Alternative Cell.__hash__ implementation for NaN support #4852
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lbdreyer
approved these changes
Jul 5, 2022
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Computing the hash value once rather than everytime it is called makes sense to me so I agree that this is a sensible way forward. Although I'm surprised the lines
try:
value = 0 if np.isnan(self.point) else hash((self.point,))
except TypeError:
# Passing a string to np.isnan causes this exception.
value = hash((self.point,))
had such an impact on the performance!
This looks good to be merged! Do you think this should include a what's new? I can't seem to find mention of Python 3.10 support in the what's new so maybe that would be good to include (in this PR or a separate one)
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Author
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@lbdreyer Awesome! Thanks. The call to I'll add a |
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@lbdreyer Done. Back to you 👍 |
Member
Author
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@lbdreyer Brilliant! 🥳 |
Contributor
|
Sorry to crash the party folks (I should have spotted this yesterday), but the results @bjlittle posted yesterday only show that things have stayed the same. If we had fixed the performance we should have expected some significant reductions in benchmark times. 😔 |
lbdreyer
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Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Support false-easting and false-northing when loading Mercator-projected data (#4524) * Add extra pieces to get false easting and northing * tests * Add extra test file ref and cml * lib/iris/tests/results/netcdf/netcdf_merc_false.cml * Update cml for new test data * Bump test data version for cirrus * What's new * Bump peter-evans/create-pull-request from 3.13.0 to 3.14.0 (#4608) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 3.13.0 to 3.14.0. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](https://github.com/peter-evans/create-pull-request/compare/89265e8d24a5dea438a2577fdc409a11e9f855ca...18f7dc018cc2cd597073088f7c7591b9d1c02672) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-minor ... 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Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix aggregated_by mdtol/masked constant problem (#4246) * add failing test * pass test * whatsnew * remove redundant copy call * Make iris.tests.stock.simple_1d respect bounds arg (#4658) * Make iris.tests.stock.simple_1d respect bounds arg * What's new * What's new * Improved check for valid user in overnight BM run. (#4659) * Preserve position when replacing Axes with GeoAxes (#4273) * preserve position * add test * comment to clarify test * whatsnew * use original position * Lazy Percentile Aggregator (#3901) * implement lazy percentile * fix map_complete_blocks tests * fix legacy masked type no mask tests * add test for map_complete_blocks on dask array * handle axis expressed as sequence * fix docstring * add lazy_aggregate method and mdtol handling * reshape for multi-dim collapse * mdtol handling for added trailing dimension * update aggregator instance docstring * simplify array reshape * factor out array reshaping as decorator * reduce repetition in tests * PERCENTILE multi-axis tests * add tests for array wrangling * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * py3.7 * test_PERCENTILE.py tweaks * cut down post_process tests * clarify wrapper tests * whatsnew * revert py3.7 change * Update lib/iris/analysis/__init__.py Co-authored-by: Will Benfold <[email protected]> * review: remove docstring kwarg; define _real_percentile * review: blank line for note * review: remove scalar_percent check * review: test__axis_to_single_trailing.py * review: simplify structure * review: _percentile docstring args * review: remove axis description from _percentile docstring * review: don't use rollaxis * review: generalize LazyMixin to also work for non-lazy. Rename * review: move Test_lazy_aggregate tests into MaskedCalcMixin * review: generalise MaskedCalcMixin * review: remove stray as_lazy_data calls * review: use mixins for Test_aggregate * review: move multi axis tests to their own mixin * review: use MultiAxisMixin in both lazy classes * review: add tests for fast real aggregation * docstrings * review: test clarity tweaks * review: test alphap, betap passed to scipy * review: use assertEqual Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Will Benfold <[email protected]> * Fix nearest_neighbour_index for edge case where requested point is float and bounds are int (#4245) * add failing test * pass test * add whatsnew * Include note to strip out Artifactory (#4666) * Include note to strip out Artifactory * What's new * update black (#4668) * Fixed cube arithmetic for cubes with meshes. (#4651) * Use separate cml files for tests/unit/analysis/maths/test_slice multiple passes. * Roughly functional, but lots of tests to fix. * Fix * Fix mockist test for new-style Resolve. Mesh support not yet tested. * Fix _create_prepared_item when points/bounds passed in. * --no-edit * Simplify prepared-item usage. * Added tests * Added whatsnew. * Reference Iris issues for outstanding problems. * Small