Merge branch 'master' of github.com:djgroen/facs

.coveragerc

@@ -0,0 +1,3 @@
+[report]
+exclude_lines =
+    if TYPE_CHECKING:

.github/workflows/pytest.yml

@@ -0,0 +1,24 @@
+name: Pytest
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements_serial.txt
+        pip install pytest
+    - name: Analysing the code with pytest
+      run: |
+        python -m pytest tests/

README.md

@@ -1,6 +1,6 @@
 # FACS: Flu And Coronavirus Simulator
 
-[![Build Status](https://travis-ci.com/djgroen/facs.svg?branch=master)](https://travis-ci.com/djgroen/facs)
+![Code Tests](https://github.com/djgroen/facs/actions/workflows/pytest.yml/badge.svg)
 [![GitHub Issues](https://img.shields.io/github/issues/djgroen/facs.svg)](https://github.com/djgroen/facs/issues)
 [![GitHub last-commit](https://img.shields.io/github/last-commit/djgroen/facs.svg)](https://github.com/djgroen/facs/commits/master)
 

covid_data/building_types_map.yml

@@ -3,18 +3,27 @@ park:
   labels:
   - park
   default_sqm: 20000
+  neighbours: 1
+  fixed: true
+  weighted: false
 
 hospital:
   index: 1
   labels:
   - hospital
   default_sqm: 1600
+  neighbours: 5
+  fixed: false
+  weighted: true
 
 supermarket:
   index: 2
   labels:
   - supermarket
   default_sqm: 400
+  neighbours: 10
+  fixed: false
+  weighted: false
 
 office:
   index: 3
@@ -27,6 +36,9 @@ office:
   - bank
   - service
   default_sqm: 1600
+  neighbours: 50
+  fixed: true
+  weighted: false
 
 school:
   index: 4
@@ -35,6 +47,9 @@ school:
   - university
   - college
   default_sqm: 1600
+  neighbours: 5
+  fixed: true
+  weighted: false
 
 leisure:
   index: 5
@@ -54,6 +69,9 @@ leisure:
   - library
   - community_centre
   default_sqm: 400
+  neighbours: 10
+  fixed: false
+  weighted: false
 
 shopping:
   index: 6
@@ -69,3 +87,6 @@ shopping:
   - shops
   - retail
   default_sqm: 200
+  neighbours: 10
+  fixed: false
+  weighted: false

covid_data/disease_measles.yml

@@ -0,0 +1,40 @@
+name: Measles
+infection_rate: 0.1
+mortality:
+  - [4.5, 0.001]     # Mortality rate for children under 5 years old
+  - [14.5, 0.02]     # Mortality rate for children aged 5-14 years
+  - [24.5, 0.1]      # Mortality rate for individuals aged 15-24 years
+  - [34.5, 0.3]      # Mortality rate for individuals aged 25-34 years
+  - [44.5, 0.5]      # Mortality rate for individuals aged 35-44 years
+  - [54.5, 1.0]      # Mortality rate for individuals aged 45-54 years
+  - [64.5, 5.0]      # Mortality rate for individuals aged 55-64 years
+  - [74.5, 10.0]     # Mortality rate for individuals aged 65-74 years
+  - [84.5, 20.0]     # Mortality rate for individuals aged 75-84 years
+  - [999, 50.0]      # Mortality rate for individuals aged 85 and older
+
+hospitalised:
+  - [4.5, 0.01]     # Hospitalisation rate for children under 5 years old
+  - [14.5, 0.02]    # Hospitalisation rate for children aged 5-14 years
+  - [24.5, 0.03]    # Hospitalisation rate for individuals aged 15-24 years
+  - [34.5, 0.04]    # Hospitalisation rate for individuals aged 25-34 years
+  - [44.5, 0.05]    # Hospitalisation rate for individuals aged 35-44 years
+  - [54.5, 0.06]    # Hospitalisation rate for individuals aged 45-54 years
+  - [64.5, 0.08]    # Hospitalisation rate for individuals aged 55-64 yearsgit
+  - [74.5, 0.1]     # Hospitalisation rate for individuals aged 65-74 years
+  - [84.5, 0.15]    # Hospitalisation rate for individuals aged 75-84 years
+  - [999, 0.2]      # Hospitalisation rate for individuals aged 85 and older
+
+mortality_period: 7.0           # Measles mortality typically occurs 7 to 10 days after symptom onset due to complications like pneumonia or encephalitis.
+recovery_period: 21.0           # Measles recovery lasts about 2 to 3 weeks from symptom onset as individuals gradually recover.
+mild_recovery_period: 14.0      # Mild measles cases may have a shorter recovery period, typically 1 to 2 weeks.
+incubation_period: 10.0         # Measles' incubation period, from virus exposure to symptom onset, is around 10 to 14 days (range: 7 to 21 days).
+period_to_hospitalisation: 7.0  # The time to hospitalisation varies; severe cases may require it within days, while mild cases may not need hospitalisation.  
+immunity_duration: 9125.0       # Natural immunity after measles recovery is usually lifelong, but waning immunity can occur over decades. MMR vaccination provides long-lasting immunity, often for life.
+genotypes:
+  D4:
+    infection_rate: 0.12
+  B3:
+    infection_rate: 0.15
+  H1:
+    infection_rate: 0.19
+

covid_data/vaccinations.yml

@@ -1,6 +1,7 @@
 date_format: "%d/%m/%Y"
 vaccine_effect_time: 21 # time between receiving vaccine and immunity conferred in days.
 vaccine_immunity_duration: 287 # average time that vaccines give immunity to persons.
+antivax_fraction: 0.05
 
