Test wrangling vs v3.0.x #4249

rcomer · 2021-07-22T09:17:21Z

🚀 Pull Request

Description

Replacement for #4192, targeting the v3.0.x branch.

This PR gets our tests running consistently under pytest and nose. We had some __init__.py files missing so some tests have not been running under nose/setuptools/nox. Once reinstated, three of the tests for PartialDateTime failed, so this PR also includes changes to address that. See inline comments for explanations of individual changes.

I have verified that pointing pytest at this new branch produces 5216 passess and 22 skips. python setup.py test also finds 5148 tests, but some are falling over with memory allocation errors 😕. So let's see how the CI fairs...

Consult Iris pull request check list

rcomer · 2021-07-22T09:17:58Z

lib/iris/tests/system_test.py

@@ -22,7 +22,7 @@


 class SystemInitialTest(tests.IrisTest):
-    def system_test_supported_filetypes(self):
+    def test_supported_filetypes(self):


pytest requires test names to start with "test" or it just won't discover them.

rcomer · 2021-07-22T09:18:09Z

lib/iris/tests/system_test.py

@@ -74,7 +74,7 @@ def horiz_cs():
                new_cube, ("system", "supported_filetype_%s.cml" % filetype)
            )

-    def system_test_imports_general(self):
+    def test_imports_general(self):


pytest requires test names to start with "test" or it just won't discover them

rcomer · 2021-07-22T09:18:56Z

lib/iris/tests/test_merge.py

@@ -25,7 +25,7 @@
 import iris.tests.stock


-class TestMixin:
+class MergeMixin:


pytest tried to run this as a test class, so errored all three tests when it couldn't find _data_path. Removing "Test" from the class name stops pytest trying to do that.

rcomer · 2021-07-22T09:23:09Z

lib/iris/tests/unit/time/test_PartialDateTime.py

@@ -224,12 +224,12 @@ def setUp(self):
        self.expected_value = EQ_EXPECTATIONS

    def test_cftime_equal(self):
-        pdt = PartialDateTime(month=3, microsecond=2)
+        pdt = PartialDateTime(month=3, second=2)


This was failing because the equality operator returned False. The microsecond comparison is skipped if other doesn't have a microsecond attribute:

iris/lib/iris/time.py

Lines 152 to 157 in a6cd220

# 'microsecond' is optional

if result and hasattr(other, "microsecond"):

attr = self.microsecond

other_attr = other.microsecond

if attr is not None and attr != other_attr:

result = False

My guess is that, when this test was written, cftime.datetimes' predecessors did not have a microsecond attribute, but they do now.

rcomer · 2021-07-22T09:27:10Z

lib/iris/time.py

+                    # behaviour (which compares using object IDs), so we raise
+                    # an exception here instead.
+                    fmt = "unable to compare PartialDateTime with {}"
+                    raise TypeError(fmt.format(type(other)))


One test compares a PartialDateTime to an int, and expects a TypeError:

iris/lib/iris/tests/unit/time/test_PartialDateTime.py

Lines 66 to 70 in 1505995

class _Test_operator:

def test_invalid_type(self):

pdt = PartialDateTime()

with self.assertRaises(TypeError):

self.op(pdt, 1)

It was getting False instead.

We previously used the __cmp__ method to stop the equality comparison falling back to object identities. But this method is not a thing in python3.

My above solution works, but feels like a bit of a hack. Alternative solutions welcome!

@rcomer Rings a bell... see Unidata/cftime#81 😉

This might explain this change in behaviour, which was kinda py2 centric 🤔

@bjlittle yup the failures I saw were just for == and != operators. So I think >=, etc. were still raising the TypeError as there's no way to check that based on identities.

@rcomer Okay, I'm fine with this.

It seems completely reasonable to me and maintains prior behaviour both within iris and for users 👍

bjlittle

@rcomer Looks good to me.

I'm going to hold this PR until #4222 lands in the v3.0.x release feature branch.

At which point please:

rebase with the latest v3.0.x
add a whatsnew entry.

You're blocked until #4222 is merged, then we're good to get this across the line 👍

bjlittle

@rcomer LGTM, thanks!

I'll merge when cirrus-ci is happy 👍

pp-mo · 2021-07-22T16:05:36Z

This is really awesome work, long overdue, and I hope means we can get serious about migrating to PyTest.

