SciCompMod · HenrZu · Mar 12, 2025 · Jan 23, 2025 · Jan 23, 2025 · Jan 23, 2025
diff --git a/.gitignore b/.gitignore
@@ -280,5 +280,7 @@ pycode/memilio-epidata/memilio/epidata/CredentialsRegio.ini
 # Docs
 docs/html
 docs/xml
+docs/source/api
+docs/source/generated
 
 # End of https://www.gitignore.io/api/c++,node,python
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,15 @@
+version: "2"
+
+build:
+  os: "ubuntu-22.04"
+  apt_packages: 
+    - libmagic1
+  tools:
+    python: "3.10"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/source/conf.py
diff --git a/docs/Doxyfile b/docs/Doxyfile
@@ -733,7 +733,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../README.md README.md ../pycode/README.md ../pycode/memilio-epidata/memilio/epidata ../cpp/README.md ../cpp/memilio/ ../cpp/models/
+INPUT                  = ../cpp/models
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -990,7 +990,7 @@ IGNORE_PREFIX          =
 # If the GENERATE_HTML tag is set to YES doxygen will generate HTML output
 # The default value is: YES.
 
-GENERATE_HTML          = YES
+GENERATE_HTML          = NO
 
 # The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of

diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# 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)
diff --git a/docs/make.bat b/docs/make.bat
@@ -0,0 +1,35 @@
+@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.http://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
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -0,0 +1,12 @@
+sphinx==7.1.2
+sphinx-rtd-theme==1.3.0rc1
+furo
+sphinx-copybutton
+breathe
+sphinx-hoverxref
+pycode/memilio-epidata
+pycode/memilio-generation
+pycode/memilio-plot
+pycode/memilio-simulation
+pycode/memilio-surrogatemodel
+exhale
diff --git a/docs/source/_templates/autosummary/class.rst b/docs/source/_templates/autosummary/class.rst
@@ -0,0 +1,38 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+
+   {% block methods %}
+   {% if '__init__' in methods %}
+   .. automethod:: __init__
+      :noindex:
+   {% endif %}
+   {% if methods %}
+   .. rubric:: Methods Summary
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Attributes
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block methods_full %}
+   {% if methods %}
+   .. rubric:: Methods
+   {% for item in methods %}
+   .. automethod:: {{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
diff --git a/docs/source/_templates/autosummary/module.rst b/docs/source/_templates/autosummary/module.rst
@@ -0,0 +1,62 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+   :members:
+   :undoc-members:
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Module Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
diff --git a/docs/source/_templates/breadcrumbs.html b/docs/source/_templates/breadcrumbs.html
@@ -0,0 +1,13 @@
+{% extends "!breadcrumbs.html" %}
+{%- block breadcrumbs_aside %}
+<li class="wy-breadcrumbs-aside", style="margin-left: 20px;">
+    <a href="https://github.com/SciCompMod/memilio" target="_blank" aria-label="GitHub">
+        <svg height="24" width="24" viewBox="0 0 16 16" fill="currentColor" aria-hidden="true">
+            <path fill-rule="evenodd"
+                d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z">
+            </path>
+        </svg>
+    </a>
+</li>
+{{ super() }}
+{% endblock %}