format

Author: nrnhines

share/lib/python/neuron/rxd/geometry.py

@@ -62,10 +62,7 @@ def _volumes1d(sec: Union[nrn.Section, "rxdsection.RxDSection"]) -> numpy.ndarra
             diam0, diam1 = diams[i : i + 2]
             pt0, pt1 = pts[i : i + 2]
             volume += (
-                numpy.pi
-                * (pt1 - pt0)
-                / 12.0
-                * (diam0**2 + diam0 * diam1 + diam1**2)
+                numpy.pi * (pt1 - pt0) / 12.0 * (diam0**2 + diam0 * diam1 + diam1**2)
             )
         vols[iseg] = volume
 

share/lib/python/neuron/rxd/multiCompartmentReaction.py

@@ -204,9 +204,7 @@ def _update_rates(self):
             msg = (
                 "sources and destinations"
                 if sources and dests
-                else "sources"
-                if sources
-                else "destinations"
+                else "sources" if sources else "destinations"
             )
             raise RxDException(
                 "Multicompartment reactions the membrane and %s must share common sections. %r"

share/lib/python/neuron/rxdtests/tests/hybrid/bistable_hybrid.py

@@ -28,10 +28,12 @@
 ca = rxd.Species(
     r,
     d=diff_constant,
-    initial=lambda node: 1
-    if (0.8 < node.x and node.segment in dend1)
-    or (node.x < 0.2 and node.segment in dend2)
-    else 0,
+    initial=lambda node: (
+        1
+        if (0.8 < node.x and node.segment in dend1)
+        or (node.x < 0.2 and node.segment in dend2)
+        else 0
+    ),
 )
 bistable_reaction = rxd.Rate(ca, -ca * (1 - ca) * (0.01 - ca))
 h.finitialize()

share/lib/python/neuron/rxdtests/tests/hybrid/bistable_hybrid_change_nthread.py

@@ -28,10 +28,12 @@
 ca = rxd.Species(
     r,
     d=diff_constant,
-    initial=lambda node: 1
-    if (0.8 < node.x and node.segment in dend1)
-    or (node.x < 0.2 and node.segment in dend2)
-    else 0,
+    initial=lambda node: (
+        1
+        if (0.8 < node.x and node.segment in dend1)
+        or (node.x < 0.2 and node.segment in dend2)
+        else 0
+    ),
 )
 bistable_reaction = rxd.Rate(ca, -ca * (1 - ca) * (0.01 - ca))
 h.finitialize()

share/lib/python/neuron/rxdtests/tests/hybrid/bistable_hybrid_cvode.py

@@ -28,10 +28,12 @@
     r,
     d=diff_constant,
     atolscale=0.1,
-    initial=lambda node: 1
-    if (0.8 < node.x and node.segment in dend1)
-    or (node.x < 0.2 and node.segment in dend2)
-    else 0,
+    initial=lambda node: (
+        1
+        if (0.8 < node.x and node.segment in dend1)
+        or (node.x < 0.2 and node.segment in dend2)
+        else 0
+    ),
 )
 bistable_reaction = rxd.Rate(ca, -ca * (1 - ca) * (0.01 - ca))
 h.finitialize()

share/lib/python/neuron/rxdtests/tests/hybrid/bistable_hybrid_cvode_change_nthread.py

@@ -28,10 +28,12 @@
     r,
     d=diff_constant,
     atolscale=0.1,
-    initial=lambda node: 1
-    if (0.8 < node.x and node.segment in dend1)
-    or (node.x < 0.2 and node.segment in dend2)
-    else 0,
+    initial=lambda node: (
+        1
+        if (0.8 < node.x and node.segment in dend1)
+        or (node.x < 0.2 and node.segment in dend2)
+        else 0
+    ),
 )
 bistable_reaction = rxd.Rate(ca, -ca * (1 - ca) * (0.01 - ca))
 h.finitialize()

share/lib/python/neuron/rxdtests/tests/hybrid/pure_diffusion_hybrid.py

@@ -34,10 +34,12 @@
 ca = rxd.Species(
     r,
     d=diff_constant,
-    initial=lambda node: 1
-    if (0.8 < node.x and node.segment in dend1)
-    or (node.x < 0.2 and node.segment in dend2)
-    else 0,
+    initial=lambda node: (
+        1
+        if (0.8 < node.x and node.segment in dend1)
+        or (node.x < 0.2 and node.segment in dend2)
+        else 0
+    ),
 )
 h.finitialize()
 initial_amount = (

share/lib/python/neuron/rxdtests/tests/hybrid/pure_diffusion_hybrid_cvode.py

@@ -34,10 +34,12 @@
 ca = rxd.Species(
     r,
     d=diff_constant,
-    initial=lambda node: 1
-    if (0.8 < node.x and node.segment in dend1)
-    or (node.x < 0.2 and node.segment in dend2)
-    else 0,
+    initial=lambda node: (
+        1
+        if (0.8 < node.x and node.segment in dend1)
+        or (node.x < 0.2 and node.segment in dend2)
+        else 0
+    ),
 )
 h.finitialize()
 initial_amount = (

share/lib/python/neuron/tests/test_all.py

@@ -4,7 +4,6 @@
 $Id$
 """
 
-
 # import your specific test here
 # and add it to the "suite" function below
 from neuron.tests import test_vector, test_neuron

share/lib/python/neuron/tests/test_rxd.py

@@ -98,9 +98,13 @@ def trivial_ecs(scale, lock, path=None):
         d=2.62,
         charge=1,
         atolscale=scale,
-        initial=lambda nd: 1.0
-        if abs(nd.x3d) <= L / 2.0 and abs(nd.y3d) <= L / 2.0 and abs(nd.z3d) <= L / 2.0
-        else 0.0,
+        initial=lambda nd: (
+            1.0
+            if abs(nd.x3d) <= L / 2.0
+            and abs(nd.y3d) <= L / 2.0
+            and abs(nd.z3d) <= L / 2.0
+            else 0.0
+        ),
     )
 
     # record the concentration at (0,0,0)