merge model support

Author: bmtgoncalves

.github/workflows/python-package.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v3
@@ -27,8 +27,8 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install flake8 pytest poetry
+        poetry install
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -37,4 +37,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest tests/test_*
+        poetry run pytest tests/test_*

docs/conf.py

@@ -0,0 +1,55 @@
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../src/epidemik/"))
+import epidemik
+
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "epidemik"
+copyright = "2024, Bruno Gonçalves"
+author = "Bruno Gonçalves"
+release = epidemik.__version__
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx_rtd_theme",
+    "sphinx.ext.duration",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
+html_theme_options = {
+    "analytics_id": "G-HKWS10TRJ1",
+    "analytics_anonymize_ip": False,
+    "logo_only": False,
+    "display_version": True,
+    "prev_next_buttons_location": "bottom",
+    "style_external_links": True,
+    "vcs_pageview_mode": "",
+    "style_nav_header_background": "white",
+    # Toc options
+    "collapse_navigation": True,
+    "sticky_navigation": True,
+    "navigation_depth": 4,
+    "includehidden": True,
+    "titles_only": False,
+}

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

poetry.lock

@@ -7,7 +7,7 @@ authors = [
 ]
 description = "A package to simulate compartmental epidemic models"
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: MIT License",
@@ -20,7 +20,9 @@ dependencies = [
  "pandas>=2.0",
  "scipy>=1.7",
  "tqdm>=4",
- "pyyaml (>=6.0.2,<7.0.0)"
+ "pyyaml (>=6.0.2,<7.0.0)",
+ "seaborn (>=0.13.2,<0.14.0)",
+ "scikit-learn (>=1.6.1,<2.0.0)",
 ]
 [project.urls]
 Homepage = "https://github.com/DataForScience/epidemik"
@@ -30,8 +32,12 @@ Documentation = "https://epidemik.readthedocs.io/"
 [tool.poetry-dynamic-versioning]
 enable = true
 
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.3.4"
+pytest-cov = "^6.0.0"
+
 [build-system]
-requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
+requires = ["poetry-core>=2.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
 build-backend = "poetry_dynamic_versioning.backend"
 
 [tool.poetry-dynamic-versioning.from-file]
@@ -40,4 +46,4 @@ source = "src/epidemik/__init__.py"
 [tool.pytest.ini_options]
 pythonpath = [
   ".", "src",
-]
+]