um_stash_source attribute improved handling #4035
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Hi @bjlittle, the tests (including the full i/o set with the test data) are all running happily on my local machine now and so hopefully this is ready for review. If you let me know the commit ids from master then I'm happy to pull these into here to get the CI tests passing too, or I'm happy to leave it for you. |
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@jonseddon Thanks, I'll update As there may be a couple to pull in... Probably easier that way 👍 |
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@jonseddon See #4044. That PR updates the Once that's merged, rebase this PR with |
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@jonseddon Perfect! Awesome job, thanks 🍻 🎉
Let's get this goodness banked for v3.0.2 👍
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* 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>
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🚀 Pull Request
Description
Resolves #4029
If in a netCDF file the
um_stash_sourceCF variable isn't fully in STASH MSI format then handle this and don't raise aValueError.It's potentially contentious that if
um_stash_sourceisn't correctly formed then its value is preserved incube.attributes. I'm happy to change this if it's not desirable behaviour.Closes #4029