adding back files to be reviewed

docs/sphinxext/LICENSE

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+The file notebook_sphinxext.py was derived from code in PyNE and yt.
+
+PyNE has the following license:
+
+-------------------------------------------------------------------------------
+Copyright 2011-2015, the PyNE Development Team. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are
+permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, this list of
+      conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, this list
+      of conditions and the following disclaimer in the documentation and/or other materials
+      provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE PYNE DEVELOPMENT TEAM ``AS IS'' AND ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+The views and conclusions contained in the software and documentation are those of the
+authors and should not be interpreted as representing official policies, either expressed
+or implied, of the stakeholders of the PyNE project or the employers of PyNE developers.
+-------------------------------------------------------------------------------
+
+yt has the following license:
+
+-------------------------------------------------------------------------------
+yt is licensed under the terms of the Modified BSD License (also known as New
+or Revised BSD), as follows:
+
+Copyright (c) 2013-, yt Development Team
+Copyright (c) 2006-2013, Matthew Turk <matthewturk@gmail.com>
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+Redistributions in binary form must reproduce the above copyright notice, this
+list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.
+
+Neither the name of the yt Development Team nor the names of its
+contributors may be used to endorse or promote products derived from this
+software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+-------------------------------------------------------------------------------

docs/sphinxext/notebook_sphinxext.py

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+import sys
+import os.path
+import re
+import time
+from docutils import io, nodes, statemachine, utils
+try:
+    from docutils.utils.error_reporting import ErrorString  # the new way
+except ImportError:
+    from docutils.error_reporting import ErrorString        # the old way
+from docutils.parsers.rst import Directive, convert_directive_function
+from docutils.parsers.rst import directives, roles, states
+from docutils.parsers.rst.roles import set_classes
+from docutils.transforms import misc
+
+from nbconvert import html
+
+
+class Notebook(Directive):
+    """Use nbconvert to insert a notebook into the environment.
+    This is based on the Raw directive in docutils
+    """
+    required_arguments = 1
+    optional_arguments = 0
+    final_argument_whitespace = True
+    option_spec = {}
+    has_content = False
+
+    def run(self):
+        # check if raw html is supported
+        if not self.state.document.settings.raw_enabled:
+            raise self.warning('"%s" directive disabled.' % self.name)
+
+        # set up encoding
+        attributes = {'format': 'html'}
+        encoding = self.options.get(
+            'encoding', self.state.document.settings.input_encoding)
+        e_handler = self.state.document.settings.input_encoding_error_handler
+
+        # get path to notebook
+        source_dir = os.path.dirname(
+            os.path.abspath(self.state.document.current_source))
+        nb_path = os.path.normpath(os.path.join(source_dir,
+                                                self.arguments[0]))
+        nb_path = utils.relative_path(None, nb_path)
+
+        # convert notebook to html
+        exporter = html.HTMLExporter(template_file='full')
+        output, resources = exporter.from_filename(nb_path)
+        header = output.split('<head>', 1)[1].split('</head>',1)[0]
+        body = output.split('<body>', 1)[1].split('</body>',1)[0]
+
+        # add HTML5 scoped attribute to header style tags
+        header = header.replace('<style', '<style scoped="scoped"')
+        header = header.replace('body {\n  overflow: visible;\n  padding: 8px;\n}\n',
+                                '')
+        header = header.replace("code,pre{", "code{")
+
+        # Filter out styles that conflict with the sphinx theme.
+        filter_strings = [
+            'navbar',
+            'body{',
+            'alert{',
+            'uneditable-input{',
+            'collapse{',
+        ]
+
+        filter_strings.extend(['h%s{' % (i+1) for i in range(6)])
+
+        line_begin = [
+            'pre{',
+            'p{margin'
+        ]
+
+        filterfunc = lambda x: not any([s in x for s in filter_strings])
+        header_lines = filter(filterfunc, header.split('\n'))
+
+        filterfunc = lambda x: not any([x.startswith(s) for s in line_begin])
+        header_lines = filter(filterfunc, header_lines)
+
+        header = '\n'.join(header_lines)
+
+        # concatenate raw html lines
+        lines = ['<div class="ipynotebook">']
+        lines.append(header)
+        lines.append(body)
+        lines.append('</div>')
+        text = '\n'.join(lines)
+
+        # add dependency
+        self.state.document.settings.record_dependencies.add(nb_path)
+        attributes['source'] = nb_path
+
+        # create notebook node
+        nb_node = notebook('', text, **attributes)
+        (nb_node.source, nb_node.line) = \
+            self.state_machine.get_source_and_line(self.lineno)
+
+        return [nb_node]
+
+
+class notebook(nodes.raw):
+    pass
+
+
+def visit_notebook_node(self, node):
+    self.visit_raw(node)
+
+
+def depart_notebook_node(self, node):
+    self.depart_raw(node)
+
+
+def setup(app):
+    app.add_node(notebook,
+                 html=(visit_notebook_node, depart_notebook_node))
+
+    app.add_directive('notebook', Notebook)