Merge pull request pybamm-team#4603 from kratman/rel/v24.11.1

Release v24.11.1

Author: kratman

CHANGELOG.md

@@ -1,5 +1,15 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+# [v24.11.1](https://github.com/pybamm-team/PyBaMM/tree/v24.11.1) - 2024-11-22
+
+## Features
+
+- Modified `quick_plot.plot` to accept a list of times and generate superimposed graphs for specified time points. ([#4529](https://github.com/pybamm-team/PyBaMM/pull/4529))
+
+## Bug Fixes
+
+- Added some dependencies which were left out of the `pyproject.toml` file ([#4602](https://github.com/pybamm-team/PyBaMM/pull/4602))
+
 # [v24.11.0](https://github.com/pybamm-team/PyBaMM/tree/v24.11.0) - 2024-11-20
 
 ## Features

CITATION.cff

@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "24.11.0"
+version: "24.11.1"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"

noxfile.py

@@ -252,9 +252,11 @@ def run_tests(session):
     set_environment_variables(PYBAMM_ENV, session=session)
     session.install("setuptools", silent=False)
     session.install("-e", ".[all,dev,jax]", silent=False)
-    specific_test_files = session.posargs if session.posargs else []
     session.run(
-        "python", "-m", "pytest", *specific_test_files, "-m", "unit or integration"
+        "python",
+        "-m",
+        "pytest",
+        *(session.posargs if session.posargs else ["-m", "unit or integration"]),
     )
 
 

pyproject.toml

@@ -13,7 +13,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pybamm"
-version = "24.11.0"
+version = "24.11.1"
 license = { file = "LICENSE.txt" }
 description = "Python Battery Mathematical Modelling"
 authors = [{name = "The PyBaMM Team", email = "[email protected]"}]
@@ -45,6 +45,8 @@ dependencies = [
     "pandas>=1.5.0",
     "pooch>=1.8.1",
     "posthog",
+    "pyyaml",
+    "platformdirs",
 ]
 
 [project.urls]

src/pybamm/plotting/quick_plot.py

@@ -1,6 +1,7 @@
 #
 # Class for quick plotting of variables from models
 #
+from __future__ import annotations
 import os
 import numpy as np
 import pybamm
@@ -479,24 +480,24 @@ def reset_axis(self):
             ):  # pragma: no cover
                 raise ValueError(f"Axis limits cannot be NaN for variables '{key}'")
 
-    def plot(self, t, dynamic=False):
+    def plot(self, t: float | list[float], dynamic: bool = False):
         """Produces a quick plot with the internal states at time t.
 
         Parameters
         ----------
-        t : float
-            Dimensional time (in 'time_units') at which to plot.
+        t : float or list of float
+            Dimensional time (in 'time_units') at which to plot. Can be a single time or a list of times.
         dynamic : bool, optional
             Determine whether to allocate space for a slider at the bottom of the plot when generating a dynamic plot.
             If True, creates a dynamic plot with a slider.
         """
 
         plt = import_optional_dependency("matplotlib.pyplot")
         gridspec = import_optional_dependency("matplotlib.gridspec")
-        cm = import_optional_dependency("matplotlib", "cm")
-        colors = import_optional_dependency("matplotlib", "colors")
 
-        t_in_seconds = t * self.time_scaling_factor
+        if not isinstance(t, list):
+            t = [t]
+
         self.fig = plt.figure(figsize=self.figsize)
 
         self.gridspec = gridspec.GridSpec(self.n_rows, self.n_cols)
@@ -508,6 +509,11 @@ def plot(self, t, dynamic=False):
         # initialize empty handles, to be created only if the appropriate plots are made
         solution_handles = []
 
