instructions, go to http://python.org.  If you do not have the
 correct Python version, install a valid version using the default options.  Most
 versions of Linux and Mac OS X have a suitable Python preinstalled.  You can
-check by typing “\ :code:`python --version`\ ” in a terminal window.
+check by typing “\ :code:`python` |--|\ :code:`version`\ ” in a terminal window.
 
 You must have a C++ compiler to install the OpenMM Python API.  If you are using
 a Mac, install Apple's Xcode development tools

docs/usersguide/samepage.py

-from docutils.parsers.rst import Directive
-from docutils.nodes import compound, raw
-
-class SamepageDirective(Directive):
-    
-    has_content = True
-
-    def run(self):
-        prefix = raw('', '\\par\\begin{samepage}', format='latex')
-        suffix = raw('', '\\end{samepage}\\par', format='latex')
-        text = '\n'.join(self.content)
-        content_node = compound(rawsource=text)
-        self.state.nested_parse(self.content, self.content_offset, content_node)
-        return [prefix, content_node, suffix]
-
-def setup(app):
-    app.add_directive('samepage', SamepageDirective)