#759 fix tests, add some doctrings and fix flake8

Author: martinjrobins

pybamm/discretisations/discretisation.py

@@ -178,9 +178,9 @@ def process_model(self, model, inplace=True, check_model=True):
         for event in model.events:
             pybamm.logger.debug("Discretise event '{}'".format(event.name))
             processed_event = pybamm.Event(
-                    event.name,
-                    self.process_symbol(event.expression),
-                    event.event_type
+                event.name,
+                self.process_symbol(event.expression),
+                event.event_type
             )
             processed_events.append(processed_event)
         model_disc.events = processed_events

pybamm/models/event.py

@@ -1,10 +1,18 @@
-import pybamm
-
 from enum import Enum
 
 
 class EventType(Enum):
-    """Defines the type of event, see Event"""
+    """
+    Defines the type of event, see Event
+
+    TERMINATION indicates an event that will terminate the solver, the expression should
+    return 0 when the event is triggered
+
+    DISCONTINUITY indicates an expected discontinuity in the solution, the expression
+    should return the time that the discontinuity occurs. The solver will integrate up
+    to the discontinuity and then restart just after the discontinuity.
+
+    """
     TERMINATION = 0
     DISCONTINUITY = 1
 
@@ -20,7 +28,7 @@ class Event:
     name: str
         A string giving the name of the event
     event_type: EventType
-        An enum defining the type of event, see EventType
+        An enum defining the type of event
     expression: pybamm.Symbol
         An expression that defines when the event occurs
 

pybamm/models/full_battery_models/lithium_ion/basic_dfn.py

@@ -180,20 +180,16 @@ def __init__(self, name="Doyle-Fuller-Newman model"):
         self.initial_conditions[c_s_n] = param.c_n_init
         self.initial_conditions[c_s_p] = param.c_p_init
         # Events specify points at which a solution should terminate
-        self.events.update(
-            {
-                "Minimum negative particle surface concentration": (
-                    pybamm.min(c_s_surf_n) - 0.01
-                ),
-                "Maximum negative particle surface concentration": (1 - 0.01)
-                - pybamm.max(c_s_surf_n),
-                "Minimum positive particle surface concentration": (
-                    pybamm.min(c_s_surf_p) - 0.01
-                ),
-                "Maximum positive particle surface concentration": (1 - 0.01)
-                - pybamm.max(c_s_surf_p),
-            }
-        )
+        self.events += [
+            pybamm.Event("Minimum negative particle surface concentration",
+                         pybamm.min(c_s_surf_n) - 0.01),
+            pybamm.Event("Maximum negative particle surface concentration",
+                         (1 - 0.01) - pybamm.max(c_s_surf_n)),
+            pybamm.Event("Minimum positive particle surface concentration",
+                         pybamm.min(c_s_surf_p) - 0.01),
+            pybamm.Event("Maximum positive particle surface concentration",
+                         (1 - 0.01) - pybamm.max(c_s_surf_p)),
+        ]
         ######################
         # Current in the solid
         ######################
@@ -245,7 +241,8 @@ def __init__(self, name="Doyle-Fuller-Newman model"):
             "right": (pybamm.Scalar(0), "Neumann"),
         }
         self.initial_conditions[c_e] = param.c_e_init
-        self.events["Zero electrolyte concentration cut-off"] = pybamm.min(c_e) - 0.002
+        self.events.append(pybamm.Event("Zero electrolyte concentration cut-off",
+                                        pybamm.min(c_e) - 0.002))
 
         ######################
         # (Some) variables
@@ -263,8 +260,10 @@ def __init__(self, name="Doyle-Fuller-Newman model"):
             "Positive electrode potential": phi_s_p,
             "Terminal voltage": voltage,
         }
-        self.events["Minimum voltage"] = voltage - param.voltage_low_cut
-        self.events["Maximum voltage"] = voltage - param.voltage_high_cut
+        self.events += [
+            pybamm.Event("Minimum voltage", voltage - param.voltage_low_cut),
+            pybamm.Event("Maximum voltage", voltage - param.voltage_high_cut),
+        ]
 
     @property
     def default_geometry(self):

pybamm/models/full_battery_models/lithium_ion/basic_spm.py

@@ -97,20 +97,16 @@ def __init__(self, name="Single Particle Model"):
         c_s_surf_n = pybamm.surf(c_s_n)
         c_s_surf_p = pybamm.surf(c_s_p)
         # Events specify points at which a solution should terminate
-        self.events.update(
-            {
-                "Minimum negative particle surface concentration": (
-                    pybamm.min(c_s_surf_n) - 0.01
-                ),
-                "Maximum negative particle surface concentration": (1 - 0.01)
-                - pybamm.max(c_s_surf_n),
-                "Minimum positive particle surface concentration": (
-                    pybamm.min(c_s_surf_p) - 0.01
-                ),
-                "Maximum positive particle surface concentration": (1 - 0.01)
-                - pybamm.max(c_s_surf_p),
-            }
-        )
+        self.events += [
+            pybamm.Event("Minimum negative particle surface concentration",
+                         pybamm.min(c_s_surf_n) - 0.01),
+            pybamm.Event("Maximum negative particle surface concentration",
+                         (1 - 0.01) - pybamm.max(c_s_surf_n)),
+            pybamm.Event("Minimum positive particle surface concentration",
+                         pybamm.min(c_s_surf_p) - 0.01),
+            pybamm.Event("Maximum positive particle surface concentration",
+                         (1 - 0.01) - pybamm.max(c_s_surf_p)),
+        ]
 
