Next release

.github/workflows/build-test.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
         os: [ubuntu-latest, windows-latest, macos-latest]
     steps:
     - uses: actions/checkout@v4

.github/workflows/coverage.yml

@@ -14,9 +14,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.11" ]
+        python-version: [ "3.12" ]
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
     - name: "pip: Python ${{ matrix.python-version }} coverage"
       uses: actions/setup-python@v5
       with:
@@ -27,7 +29,7 @@ jobs:
         python -m pip install pybind11 pytest
     - name: Build
       run: |
-        CFLAGS=-coverage python -m pip install .
+        CXXFLAGS=-coverage python -m pip install .
     - name: Test
       run: |
         python -m pytest

.github/workflows/mpi-test.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.11"]
+        python-version: ["3.12"]
     steps:
       - uses: actions/checkout@v4
       - name: "pip: Python ${{ matrix.python-version }}"

codecov.yml

@@ -6,4 +6,4 @@ coverage:
         threshold: 1%  # leeway
     patch:
       default:
-        target: 80%
+        target: 75%

docs/custom_timeline.py

@@ -2,45 +2,46 @@
 
 
 class AsymptoticTimeline(neworder.Timeline):
-  def __init__(self) -> None:
-    super().__init__()
-    self.t = 1.0
+    def __init__(self) -> None:
+        super().__init__()
+        self.t = 1.0
 
-  @property
-  def start(self) -> float:
-    return 0.0
+    @property
+    def start(self) -> float:
+        return 0.0
 
-  @property
-  def end(self) -> float:
-    return 1.0
+    @property
+    def end(self) -> float:
+        return 1.0
 
-  @property
-  def nsteps(self) -> int:
-    return -1
+    @property
+    def nsteps(self) -> int:
+        return -1
 
-  @property
-  def time(self) -> float:
-    return 1.0 - self.t
+    @property
+    def time(self) -> float:
+        return 1.0 - self.t
 
-  @property
-  def dt(self) -> float:
-    return self.t / 2
+    @property
+    def dt(self) -> float:
+        return self.t / 2
 
-  def _next(self) -> None:
-    self.t /= 2
+    def _next(self) -> None:
+        self.t /= 2
 
-  @property
-  def at_end(self) -> bool:
-    return False
+    @property
+    def at_end(self) -> bool:
+        return False
 
 
 class Model(neworder.Model):
-  def __init__(self) -> None:
-    super().__init__(AsymptoticTimeline())
+    def __init__(self) -> None:
+        super().__init__(AsymptoticTimeline())
+
+    def step(self) -> None:
+        neworder.log(f"{self.timeline.index}: {self.timeline.time}")
+        if self.timeline.time > 0.99:
+            self.halt()
 
-  def step(self) -> None:
-    neworder.log(f"{self.timeline.index}: {self.timeline.time}")
-    if self.timeline.time > 0.99:
-      self.halt()
 
 neworder.run(Model())

docs/macros.py

@@ -19,7 +19,9 @@
 }
 
 # this is the overall record id, not a specific version
-_NEWORDER_ZENODO_ID = 4031821  # search using this (or DOI 10.5281/zenodo.4031821) just doesnt work
+_NEWORDER_ZENODO_ID = (
+    4031821  # search using this (or DOI 10.5281/zenodo.4031821) just doesnt work
+)
 
 
 @cache

examples/chapter1/model.py

@@ -3,6 +3,7 @@
 This is a direct neworder cover version of the Basic Cohort Model from the Belanger & Sabourin book
 See https://www.microsimulationandpopulationdynamics.com/
 """
+
 import numpy as np
 from person import People
 

examples/competing/model.py

@@ -1,6 +1,7 @@
 """
 Competing risks - fertility & mortality
 """
+
 # model implementation
 from people import People
 

examples/daisyworld/daisyworld.py

@@ -114,15 +114,15 @@ def __calc_local_heating(self) -> np.ndarray[np.float64, np.dtype[np.float64]]:
 
         # get absorbed luminosity from state
         def fs(
-            state: np.ndarray[np.int64, np.dtype[np.int64]]
+            state: np.ndarray[np.int64, np.dtype[np.int64]],
         ) -> np.ndarray[np.float64, np.dtype[np.float64]]:
             return (1.0 - self.albedo[state]) * solar_luminosity
 
         abs_lum = fs(self.domain.state)
 
         # get local heating from absorbed luminosity
         def fl(
-            lum: np.ndarray[np.float64, np.dtype[np.float64]]
+            lum: np.ndarray[np.float64, np.dtype[np.float64]],
         ) -> np.ndarray[np.float64, np.dtype[np.float64]]:
             return 72.0 * np.log(lum) + 80.0
 

examples/infection/run.py

@@ -19,5 +19,14 @@
 # probability of dying from infection at any point during the infection
 MORTALITY = 0.01
 
-m = Infection(POINT, RADIUS, NUM_AGENTS, NUM_INFECTED, SPEED, INFECTION_RADIUS, RECOVERY_TIME, MORTALITY)
+m = Infection(
+    POINT,
+    RADIUS,
+    NUM_AGENTS,
+    NUM_INFECTED,
+    SPEED,
+    INFECTION_RADIUS,
+    RECOVERY_TIME,
+    MORTALITY,
+)
 no.run(m)

examples/option/black_scholes.py

@@ -1,4 +1,4 @@
-""" Black-Scholes model implementations: analytic and MC """
+"""Black-Scholes model implementations: analytic and MC"""
 
 from typing import Any
 

examples/people/model.py

@@ -1,6 +1,7 @@
 """
 model.py: Population Microsimulation - births, deaths and migration by age, gender and ethnicity
 """
+
 import time
 from datetime import date
 

examples/people/population.py

@@ -1,5 +1,5 @@
 """
- population.py: Model implementation for population microsimulation
+population.py: Model implementation for population microsimulation
 """
 
 import os

examples/people/pyramid.py

@@ -1,4 +1,5 @@
-""" pyramid plots """
+"""pyramid plots"""
+
 from __future__ import annotations
 
 from typing import Any

examples/riskpaths/model.py

@@ -16,6 +16,7 @@
   available at www.statcan.gc.ca/microsimulation/modgen/modgen-eng.htm'
 
 """
+
 from riskpaths import RiskPaths
 from visualisation import plot