Praise @bjlittle @rcomer 💐 🍻

@trexfeathers

* Add release highlights and pin rc version (#3898) * Add release highlights and pin rc version * review actions * reorder release highlights (#3899) Tweak release highlights * Add whatsnew announcement (#3900) * Fix spelling (#3903) * Fix unit label handling (#3902) * Add failing test of plotting * Implement fix to pass test * Update idiff to ignore irrelevant hyphens in path * Update imagerepo (following docs) * Update after review by @trexfeathers * Add whatsnew entries * Move whatsnew entries into correct file * Release Docs Improvements (#3895) * Minor phrasing change in 'Release candidate'. * Before release deprecations. * Whatsnew highlights section. * Relax setup.py setup requirements (#3909) * Updated CF saver version in User Guide and docstring (#3925) * Updated CF saver version in User Guide and docstring * Remove references to CF version of the loader in docstrings * Added whatsnew * Pin cftime<1.3.0 * Migrate to cirrus-ci (#3928) * migrate from travis-ci to cirrus-ci * added whatsnew entries * ignore url for doc link check (#3929) * whatsnew for coord default units (#3924) * Cube._summary_coord_extra: efficiency and bugfix (#3922) * Add Documentation Title Case Capitalization (#3940) * Use Title Case Capitalisation for Documentation * add whatsnew enter * CI requirements drop pip packages (#3939) * requirements pip to conda * use pip install over develop * default PY_VER to python versions * update links (#3942) * update links * added s to http * Add support for 1-d weights in collapse. (#3943) * Remove warning for convert_units on lazy data (#3951) * drop stickler references in docs (#3953) * drop stickler references in docs * remove sticker from common links * update docs for travis-ci to cirrus-ci (#3954) * update docs for travis-ci to cirrus-ci * add 'travis-ci' reference locally to whatsnew * update whatsnew comment * docs for nox (#3955) * docs for nox * add titles, notices and additional detail * review actions * Resolve test coverage (#3947) * test coverage for __init__ and __call__ * test coverage for metadata resolve and coverage * partial test coverage for metadata mapping * python 3.6 workaround for deepcopy of mock.sentinel * test coverage for Resolve._free_mapping * test coverage for Resolve convenience methods * add test stub for Resolve._metadata_mapping * fix Test__tgt_cube_position * test coverage for shape * test coverage for _as_compatible_cubes * test coverage for Resolve._metadata_mapping * test coverage for Resolve._prepare_common_dim_payload * test coverage for Resolve._prepare_common_aux_payload * test coverage for Resolve._prepare_points_and_bounds * test coverage for Resolve._create_prepared_item * test coverage for Resolve._prepare_local_payload_dim * test coverage for Resolve._prepare_local_payload_aux * test coverage for Resolve._prepare_local_payload_scalar + docs URL skip * test coverage for Resolve._prepare_local_payload * test coverage for Resolve._metadata_prepare * added docs URL linkcheck skip * test coverage for Resolve._prepare_factory_payload * test coverage for Resolve._get_prepared_item * review actions * test coverage for Resolve.cube * pin v3.0.0 version and whatnew date (#3956) * update github ci checks image (#3957) * Promote unknown units to dimensionless in aux factories (#3965) * promote unknown to dimensionless units in aux factories * patch aux factories to promote unknown to dimensionless units for formula terms * add whatnew PR for entry * Release branch prepare for v3.0.2 (#4044) * update intersphinx mapping and matplotlib urls (#4003) * update intersphinx mapping and matplotlib urls * use matplotlib intersphinx where possible * review actions * review actions * cirrus-ci compute credits (#4007) * cirrus-ci conditional tasks (#4019) * cirrus-ci conditional tasks * use bc for bash arithmetic * revert back to sed * use expr * reword * minor documentation changes * review actions * prepare v3.0.2 release * Fix test_incompatible_dimensions test (#3977) * test_incompatible_dimensions used a ragged array for the test, which has been deprecated in numpy, and now fails if dtype is anything other than object. This test appears to be checking that the addition of a [2x4] masked array to a [2x3] masked cube should raise a ValueError. This commit fixes the creation of `data3` object to be a [2x4] non-ragged array. * Added entry to what's new * Added name to core developer list :) * Update latest.rst Fixed space in PR macro call * update whatsnew v3.0.2 Co-authored-by: James Penn <james@jamespenn.co.uk> * um_stash_source attribute improved handling (#4035) * Modified pyke rule * Tests added * Black and whatsnew * Include PR number * Remove latest.rst * Add what's new * Support for py38 and Cartopy 0.19 (#4130) * mpl 3.4.1 updates (#4087) * replace most recent hashes (#4112) * Corrected plot_anomaly_log_colouring for new Matplotlib linscale rules. (#4115) * Cartopy 0.19 updates (#4128) * Use assertArrayAllClose for sqrt test (#4118) * using AllClose for sqrt test * Omitting the checksum from test cml * use ArrayAllClose (rebase reset it?) * Iris py38 (#3976) * support for py38 * update CI and noxfile * enforce alphabetical xml element attribute order * full tests for py38 + fix docs-tests * add whatsnew entry * update doc-strings + review actions * Alternate xml handling routine (#29) * all xml tests pass for nox tests-3.8 * restored docstrings * move sort_xml_attrs * make sort_xml_attrs a classmethod * update sort_xml_attr doc-string Co-authored-by: Bill Little <bill.james.little@gmail.com> * add jamesp to whatsnew + minor tweak Co-authored-by: James Penn <james@jamespenn.co.uk> * reinstate black and nox links * Linkcheck update (#4104) * Updated links * Added login remark * Removed extra space * change to kick cirrus * kick cirrus * test verbose on cirrus * Removed test settings. Co-authored-by: Bill Little <bill.james.little@gmail.com> Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: James Penn <james.penn@metoffice.gov.uk> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> * Intersection bounds fix (replacement PR) (#4059) * fix intersection out of bounds point * fix intersection out of bounds point take 2 * add referencing comment * bootstrap ci for 3.0.x (#4154) * add cirrus-ci docker support * wip * wip * wip * wip * wip * add pip * revert docker * fix add_weekday (#32) * fix add_weekday * fix black link * fix link Co-authored-by: Ruth Comer <10599679+rcomer@users.noreply.github.com> * Tweak to speed up dask wrapping of netcdf variables (#4135) * Use 'meta' in da.from_array to stop it sampling netcdf variables, which is quite slow. * Fix PR number. * Fix test. * Review changes. * Update docs/iris/src/whatsnew/3.0.2.rst Co-authored-by: lbdreyer <lbdreyer@users.noreply.github.com> * Fb fix cube coord arithmetic (#4159) * fix coord with cube arithmetic * add coord arithmetic test coverage * add a whatsnew entry * Pp daskfix (#4141) * Remove workaround when dask-wrapping PP data, obsoleted by #4135. * Remove old slice testing * Add whats new * move whitespace? * missing line Co-authored-by: lbdreyer <laura.dreyer@metoffice.gov.uk> * add release date to v3.0.2 whatsnew (#4160) * update readme logo img src and href (#4006) (#4216) * In cube.intersection, find split cells using a tolerant equality check (#4220) * In cube.intersection, find split cells using a tolerant equality check * remove unused var * Add bounds check to tests; add what's new * Fix whats new; update version number * Update 3.0.3.rst Update release date in `3.0.3.rst` * Wide cubestr fix 3v0vx v2 (#4233) * Widen cube printout for long ancil or cell-measure names. * Adjust result for fixed cube-units printout. * Added whatsnew. * Include newest whatsnew in index. * Review: fix whatsnew structure. * Fix initial sections display. * Fix some typos in the cube maths docs (#4248) * (More of) Wide cubestr fix 3v0vx v2 (#4238) * Fix whatsnew for #4233. * Move 'empty slicings' whatsnew entry to 3.0.2 section. * unpin cftime (#4222) * Test wrangling vs v3.0.x (#4249) * test changes * add awol init * rename system test cases * fix PartialDateTime tests * fix typo * add whatsnew * Fix mergeback PR #4035 * Fix mergeback PR #4035 tests * Update mergeback nox conda-lock files Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: Zeb Nicholls <zebedee.nicholls@climate-energy-college.org> Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com> Co-authored-by: Jon Seddon <17068361+jonseddon@users.noreply.github.com> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk> Co-authored-by: James Penn <james@jamespenn.co.uk> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: James Penn <james.penn@metoffice.gov.uk> Co-authored-by: Ruth Comer <10599679+rcomer@users.noreply.github.com> Co-authored-by: lbdreyer <lbdreyer@users.noreply.github.com> Co-authored-by: lbdreyer <laura.dreyer@metoffice.gov.uk>

