#923 merge develop

CHANGELOG.md

@@ -1,4 +1,17 @@
-# [Unreleased](https://github.com/pybamm-team/PyBaMM)
+# [Unreleased](https://github.com/pybamm-team/PyBaMM/)
+
+## Optimizations
+
+-   Sped up model building ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
+-   Changed default solver for lead-acid to `CasadiSolver` ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
+
+## Bug fixes
+
+-   Reformatted electrolyte submodels ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
+
+# [v0.2.1](https://github.com/pybamm-team/PyBaMM/tree/v0.2.1) - 2020-03-31
+
+New expression tree node types, models, parameter sets and solvers, as well as general bug fixes and new examples.
 
 ## Features
 
@@ -9,9 +22,6 @@
 -   Added functionality to broadcast to edges ([#891](https://github.com/pybamm-team/PyBaMM/pull/891))
 -   Reformatted and cleaned up `QuickPlot` ([#886](https://github.com/pybamm-team/PyBaMM/pull/886))
 -   Added thermal effects to lead-acid models ([#885](https://github.com/pybamm-team/PyBaMM/pull/885))
--   Add new symbols `VariableDot`, representing the derivative of a variable wrt time,
-    and `StateVectorDot`, representing the derivative of a state vector wrt time
-    ([#858](https://github.com/pybamm-team/PyBaMM/issues/858))
 -   Added a helper function for info on function parameters ([#881](https://github.com/pybamm-team/PyBaMM/pull/881))
 -   Added additional notebooks showing how to create and compare models ([#877](https://github.com/pybamm-team/PyBaMM/pull/877))
 -   Added `Minimum`, `Maximum` and `Sign` operators
@@ -24,14 +34,9 @@
     and `StateVectorDot`, representing the derivative of a state vector wrt time
     ([#858](https://github.com/pybamm-team/PyBaMM/issues/858))
 
-## Optimizations
-
--   Sped up model building ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
--   Changed default solver for lead-acid to `CasadiSolver` ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
-
 ## Bug fixes
 
--   Reformatted electrolyte submodels ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
+-   Fixed tight layout for QuickPlot in jupyter notebooks ([#930](https://github.com/pybamm-team/PyBaMM/pull/930))
 -   Fixed bug raised if function returns a scalar ([#919](https://github.com/pybamm-team/PyBaMM/pull/919))
 -   Fixed event handling in `ScipySolver` ([#905](https://github.com/pybamm-team/PyBaMM/pull/905))
 -   Made input handling clearer in solvers ([#905](https://github.com/pybamm-team/PyBaMM/pull/905))

docs/conf.py

@@ -28,7 +28,7 @@
 # The short X.Y version
 version = "0.2"
 # The full version, including alpha/beta/rc tags
-release = "0.2.0"
+release = "0.2.1"
 
 
 # -- General configuration ---------------------------------------------------

pybamm/__init__.py

@@ -220,7 +220,7 @@ def version(formatted=False):
 # other
 #
 from .processed_variable import ProcessedVariable
-from .quick_plot import QuickPlot, ax_min, ax_max
+from .quick_plot import QuickPlot, dynamic_plot, ax_min, ax_max
 
 from .simulation import Simulation, load_sim, is_notebook
 

pybamm/quick_plot.py

@@ -3,7 +3,6 @@
 #
 import numpy as np
 import pybamm
-import warnings
 from collections import defaultdict
 
 
@@ -45,6 +44,24 @@ def split_long_string(title, max_words=4):
         return first_line + "\n" + second_line
 
