[WIP] Website

sphinx/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+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/README.md

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+The following are needed for the documentation set-up:
+
+- conda install sphinx
+- conda install sphinxcontrib-bibtex
+- conda install sphinx-book-theme
+
+(See e.g. https://sphinx-themes.org/ for other choices of themes)
+
+
+From within the sphinx directory:
+
+- sphinx-build -b html source build
+- or 'make html'
+
+
+Then 'open build/html/index.html' will open the webpage.
+
+
+Important files:
+
+- sphinx/source/conf.py configures the set-up.  The project name, authors, version as well as extensions and project theme can all be changed here.
+- sphinx/source/index.rst is the 'front page', and table of contents etc are specified here
+- sphinx/source/simunet_analysis.rst contains some first basic examples of how we can generate documentation directly from the code docstrings.
+
+
+See also https://www.sphinx-doc.org/en/master/index.html for much more info on Sphinx

sphinx/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

sphinx/source/_static/custom.css

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+/* To apply full justification to the entire body text */
+body {
+    text-align: justify;
+}
+
+/* To apply center alignment to headings */
+/*h1, h2, h3, h4, h5, h6 {
+    text-align: center;
+}

sphinx/source/bibliography.rst

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+**Bibliography**
+================
+
+.. bibliography:: simunet.bib

sphinx/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- 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,'.')
+
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'SIMUnet'
+copyright = '2023, PBSP'
+author = 'PBSP'
+
+
+# -- General configuration ---------------------------------------------------
+
+# 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.autodoc","sphinxcontrib.bibtex","sphinx.ext.autosummary"]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# 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 = []
+
+
+# Bibtex
+bibtex_bibfiles = ['simunet.bib']
+bibtex_default_style = 'unsrt'
+bibtex_reference_style = 'author_year'
+
+# -- 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_book_theme'
+
+html_theme_options = {
+    'sidebar': 'none',
+}
+
+html_logo = "_static/PBSP_logo.png"
+
+# 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']
+html_static_path = ['_static']
+html_css_files = ['custom.css']