change numpy representations just within the test

instead of setting an environment-specific number representation within
numpy, this commit sets the number representation per test case and with
a suggestion on how to change it once numpy>=2.0 is the minimal
requirement.

navis/core/base.py

@@ -608,7 +608,12 @@ def convert_units(
 
         Examples
         --------
+        (Set up numpy number representation within the test, see NEP51.
+        Once numpy<=2 is dropped from requirements, the doctest comparissons
+        should become `np.float32(266476.88)` instead of `266476.8`)
         >>> import navis
+        >>> if int(np.version.version.split('.')[0])>=2:
+                np.set_printoptions(legacy="1.25")
         >>> n = navis.example_neurons(1)
         >>> n.units
         <Quantity(8, 'nanometer')>

navis/core/skeleton.py

@@ -1422,7 +1422,12 @@ def snap(self, locs, to='nodes'):
 
         Examples
         --------
+        (Set up numpy number representation within the test, see NEP51.
+        Once numpy<=2 is dropped from requirements, the doctest comparissons
+        should become `np.int32(1124)` instead of `1124`)
         >>> import navis
+        >>> if int(np.version.version.split('.')[0])>=2:
+                np.set_printoptions(legacy="1.25")
         >>> n = navis.example_neurons(1)
         >>> id, dist = n.snap([0, 0, 0])
         >>> id

navis/graph/graph_utils.py

@@ -1078,7 +1078,12 @@ def find_main_branchpoint(
 
     Examples
     --------
+    (Set up numpy number representation within the test, see NEP51.
+    Once numpy<=2 is dropped from requirements, the doctest comparissons
+    should become `np.int32(110)` instead of `110`)
     >>> import navis
+    >>> if int(np.version.version.split('.')[0])>=2:
+            np.set_printoptions(legacy="1.25")
     >>> n = navis.example_neurons(1)
     >>> navis.find_main_branchpoint(n, reroot_soma=True)
     110

navis/intersection/intersect.py

@@ -198,7 +198,14 @@ def in_volume(x: Union['core.NeuronObject', Sequence, pd.DataFrame],
     --------
     Prune neuron to volume
 
+    (Set up numpy number representation within the test, see NEP51.
+    Once numpy<=2 is dropped from requirements, the doctest comparissons
+    should become `array([False, False, False, ..., False, False, False], shape=(4465,))` 
+    instead of `array([False, False, False, ..., False, False, False])`)
+
     >>> import navis
+    >>> if int(np.version.version.split('.')[0])>=2:
+            np.set_printoptions(legacy="1.25")
     >>> n = navis.example_neurons(1)
     >>> lh = navis.example_volume('LH')
     >>> n_lh = navis.in_volume(n, lh, inplace=False)

navis/morpho/mmetrics.py

@@ -147,7 +147,13 @@ def strahler_index(
 
     Examples
     --------
+    (Set up numpy number representation within the test, see NEP51.
+    Once numpy<=2 is dropped from requirements, the doctest comparissons
+    should become `np.int16(6)` instead of `91234`)
+
     >>> import navis
+    >>> if int(np.version.version.split('.')[0])>=2:
+            np.set_printoptions(legacy="1.25")
     >>> n = navis.example_neurons(2, kind='skeleton')
     >>> n.reroot(n.soma, inplace=True)
     >>> _ = navis.strahler_index(n)
@@ -550,7 +556,13 @@ def arbor_segregation_index(x: "core.NeuronObject") -> "core.NeuronObject":
 
     Examples
     --------
+    (Set up numpy number representation within the test, see NEP51.
+    Once numpy<=2 is dropped from requirements, the doctest comparissons
+    should become `np.float64(0.277)` instead of `0.277`)
+
     >>> import navis
+    >>> if int(np.version.version.split('.')[0])>=2:
+            np.set_printoptions(legacy="1.25")
     >>> n = navis.example_neurons(1)
     >>> n.reroot(n.soma, inplace=True)
     >>> _ = navis.arbor_segregation_index(n)
@@ -699,7 +711,13 @@ def bending_flow(x: "core.NeuronObject") -> "core.NeuronObject":
 
     Examples
     --------
+    (Set up numpy number representation within the test, see NEP51.
+    Once numpy<=2 is dropped from requirements, the doctest comparissons
+    should become `np.int64(785645)` instead of `785645`)
+
     >>> import navis
+    >>> if int(np.version.version.split('.')[0])>=2:
+            np.set_printoptions(legacy="1.25")
     >>> n = navis.example_neurons(1)
     >>> n.reroot(n.soma, inplace=True)
     >>> _ = navis.bending_flow(n)
@@ -969,7 +987,13 @@ def synapse_flow_centrality(
 
     Examples
     --------
+    (Set up numpy number representation within the test, see NEP51.
+    Once numpy<=2 is dropped from requirements, the doctest comparissons
+    should become `np.int64(786969)` instead of `786969`)
+
     >>> import navis
+    >>> if int(np.version.version.split('.')[0])>=2:
+            np.set_printoptions(legacy="1.25")
     >>> n = navis.example_neurons(2)
     >>> n.reroot(n.soma, inplace=True)
     >>> _ = navis.synapse_flow_centrality(n)
@@ -1174,7 +1198,13 @@ def flow_centrality(x: "core.NeuronObject") -> "core.NeuronObject":
 
     Examples
     --------
+    (Set up numpy number representation within the test, see NEP51.
+    Once numpy<=2 is dropped from requirements, the doctest comparissons
+    should become `np.int64(91234)` instead of `91234`)
+
     >>> import navis
+    >>> if int(np.version.version.split('.')[0])>=2:
+            np.set_printoptions(legacy="1.25")
     >>> n = navis.example_neurons(2)
     >>> n.reroot(n.soma, inplace=True)
     >>> _ = navis.flow_centrality(n)
@@ -1326,7 +1356,7 @@ def tortuosity(
     should become `np.float64(1.074)` instead of `1.074`)
     >>> import navis
     >>> if int(np.version.version.split('.')[0])>=2:
-        np.set_printoptions(legacy="1.25")
+            np.set_printoptions(legacy="1.25")
     >>> n = navis.example_neurons(1)
     >>> # Calculate tortuosity as-is
     >>> T = navis.tortuosity(n)
@@ -1635,7 +1665,13 @@ def betweeness_centrality(
 
     Examples
     --------
+    (Set up numpy number representation within the test, see NEP51.
+    Once numpy<=2 is dropped from requirements, the doctest comparissons
+    should become `np.int64(436866)` instead of `436866`)
+
     >>> import navis
+    >>> if int(np.version.version.split('.')[0])>=2:
+            np.set_printoptions(legacy="1.25")
     >>> n = navis.example_neurons(2, kind='skeleton')
     >>> n.reroot(n.soma, inplace=True)
     >>> _ = navis.betweeness_centrality(n)

navis/nbl/utils.py

@@ -199,7 +199,12 @@ def update_scores(queries, targets, scores_ex, nblast_func, **kwargs):
 
     Mostly for testing but also illustrates the principle:
 
+    (Set up numpy number representation within the test, see NEP51.
+    Once numpy<=2 is dropped from requirements, the doctest comparissons
+    should become `np.True_` instead of `True`)
     >>> import navis
+    >>> if int(np.version.version.split('.')[0])>=2:
+            np.set_printoptions(legacy="1.25")
     >>> import numpy as np
     >>> nl = navis.example_neurons(n=5)
     >>> dp = navis.make_dotprops(nl, k=5) / 125