Test skipping based on module (esp. healpix) availability

.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

@@ -1,33 +1,49 @@
 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."
+            )
+        else:
+            # 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 = [  # noqa: F841
+                i + 4 ** (1 + r)
+                for r, i in zip(refinement_levels, nested_indices)
+            ]
+
+            zuniq_indices = [  # noqa: F841
+                (2 * i + 1) * 4 ** (29 - r)
+                for r, i in zip(refinement_levels, nested_indices)
+            ]
+
     def test_HEALPix_uniq2zuniq(self):
         """Test _uniq2zuniq"""
         from cf.data.dask_utils_healpix import _uniq2zuniq

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

cf/test/test_regrid.py

@@ -11,6 +11,12 @@
 
 import cf
 
+esmpy_imported = True
+try:
+    import esmpy  # noqa: F401
+except ImportError:
+    esmpy_imported = False
+
 n_tmpfiles = 1
 tmpfiles = [
     tempfile.mkstemp("_test_regrid.nc", dir=os.getcwd())[1]
@@ -30,14 +36,6 @@ def _remove_tmpfiles():
 
 atexit.register(_remove_tmpfiles)
 
-
-esmpy_imported = True
-try:
-    import esmpy  # noqa: F401
-except ImportError:
-    esmpy_imported = False
-
-
 all_methods = (
     "linear",
     "conservative",
@@ -140,19 +138,27 @@ def esmpy_regrid_Nd(coord_sys, method, src, dst, **kwargs):
 
 
 class RegridTest(unittest.TestCase):
-    # Get the test source and destination fields
-    filename = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "regrid.nc"
-    )
-    dst_src = cf.read(filename)
-    dst = dst_src[0]
-    src = dst_src[1]
 
-    filename_xyz = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "regrid_xyz.nc"
-    )
+    def setUp(self):
+        """Preparations called immediately before each test method."""
+        # Skip all if esmpy module not available!
+        if not esmpy_imported:
+            self.skipTest(
+                "Test module requires 'esmpy' package. Install it to run all."
+            )
+        else:
+            # Get the test source and destination fields
+            filename = os.path.join(
+                os.path.dirname(os.path.abspath(__file__)), "regrid.nc"
+            )
+            dst_src = cf.read(filename)
+            dst = dst_src[0]  # noqa: F841
+            src = dst_src[1]  # noqa: F841
+
+            filename_xyz = os.path.join(  # noqa: F841
+                os.path.dirname(os.path.abspath(__file__)), "regrid_xyz.nc"
+            )
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_Field_regrid_2d_field(self):
         """2-d regridding with Field destination grid."""
         self.assertFalse(cf.regrid_logging())
@@ -304,7 +310,6 @@ def test_Field_regrid_2d_field(self):
             with self.assertRaises(ValueError):
                 src.regrids(dst, method=method).array
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_Field_regrids_coords(self):
         """Spherical regridding with coords destination grid."""
         self.assertFalse(cf.regrid_logging())
@@ -374,7 +379,6 @@ def test_Field_regrids_coords(self):
         d1 = src.regrids(r)
         self.assertTrue(d1.data.equals(d0.data, atol=atol, rtol=rtol))
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_Field_regridc_2d_coords(self):
         """2-d Cartesian regridding with coords destination grid."""
         self.assertFalse(cf.regrid_logging())
@@ -418,7 +422,6 @@ def test_Field_regrids_bad_dst(self):
         with self.assertRaises(ValueError):
             self.src.regrids("foobar", method="conservative")
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_Field_regrids_domain(self):
         """Spherical regridding with Domain destination grid."""
         self.assertFalse(cf.regrid_logging())
@@ -442,7 +445,6 @@ def test_Field_regrids_domain(self):
         d1 = src.regrids(r)
         self.assertTrue(d1.equals(d0, atol=atol, rtol=rtol))
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_Field_regridc_domain(self):
         """Spherical regridding with Domain destination grid."""
         self.assertFalse(cf.regrid_logging())
@@ -468,7 +470,6 @@ def test_Field_regridc_domain(self):
         d1 = src.regridc(r)
         self.assertTrue(d1.equals(d0, atol=atol, rtol=rtol))
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_Field_regrids_field_operator(self):
         """Spherical regridding with operator destination grid."""
         self.assertFalse(cf.regrid_logging())
@@ -506,7 +507,6 @@ def test_Field_regrids_field_operator(self):
         with self.assertRaises(ValueError):
             dst.regrids(r)
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_Field_regrids_non_coordinates(self):
         """Check setting of non-coordinate metadata."""
         self.assertFalse(cf.regrid_logging())
@@ -555,7 +555,6 @@ def test_Field_regrids_non_coordinates(self):
         # Cell measures
         self.assertFalse(d1.cell_measures())
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_Field_regridc_3d_field(self):
         """3-d Cartesian regridding with Field destination grid."""
         self.assertFalse(cf.regrid_logging())
@@ -659,7 +658,6 @@ def test_Field_regridc_3d_field(self):
             with self.assertRaises(ValueError):
                 src.regridc(dst, method=method, axes=axes)
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_Field_regridc_1d_field(self):
         """1-d Cartesian regridding with Field destination grid."""
         self.assertFalse(cf.regrid_logging())
@@ -750,7 +748,6 @@ def test_Field_regridc_1d_field(self):
             with self.assertRaises(ValueError):
                 src.regridc(dst, method=method, axes=axes)
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_Field_regridc_1d_coordinates_z(self):
         """1-d Z Cartesian regridding with coordinates destination grid."""
         self.assertFalse(cf.regrid_logging())
@@ -763,7 +760,6 @@ def test_Field_regridc_1d_coordinates_z(self):
         z = d.dimension_coordinate("Z")
         self.assertTrue(z.data.equals(dst.data))
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_Field_regrid_chunks(self):
         """Regridding of chunked axes"""
         self.assertFalse(cf.regrid_logging())
@@ -780,7 +776,6 @@ def test_Field_regrid_chunks(self):
         d0 = src.regrids(dst, method="linear")
         self.assertEqual(d0.data.numblocks, (1, 1, 1))
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_Field_regrid_weights_file(self):
         """Regridding creation/use of weights file"""
         self.assertFalse(cf.regrid_logging())
@@ -816,7 +811,6 @@ def test_Field_regrid_weights_file(self):
                 src.regrids(r1, method="linear", weights_file=tmpfile)
             )
 
-    @unittest.skipUnless(esmpy_imported, "Requires esmpy/ESMF package.")
     def test_return_esmpy_regrid_operator(self):
         """esmpy regrid operator returns esmpy.Regrid in regrids and regridc"""
         self.assertFalse(cf.regrid_logging())