Add static build of docs

sphinx/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

sphinx/conf.py

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+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# 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.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'opendihu'
+copyright = u'2020, Benjamin Maier. MIT licence, see LICENSE for details.'
+author = u'Benjamin Maier'
+
+# The short X.Y version
+version = u''
+# The full version, including alpha/beta/rc tags
+release = u'1.4'
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# 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.mathjax',
+    'sphinx.ext.githubpages',
+    'recommonmark'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = [u'_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+#html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+html_sidebars = {'**': ['localtoc.html']}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'opendihudoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# 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 = [
+    (master_doc, 'opendihu.tex', u'opendihu Documentation',
+     u'Benjamin Maier', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'opendihu', u'opendihu Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'opendihu', u'opendihu 1.4 Documentation',
+     author, 'opendihu', 'Computational framework for the DiHu multi-scale muscle model and variants.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------
+numfig = True

sphinx/developer/contributors.rst

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+
+Contributors
+========================
+
+Over time, numerous people make changes in the code. The following list aims to give an overview who was using it when and in which context. Please update the list with new people.
+Only people that contributed to the code are listed, not solely "users".
+Most recent on top:
+
+.. - **Julia Kühnert**
+
+- **Matthias Tompert**
+
+  - Bachelor thesis with Benjamin
+  - 06/2020 - 12/2020
+  - Parser for python settings and c++ main files, web application and/or GUI to edit existing examples and create new ones
+
+- **Marius Nitzsche**
+
+  - Master thesis with Benjamin and Aaron
+  - 09/2019 - 09/2020
+  - Parallel-in-time algorithm for Multidomain, Integrate multigrid-reduction-in-time scheme provided by external library `xbraid`. Examples: `Pint_diffusion`, `multidomain_no_fat`
+
+- **Felix Huber**
+
+  - PhD student with Dominik Göddeke and Miriam Mehl, IANS/SGS
+  - from 10/2019
+
+- **Sebastian Kreuder**
+
+  - Bachelor thesis with Benjamin
+  - 11/2018 - 05/2019
+  - Heun with adaptive timestep widths, dynamic rebalancing of workload between the processes that compute a single muscle fiber. Implemented `LoadBalancing` and `HeunAdaptive` classes.
+
+- **Pascal Litty**
+
+  - Bachelor thesis with Nehzat
+  - 08/2017 - 02/2018
+  - topic same as Nehzat, implemented `svd_utility`
+
+- **Nehzat Emamy**
+
+  - Post-doc with Miriam Mehl
+  - 02/2019 - 08/2019
+  - Model order reduction, POD-Galerkin and POD-DEIM, prototype in MATLAB, started implementation in opendihu, the snapshot matrix needs to be generated externally. Directories `core/src/model_order_reduction` and `examples/electrophysiology/monodomain/pod`.
+
+- **Dominik Sellenthin**
+
+  - Bachelor student with Benjamin
+  - 02/2018 - 07/2018
+  - Quadrature schemes, implemented/investigated Gauss, Clenshaw-Curtis and Newton-Cotes quadratures.
+
+- **Aaron Krämer**
+
+  - PhD student with Dominik Göddeke
+  - from 03/2018
+  - Numerics, GPU offloading with PGI compiler
+
+- **Benjamin Maier**
+
+  - PhD student with Miriam Schulte
+  - 07/2017 - 05/2021