+        # Generate distinct colors for each time point
+        time_colors = plt.cm.coolwarm(
+            np.linspace(0, 1, len(t))
+        )  # Use a colormap for distinct colors
+
         for k, (key, variable_lists) in enumerate(self.variables.items()):
             ax = self.fig.add_subplot(self.gridspec[k])
             self.axes.add(key, ax)
@@ -518,19 +524,17 @@ def plot(self, t, dynamic=False):
             ax.xaxis.set_major_locator(plt.MaxNLocator(3))
             self.plots[key] = defaultdict(dict)
             variable_handles = []
-            # Set labels for the first subplot only (avoid repetition)
+
             if variable_lists[0][0].dimensions == 0:
-                # 0D plot: plot as a function of time, indicating time t with a line
+                # 0D plot: plot as a function of time, indicating multiple times with lines
                 ax.set_xlabel(f"Time [{self.time_unit}]")
                 for i, variable_list in enumerate(variable_lists):
                     for j, variable in enumerate(variable_list):
-                        if len(variable_list) == 1:
-                            # single variable -> use linestyle to differentiate model
-                            linestyle = self.linestyles[i]
-                        else:
-                            # multiple variables -> use linestyle to differentiate
-                            # variables (color differentiates models)
-                            linestyle = self.linestyles[j]
+                        linestyle = (
+                            self.linestyles[i]
+                            if len(variable_list) == 1
+                            else self.linestyles[j]
+                        )
                         full_t = self.ts_seconds[i]
                         (self.plots[key][i][j],) = ax.plot(
                             full_t / self.time_scaling_factor,
@@ -542,128 +546,104 @@ def plot(self, t, dynamic=False):
                     solution_handles.append(self.plots[key][i][0])
                 y_min, y_max = ax.get_ylim()
                 ax.set_ylim(y_min, y_max)
-                (self.time_lines[key],) = ax.plot(
-                    [
-                        t_in_seconds / self.time_scaling_factor,
-                        t_in_seconds / self.time_scaling_factor,
-                    ],
-                    [y_min, y_max],
-                    "k--",
-                    lw=1.5,
-                )
+
+                # Add vertical lines for each time in the list, using different colors for each time
+                for idx, t_single in enumerate(t):
+                    t_in_seconds = t_single * self.time_scaling_factor
+                    (self.time_lines[key],) = ax.plot(
+                        [
+                            t_in_seconds / self.time_scaling_factor,
+                            t_in_seconds / self.time_scaling_factor,
+                        ],
+                        [y_min, y_max],
+                        "--",  # Dashed lines
+                        lw=1.5,
+                        color=time_colors[idx],  # Different color for each time
+                        label=f"t = {t_single:.2f} {self.time_unit}",
+                    )
+                ax.legend()
+
             elif variable_lists[0][0].dimensions == 1:
-                # 1D plot: plot as a function of x at time t
-                # Read dictionary of spatial variables
+                # 1D plot: plot as a function of x at different times
                 spatial_vars = self.spatial_variable_dict[key]
                 spatial_var_name = next(iter(spatial_vars.keys()))
-                ax.set_xlabel(
-                    f"{spatial_var_name} [{self.spatial_unit}]",
-                )
-                for i, variable_list in enumerate(variable_lists):
-                    for j, variable in enumerate(variable_list):
-                        if len(variable_list) == 1:
-                            # single variable -> use linestyle to differentiate model
-                            linestyle = self.linestyles[i]
-                        else:
-                            # multiple variables -> use linestyle to differentiate
-                            # variables (color differentiates models)
-                            linestyle = self.linestyles[j]
-                        (self.plots[key][i][j],) = ax.plot(
-                            self.first_spatial_variable[key],
-                            variable(t_in_seconds, **spatial_vars),
-                            color=self.colors[i],
-                            linestyle=linestyle,
-                            zorder=10,
-                        )
-                        variable_handles.append(self.plots[key][0][j])
-                    solution_handles.append(self.plots[key][i][0])
-                # add lines for boundaries between subdomains
-                for boundary in variable_lists[0][0].internal_boundaries:
-                    boundary_scaled = boundary * self.spatial_factor