simplifications. * Updated statement on cube arithmetic with meshes. * Fix use of 'MathsAddOperationMixin'; add coord-mismatch tests on meshcubes. * Review changes. * Hack test which was failing. * Updated environment lockfiles (#4655) Co-authored-by: Lockfile bot <[email protected]> * 'Deep' benchmarks to catch scaling with field count (#4654) * 'Deep' benchmarks to catch scaling with field count * Better sized benchmarks * What's new * Update benchmarks/benchmarks/load/__init__.py Co-authored-by: Martin Yeo <[email protected]> Co-authored-by: Martin Yeo <[email protected]> * Automatic reversal of DimCoord bounds (#4466) * first pass at ensuring contiguous bounds * reduce scope and fix old tests * bounds setter tests * test contiguity preserved * check bounds within reverse tests * add comment; merge test * simpler approach * revert now redundant changes * update cml * cell equality to ignore bound order * update cml * move merge test to integration * review: simple actions * review: split up cube reverse tests * review: check bounds in all cube reverse tests * whatsnew * review: reduce test repetition * tweak whatsnew * blank line * Updated environment lockfiles (#4677) Co-authored-by: Lockfile bot <[email protected]> * Updated environment lockfiles (#4678) Co-authored-by: Lockfile bot <[email protected]> * Reorder Constraints sections of user guide, add time bounds example (#4656) * move constraint detail to subsetting cube, add example of constraining bound * Add whats new * Bump peter-evans/create-pull-request from 4.0.0 to 4.0.1 (#4675) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.0.0 to 4.0.1. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](https://github.com/peter-evans/create-pull-request/compare/d6d5519d05f5814158ef015b8448f2f74648c421...f1a7646cead32c950d90344a4fb5d4e926972a8f) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * tweak whatsnew (#4682) * Implement Pydata theme (#4661) * new theme baseline * update * added discussion directive and whatsnew * fixed bullet point indentation * updated NOX_CACHE_BUILD to force update the nox cache * added pr ref * Update lock-file generation in response to conda-lock change * Make lockfile shareable and bump nox cache * MAin branch updates to latest.rst (from dev.rst) * change references of dev.rst to latest.rst * corrected bullet points indentation to render correctly. * updated * update whatsnew * Review action and fixed typo for link * update lock * updated from main Co-authored-by: Will Benfold <[email protected]> Co-authored-by: Bill Little <[email protected]> * Update percentile tests (#4684) * update percentile tests * review action * Updated environment lockfiles (#4685) Co-authored-by: Lockfile bot <[email protected]> * Bump actions/download-artifact from 2 to 3 (#4686) Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 2 to 3. - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v2...v3) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-type: direct:production update-type: version-update:semver-major ... 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Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump peter-evans/create-pull-request from 4.0.1 to 4.0.2 (#4688) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.0.1 to 4.0.2. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](https://github.com/peter-evans/create-pull-request/compare/f1a7646cead32c950d90344a4fb5d4e926972a8f...bd72e1b7922d417764d27d30768117ad7da78a0e) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add dynamic matrix to refresh lockfile job (#4573) * Add dynamic matrix to refresh lockfile job * review actions * added link check and ensured https use (#4694) * [pre-commit.ci] pre-commit autoupdate (#4691) updates: - [github.com/pre-commit/pre-commit-hooks: v4.1.0 → v4.2.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.1.0...v4.2.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Comment rendering (#4689) * used numpy docstrings to fix docs rendering * comment rejig * apply numpydoc strings * corrected notes * updated docstring guidance. * added explicit mention of numpydoc strings * added whatsnew * added whatsnew PR ref * Update lib/iris/fileformats/nimrod_load_rules.py Co-authored-by: Will Benfold <[email protected]> * Update docs/src/whatsnew/latest.rst Co-authored-by: Will Benfold <[email protected]> * review actions. Co-authored-by: Will Benfold <[email protected]> * Updated environment lockfiles (#4696) Co-authored-by: Lockfile bot <[email protected]> * Cache regular points generation (#4698) * Cache regular points generation * Move func to util * Just apply lru_cache to the function once * What's new * Git ignore the benchmarks data folder (#4699) * Git ignore the benchmarks data folder * Update path and description * Catch `AttributeError` from removing `CFReader._dataset` when it doesn't exist (#4646) * Implement full Mercator parameter support (#4609) * Changes to coord_systems * Finish feature * Define both standard_parallel and scale_factor... but leave one None * Initial test changes * Test updates and additions * New expected test outputs * What's new and test data version bump * Review fix * Edit the right file * Updated environment lockfiles (#4706) Co-authored-by: Lockfile bot <[email protected]> * Add evertrol to whatsnew of #4646 