Merge pull request #944 from sadielbartholomew/test-skipping-post3.20

Test skipping based on module (esp. `healpix`) availability

Author: sadielbartholomew

.flake8

@@ -30,3 +30,7 @@ per-file-ignores =
     # https://stackoverflow.com/questions/59167405/)
     __init__.py: F401
     */__init__.py: F401
+    # Whole-module test skips (via setUp method) for these cases means exit
+    # before reach undefined vars where need given module for defining those.
+    # This is the cleanest way but sets off F821 code en-masse so ignore that.
+    cf/test/test_HEALPix_utils.py: F821

cf/test/test_Domain.py

@@ -1,6 +1,7 @@
 import datetime
 import re
 import unittest
+from importlib.util import find_spec
 
 import numpy as np
 
@@ -494,6 +495,9 @@ def test_Domain_cyclic_iscyclic(self):
         d2.cyclic("X", iscyclic=False)
         self.assertTrue(d2.iscyclic("X"))
 
+    # Note: here only need healpix for cf under-the-hood code, not in test
+    # directly, so no need to actually import healpix, just test it is there.
+    @unittest.skipUnless(find_spec("healpix"), "Requires 'healpix' package.")
     def test_Domain_create_healpix(self):
         """Test Domain.create_healpix."""
         d = cf.Domain.create_healpix(0)

cf/test/test_Field.py

@@ -16,6 +16,12 @@
 
 import cf
 
+healpix_available = False
+# Note: here only need healpix for cf under-the-hood code, not in test
+# directly, so no need to actually import healpix, just test it is there.
+if find_spec("healpix"):
+    healpix_available = True
+
 n_tmpfiles = 1
 tmpfiles = [
     tempfile.mkstemp("_test_Field.nc", dir=os.getcwd())[1]
@@ -3137,6 +3143,7 @@ def test_Field_to_units(self):
         with self.assertRaises(ValueError):
             g.to_units("degC")
 
+    @unittest.skipUnless(healpix_available, "Requires 'healpix' package.")
     def test_Field_healpix_change_indexing_scheme(self):
         """Test Field.healpix_change_indexing_scheme."""
         # HEALPix field
@@ -3236,6 +3243,7 @@ def test_Field_healpix_change_indexing_scheme(self):
         with self.assertRaises(ValueError):
             self.f0.healpix_change_indexing_scheme("ring")
 
+    @unittest.skipUnless(healpix_available, "Requires 'healpix' package.")
     def test_Field_healpix_to_ugrid(self):
         """Test Field.healpix_to_ugrid."""
         # HEALPix field
@@ -3276,6 +3284,7 @@ def test_Field_healpix_to_ugrid(self):
         with self.assertRaises(ValueError):
             self.f0.healpix_to_ugrid()
 
+    @unittest.skipUnless(healpix_available, "Requires 'healpix' package.")
     def test_Field_create_latlon_coordinates(self):
         """Test Field.create_latlon_coordinates."""
         # ------------------------------------------------------------
@@ -3334,6 +3343,7 @@ def test_Field_create_latlon_coordinates(self):
             self.assertTrue(mc[:16].equals(l2.auxiliary_coordinate(c)[:16]))
             self.assertTrue(mc[16:].equals(l1.auxiliary_coordinate(c)[4:]))
 
+    @unittest.skipUnless(healpix_available, "Requires 'healpix' package.")
     def test_Field_healpix_subspace(self):
         """Test Field.subspace for HEALPix grids"""
         f = self.f12
@@ -3369,6 +3379,7 @@ def test_Field_healpix_subspace(self):
             np.array_equal(g.coordinate("healpix_index"), [13, 12])
         )
 
+    @unittest.skipUnless(healpix_available, "Requires 'healpix' package.")
     def test_Field_healpix_decrease_refinement_level(self):
         """Test Field.healpix_decrease_refinement_level."""
         f = self.f12
@@ -3469,6 +3480,7 @@ def my_mean(a, axis=None):
         with self.assertRaises(ValueError):
             self.f0.healpix_decrease_refinement_level(0, "mean")
 
+    @unittest.skipUnless(healpix_available, "Requires 'healpix' package.")
     def test_Field_healpix_increase_refinement_level(self):
         """Test Field.healpix_increase_refinement_level."""
         f = self.f12

cf/test/test_HEALPix_utils.py

@@ -1,62 +1,78 @@
 import datetime
 import unittest
 
-import healpix
 import numpy as np
 
 import cf
 
-# Create matching lists of selected nested, ring, nuniq and zuniq
-# indices for every refinement level.
-indices = [
-    (r, i, healpix.nest2ring(healpix.order2nside(r), i))
-    for r in range(30)
-    for i in (0, 7, (12 * 4**r) - 1)
-]
-refinement_levels, nested_indices, ring_indices = map(list, zip(*indices))
-
-nuniq_indices = [
-    i + 4 ** (1 + r) for r, i in zip(refinement_levels, nested_indices)
-]
-
-zuniq_indices = [
-    (2 * i + 1) * 4 ** (29 - r)
-    for r, i in zip(refinement_levels, nested_indices)
-]
+healpix_imported = True
+try:
+    import healpix  # noqa: F401
+except ImportError:
+    healpix_imported = False
 
 
 class DataTest(unittest.TestCase):
     """Unit tests for HEALPix utilities."""
 