-                    ax.axvline(boundary_scaled, color="0.5", lw=1, zorder=0)
+                ax.set_xlabel(f"{spatial_var_name} [{self.spatial_unit}]")
+
+                for idx, t_single in enumerate(t):
+                    t_in_seconds = t_single * self.time_scaling_factor
+
+                    for i, variable_list in enumerate(variable_lists):
+                        for j, variable in enumerate(variable_list):
+                            linestyle = (
+                                self.linestyles[i]
+                                if len(variable_list) == 1
+                                else self.linestyles[j]
+                            )
+                            (self.plots[key][i][j],) = ax.plot(
+                                self.first_spatial_variable[key],
+                                variable(t_in_seconds, **spatial_vars),
+                                color=time_colors[idx],  # Different color for each time
+                                linestyle=linestyle,
+                                label=f"t = {t_single:.2f} {self.time_unit}",  # Add time label
+                                zorder=10,
+                            )
+                            variable_handles.append(self.plots[key][0][j])
+                        solution_handles.append(self.plots[key][i][0])
+
+                # Add a legend to indicate which plot corresponds to which time
+                ax.legend()
+
             elif variable_lists[0][0].dimensions == 2:
-                # Read dictionary of spatial variables
+                # 2D plot: superimpose plots at different times
                 spatial_vars = self.spatial_variable_dict[key]
-                # there can only be one entry in the variable list
                 variable = variable_lists[0][0]
-                # different order based on whether the domains are x-r, x-z or y-z, etc
-                if self.x_first_and_y_second[key] is False:
-                    x_name = list(spatial_vars.keys())[1][0]
-                    y_name = next(iter(spatial_vars.keys()))[0]
-                    x = self.second_spatial_variable[key]
-                    y = self.first_spatial_variable[key]
-                    var = variable(t_in_seconds, **spatial_vars)
-                else:
-                    x_name = next(iter(spatial_vars.keys()))[0]
-                    y_name = list(spatial_vars.keys())[1][0]
+
+                for t_single in t:
+                    t_in_seconds = t_single * self.time_scaling_factor
                     x = self.first_spatial_variable[key]
                     y = self.second_spatial_variable[key]
                     var = variable(t_in_seconds, **spatial_vars).T
-                ax.set_xlabel(f"{x_name} [{self.spatial_unit}]")
-                ax.set_ylabel(f"{y_name} [{self.spatial_unit}]")
-                vmin, vmax = self.variable_limits[key]
-                # store the plot and the var data (for testing) as cant access
-                # z data from QuadMesh or QuadContourSet object
-                if self.is_y_z[key] is True:
-                    self.plots[key][0][0] = ax.pcolormesh(
-                        x,
-                        y,
-                        var,
-                        vmin=vmin,
-                        vmax=vmax,
-                        shading=self.shading,
+
+                    ax.set_xlabel(
+                        f"{next(iter(spatial_vars.keys()))[0]} [{self.spatial_unit}]"
                     )
-                else:
-                    self.plots[key][0][0] = ax.contourf(
-                        x, y, var, levels=100, vmin=vmin, vmax=vmax
+                    ax.set_ylabel(
+                        f"{list(spatial_vars.keys())[1][0]} [{self.spatial_unit}]"
                     )
-                self.plots[key][0][1] = var
-                if vmin is None and vmax is None:
-                    vmin = ax_min(var)
-                    vmax = ax_max(var)
-                self.colorbars[key] = self.fig.colorbar(
-                    cm.ScalarMappable(colors.Normalize(vmin=vmin, vmax=vmax)),
-                    ax=ax,
-                )
-            # Set either y label or legend entries
-            if len(key) == 1:
-                title = split_long_string(key[0])
-                ax.set_title(title, fontsize="medium")
-            else:
-                ax.legend(
-                    variable_handles,
-                    [split_long_string(s, 6) for s in key],
-                    bbox_to_anchor=(0.5, 1),
-                    loc="lower center",
-                )
+                    vmin, vmax = self.variable_limits[key]
+
+                    # Use contourf and colorbars to represent the values
+                    contour_plot = ax.contourf(
+                        x, y, var, levels=100, vmin=vmin, vmax=vmax, cmap="coolwarm"
+                    )
+                    self.plots[key][0][0] = contour_plot
+                    self.colorbars[key] = self.fig.colorbar(contour_plot, ax=ax)
 
