Main

docs/Makefile

@@ -4,9 +4,9 @@
 # You can set these variables from the command line, and also
 # from the environment for the first two.
 SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
-BUILDDIR      = _build
+SPHINXBUILD   ?= sphinx-build 
+SOURCEDIR     = source
+BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".
 help:

docs/make.bat

@@ -7,8 +7,8 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
-set SOURCEDIR=.
-set BUILDDIR=_build
+set SOURCEDIR=source
+set BUILDDIR=build
 
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (

docs/source/conf.py

@@ -0,0 +1,61 @@
+# 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, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+import epidemik
+
+project = 'epidemik'
+copyright = '2024, Bruno Gonçalves'
+author = 'Bruno Gonçalves'
+
+# The full version, including alpha/beta/rc tags
+release = epidemik.__version__ 
+
+
+# -- 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',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx_autodoc_typehints',
+]
+
+# 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 = []
+
+
+# -- 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 = 'sphinx_rtd_theme'
+
+# 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']

docs/index.rst → docs/source/index.rst

@@ -1,5 +1,5 @@
 .. epidemik documentation master file, created by
-   sphinx-quickstart on Mon Apr 15 09:20:13 2024.
+   sphinx-quickstart on Sun Mar 30 10:52:07 2025.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
@@ -10,7 +10,7 @@ Welcome to epidemik's documentation!
    :maxdepth: 2
    :caption: Contents:
 
-
+   modules
 
 Indices and tables
 ==================

docs/modules.rst → docs/source/modules.rst

@@ -1,5 +1,5 @@
-epidemik
-========
+src
+===
 
 .. toctree::
    :maxdepth: 4

models/SEIIR.yaml

@@ -0,0 +1,20 @@
+# Epidemic Model with 5 compartments and 6 transitions:
+Name: SEIIR
+
+Parameters:
+  rate : 0.166667
+  beta : 0.222222
+  epsilon_a : 0.160000
+  epsilon_s : 0.240000
+  mu : 0.100000
+
+
+Transitions:
+  - S + Ia = E rate
+  - S + Is = E beta
+  - E -> Ia epsilon_a
+  - E -> Is epsilon_s
+  - Ia -> R mu
+  - Is -> R mu
+
+# R0=2.00

models/SEIIRD.yaml

@@ -0,0 +1,23 @@
+# Epidemic Model with 6 compartments and 7 transitions:
+Name: SEIIRD
+
+Parameters:
+  rbeta : 0.166667
+  beta : 0.222222
+  epsilon_a : 0.160000
+  epsilon_s : 0.240000
+  mu : 0.100000
+  mu_nd : 0.090000
+  mu_d : 0.010000
+
+
+Transitions:
+  - S + Ia = E rbeta
+  - S + Is = E beta
+  - E -> Ia epsilon_a 
+  - E -> Is epsilon_s
+  - Ia -> R mu
+  - Is -> R mu_nd
+  - Is -> D mu_d
+
+# R0=2.00

models/SEIR.yaml

@@ -0,0 +1,15 @@
+# Epidemic Model with 4 compartments and 3 transitions:
+Name: SEIR
+
+Parameters:
+  beta : 0.200000
+  epsilon : 0.400000
+  mu : 0.100000
+
+
+Transitions:
+  - S + I = E beta
+  - E -> I epsilon 
+  - I -> R mu
+
+# R0=2.00

models/SEIRS.yaml

@@ -0,0 +1,15 @@
+# Epidemic Model with 4 compartments and 4 transitions:
+Name: SEIRS
+
+Parameters:
+  beta : 0.200000
+  epsilon : 0.400000
+  mu : 0.100000
+  rho : 0.300000
+
+
+Transitions:
+  - S + I = E beta
+  - E -> I epsilon 
+  - I -> R mu
+  - R -> S rho

models/SI.yaml

@@ -0,0 +1,8 @@
+# Epidemic Model with 2 compartments and 1 transitions:
+
+Parameters:
+  beta : 0.200000
+
+
+Transitions:
+  - S + I = I beta

models/model_list.txt

@@ -0,0 +1,6 @@
+SEIIR.yaml
+SEIIRD.yaml
+SEIR.yaml
+SEIRS.yaml
+SI.yaml
+SIR.yaml