lint: fix NPY002 for examples/models/sir/sir_python.py

Fixed NPY002 issues in SIR models implemented in examples/models/sir/sir_python.py.

Added tests to verify the new seed management works.

.gitignore

@@ -362,3 +362,5 @@ Java\ model/
 
 examples/output
 
+!tests/fixtures/data/test_sir_python.npy
+!tests/fixtures/data/test_sir_python_w_breaks_python.npy

examples/models/sir/sir_python.py

@@ -46,12 +46,10 @@ def SIR(theta: NDArray, N: int, seed: int | None) -> NDArray:  # noqa: N802, N80
     Returns:
         simulated series
     """
-    np.random.seed(seed=seed)
-
     num_agents = 100000
     g = nx.watts_strogatz_graph(num_agents, int(theta[0]), theta[1], seed=theta[5])
 
-    model = ep.SIRModel(g)
+    model = ep.SIRModel(g, seed=seed)
 
     cfg = ModelConfig.Configuration()
     cfg.add_model_parameter("beta", theta[3])  # infection rate
@@ -102,12 +100,10 @@ def SIR_w_breaks(  # noqa: N802
     Returns:
         simulated series
     """
-    np.random.seed(seed=seed)
-
     num_agents = 100000
     g = nx.watts_strogatz_graph(num_agents, int(theta[0]), theta[1], seed=theta[11])
 
-    model = ep.SIRModel(g)
+    model = ep.SIRModel(g, seed=seed)
 
     cfg = ModelConfig.Configuration()
     cfg.add_model_parameter("beta", theta[3])  # infection rate

tests/test_examples/test_sir_python.py

@@ -0,0 +1,96 @@
+# Black-box ABM Calibration Kit (Black-it)
+# Copyright (C) 2021-2023 Banca d'Italia
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+"""Test the SIR model implementation in Python."""
+
+import numpy as np
+import pytest
+
+try:
+    from examples.models.sir.sir_python import SIR, SIR_w_breaks
+except ModuleNotFoundError as e:
+    pytest.skip(
+        f"skipping tests for SIR python models, reason: {str(e)}",
+        allow_module_level=True,
+    )
+
+from tests.conftest import TEST_DIR
+
+
+def test_sir() -> None:
+    """Test the 'SIR' function in examples/models/sir/sir_python.py."""
+    expected_output = np.load(TEST_DIR / "fixtures" / "data" / "test_sir_python.npy")
+    model_seed = 0
+
+    lattice_order = 20
+    rewire_probability = 0.2
+    percentage_infected = 0.05
+    beta = 0.2
+    gamma = 0.15
+    networkx_seed = 0
+    theta = [
+        lattice_order,
+        rewire_probability,
+        percentage_infected,
+        beta,
+        gamma,
+        networkx_seed,
+    ]
+
+    n = 100
+    output = SIR(theta, n, seed=model_seed)
+
+    assert np.isclose(output, expected_output).all()
+
+
+def test_sir_w_breaks() -> None:
+    """Test the 'SIR_w_breaks' function in examples/models/sir/sir_python.py."""
+    expected_output = np.load(
+        TEST_DIR / "fixtures" / "data" / "test_sir_w_breaks_python.npy",
+    )
+    model_seed = 0
+
+    lattice_order = 20
+    rewire_probability = 0.2
+    percentage_infected = 0.05
+    beta_1 = 0.2
+    gamma_1 = 0.15
+    beta_2 = 0.3
+    beta_3 = 0.1
+    beta_4 = 0.01
+    t_break_1 = 10
+    t_break_2 = 20
+    t_break_3 = 30
+    networkx_seed = 0
+    theta = [
+        lattice_order,
+        rewire_probability,
+        percentage_infected,
+        beta_1,
+        gamma_1,
+        beta_2,
+        beta_3,
+        beta_4,
+        t_break_1,
+        t_break_2,
+        t_break_3,
+        networkx_seed,
+    ]
+
+    n = 100
+    output = SIR_w_breaks(theta, n, seed=model_seed)
+
+    assert np.isclose(output, expected_output).all()