-        # Set global legend
+                    self.plots[key][0][1] = var
+
+                    ax.set_title(f"t = {t_single:.2f} {self.time_unit}")
+
+        # Set global legend if there are multiple models
         if len(self.labels) > 1:
             fig_legend = self.fig.legend(
                 solution_handles, self.labels, loc="lower right"
             )
-            # Get the position of the top of the legend in relative figure units
-            # There may be a better way ...
-            try:
-                legend_top_inches = fig_legend.get_window_extent(
-                    renderer=self.fig.canvas.get_renderer()
-                ).get_points()[1, 1]
-                fig_height_inches = (self.fig.get_size_inches() * self.fig.dpi)[1]
-                legend_top = legend_top_inches / fig_height_inches
-            except AttributeError:  # pragma: no cover
-                # When testing the examples we set the matplotlib backend to "Template"
-                # which means that the above code doesn't work. Since this is just for
-                # that particular test we can just skip it
-                legend_top = 0
         else:
-            legend_top = 0
+            fig_legend = None
 
-        # Fix layout
+        # Fix layout for sliders if dynamic
         if dynamic:
             slider_top = 0.05
         else:
             slider_top = 0
-        bottom = max(legend_top, slider_top)
+        bottom = max(
+            fig_legend.get_window_extent(
+                renderer=self.fig.canvas.get_renderer()
+            ).get_points()[1, 1]
+            if fig_legend
+            else 0,
+            slider_top,
+        )
         self.gridspec.tight_layout(self.fig, rect=[0, bottom, 1, 1])
 
     def dynamic_plot(self, show_plot=True, step=None):

src/pybamm/version.py

@@ -1 +1 @@
-__version__ = "24.11.0"
+__version__ = "24.11.1"

tests/unit/test_plotting/test_quick_plot.py

@@ -252,6 +252,41 @@ def test_simple_ode_model(self, solver):
                 solution, ["a", "b broadcasted"], variable_limits="bad variable limits"
             )
 
+        # Test with a list of times
+        # Test for a 0D variable
+        quick_plot = pybamm.QuickPlot(solution, ["a"])
+        quick_plot.plot(t=[0, 1, 2])
+        assert len(quick_plot.plots[("a",)]) == 1
+
+        # Test for a 1D variable
+        quick_plot = pybamm.QuickPlot(solution, ["c broadcasted"])
+
+        time_list = [0.5, 1.5, 2.5]
+        quick_plot.plot(time_list)
+
+        ax = quick_plot.fig.axes[0]
+        lines = ax.get_lines()
+
+        variable_key = ("c broadcasted",)
+        if variable_key in quick_plot.variables:
+            num_variables = len(quick_plot.variables[variable_key][0])
+        else:
+            raise KeyError(
+                f"'{variable_key}' is not in quick_plot.variables. Available keys: "
+                + str(quick_plot.variables.keys())
+            )
+
+        expected_lines = len(time_list) * num_variables
+
+        assert (
+            len(lines) == expected_lines
+        ), f"Expected {expected_lines} superimposed lines, but got {len(lines)}"
+
+        # Test for a 2D variable
+        quick_plot = pybamm.QuickPlot(solution, ["2D variable"])
+        quick_plot.plot(t=[0, 1, 2])
+        assert len(quick_plot.plots[("2D variable",)]) == 1
+
         # Test errors
         with pytest.raises(ValueError, match="Mismatching variable domains"):
             pybamm.QuickPlot(solution, [["a", "b broadcasted"]])

vcpkg.json

@@ -1,6 +1,6 @@
 {
   "name": "pybamm",
-  "version-string": "24.11.0",
+  "version-string": "24.11.1",
   "dependencies": [
     "casadi",
     {