small fixes (#11)

- use isinstance instead of type
- check shape of array in concentration heatmap image
- removed unused imports
- increase tolerance of minimize test

sme_contrib/plot.py

@@ -4,7 +4,6 @@
 from matplotlib import pyplot as plt
 from matplotlib.colors import LinearSegmentedColormap as lscmap
 from matplotlib import animation
-import sme
 
 
 def colormap(color, name="my colormap"):

sme_contrib/tests/test_optimize.py

@@ -46,8 +46,8 @@ def test_minimize() -> None:
         iterations=20,
         ps_options={"c1": 2.025, "c2": 2.025, "w": 0.5},
     )
-    assert np.abs(res[0] - 0.375) < 0.100
-    assert np.abs(res[1] + 0.900) < 0.100
+    assert np.abs(res[0] - 0.375) < 0.200
+    assert np.abs(res[1] + 0.900) < 0.200
 
 
 def test_rescale() -> None:
@@ -97,21 +97,21 @@ def test_steady_state() -> None:
 
     # just check plots have correct titles for now
     ax = ss.plot_target_concentration()
-    assert type(ax) == matplotlib.axes._subplots.Subplot
+    assert isinstance(ax, matplotlib.axes._subplots.Subplot)
     assert ax.get_title() == "Target Concentration"
 
     ax = ss.plot_model_concentration()
-    assert type(ax) == matplotlib.axes._subplots.Subplot
+    assert isinstance(ax, matplotlib.axes._subplots.Subplot)
     assert ax.get_title() == "Model Concentration"
 
     ax = ss.plot_cost_history()
-    assert type(ax) == matplotlib.axes._subplots.Subplot
+    assert isinstance(ax, matplotlib.axes._subplots.Subplot)
     assert ax.get_title() == "Best cost history"
 
     ax = ss.plot_cost_history_pbest()
-    assert type(ax) == matplotlib.axes._subplots.Subplot
+    assert isinstance(ax, matplotlib.axes._subplots.Subplot)
     assert ax.get_title() == "Mean particle best cost history"
 
     ax = ss.plot_timeseries(1, 1)
-    assert type(ax) == matplotlib.axes._subplots.Subplot
+    assert isinstance(ax, matplotlib.axes._subplots.Subplot)
     assert ax.get_title() == "Concentration time series"

sme_contrib/tests/test_plot.py

@@ -1,5 +1,4 @@
 import sme_contrib.plot as smeplot
-import numpy as np
 import sme
 import os.path
 
@@ -32,15 +31,21 @@ def test_concentration_heatmap() -> None:
     # single species
     ax, im = smeplot.concentration_heatmap(results[-1], ["A_nucl"])
     assert ax.title.get_text() == "Concentration of A_nucl at time 10.0"
+    assert im.get_array().shape == (100, 100)
+    assert im.get_array()[0, 0] == 0.0
     # two species
     ax, im = smeplot.concentration_heatmap(results[-1], ["A_nucl", "A_cell"])
     assert ax.title.get_text() == "Concentration of A_nucl, A_cell at time 10.0"
+    assert im.get_array().shape == (100, 100)
+    assert im.get_array()[0, 0] == 0.0
     # specify title, existing plot axis & colormap
     colormap = smeplot.colormap((1, 0, 0), "red1")
     ax, im = smeplot.concentration_heatmap(
         results[-1], ["A_nucl", "A_cell"], "my Title", ax, colormap
     )
     assert ax.title.get_text() == "my Title"
+    assert im.get_array().shape == (100, 100)
+    assert im.get_array()[0, 0] == 0.0
 
 
 def test_concentration_heatmap_animation() -> None: