Test skipping based on module (esp. `healpix`) availability by sadielbartholomew · Pull Request #944 · NCAS-CMS/cf-python

sadielbartholomew · 2026-04-15T16:18:57Z

We have some test skipping for lack of required module availability, including cases where it is an 'optional' dependency not enforced by packaging requirements, but not comprehensive and not accounting for the new healpix optional dependency.

In the background to the EXPECT GA I've went in and added all skips required, replacing those on individual methods with module-level skipping for relevant test modules (regrid-related tests which all need esmpy including one case where there was a false positive i.e. test pass from lack of skip, and tests requiring an explicit or under-the-hood use of healpix).

@davidhassell a sanity check would be useful but feel free to approve if you don't think a review is necessary given this PR is only trivial test infra changes.

sadielbartholomew · 2026-05-27T11:06:57Z

@davidhassell just a reminder as per our meeting today that it would be great to get this reviewed and merged when you have a change to look. Thanks.

davidhassell

Hi Sadie,

I find that the setup variables are not available to the test methods ... is that what you get?

>>python test_HEALPix_utils.py 
Run date: 2026-05-30 12:00:00.673592
Platform: Linux-6.8.0-124-generic-x86_64-with-glibc2.39 

<snip>

test_HEALPix_pix2zuniq (__main__.DataTest.test_HEALPix_pix2zuniq)
Test _pix2zuniq ... ERROR
test_HEALPix_uniq2zuniq (__main__.DataTest.test_HEALPix_uniq2zuniq)
Test _uniq2zuniq ... ERROR
test_HEALPix_zuniq2pix (__main__.DataTest.test_HEALPix_zuniq2pix)
Test _zuniq2pix ... ERROR
test_HEALPix_zuniq2uniq (__main__.DataTest.test_HEALPix_zuniq2uniq)
Test _zuniq2uniq ... ERROR

======================================================================
ERROR: test_HEALPix_pix2zuniq (__main__.DataTest.test_HEALPix_pix2zuniq)
Test _pix2zuniq
----------------------------------------------------------------------
Traceback (most recent call last):
  File "cf-python/cf/test/test_HEALPix_utils.py", line 84, in test_HEALPix_pix2zuniq
    for r, i in zip(refinement_levels, nested_indices)
                    ^^^^^^^^^^^^^^^^^
NameError: name 'refinement_levels' is not defined

======================================================================
ERROR: test_HEALPix_uniq2zuniq (__main__.DataTest.test_HEALPix_uniq2zuniq)
Test _uniq2zuniq
----------------------------------------------------------------------
Traceback (most recent call last):
  File "cf-python/cf/test/test_HEALPix_utils.py", line 52, in test_HEALPix_uniq2zuniq
    np.array_equal(_uniq2zuniq(nuniq_indices), zuniq_indices)
                               ^^^^^^^^^^^^^
NameError: name 'nuniq_indices' is not defined

======================================================================
ERROR: test_HEALPix_zuniq2pix (__main__.DataTest.test_HEALPix_zuniq2pix)
Test _zuniq2pix
----------------------------------------------------------------------
Traceback (most recent call last):
  File "cf-python/cf/test/test_HEALPix_utils.py", line 68, in test_HEALPix_zuniq2pix
    order, i = _zuniq2pix(zuniq_indices, nest=True)
                          ^^^^^^^^^^^^^
NameError: name 'zuniq_indices' is not defined

======================================================================
ERROR: test_HEALPix_zuniq2uniq (__main__.DataTest.test_HEALPix_zuniq2uniq)
Test _zuniq2uniq
----------------------------------------------------------------------
Traceback (most recent call last):
  File "cf-python/cf/test/test_HEALPix_utils.py", line 60, in test_HEALPix_zuniq2uniq
    np.array_equal(_zuniq2uniq(zuniq_indices), nuniq_indices)
                               ^^^^^^^^^^^^^
NameError: name 'zuniq_indices' is not defined

----------------------------------------------------------------------
Ran 4 tests in 0.009s

FAILED (errors=4)
>>

sadielbartholomew · 2026-06-01T15:53:11Z

Good spot @davidhassell, thanks - I thought I'd sorted that in a clever way but forgot to check how it was handled when healpix is installed which is by far the most important use case! Will get this updated to fix it...

davidhassell · 2026-06-09T08:34:42Z

Hi Sadie - nearly there :) test_regrid.py still has a bug:

test_Field_regrid_2d_field (__main__.RegridTest.test_Field_regrid_2d_field)
2-d regridding with Field destination grid. ... ERROR
test_Field_regrid_chunks (__main__.RegridTest.test_Field_regrid_chunks)
Regridding of chunked axes ... ok
test_Field_regrid_weights_file (__main__.RegridTest.test_Field_regrid_weights_file)
Regridding creation/use of weights file ... ERROR
test_Field_regridc_1d_coordinates_z (__main__.RegridTest.test_Field_regridc_1d_coordinates_z)
1-d Z Cartesian regridding with coordinates destination grid. ... ERROR
test_Field_regridc_1d_field (__main__.RegridTest.test_Field_regridc_1d_field)
1-d Cartesian regridding with Field destination grid. ... ERROR
test_Field_regridc_2d_coords (__main__.RegridTest.test_Field_regridc_2d_coords)
2-d Cartesian regridding with coords destination grid. ... ERROR
test_Field_regridc_3d_field (__main__.RegridTest.test_Field_regridc_3d_field)
3-d Cartesian regridding with Field destination grid. ... ERROR
test_Field_regridc_domain (__main__.RegridTest.test_Field_regridc_domain)
Spherical regridding with Domain destination grid. ... ERROR
test_Field_regrids_bad_dst (__main__.RegridTest.test_Field_regrids_bad_dst)
Disallowed destination grid types raise an exception. ... ERROR
test_Field_regrids_coords (__main__.RegridTest.test_Field_regrids_coords)
Spherical regridding with coords destination grid. ... ERROR
test_Field_regrids_domain (__main__.RegridTest.test_Field_regrids_domain)
Spherical regridding with Domain destination grid. ... ERROR
test_Field_regrids_field_operator (__main__.RegridTest.test_Field_regrids_field_operator)
Spherical regridding with operator destination grid. ... ERROR
test_Field_regrids_non_coordinates (__main__.RegridTest.test_Field_regrids_non_coordinates)
Check setting of non-coordinate metadata. ... ERROR
test_return_esmpy_regrid_operator (__main__.RegridTest.test_return_esmpy_regrid_operator)
esmpy regrid operator returns esmpy.Regrid in regrids and regridc ... ERROR

======================================================================
ERROR: test_Field_regrid_2d_field (__main__.RegridTest.test_Field_regrid_2d_field)
2-d regridding with Field destination grid.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/david/cf-python/cf/test/test_regrid.py", line 166, in test_Field_regrid_2d_field
    dst = self.dst.copy()
          ^^^^^^^^
AttributeError: 'RegridTest' object has no attribute 'dst'

======================================================================
ERROR: test_Field_regrid_weights_file (__main__.RegridTest.test_Field_regrid_weights_file)
Regridding creation/use of weights file
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/david/cf-python/cf/test/test_regrid.py", line 783, in test_Field_regrid_weights_file
    dst = self.dst
          ^^^^^^^^
AttributeError: 'RegridTest' object has no attribute 'dst'

======================================================================
ERROR: test_Field_regridc_1d_coordinates_z (__main__.RegridTest.test_Field_regridc_1d_coordinates_z)
1-d Z Cartesian regridding with coordinates destination grid.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/david/cf-python/cf/test/test_regrid.py", line 755, in test_Field_regridc_1d_coordinates_z
    src = cf.read(self.filename_xyz)[0]
                  ^^^^^^^^^^^^^^^^^
AttributeError: 'RegridTest' object has no attribute 'filename_xyz'

======================================================================
ERROR: test_Field_regridc_1d_field (__main__.RegridTest.test_Field_regridc_1d_field)
1-d Cartesian regridding with Field destination grid.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/david/cf-python/cf/test/test_regrid.py", line 669, in test_Field_regridc_1d_field
    dst = self.dst.copy()
          ^^^^^^^^
AttributeError: 'RegridTest' object has no attribute 'dst'

======================================================================
ERROR: test_Field_regridc_2d_coords (__main__.RegridTest.test_Field_regridc_2d_coords)
2-d Cartesian regridding with coords destination grid.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/david/cf-python/cf/test/test_regrid.py", line 386, in test_Field_regridc_2d_coords
    dst = self.dst.copy()
          ^^^^^^^^
AttributeError: 'RegridTest' object has no attribute 'dst'

======================================================================
ERROR: test_Field_regridc_3d_field (__main__.RegridTest.test_Field_regridc_3d_field)
3-d Cartesian regridding with Field destination grid.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/david/cf-python/cf/test/test_regrid.py", line 565, in test_Field_regridc_3d_field
    dst = self.dst.copy()
          ^^^^^^^^
AttributeError: 'RegridTest' object has no attribute 'dst'

======================================================================
ERROR: test_Field_regridc_domain (__main__.RegridTest.test_Field_regridc_domain)
Spherical regridding with Domain destination grid.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/david/cf-python/cf/test/test_regrid.py", line 452, in test_Field_regridc_domain
    dst = self.dst
          ^^^^^^^^
AttributeError: 'RegridTest' object has no attribute 'dst'