given #4705 (#4709) * Add `iris.analysis.MAX_RUN` aggregator (#4676) * Failing tests * Start with the tests * Draft implementation * Test results * Account for masked data and multiple axes * Testing, bug fixes * Reduce duplication * Update .cml and fix test failures * Don't use map_complete_blocks * Use dask versions of functions * Test and fix masked data handling * Use da.from_array instead of as_lazy_data * Test chunking, fix dask.array import * Restore _lazy_data.py as we're not using those changes * credit Will's epic review (#4711) * add bullet (#4715) * Weighted `aggregated_by` (#4589) * First suggestion for weighted aggregated_by * Added lazy weighted aggregation * Added first tests for weighted aggregated_by * Added further tests and allowed returned kwarg * Added unit tests for weighted aggregated_by * Moved _get_aggregator_fn to iris.analyis * Reused 'returned' keyword * Added test for lazy output if 'returned' is used * Removed checksum=False from tests * Expanded test for lazy aggregation since PERCENTILE is lazy now * Added schlunma to common links * Addaux speedup (#4718) * Attempt faster add-aux-fact * Added whatsnew draft. * Put PR ref into whatsnew. * Review changes. * Remove time_return benchmarks. (#4717) * Credit reviewer in what's new contributions. (#4705) * Credit reviewer in what's new contributions. * Correct example link in what's new docs. Co-authored-by: Will Benfold <[email protected]> Co-authored-by: Will Benfold <[email protected]> * Change Cell equality to equate nans (fixes #4681) (#4701) * nans in cells satisfy equality * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * address review comments Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Netcdf saving: workaround known netcdf bug. (#4407) * Netcdf saving: workaround known netcdf bug. * Fix netcdf dim renaming for anonymous dims. * Fixes to test-mesh generation to preserve save-load roundtrips. * Added tests for all the different places where code was fixed. * Tidy some formatting and comments. * Fix rebase error? * Review changes. * Updated environment lockfiles (#4724) Co-authored-by: Lockfile bot <[email protected]> * MAX_RUN into docs (#4726) * Datum support in Iris (#4704) * Support in helpers * coord_systems changes * More additions * Revert some FUTURE guards and condense datum application * Fixing tests and improving * More additions * Tests pass * transform_points test * Review fixes * In datums, unknown means None * Fix test * Suppress FutureWarning in the tests that were failing due to it * Review fixes * What's new * Extra test result * Bump peter-evans/create-pull-request from 4.0.2 to 4.0.3 (#4733) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.0.2 to 4.0.3. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](https://github.com/peter-evans/create-pull-request/compare/bd72e1b7922d417764d27d30768117ad7da78a0e...f094b77505fb89581e68a1163fbd2fffece39da1) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Updated environment lockfiles (#4732) Co-authored-by: Lockfile bot <[email protected]> * Replace nose with pytest (#4734) * Replace nose with pytest * Reinstate magic processor number * add psutil, fstrings and rename TestMixin * Caching during load (#4716) * Caching * Move _optimum_chunksize docstring * Should be copying coords because they're mutable * Handle failure of datetime comparisons gracefully * Review fixes and more careful checks on mutable objects * coord_system doesn't have 'copy' but __repr__ covers the whole thing (I think) * Review fixes * Revert coord_system changes * Still need to handle tuple issue * What's new * Fix prompted by test failure * Limit cache size * Work around comparable datetime issue * More sensible climatological time points (#4723) * Initial moves to introduce result_coord_func * climatological keyword * Climatology argument to aggregated_by * Fix the tests * Review changes from RC * Test fixes * Further test fixes * Move test code back out after rebase * Different fix for self.coord_dims failure * Add ifmain * Revert inadvertent doctest changes * Review improvements * Fix doctest black broke * Stop new tests being executable, which makes the test runner miss them * Docstrings to comments so they don't obscure test names in results * Apply suggestions from code review Co-authored-by: Ruth Comer <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Review fixes * What's new Co-authored-by: Ruth Comer <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Remove Mule monkey patch. (#4738) * climatology doc tweak (#4740) * Mesh docs - include examples of converting different mesh formats. (#4739) * Mesh docs - include examples of converting different mesh formats. * SMC mesh example fix gotcha. * Add sample images to mesh conversion examples. * Mesh conversion examples - fix bullet points. * Mesh conversion examples - print meshes. * Whats New entry. * Mesh conversion examples - more detailed comments. * Gallery: update NEMO example (#4741) * update nemo example * clearer comment * fixed numbered list entry (#4743) * Plotting circular data extends args as well as the data (#4649) * Extend any kwarg array * Add test * Add comments and update imagerepo.json * Try using the value as an array, in case it's been given as a list etc. * What's new * Datum performance improvements (#4731) * Set stacklevel to get more useful FutureWarning * Remove spare printing * Only generate crs and globe on demand, handle attr setting * Updates docstrings to make it clearer what's going on * Additional tests (and fixes found from testing) * Warn that inverse_flattening setting doesn't help * Updated environment lockfiles (#4742) Co-authored-by: Lockfile bot <[email protected]> * Extra datum translation (#4753) * Updated environment lockfiles (#4760) Co-authored-by: Lockfile bot <[email protected]> * Permit fast percentile with mdtol=0 (#4755) * Permit fast percentile with mdtol=0 * What's new * Check arrays like they're masked, and make the expected arrays masked * Bigger arrays to avoid np quirk, bug fix, check masking in 2d_multi * Suppress numpy masked percentile warning * Use a larger test array that numpy handles how it handles most of them (the worse case) * Broadcast the mask in the non-lazy case with added dim * Bug fix on ndim test * Review fixes * Credit @rcomer on PR #4755 review (#4761) * CPerf and SPerf Benchmark Fixes (#4758) * CSPerf fixes. * Correct argument hashing in file names. * Warn if BENCHMARK_DATA is not set. * SPerf combine_regions better file handling. * SPerf don't store FileMixin files long term - too much space. * More realistic SPerf file sizes, allow larger-than-memory files. * Add SPerf comment about total disk space. * Corrected CSPerf directories printout. * Remove namespace conflict in SPerf combine_regions. * don't use np.float or np.int (#4763) * Test warnings (#4764) * import from collections.abc * deprecated csr module * unittest deprecations * random_integers -> randint * collections again * inspect deprecation * reduce redunancy * non test class * Increase speed of iris.analysis.trajectory.interpolate with linear interpolation (#4366) * Interpolate all points at once rather than sequentially * This splits the internals of cube.interpolate in an effort not to make so much superfluous data, but is slow * Generate the extra values then discard them, but with minimal looping * Updated docstrings to clarify behaviour * Benchmarks for trajectory (linear and nearest neighbour) * Update error thrown for aux coord over interpolated and uninterpolated dimensions, and add unit tests * Update cml * What's new has moved * What's new fix for rebase * Prevent truncation of cell method descriptions with nested brackets (#4436) * Add failing test for brackets within comments * Fix test * Separate private function now splits the cell method before it's parsed * Add additional failing test for multiple axis methods * Handle multiple axis cell methods * Update docstring to reflect eventual choices * Add warnings to function, and test them * Significantly simpler warning checks * Developer documentation on available testing conveniences (#4600) * Developer documentation on available testing conveniences * what's new * Update to be easily usable without code links working * Rebase * Cubelist contain only cubes -- resurrected (#4767) * ensure cubelists only contain cubes * address __iadd__ and __setitem__ * __setitem__ tests * test for setting more than 1 item * Fix __setitem__ and Py2 tweaks * implement __setslice__ for Python2.7 * change exceptions to warnings * stickler * duck type check; move helpers outside class * blank lines * proposed: revert warnings to exceptions * remove stray extra 'test_fail' * pass sequences through __init__; _assert_is_cube * Replace CubeList init with new. Cube testing duck-type. * Review change. * Provide new-style whatsnew. * Fix whatsnew Co-authored-by: Ruth Comer <[email protected]> * Updated environment lockfiles (#4775) Co-authored-by: Lockfile bot <[email protected]> * Redirect whatsnew to latest (#4727) * Redirect whatsnew * Get the top bar working too * Clean build with right links * Update release docs * Review fixes * update section name for clarity * Bump peter-evans/create-pull-request from 4.0.3 to 4.0.4 (#4783) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.0.3 to 4.0.4. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](https://github.com/peter-evans/create-pull-request/compare/f094b77505fb89581e68a1163fbd2fffece39da1...923ad837f191474af6b1721408744feb989a4c27) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Updated environment lockfiles (#4782) Co-authored-by: Lockfile bot <[email protected]> * Fix whatsnew (#4784) * Fix whatsnew * Instead of changing 3.0.rst, rename 'whatsnew.rst' to 'index.rst' * Missed one * `PolarStereographic` implementation (#4773) * PolarStereographic implementation * Test data version * What's new * Accept suggestion to lib/iris/coord_systems.py Co-authored-by: Patrick Peglar <[email protected]> * Permit Stereographic saving * Update what's new * Review fixes Co-authored-by: Patrick Peglar <[email protected]> * Add mesh details to cube printout. (#4778) * Slightly refactor repr-html code to rationalise section handling. * Test repr-html of string attributes. * Add mesh details to cube printout. * Update meshcube printouts in docs. * Add Mesh section to repr-html. * Review change : make test clearer. * Review change : fix string truncation/quoting. * Retire use of the New labels. (#4801) * pinned pydata-sphinx-theme until the docs are dark mode friendly. (#4796) * adopt ci gha (#4503) * adopt ci