Merge pull request #176 from floesche/fix_numpy_doctest

Fix numpy doctest

.github/workflows/test-package.yml

@@ -58,4 +58,5 @@ jobs:
         with:
           run: |
             export NAVIS_HEADLESS=TRUE
+            export NAVIS_TEST_ENV=TRUE
             pytest --verbose

navis/config.py

@@ -59,6 +59,12 @@ def get_logger(name: str):
         return logging.getLogger(name)
     return logger
 
+# Set up numpy number representation, see NEP51
+# Once numpy<=2 is dropped from requirements, the doctest comparissons
+# should become `np.float64(1.074)` instead of `1.074`
+if os.environ.get('NAVIS_TEST_ENV', '').lower() == 'true':
+    import numpy as np
+    np.set_printoptions(legacy="1.25")
 
 # Default settings for progress bars
 pbar_hide = False

navis/morpho/mmetrics.py

@@ -30,6 +30,7 @@
 # Set up logging
 logger = config.get_logger(__name__)
 
+
 __all__ = sorted(
     [
         "strahler_index",

navis/plotting/plot_utils.py

@@ -190,7 +190,7 @@ def make_tube(segments, radii=1.0, tube_points=8, use_normals=True):
     faces :         np.ndarray
 
     """
-    vertices = np.empty((0, 3), dtype=np.float_)
+    vertices = np.empty((0, 3), dtype=np.float64)
     indices = np.empty((0, 3), dtype=np.uint32)
 
     if not isinstance(radii, Iterable):
@@ -219,7 +219,7 @@ def make_tube(segments, radii=1.0, tube_points=8, use_normals=True):
         # Vertices for each point on the circle
         verts = np.repeat(points, tube_points, axis=0)
 
-        v = np.arange(tube_points, dtype=np.float_) / tube_points * 2 * np.pi
+        v = np.arange(tube_points, dtype=np.float64) / tube_points * 2 * np.pi
 
         all_cx = (
             radius

pytest.ini

@@ -3,3 +3,4 @@ doctest_optionflags = IGNORE_EXCEPTION_DETAIL NUMBER NORMALIZE_WHITESPACE
 addopts = --doctest-modules
 env =
     NAVIS_HEADLESS=TRUE
+    NAVIS_TEST_ENV=TRUE