======================================================================
ERROR: test_Field_regrids_bad_dst (__main__.RegridTest.test_Field_regrids_bad_dst)
Disallowed destination grid types raise an exception.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/david/cf-python/cf/test/test_regrid.py", line 417, in test_Field_regrids_bad_dst
    self.src.regrids(999, method="conservative")
    ^^^^^^^^
AttributeError: 'RegridTest' object has no attribute 'src'

======================================================================
ERROR: test_Field_regrids_coords (__main__.RegridTest.test_Field_regrids_coords)
Spherical regridding with coords destination grid.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/david/cf-python/cf/test/test_regrid.py", line 317, in test_Field_regrids_coords
    dst = self.dst.copy()
          ^^^^^^^^
AttributeError: 'RegridTest' object has no attribute 'dst'

======================================================================
ERROR: test_Field_regrids_domain (__main__.RegridTest.test_Field_regrids_domain)
Spherical regridding with Domain destination grid.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/david/cf-python/cf/test/test_regrid.py", line 429, in test_Field_regrids_domain
    dst = self.dst
          ^^^^^^^^
AttributeError: 'RegridTest' object has no attribute 'dst'

======================================================================
ERROR: test_Field_regrids_field_operator (__main__.RegridTest.test_Field_regrids_field_operator)
Spherical regridding with operator destination grid.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/david/cf-python/cf/test/test_regrid.py", line 477, in test_Field_regrids_field_operator
    dst = self.dst
          ^^^^^^^^
AttributeError: 'RegridTest' object has no attribute 'dst'

======================================================================
ERROR: test_Field_regrids_non_coordinates (__main__.RegridTest.test_Field_regrids_non_coordinates)
Check setting of non-coordinate metadata.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/david/cf-python/cf/test/test_regrid.py", line 515, in test_Field_regrids_non_coordinates
    src = self.src
          ^^^^^^^^
AttributeError: 'RegridTest' object has no attribute 'src'

======================================================================
ERROR: test_return_esmpy_regrid_operator (__main__.RegridTest.test_return_esmpy_regrid_operator)
esmpy regrid operator returns esmpy.Regrid in regrids and regridc
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/david/cf-python/cf/test/test_regrid.py", line 818, in test_return_esmpy_regrid_operator
    dst = self.dst
          ^^^^^^^^
AttributeError: 'RegridTest' object has no attribute 'dst'

----------------------------------------------------------------------
Ran 14 tests in 3.044s

FAILED (errors=13)

sadielbartholomew · 2026-06-09T16:51:38Z

Ah yes, sorry somehow my main environment on Python 3.14 which is meant to have everything optional in didn't have esmpy installed so those tests got skipped and I missed it, oops! Pushing a commit to fix it now.

sadielbartholomew · 2026-06-09T17:42:39Z

Thanks @davidhassell, should now (finally, sorry!) be good.

davidhassell

Thanks - all tests pass for me :) Merge away ...

sadielbartholomew added 10 commits April 14, 2026 16:06

Add missing ESMPy module availability test skips

f106360

Add test_Domain healpix module availability test skipping

2e885f2

Add test_weights healpix module availability test skipping

44357b8

Add healpix module availability test skips to field-related tests

b39b402

Add module availability module-level test skip for test_HEALPix_utils

d77c424

Add subtle esmpy availability test_regrid skip to avoid false positive

cad2ba4

Convert test_regrid esmpy availability test skips to module-level

45dbe80

Add last required healpix availability skip from full test suite run

7567ac7

Tidy test skip on lone methods to avoid use of flag

f674572

Convert test skipping to module-level for test_RegridOperator

2088b7e

sadielbartholomew requested a review from davidhassell April 15, 2026 16:18

sadielbartholomew self-assigned this Apr 15, 2026

sadielbartholomew added the testing Issues related to units tests and their coverage label Apr 15, 2026

davidhassell requested changes May 30, 2026

View reviewed changes

Fix scoping issues in test_HEALPix_utils

7c3205a

sadielbartholomew added 2 commits June 9, 2026 18:10

Fix scoping issue in test_regrid

284a47d

Fix logic issue and redundant 'noqa' markers in test_regrid

9c28b79

davidhassell approved these changes Jun 9, 2026

View reviewed changes

sadielbartholomew merged commit 6b4623b into NCAS-CMS:main Jun 10, 2026

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Test skipping based on module (esp. `healpix`) availability#944

Test skipping based on module (esp. `healpix`) availability#944
sadielbartholomew merged 13 commits into
NCAS-CMS:mainfrom
sadielbartholomew:test-skipping-post3.20

sadielbartholomew commented Apr 15, 2026

Uh oh!

sadielbartholomew commented May 27, 2026

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sadielbartholomew commented Apr 15, 2026

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sadielbartholomew commented Jun 1, 2026

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davidhassell commented Jun 9, 2026

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