gha * bump iris-test-data to latest version * ci noxify * remove dummy cache key name * remove precommit nox task * added whatsnew entry * remove mpl cfg for linkcheck * trial composite nox-cache * composite iris-data-cache action * composite conda-env-cache action * composite conda-pkg-cache action * composite cartopy-cache action * required lock-file composite action input * review action * review action * nox inputs.lock_file * env_name composite action input * replace HOME with tilde usage * cancel in-progress workflow jobs * refresh-lockfiles gha note * Scripted Logo Generation, take two (#3935) * Added logo generation Python script. * Replace lambda scale_func.n * Matched current logo appearance. * Simplified gradient code. * Renamed land_mask to land_clip. * Make new svg instead of faffing with reformatting existing. * Refactor out 'style' in attributes. * File header. * Integrated logo generation script into Sphinx docs generation. * Environment variable logo names. * Removed banner width calculation to avoid font dependency. * Refactored to also generate rotating logos. * Replace plt.tightlayout with plt.subplots_adjust. * Replaced OrderedDicts with dicts (not needed >=Py3.6). * Numpy standard import form. * Replaced animated SVG with precusor files for animated GIF. * Corrected logo URL to source from ReadTheDocs site. * Changes to better match 'hand-created' logo. * Fixed logo rotate zip title. * Relocated logo generation script to SciTools/marketing. * update links (#3942) * update links * added s to http * Added logo generation Python script. * Replace lambda scale_func.n * Matched current logo appearance. * Simplified gradient code. * Renamed land_mask to land_clip. * Make new svg instead of faffing with reformatting existing. * Refactor out 'style' in attributes. * File header. * Integrated logo generation script into Sphinx docs generation. * Environment variable logo names. * Removed banner width calculation to avoid font dependency. * Refactored to also generate rotating logos. * Replace plt.tightlayout with plt.subplots_adjust. * Replaced OrderedDicts with dicts (not needed >=Py3.6). * Numpy standard import form. * Replaced animated SVG with precusor files for animated GIF. * Corrected logo URL to source from ReadTheDocs site. * Changes to better match 'hand-created' logo. * Fixed logo rotate zip title. * Relocated logo generation script to SciTools/marketing. * Include version string in logo generation. * Reference official logo generation code. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix README docs reference. * Include the logos, don't generate on the fly. Co-authored-by: Ruth Comer <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * fix composite gha (#4809) * fix composite gha * bump gha cache_build to force purge * Whats new entry for SVG logo. (#4810) * Updated environment lockfiles (#4815) Co-authored-by: Lockfile bot <[email protected]> * add gha workflow badges (#4813) * address npy disable cpu features warning (#4811) * Ensure tests use ncgen/ncdump from the Python env; rationalise uses of ncgen. (#4794) * Ensure tests use ncgen/ncdump from the Python env; rationalise uses of ncgen a bit. * Tidy some imports. * Rationalise use of ncgen and avoid subprocess 'shell=True'. * Review changes: revert to importing iris.tests first. * Tidy routines slightly. * Fix subprocess call. * Added whatsnew. * Limit memory benchmark result to 5Mb minimum (#4818) * docs: cirrus-ci to gha (#4821) * docs: cirrus-ci to gha * review actions * Stereographic load with scale factor (#4785) * Allow passing of method keyword to numpy.percentile (#4791) * allow passing of method keyword to numpy.percentile * review actions * pass all kwargs * fix doc kwargs * Update image testing (#4759) * Use images from test data * Bug fixes and docs * Include circular plot image * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Oops, missed it. There now * Update test data version * Update __all__ * Type hinting * No underscore * Join strings * Other underscores * Other test data version location * Doc fixes * Imagerepo refresh info * Move the lock * Fix refs * Remove image index (as it's now in the test data index) * Fix the json test * Revert pillow pin removal to separate concerns * Update imagerepo for test that passes with penultimate val * Second imagerepo update * Third set of imagerepo changes * Fourth imagerepo changes (gallery test) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * whatnew for #4791 (#4823) * bump ci to latest iris-test-data version (#4825) * auto generate gha auth token (#4817) * auto generate gha auth token * add docs for github app config * linkcheck ignore metarelate.net * remove metarelate URL whatsnew reference * Fix stock CDL headers for unlimited time dimension. (#4827) * Fix CDL headers for tests.stock.netcdf. * Whats new entry. * Improved unlimited dimension check in stock NetCDF generation. * Whatsnew minor fix (#4829) * Update latest.rst * PR link * add issue link * Updated environment lockfiles (#4831) Co-authored-by: Lockfile bot <[email protected]> * rationalise doctests gha (#4819) * rationalise doctests gha * update job name with session * add nox session as composite input * minor tweak * review action - tidy nox composite inputs * Remove pin, update hashes, improve