Resolve warnings #317 & and Fix Issue: #355

docs/source/ext/github_tools.py

@@ -42,6 +42,11 @@
 
 
 def fetch_url(url):
+    """This was pointed out as a Security issue in bandit.
+    please look at issue #355,
+    we fixed it, but the bandit warning might remain,
+    need to suppress it manually (just ignore it)
+    """
     req = Request(url)
     if GH_TOKEN:
         req.add_header('Authorization', 'token {0}'.format(GH_TOKEN))
@@ -50,6 +55,9 @@ def fetch_url(url):
         # url = Request(url,
         #               headers={'Accept': 'application/vnd.github.v3+json',
         #                        'User-agent': 'Defined'})
+        if not url.lower().startswith('http'):
+            msg = "Please make sure you use http/https connection"
+            raise ValueError(msg)
         f = urlopen(req)
     except Exception as e:
         print(e)

fury/tests/test_actors.py

@@ -950,7 +950,7 @@ def test_cones_vertices_faces(interactive=False):
     if interactive:
         window.show(scene, order_transparent=True)
     arr = window.snapshot(scene)
-    report = window.analyze_snapshot(arr, colors=[colors])
+    report = window.analyze_snapshot(arr, colors=colors)
     npt.assert_equal(report.objects, 3)
     scene.clear()
 

fury/tests/test_convert.py

@@ -0,0 +1,37 @@
+import os
+import pytest
+import numpy.testing as npt
+from tempfile import TemporaryDirectory
+from fury.io import load_image
+# Optional packages
+from fury.optpkg import optional_package
+matplotlib, have_matplotlib, _ = optional_package('matplotlib')
+
+if have_matplotlib:
+    import matplotlib.pyplot as plt
+    from fury.convert import matplotlib_figure_to_numpy
+
+
+@pytest.mark.skipif(not have_matplotlib, reason="Requires MatplotLib")
+def test_convert():
+    names = ['group_a', 'group_b', 'group_c']
+    values = [1, 10, 100]
+
+    fig = plt.figure(figsize=(9, 3))
+    plt.subplot(131)
+    plt.bar(names, values)
+    plt.subplot(132)
+    plt.scatter(names, values)
+    plt.subplot(133)
+    plt.plot(names, values)
+    plt.suptitle('Categorical Plotting')
+    arr2 = matplotlib_figure_to_numpy(fig, transparent=False,
+                                      flip_up_down=False)
+
+    with TemporaryDirectory() as tmpdir:
+        fname = os.path.join(tmpdir, 'tmp.png')
+        dpi = 100
+        fig.savefig(fname, transparent=False, bbox_inches='tight',
+                    pad_inches=0)
+        arr1 = load_image(fname)
+        npt.assert_array_equal(arr1, arr2)

fury/tests/test_utils.py

@@ -130,9 +130,9 @@ def trilinear_interp_numpy(input_array, indices):
     y_indices = indices[:, 1]
     z_indices = indices[:, 2]
 
-    x0 = x_indices.astype(np.integer)
-    y0 = y_indices.astype(np.integer)
-    z0 = z_indices.astype(np.integer)
+    x0 = x_indices.astype(int)
+    y0 = y_indices.astype(int)
+    z0 = z_indices.astype(int)
     x1 = x0 + 1
     y1 = y0 + 1
     z1 = z0 + 1

fury/window.py

@@ -1082,7 +1082,8 @@ def __str__(self):
         flags = [False] * len(colors)
         for (i, col) in enumerate(colors):
             # find if the current color exist in the array
-            flags[i] = np.any(np.any(np.all(im[..., :3] == col[:3], axis=-1)))
+            flags[i] = np.any(np.any(np.all(np.equal(im[..., :3], col[:3]),
+                                            axis=-1)))
 
         report.colors_found = flags