         # Note that the SPM does not have any algebraic equations, so the `algebraic`
         # dictionary remains empty
@@ -164,8 +160,10 @@ def __init__(self, name="Single Particle Model"):
             ),
             "Terminal voltage": V,
         }
-        self.events["Minimum voltage"] = V - param.voltage_low_cut
-        self.events["Maximum voltage"] = V - param.voltage_high_cut
+        self.events += [
+            pybamm.Event("Minimum voltage", V - param.voltage_low_cut),
+            pybamm.Event("Maximum voltage", V - param.voltage_high_cut),
+        ]
 
     @property
     def default_geometry(self):

pybamm/solvers/base_solver.py

@@ -426,7 +426,8 @@ def solve(self, model, t_eval, external_variables=None, inputs=None):
 
         # Calculate discontinuities
         discontinuities = [
-            event.expression.evaluate(u=inputs) for event in model.discontinuity_events_eval
+            event.expression.evaluate(u=inputs)
+            for event in model.discontinuity_events_eval
         ]
 
         # make sure they are increasing in time
@@ -436,31 +437,33 @@ def solve(self, model, t_eval, external_variables=None, inputs=None):
         )
         # remove any identical discontinuities
         discontinuities = [
-                v for i, v in enumerate(discontinuities)
-                    if i==len(discontinuities)-1 or discontinuities[i] < discontinuities[i+1]
-                    ]
+            v for i, v in enumerate(discontinuities)
+            if i == len(discontinuities) - 1
+            or discontinuities[i] < discontinuities[i + 1]
+        ]
 
         # insert time points around discontinuities in t_eval
         # keep track of sub sections to integrate by storing start and end indices
         start_indices = [0]
         end_indices = []
         for dtime in discontinuities:
             dindex = np.searchsorted(t_eval, dtime, side='left')
-            end_indices.append(dindex+1)
-            start_indices.append(dindex+1)
+            end_indices.append(dindex + 1)
+            start_indices.append(dindex + 1)
             if t_eval[dindex] == dtime:
                 t_eval[dindex] += sys.float_info.epsilon
                 t_eval = np.insert(t_eval, dindex, dtime - sys.float_info.epsilon)
             else:
                 t_eval = np.insert(t_eval, dindex,
-                                   [dtime - sys.float_info.epsilon, dtime + sys.float_info.epsilon])
+                                   [dtime - sys.float_info.epsilon,
+                                    dtime + sys.float_info.epsilon])
         end_indices.append(len(t_eval))
 
         old_y0 = model.y0
         solution = None
         for start_index, end_index in zip(start_indices, end_indices):
             pybamm.logger.info("Calling solver for {} < t < {}"
-                               .format(t_eval[start_index], t_eval[end_index-1]))
+                               .format(t_eval[start_index], t_eval[end_index - 1]))
             timer.reset()
             if solution is None:
                 solution = self._integrate(
@@ -479,14 +482,15 @@ def solve(self, model, t_eval, external_variables=None, inputs=None):
                 # setup for next integration subsection
                 y0_guess = solution.y[:, -1]
                 if model.algebraic:
-                    model.y0 = self.calculate_consistent_state(model, t_eval[end_index], y0_guess)
+                    model.y0 = self.calculate_consistent_state(
+                        model, t_eval[end_index], y0_guess)
                 else:
                     model.y0 = y0_guess
 
                 last_state = solution.y[:, -1]
                 if len(model.algebraic) > 0:
                     model.y0 = self.calculate_consistent_state(
-                            model, t_eval[end_index], last_state)
+                        model, t_eval[end_index], last_state)
                 else:
                     model.y0 = last_state
 

pybamm/solvers/casadi_solver.py

@@ -104,7 +104,8 @@ def _integrate(self, model, t_eval, inputs=None):
         elif self.mode == "safe":
             # Step-and-check
             init_event_signs = np.sign(
-                np.concatenate([event(0, model.y0) for event in model.terminate_events_eval])
+                np.concatenate([event(0, model.y0)
+                                for event in model.terminate_events_eval])
             )
             pybamm.logger.info(
                 "Start solving {} with {} in 'safe' mode".format(model.name, self.name)

tests/unit/test_solvers/test_scikits_solvers.py

@@ -6,6 +6,7 @@
 import unittest
 import warnings
 from tests import get_mesh_for_testing, get_discretisation_for_testing
+import sys
 
 
 @unittest.skipIf(not pybamm.have_scikits_odes(), "scikits.odes not installed")