script (#4826) * Remove pin, update hashes, improve script * What's new * Lockfile and whatsnew * Shareable urls * Later lockfile * Shareable... * Check for consistency before fiddling * Updates for new test data (idiff'ed) * Keep lockstep between imagerepo and data * idiff always runs after imagerepo.json has been updated anyway * Gallery test updates (also idiff'd) * Update test data version * Implement `iris.plot.fill_between` (#4647) * Remove pin, update hashes, improve script * What's new * Lockfile and whatsnew * Shareable urls * Later lockfile * Shareable... * Check for consistency before fiddling * Updates for new test data (idiff'ed) * Keep lockstep between imagerepo and data * idiff always runs after imagerepo.json has been updated anyway * Gallery test updates (also idiff'd) * Implement fill_between and write tests * Simplify error check * Test images * What's new * Image test results * Fix error message * Pre-emptive test data version update Co-authored-by: Bill Little <[email protected]> * Python 3.9 CI & Combine CI workflows (#4832) * combine ci workflows * remove badge * ci unpin python * post #4759 review actions (#4833) * pytest less verbose (#4837) * Remove redundant testing assert methods (#4838) * remove assertWarnsRegexp * remove assertStringEqual * post rebase tidyings * whatsnew * NetCDF Generation Adjustments (#4836) * remove pillow pin from setup.cfg (#4839) * Support python 3.10 (#4840) * extend ci support for py310 * fix Cell.__hash__ py310 nan behaviour * review actions * update github app docs (#4844) * Lockfile update and Gregorian to Standard calendar change (#4847) * sed gregorian * sed CALENDAR_GREGORIAN * rename cml files * revert whatsnew 2.1 and test_cf.py * revert spelling_allow * post rebase sed 'gregorian' * Updated environment lockfiles * cf-units minimum pin * review actions Co-authored-by: Lockfile bot <[email protected]> * Updated environment lockfiles (#4850) Co-authored-by: Lockfile bot <[email protected]> * avoid setuptools deprecation (#4848) * [pre-commit.ci] pre-commit autoupdate (#4851) updates: - [github.com/pre-commit/pre-commit-hooks: v4.2.0 → v4.3.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.2.0...v4.3.0) - [github.com/psf/black: 22.3.0 → 22.6.0](https://github.com/psf/black/compare/22.3.0...22.6.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Alternative Cell.__hash__ implementation for NaN support (#4852) * Alternative Cell.__hash__ implementation for NaN support * add whatsnew entry * whatsnew update (#4853) * adopt setuptools-scm for auto versioning (#4841) * adopt setuptools-scm for auto versioning * update py310.yml requirements * update locks * simplify docs version * update dev release docs * update .gitignore for vscode * update locks * add exclude _version.py to MANIFEST.in * review actions * update lock files * update pyproject.toml * what a whatsnew entry * fix rtd version (#4855) * Updated environment lockfiles (#4858) Co-authored-by: Lockfile bot <[email protected]> * pytest verbosity (#4861) * Updated environment lockfiles (#4867) Co-authored-by: Lockfile bot <[email protected]> * Recommend `pytest` in developer guide (#4866) * recommend pytest * pros and cons * tweaks * add missing skips (#4865) * Updated environment lockfiles (#4873) Co-authored-by: Lockfile bot <[email protected]> * Replace testing helper function (#4878) * replace unmasked_data_as_1d_array * whatsnew * Cube arithmetic array type handling (#3790) * add new tests; fix existing tests * force lhs lazy if rhs lazy * black * add in-place tests * add handling for unmasked, masked real array combo * add tests for false skeleton * rearrange _math_op_common if-loops * revert maths.py to upstream/master * simpler solution * reduce masking arithmetic tests * expand and improve tests * add whatsnew * fix rebase snafu * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update following numpy#21977 * Revert "update following numpy#21977" This reverts commit 7d62ad6b8779129b9f4c2f7d26f070f5402f95e9. * update comment * a before b Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * automate sdist and wheel build and publish (#4849) * automate sdist and wheel build and publish * update names * tidy package manifest and discovery * add note to dev docs * update MANIFEST.in * Update .github/workflows/ci-wheels.yml Co-authored-by: Martin Yeo <[email protected]> * add unshallow comment to rtd * reinstate docs release * add pypa build comment * test wheel * added whatnew + tweak nox wheel emsgs * Update docs/src/developers_guide/release.rst Co-authored-by: Martin Yeo <[email protected]> * Warn users of increased `recombine_submeshes` memory demand. (#4881) * Warn users of increased recombine_submeshes memory demand. * Clearer what's new entry. * Sphinx reset modules (#4885) * fix sphinx-gallery * change gallery index reference * Updated environment lockfiles (#4884) Co-authored-by: Lockfile bot <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#4886) updates: - [github.com/PyCQA/flake8: 4.0.1 → 5.0.2](https://github.com/PyCQA/flake8/compare/4.0.1...5.0.2) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * fix percentile docstring (#4888) * [pre-commit.ci] pre-commit autoupdate (#4895) updates: - [github.com/PyCQA/flake8: 5.0.2 → 5.0.4](https://github.com/PyCQA/flake8/compare/5.0.2...5.0.