TheVirtualBrain:

TheDocumentationwebsite.

Source code for tvb.interfaces.web.controllers.burst.matjax

# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Framework Package. This package holds all Data Management, and
# Web-UI helpful to run brain-simulations. To use it, you also need do download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also http://www.thevirtualbrain.org
#
# (c) 2012-2022, Baycrest Centre for Geriatric Care ("Baycrest") and others
#
# This program is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software Foundation,
# either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.  See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this
# program.  If not, see <http://www.gnu.org/licenses/>.
#
#
#   CITATION:
# When using The Virtual Brain for scientific publications, please cite it as follows:
#
#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
#       The Virtual Brain: a simulator of primate brain network dynamics.
#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
#
#

"""
Functions responsible for collecting and rendering the descriptions and the documentations
of the dynamic models in Simulator/Phase Plane.

.. moduleauthor:: Mihai Andrei <mihai.andrei@codemart.ro>
.. moduleauthor:: Robert Vincze <robert.vincze@codemart.ro>
"""


[docs]def configure_matjax_doc(available_models): """ Builds a list containing the model names, inline descriptions and descriptions, which will be displayed in the Simulation/Phase Plane section. """ models_docs = [] for clz_name, clz in available_models.items(): models_docs.append({ 'name': clz_name.replace(' ', '_'), 'inline_description': _dfun_math_directives_to_matjax(clz), 'description': _format_doc(clz.__doc__) }) return models_docs
def _dfun_math_directives_to_matjax(model): """ Looks for sphinx math directives if the docstring of the dfun function of a model. It converts them in html text that will be interpreted by mathjax The parsing is simplistic, not a full rst parser. """ try: doc = model.dfun.__doc__ except AttributeError: doc = None if doc is not None: return _format_doc(doc) # try the parent __doc__ try: doc = model.__mro__[1].dfun.__doc__ except (AttributeError, IndexError): doc = None if doc is not None: return _format_doc('Documentation is missing. Copy-ed from parent\n' + doc) return 'Documentation is missing. ' def _format_doc(doc): return _multiline_math_directives_to_matjax(doc).replace('&', '&amp;').replace('.. math::', '') def _multiline_math_directives_to_matjax(doc): """ Looks for multi-line sphinx math directives in the given rst string It converts them in html text that will be interpreted by mathjax The parsing is simplistic, not a rst parser. Wraps .. math :: body in \[\begin{split}\end{split}\] """ # doc = text | math BEGIN = r'\[\begin{split}' END = r'\end{split}\]' in_math = False # 2 state parser out_lines = [] indent = '' for line in doc.splitlines(): if not in_math: # math = indent directive math_body indent, sep, _ = line.partition('.. math::') if sep: out_lines.append(BEGIN) in_math = True else: out_lines.append(line) else: # math body is at least 1 space more indented than the directive, but we tolerate empty lines if line.startswith(indent + ' ') or line.strip() == '': out_lines.append(line) else: # this line is not properly indented, math block is over out_lines.append(END) out_lines.append(line) in_math = False if in_math: # close math tag out_lines.append(END) return '\n'.join(out_lines)