+    def setUp(self):
+        """Preparations called immediately before each test method."""
+        # Skip all if healpix module not available!
+        if not healpix_imported:
+            self.skipTest(
+                "Test module requires 'healpix' package. Install it to run all."
+            )
+
+        # Create matching lists of selected nested, ring, nuniq and zuniq
+        # indices for every refinement level.
+        indices = [
+            (r, i, healpix.nest2ring(healpix.order2nside(r), i))
+            for r in range(30)
+            for i in (0, 7, (12 * 4**r) - 1)
+        ]
+        self.refinement_levels, self.nested_indices, self.ring_indices = map(
+            list, zip(*indices)
+        )
+
+        self.nuniq_indices = [  # noqa: F841
+            i + 4 ** (1 + r)
+            for r, i in zip(self.refinement_levels, self.nested_indices)
+        ]
+
+        self.zuniq_indices = [  # noqa: F841
+            (2 * i + 1) * 4 ** (29 - r)
+            for r, i in zip(self.refinement_levels, self.nested_indices)
+        ]
+
     def test_HEALPix_uniq2zuniq(self):
         """Test _uniq2zuniq"""
         from cf.data.dask_utils_healpix import _uniq2zuniq
 
         self.assertTrue(
-            np.array_equal(_uniq2zuniq(nuniq_indices), zuniq_indices)
+            np.array_equal(_uniq2zuniq(self.nuniq_indices), self.zuniq_indices)
         )
 
     def test_HEALPix_zuniq2uniq(self):
         """Test _zuniq2uniq"""
         from cf.data.dask_utils_healpix import _zuniq2uniq
 
         self.assertTrue(
-            np.array_equal(_zuniq2uniq(zuniq_indices), nuniq_indices)
+            np.array_equal(_zuniq2uniq(self.zuniq_indices), self.nuniq_indices)
         )
 
     def test_HEALPix_zuniq2pix(self):
         """Test _zuniq2pix"""
         from cf.data.dask_utils_healpix import _zuniq2pix
 
         # nested
-        order, i = _zuniq2pix(zuniq_indices, nest=True)
+        order, i = _zuniq2pix(self.zuniq_indices, nest=True)
 
-        self.assertTrue(np.array_equal(order, refinement_levels))
-        self.assertTrue(np.array_equal(i, nested_indices))
+        self.assertTrue(np.array_equal(order, self.refinement_levels))
+        self.assertTrue(np.array_equal(i, self.nested_indices))
 
         # ring
         with self.assertRaises(NotImplementedError):
-            _zuniq2pix(zuniq_indices, nest=False)
+            _zuniq2pix(self.zuniq_indices, nest=False)
 
     def test_HEALPix_pix2zuniq(self):
         """Test _pix2zuniq"""
@@ -65,18 +81,18 @@ def test_HEALPix_pix2zuniq(self):
         # nested
         z = [
             _pix2zuniq(r, i, nest=True)
-            for r, i in zip(refinement_levels, nested_indices)
+            for r, i in zip(self.refinement_levels, self.nested_indices)
         ]
 
-        self.assertTrue(np.array_equal(z, zuniq_indices))
+        self.assertTrue(np.array_equal(z, self.zuniq_indices))
 
         # ring
         z = [
             _pix2zuniq(r, i, nest=False)
-            for r, i in zip(refinement_levels, ring_indices)
+            for r, i in zip(self.refinement_levels, self.ring_indices)
         ]
 
-        self.assertTrue(np.array_equal(z, zuniq_indices))
+        self.assertTrue(np.array_equal(z, self.zuniq_indices))
 
 
 if __name__ == "__main__":

cf/test/test_RegridOperator.py

@@ -19,11 +19,16 @@
 class RegridOperatorTest(unittest.TestCase):
 
     def setUp(self):
-        src = cf.example_field(0)
-        dst = cf.example_field(1)
-        self.r = src.regrids(dst, "linear", return_operator=True)
+        # Skip all if espmy module not available!
+        if not esmpy_imported:
+            self.skipTest(
+                "Test module requires 'esmpy' package. Install it to run all."
+            )
+        else:
+            src = cf.example_field(0)
+            dst = cf.example_field(1)
+            self.r = src.regrids(dst, "linear", return_operator=True)
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_RegridOperator_attributes(self):
         self.assertEqual(self.r.coord_sys, "spherical")
         self.assertEqual(self.r.method, "linear")
@@ -51,7 +56,6 @@ def test_RegridOperator_attributes(self):
         self.assertIsNone(self.r.dst_z)
         self.assertFalse(self.r.ln_z)
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_RegridOperator_copy(self):
         self.assertIsInstance(self.r.copy(), self.r.__class__)
 

cf/test/test_collapse.py

@@ -4,6 +4,7 @@
 import os
 import tempfile
 import unittest
+from importlib.util import find_spec
 
 import numpy as np
 
@@ -825,6 +826,9 @@ def test_Field_collapse_ugrid(self):
         # Check the collpsed fields writes
         cf.write(f, tmpfile)
 
+    # Note: here only need healpix for cf under-the-hood code, not in test
+    # directly, so no need to actually import healpix, just test it is there.
+    @unittest.skipUnless(find_spec("healpix"), "Requires 'healpix' package.")
     def test_Field_collapse_HEALPix(self):
         """Test HEALPix collapses."""
         f0 = cf.example_field(12)

cf/test/test_functions.py

@@ -4,6 +4,7 @@
 import platform
 import sys
 import unittest
+from importlib.util import find_spec
 
 import dask.array as da
 import numpy as np
@@ -487,6 +488,9 @@ def test_normalize_slice(self):
             with self.assertRaises(IndexError):
                 cf.normalize_slice(index, 8, cyclic=True)
 
+    # Note: here only need healpix for cf under-the-hood code, not in test
+    # directly, so no need to actually import healpix, just test it is there.
+    @unittest.skipUnless(find_spec("healpix"), "Requires 'healpix' package.")
     def test_locate(self):
         """Test cf.locate"""
         # HEALPix