 1/12/2020:
   vaccines_per_day: 500 # Total no. of vaccines handed out daily.

facs/base/disease.py

@@ -1,7 +1,10 @@
 """Module for Disease class."""
 
 import sys
+import warnings
 from dataclasses import dataclass, field
+
+
 from .utils import get_interpolated_lists
 
 AGE_CLASSES = 91
@@ -24,19 +27,91 @@ class Disease:
     hospital: list[float] = field(default_factory=list, init=False, repr=False)
     mortality: list[float] = field(default_factory=list, init=False, repr=False)
     mutations: dict[str, dict] = field(default_factory=list, init=False, repr=False)
+    genotypes: dict[str, dict] = field(default_factory=list, init=False, repr=False)
+
+    def __post_init__(self):
+        """Ensure that all the parameters are positive floats."""
+
+        positive_attributes = [
+            "infection_rate",
+            "incubation_period",
+            "mild_recovery_period",
+            "recovery_period",
+            "mortality_period",
+            "period_to_hospitalisation",
+            "immunity_duration",
+        ]
+
+        for attr in positive_attributes:
+            if not isinstance(getattr(self, attr), float) and not isinstance(
+                getattr(self, attr), int
+            ):
+                raise TypeError(f"{attr} must be int or float")
+
+            if getattr(self, attr) < 0:
+                raise ValueError(f"{attr} must not be negative")
+
+            if getattr(self, attr) == 0:
+                warnings.warn(f"{attr} is zero", RuntimeWarning)
+
+    def array_sanity_check(self, array: list[list[float]], name: str):
+        """Sanity check for Hospitalisation and Mortality parameters."""
+
+        for item in array:
+            if len(item) != 2:
+                raise ValueError(f"{name} chances must be a list of pairs")
+
+        ages = [item[0] for item in array]
+        probs = [item[1] for item in array]
+
+        if ages != sorted(ages):
+            raise ValueError(f"{name} chances must be sorted by age")
+
+        if min(ages) < 0 or max(ages) > AGE_CLASSES - 1:
+            raise ValueError(f"{name} chances must be between 0 and {AGE_CLASSES - 1}")
+
+        if len(ages) != len(set(ages)):
+            raise ValueError(f"{name} chances must be unique for each age")
+
+        if min(probs) < 0 or max(probs) > 1:
+            raise ValueError(f"{name} chances must be between 0 and 1")
+
+    def dict_sanity_check(self, dictionary: dict[str, dict], name: str):
+        """Sanity check for mutations and genotypes parameters."""
+
+        for key in dictionary:
+            if not isinstance(dictionary[key], dict):
+                raise TypeError(f"{name} must be a dictionary of dictionaries")
+
+            if not isinstance(key, str):
+                raise TypeError(f"{name} key must be string")
 
     def add_hospitalisation_chances(self, hosp_array: list[list[float]]):
         """Add age-dependent hospitalisation chances."""
 
+        self.array_sanity_check(hosp_array, "Hospitalisation")
+
         self.hospital = get_interpolated_lists(AGE_CLASSES, hosp_array)
 
     def add_mortality_chances(self, mort_array: list[list[float]]):
         """Add age-dependent mortality chances."""
 
+        self.array_sanity_check(mort_array, "Mortality")
+
         self.mortality = get_interpolated_lists(AGE_CLASSES, mort_array)
 
     def add_mutations(self, mutations: dict[str, dict]):
         """Add mutations."""
 
+        self.dict_sanity_check(mutations, "Mutations")
+
         print("Loading mutations:", mutations, file=sys.stderr)
         self.mutations = mutations
+
+    def add_genotypes(self, genotypes: dict[str, dict]):
+        """Add genotype with its parameters."""
+
+        self.dict_sanity_check(genotypes, "Genotypes")
+
+        print("Loading genotypes:", genotypes, file=sys.stderr)
+        self.genotypes = genotypes

facs/base/facs.py

@@ -337,14 +337,15 @@ def update_nearest_locations(self, dump_and_exit=False):
             print(",".join(f"{x}" for x in building_types), file=f)
 
         count = 0
+        print("Updating nearest locations...", file=sys.stderr)
         for h in self.houses:
             ni = h.find_nearest_locations(self)
             if dump_and_exit == True:
                 print(",".join(f"{x}" for x in ni), file=f)
             count += 1
             if count % 1000 == 0:
-                print(count, "houses scanned.", file=sys.stderr)
-        print(count, "houses scanned.", file=sys.stderr)
+                print(f"{count} houses scanned.", file=sys.stderr, end="\r")
+        print(f"Total {count} houses scanned.", file=sys.stderr)
 
         print(dump_and_exit)
 
@@ -478,7 +479,7 @@ def evolve(self, reduce_stochasticity=False):
             h = self.houses[i]
             for hh in h.households:
                 for a in hh.agents:
-                    a.plan_visits(self, reduce_stochasticity)
+                    a.plan_visits(self)
                     a.progress_condition(self, self.time, self.disease)
 
                     if (