Merge pull request #78 from ndukler/lapierre_qc

Lapierre qc

qc/e_coli_qc.py

@@ -0,0 +1,20 @@
+import msprime
+import numpy as np
+import math
+import stdpopsim.models as models
+
+class LapierreConstant(models.Model):
+    def __init__(self):
+        super().__init__()
+        # From paper https://doi.org/10.1093/molbev/msw048
+        # Ne taken from Table 2
+        Ne = 1.8e8
+
+        # Single pop with initial size Ne
+        self.population_configurations = [
+            msprime.PopulationConfiguration(initial_size=Ne),
+        ]
+        # No migration
+        self.migration_matrix = [[0]]
+        # No demographic events
+        self.demographic_events = []

tests/test_e_coli.py

@@ -0,0 +1,24 @@
+"""
+Tests for the e. coli data definitions.
+"""
+import unittest
+import io
+
+from stdpopsim import e_coli
+from qc import e_coli_qc
+
+
+class TestLapierreConstant(unittest.TestCase):
+    """
+    Basic tests for the LapierreConstant model.
+    """
+    def test_debug_runs(self):
+        model = e_coli.LapierreConstant()
+        output = io.StringIO()
+        model.debug(output)
+        s = output.getvalue()
+        self.assertGreater(len(s), 0)
+
+    def test_qc_model_equal(self):
+        model = e_coli.LapierreConstant()
+        self.assertTrue(model.equals(e_coli_qc.LapierreConstant()))