updated tests

Author: KatyBrown

tests/helper_functions.py

@@ -1,7 +1,13 @@
 #!/usr/bin/env python3
 import numpy as np
 import matplotlib
+import matplotlib.pyplot as plt
 from PIL import Image
+matplotlib.use('Agg')
+plt.rcParams.update({
+    'font.family': 'DejaVu Sans',  # Or another reliable cross-platform font
+    'figure.dpi': 100              # Set a fixed DPI
+})
 
 
 def compare_images(f1, f2, tol):
@@ -10,8 +16,8 @@ def compare_images(f1, f2, tol):
 
     f1arr_sub = f1arr[500:1500, 500:1500, :]
     f2arr_sub = f2arr[500:1500, 500:1500, :]
-    im1 = Image.fromarray((f1arr_sub* 255).astype(np.uint8))
-    im2 = Image.fromarray((f2arr_sub* 255).astype(np.uint8))
+    im1 = Image.fromarray((f1arr_sub * 255).astype(np.uint8))
+    im2 = Image.fromarray((f2arr_sub * 255).astype(np.uint8))
     size1 = np.shape(f1arr)
     size2 = np.shape(f2arr)
     t1 = compare_floats(size1[0], size2[0])

tests/test_amend_tree.py

@@ -8,6 +8,14 @@
 import ete3
 import pickle
 import helper_functions
+import matplotlib
+matplotlib.use('Agg')
+
+
+plt.rcParams.update({
+    'font.family': 'DejaVu Sans',
+    'figure.dpi': 100              # Set a fixed DPI
+})
 
 
 @pytest.mark.parametrize(test_rev_align_vars,

tests/test_plot_phylo.py

@@ -7,7 +7,15 @@
                                   test_plot_phylo_nams)
 import os
 import shutil
-import helper_functions
+import matplotlib
+from matplotlib.testing.compare import compare_images
+matplotlib.use('Agg')
+
+
+plt.rcParams.update({
+    'font.family': 'DejaVu Sans',
+    'figure.dpi': 100              # Set a fixed DPI
+})
 
 
 # Tests all parameters with plot_phylo with three different trees
@@ -45,8 +53,6 @@ def test_plot_phylo_params(xpos,
 
     f = plt.figure(figsize=(10, 20))
     a = f.add_subplot(111)
-    a.set_xlim(-10, 20)
-    a.set_ylim(-1, ylim)
     plot_phylo.plot_phylo(tree=tree, ax=a,
                           xpos=xpos,
                           ypos=ypos,
@@ -80,14 +86,12 @@ def test_plot_phylo_params(xpos,
 
     exp = expected_figure.replace(".png", "_%s.png" % tree_stem)
     # Compare the Matplotlib figures as images
-    result, f1, f2 = helper_functions.compare_images(
-                            "test_temp/%s_%s.png" % (ID, tree_stem),
-                            exp, tol=1)
-    f1.save(f"test_temp/f1_{ID}_{tree_stem}_frag.png")
-    f2.save(f"test_temp/f2_{ID}_{tree_stem}_frag.png")
-    # shutil.rmtree("test_temp")
+    result = compare_images("test_temp/%s_%s.png" % (ID, tree_stem),
+                            exp, tol=0.01)
+
+    shutil.rmtree("test_temp")
     # Assert that the images are similar
-    assert result
+    assert result is None
 
 
 @pytest.mark.parametrize(test_plot_phylo_vars,
@@ -119,8 +123,6 @@ def test_bad_tree(xpos,
                   auto_ax):
     f = plt.figure(figsize=(10, 20))
     a = f.add_subplot(111)
-    a.set_xlim(-10, 20)
-    a.set_ylim(-1, ylim)
     with pytest.raises(RuntimeError,
                        match="Error in parsing Newick"):
         plot_phylo.plot_phylo(tree=tree, ax=a,