 
+def dynamic_plot(*args, **kwargs):
+    """
+    Creates a :class:`pybamm.QuickPlot` object (with arguments 'args' and keyword
+    arguments 'kwargs') and then calls :meth:`pybamm.QuickPlot.dynamic_plot`.
+    The key-word argument 'testing' is passed to the 'dynamic_plot' method, not the
+    `QuickPlot' class.
+
+    Returns
+    -------
+    plot : :class:`pybamm.QuickPlot`
+        The 'QuickPlot' object that was created
+    """
+    kwargs_for_class = {k: v for k, v in kwargs.items() if k != "testing"}
+    plot = pybamm.QuickPlot(*args, **kwargs_for_class)
+    plot.dynamic_plot(kwargs.get("testing", False))
+    return plot
+
+
 class QuickPlot(object):
     """
     Generates a quick plot of a subset of key outputs of the model so that the model
@@ -615,6 +632,10 @@ def plot(self, t):
         if len(solution_handles) > 0:
             self.fig.legend(solution_handles, self.labels, loc="lower right")
 
+        # Fix layout
+        bottom = 0.05 + 0.03 * max((len(self.labels) - 2), 0)
+        self.gridspec.tight_layout(self.fig, rect=[0, bottom, 1, 1])
+
     def dynamic_plot(self, testing=False, step=None):
         """
         Generate a dynamic plot with a slider to control the time.
@@ -651,12 +672,6 @@ def dynamic_plot(self, testing=False, step=None):
             )
             self.slider.on_changed(self.slider_update)
 
-            # ignore the warning about tight layout
-            warnings.simplefilter("ignore")
-            bottom = 0.05 + 0.03 * max((len(self.labels) - 2), 0)
-            self.gridspec.tight_layout(self.fig, rect=[0, bottom, 1, 1])
-            warnings.simplefilter("always")
-
             if not testing:  # pragma: no cover
                 plt.show()
 

pybamm/simulation.py

@@ -46,13 +46,12 @@ class Simulation:
     ----------
     model : :class:`pybamm.BaseModel`
         The model to be simulated
-    experiment : : class:`pybamm.Experiment` (optional)
+    experiment : :class:`pybamm.Experiment` (optional)
         The experimental conditions under which to solve the model
     geometry: :class:`pybamm.Geometry` (optional)
         The geometry upon which to solve the model
-    parameter_values: dict (optional)
-        A dictionary of parameters and their corresponding numerical
-        values
+    parameter_values: :class:`pybamm.ParameterValues` (optional)
+        Parameters and their corresponding numerical values.
     submesh_types: dict (optional)
         A dictionary of the types of submesh to use on each subdomain
     var_pts: dict (optional)
@@ -533,9 +532,9 @@ def plot(self, quick_plot_vars=None, testing=False):
         if quick_plot_vars is None:
             quick_plot_vars = self.quick_plot_vars
 
-        plot = pybamm.QuickPlot(self._solution, output_variables=quick_plot_vars)
-
-        plot.dynamic_plot(testing=testing)
+        self.quick_plot = pybamm.dynamic_plot(
+            self._solution, output_variables=quick_plot_vars, testing=testing
+        )
 
     @property
     def model(self):

pybamm/solvers/solution.py

@@ -233,10 +233,10 @@ def save_data(self, filename, variables=None, to_format="pickle"):
             savemat(filename, data)
         elif to_format == "csv":
             for name, var in data.items():
-                if var.ndim == 2:
+                if var.ndim >= 2:
                     raise ValueError(
-                        "only 1D variables can be saved to csv, but '{}' is 2D".format(
-                            name
+                        "only 0D variables can be saved to csv, but '{}' is {}D".format(
+                            name, var.ndim - 1
                         )
                     )
             df = pd.DataFrame(data)

pybamm/version

@@ -1 +1 @@
-0, 2, 0
+0, 2, 1

tests/unit/test_solvers/test_solution.py

@@ -125,7 +125,7 @@ def test_save(self):
 
         # to csv
         with self.assertRaisesRegex(
-            ValueError, "only 1D variables can be saved to csv"
+            ValueError, "only 0D variables can be saved to csv"
         ):
             solution.save_data("test.csv", to_format="csv")
         # only save "c" and "2c"