Update .flake8 config to reflect 5 -> 6 update

.flake8

@@ -1,11 +1,17 @@
 [flake8]
 ignore =
-    E121, E123, E133, E226, E24, ; default
-    E231, ; sometimes no whitespace between commas is clearer
-    W503, ; W503 conflicts with W504 standard
-    E402, ; must define path before some local imports
-    E741, ; ignoring ambiguous variable name 'l'
-    E743, ; ignoring ambiguous function name 'I'
+    ; default
+    E121, E123, E133, E226, E24,
+    ; sometimes no whitespace between commas is clearer
+    E231,
+    ; W503 conflicts with W504 standard
+    W503,
+    ; must define path before some local imports
+    E402,
+    ; ignoring ambiguous variable name 'l'
+    E741,
+    ; ignoring ambiguous function name 'I'
+    E743,
 max-line-length = 79
 per-file-ignores =
     simpar/__init__.py:F401

simpar/groups.py

@@ -62,8 +62,8 @@ def infection_matrix(self, infections_per_contact_unit: float):
     def outside_rate(self, outside_rate: float):
         """Return the outside rate."""
         # Outside rate assumes well-mixed with external population
-        return outside_rate * (self.pop * self.contact_units /
-                               np.sum(self.pop * self.contact_units))
+        return outside_rate * (self.pop * self.contact_units
+                               / np.sum(self.pop * self.contact_units))
 
     def get_init_SIR_and_DH(self, init_infections: float,
                             init_recovered: float,

simpar/sim.py

@@ -212,7 +212,7 @@ def step(self, n: int = 1, infection_rate: np.ndarray = None,
             outside_rate (np.ndarray): infections per time period, weighed by \
                 population of each group in a meta-group.
         """
-        assert(n >= 1)
+        assert (n >= 1)
         if n > 1:
             for _ in range(n):
                 self.step(infection_rate=infection_rate,
@@ -241,7 +241,7 @@ def step(self, n: int = 1, infection_rate: np.ndarray = None,
 
         t = self._t
 
-        assert(t < self.max_T)  # enforce max generation
+        assert (t < self.max_T)  # enforce max generation
 
         # Fraction susceptible in each group
         # self._S[t] / (self._S[t] + self._I[t] + self._R[t])

simpar/strategy.py

@@ -303,7 +303,7 @@ def from_dictionary(d: Dict, arrival_testing_regimes: Dict,
             arrival_regime = arrival_testing_regimes[arrival_regime]
         isolation_regime = d.get("isolation_regime", None)
         if isolation_regime is not None:
-            if type(isolation_regime) == str:
+            if isolation_regime is str:
                 isolation_regime = isolation_regimes[isolation_regime]
             else:
                 isolation_regime = \

simpar/tests/test_groups.py

@@ -48,4 +48,4 @@ def test_sim8():
     s.step(T)
 
     inf_2 = sim.I
-    assert(np.isclose(inf_1, inf_2).all())
+    assert (np.isclose(inf_1, inf_2).all())