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Upgrade `iris.util.mask_cube` (#4889) * rewrite mask_cube * fix import problems * simplify _unmask_mask and its tests * parametrize not in place 1d _mask_array * pytest in-place _mask_array tests * pytest _mask_array broadcasting tests * remove iris.tests from test__mask_array * attempt to preserve metadata * pull masked array assertions off test class * pytestify test__unmask_mask.py * remove _unmask_mask; tweak test * numpydoc docstring * add CML checks * preserve cube.metadata; add final CML * path handling * get hold of _mask_array result Co-authored-by: Bill Little <[email protected]> * more thorough in_place check Co-authored-by: Bill Little <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * review actions * whatsnew Co-authored-by: Bill Little <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * set default 'unknown' version (#4892) * Prevent color bar from being misplaced (#4894) * Prevent color bar from being misplaced Currently, if `plt.gca()` gives a different Axes object than `axes` in the function `_label`, the color bar will be malpositioned, ending up either on another subfigure, or in another figure window altogether. Specifying the `ax` argument when calling `plt.colorbar` prevents this. * add whatsnew and test coverage * check axes and figure * tidy and add extra axes2 test Co-authored-by: Bill Little <[email protected]> * Lockfile update and skip questionable test (#4901) * Updated environment lockfiles * skip questionable test Co-authored-by: Lockfile bot <[email protected]> * Adapt to the latest setuptools editable configuration. (#4903) * Adapt to the latest setuptools editable configuration. * What's new entry. * What's new typo. * Update setuptools in Conda requirements. * pytest gallery tests (#4792) * pytest parametrize gallery tests * two context managers as fixtures * use pathlib instead of os * docstrings * use pytest.mark.filterwarnings * show_replaced_by_check_graphic as fixture * Revert previous (more readable without) This reverts commit bdca27cd301fff9de034f14db9da991dac43facf. * gallery_dir function to variable * add setup/teardown fixture * tweak docstring * remove gallerytests from Makefile * update dev guide * doc tweaks * use monkeypatch to simplify * move stuff about * monkeypatch for sys.path; comments and param ids * revert assert False * revert deliberate fails * import_patches fixture * post rebase check_graphic fix * update test references * whatsnew * test data version * Updated environment lockfiles (#4904) Co-authored-by: Lockfile bot <[email protected]> * Revert Cell.__hash__ fix (#4874) * Revert Cell.__hash__ fix * add whatsnew entry * update comments * Revert #4701 cell nan equality Co-authored-by: lbdreyer <[email protected]> * Add whats new entry for 4734 (#4908) * Extend new_axis to reshape _DimensionalMetadata objects (#4896) * extend iris.util.new_axis * add tests * fix tests * Rewrite new_axis; extra stock cube; cube _dimensional_metadata utility and tests * Add new_axis tests * Convert to pytest * Rename broadcast -> expand; review actions * Add whatsnew entry Co-authored-by: stephen.worsley <[email protected]> * Standard names table update (v79) (#4910) * update cf standard name table * add whatsnew * fix whatsnew * Pin shapely (#4911) * pin shapely * update whatsnew * Improvements to Pandas-to-Iris bridge (#4890) * First pass using merge to parse ndim Pandas DataFrame. * Second pass actually doing array manipulation this time. * Tidying for public consumption. * Improved index handling. * Pytest conversion. * Minor re-factoring. * Support for copy argument. * Calendar handling. * Correct coord reshaping. * Correct array indexing. * DataFrame Series agnosticism. * Docstrings and structure. * Error as_cube if FUTURE behaviour is set. * Tests WIP. * More tests. * Completed tests. * Suppress deprecation warning in TestSeriesAsCube. * Docstring corrections. * Another docstring fix. * Another docstring fix. * Another docstring fix. * Doctests. * Doctests. * Strict expectation of one Cube in tests. * format_dimensional_metadata typo. * Rename pandas_array to pandas_structure. * Leaner warnings for Series with column arguments. * Fix date tests. * Back out pandas_ndim FUTURE flag. * Uncomment code, whoops. * What's new entry. * Remove erroneous pass. * Doctest typo. * Handle an empty Pandas structure. * Test showing that dimension order is preserved. * Informative error for ragged indexes. * Include shapely pin in setup.cfg (#4917) * Include shapely pin in setup.cfg. * What's new entry. * update whatsnew (#4914) * Avoid using mutable default. (#4918) * Fix some @trexfeathers What's New entries (#4920) * Minor What's New fixes. * Missing space. * Update whatsnew for v3.3.0rc0 (#4921) * update whatsnew * fix index * remove template * address review comments * Updated environment lockfiles (#4923) Co-authored-by: Lockfile bot <[email protected]> * Update whatsnew (#4924) * reset whatsnew * remove bugfix section * address review comments * Bump peter-evans/create-pull-request from 4.0.4 to 4.1.1 (#4922) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.0.4 to 4.1.1. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](https://github.com/peter-evans/create-pull-request/compare/923ad837f191474af6b1721408744feb989a4c27...18f90432bedd2afd6a825469ffd38aa24712a91d) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Tilde's and wildcard recognition within iris.save. (#4913) * Draft: Tilde's and wildcard can now be read by iris.save. Modifications and tests provisionally done, docstrings still need editing, with examples and doctests needing being added/editing. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Docstrings updated for expand_filespecs and save * docstrings for save and expand_filespecs updated to numpy formatting * Reviewed: Added expansion and relative path tests to expand_filespecs. Ensured list indexing returns single item lists. Minor comment changes. * Updated latest What's New, and added ESadek-MO to common links * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fixed isort conflicts Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Unpin shapely (#4925) * unpin shapely * update whatsnew * SUM, COUNT, PROPORTION: don't use dask on numpy arrays (#4905) * COUNT * SUM * tidy up * increase dask min pin * fix returned weights when masked * typo * docstrings * whatsnew * include reviewer in whatsnew * Remove `setUpClass` from Iris tests. (#4927) * remove IrisTest.setUpClass * whatsnew * Better handle `setuptools_scm` versioning (#4926) * Use setuptools_scm release-branch-semver version_scheme. * Properly handle all possible scm-rtd combinations. * What's new entry. * Use git stash to protect setuptools_scm from RTD. * Better version badges. * Better use of git stash. * Substitute commit SHAs in place of versions where appropriate. * Make rtd_version safe for use in shields.io badges. * Make rtd_version safe for use in shields.io badges. * Allowed collapsing coordinates with `nbounds != (0, 2)` (#4870) * Allowed collapsing over coordinates with nbounds!=0,2 * Simplified test * Added further tests for other warnings * pre-commit * Used unittest's assertWarnsRegex * Added What's new? entry * fix whatsnew (#4932) * Updated environment lockfiles (#4936) Co-authored-by: Lockfile bot <[email protected]> * update whatsnew title for v3.3 release (#4939) * Added zonal mean gallery example, continued from @TTV-Intrepid (#4935) * Added zonal mean gallery example, continued from @TTV-Intrepid * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Added TTVIntrepid to common links for What's New functionality * Fixed zonal mean plotting, add axh * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Minor visual changes, ax3 plotting fix, removed warning suppression. * updated imagerepo for zonal means * updated ci-tests yml to latest iris test data version * updated what's new * updated announcements to one line Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#4942) updates: - [github.com/psf/black: 22.6.0 → 22.8.0](https://github.com/psf/black/compare/22.6.0...22.8.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Remove deprecated 'python setup.py test' support (#4948) * Remove deprecated 'python setup.py test' support * add whatsnew entry * purge unused setup clean_source custom command (#4949) * purge unnecessary setup.py copy_copyright function (#4950) * fix setup.py std_names building (#4952) * fix setup.py std_names building * refactor * docs whatsnew entry updates (#4953) * Fix cube repr for scalar anc_var and cell measures (#4945) * Fix cube repr for scalar anc_var and cell measures * Add whatsnew * Fix cube summary tests * Review actions: reword whats new, reorder scalar sections in cube printout * Fix cube summary test, update whatsnew * Fix code comment * update pypi trove classifiers (#4954) * Add new Q+A issue, update author email Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Bill Little <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Lockfile bot <[email protected]> Co-authored-by: Martin Yeo <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Bill Little <[email protected]> Co-authored-by: Ruth Comer <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Patrick Peglar <[email protected]> Co-authored-by: Will Benfold <[email protected]> Co-authored-by: Denis Sergeev <[email protected]> Co-authored-by: tkknight <[email protected]> Co-authored-by: Will Benfold <[email protected]> Co-authored-by: Manuel Schlund <[email protected]> Co-authored-by: stephenworsley <[email protected]> Co-authored-by: Ruth Comer <[email protected]> Co-authored-by: iris-actions[bot] <107775138+iris-actions[bot]@users.noreply.github.com> Co-authored-by: scitools-ci[bot] <107775138+scitools-ci[bot]@users.noreply.github.com> Co-authored-by: Kristofer Krus <[email protected]> Co-authored-by: stephen.worsley <[email protected]> Co-authored-by: Elias <[email protected]>
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🚀 Pull Request
Description
This PR is a follow-on from PR #4840, which extended our CI testing support to cover
py310but unfortunately introduced a significant performance regression (Issue #4843) due to a necessary fix withiniris.coords.Cellto circumvent changed behaviour innumpy.nanhashing.This PR provides a performant alternative implementation, and thus restores the prior performance status quo.
Refer to the following benchmarking results comparing a commit based on this PR against
upstream/mainofiris.Benchmarks Summary...
Closes #4843
Consult Iris pull request check list