rcomer commented Jul 22, 2021

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rcomer added Release: Patch Type: Testing labels Jul 22, 2021

rcomer added this to In progress in Iris v3.0.x via automation Jul 22, 2021

rcomer mentioned this pull request Jul 22, 2021

Test Wrangling #4192

Closed

Iris v3.0.x automation moved this from In progress to Review in progress Jul 22, 2021

bjlittle requested changes Jul 22, 2021

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rcomer added 6 commits July 22, 2021 16:23

test changes

4b90c88

add awol init

3a46136

rename system test cases

3b27a6b

fix PartialDateTime tests

9b5691b

fix typo

7b9df30

add whatsnew

7ff16a7

rcomer force-pushed the test-wrangling branch from 5b21e44 to 7ff16a7 Compare July 22, 2021 15:38

bjlittle approved these changes Jul 22, 2021

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Iris v3.0.x automation moved this from Review in progress to Reviewer approved Jul 22, 2021

bjlittle merged commit 1af2060 into SciTools:v3.0.x Jul 22, 2021

Iris v3.0.x automation moved this from Reviewer approved to Done Jul 22, 2021

rcomer deleted the test-wrangling branch September 24, 2021 08:29

rcomer mentioned this pull request May 9, 2022

Replace nose with pytest #4734

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Test wrangling vs v3.0.x #4249

Test wrangling vs v3.0.x #4249

rcomer commented Jul 22, 2021

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pp-mo commented Jul 22, 2021

	# 'microsecond' is optional
	if result and hasattr(other, "microsecond"):
	attr = self.microsecond
	other_attr = other.microsecond
	if attr is not None and attr != other_attr:
	result = False

	class _Test_operator:
	def test_invalid_type(self):
	pdt = PartialDateTime()
	with self.assertRaises(TypeError):
	self.op(pdt, 1)

Test wrangling vs v3.0.x #4249

Test wrangling vs v3.0.x #4249

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rcomer commented Jul 22, 2021

🚀 Pull Request

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