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Dask merge back #2597
Dask merge back #2597
Commits on May 26, 2017
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Use Dask for concatenate (#38)
* Swap out Biggus concatenate for Dask concatenate * Re-enable passing concatenate tests
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typo fix and fill_value guarantee (#39)
* fixed typo lazy_array to lazy_data; give fill_value attribute to all lazy data
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Fixes for biggus array checks (#41)
* Changed most occurrences of biggus.Array instance checks to either dask.array.Array instance checks or lazy data checks * updated headers
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* header dates corrected whitespace removed
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Core refactor for dask usage
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first run at daskifying stats and maths (SciTools#2402)
* daskifying stats and maths
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Refactor AuxCoordFactory unit tests to remove biggus references (SciT…
…ools#2401) * Refactor AuxCoordFactory unit tests to remove biggus references
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passing tests unskipped (SciTools#2408)
* passing tests unskipped * esmpy regrid skips removed
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* Existing lazy stats working, mean / std / var, with mdtol-action wrapper. * Enable and test lazy collapse over multiple dimensions.
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PPfield core_data (SciTools#2410)
* Fix FieldCollation.data; Replace uses of PPField._data outside the class with core_data or data. Fix unittests
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Replace intersection (SciTools#2409)
* daskify_intersection * removed skippers for passing tests
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Reinstate
as_lazy_data
(SciTools#2421)* Reinstate func and uses in Iris code * Tests use new func, tests for new func * lazy data func handles masked arrays * Review actions * Remove missed spurious chunk sizes * Review action: reference a function as a function
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Commits on May 30, 2017
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Reuse multidim_daskstack in merge + fast um loading. (SciTools#2423)
Use multidimension dask stacks in merge and fast um loading.
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Tighten purpose of
array_masked_to_nans
(SciTools#2424)Tighten purpose of `array_masked_to_nans`
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fill_value and dtype (SciTools#2433)
* Testing ideas for cube data/dtype/fill_value interaction (not passing -- need new API). * Add checks for realisation; fix dtype tests; use 'lazy' keyword instead of 'real'. * With test failures to investigate. * Fixed tests for new code from SciTools#2433. * Fix tests * Pep8 fix. * Fixed data_dtype_fillvalue test fails (other things now failing). * Fix bug in clearing _dask_array when assigning real data. * Keep fill value of cube when resetting the cube's data * Fix concatenate tests. * Keep fill values during stats operations; cast cml fill values to float64. * Keep fill values during regrid test. * Fix basic maths tests. * Tidy cube.__init__ for dtype setting. * Review actions. * Rename concatenate unit tests. * Review actions. * pep8
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Consistent check for masked array types (SciTools#2434)
* Consistent checking for ma * License headers * Fix missed instances
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NetCDF save with dask support (SciTools#2411)
* NetCDF save with dask support * Refactor and use array_nans_to_masked * Add array_nans_to_masked test coverage. * Refactor. * Working tests. * Update comment detail for convert usage. * Use array.dtype in convert_nans_array * Review actions. * Review actions.
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Replace dask 'compute()' usage with a common realisation call. (#2) (S…
…ciTools#2447) Replace dask 'compute()' usage with a common realisation call.
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Only use truediv in cubes (SciTools#2458)
Only use truediv
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Remove the last bits of biggus (SciTools#2451)
Remove biggus imports
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Remove biggus test skipper: fix pp field data (SciTools#2473)
* pp save return field's data as masked array; fix test to check fill value of cube not data, and cube's dtype * Fix bmdis of fields that were saved from global.pp test data
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Dask options for Iris processing (SciTools#2511)
Dask opts controlled by simple function
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Fix iris_grib integration tests.
Fix translation generator tool to use internal grib module.
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DataManager used for cell measures (SciTools#2513)
* Use DataManager for CellMeasures data. * Review changes: clearer comments. * Add lazy data tests * Add masked saving test * Review actions: license dates, test updates * Prevent sliced measures data being a view on the parent. * Pep8 fix. * Review changes.
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Dask cube and data manager integration (SciTools#2492)
* Initial integration * Renames + data_manager tests. * Add missing cube.copy return + pep8 * Fixed concatenate + added cube.replace with tests * Fix test_Cube.py * Fix test_fast_load.py dtype setter. * Fix test_cdm.py metadata. * Fix merge + fill-value failures * licence years + numpy maskedconstant dtype fix * Fix merge as_concrete_data result_dtype * Use Cube.replace for data + fill-value setting. * Remove _lazy_data imports from cube. * Minor refactor of _deepcopy. * Minor ProtoCube._get_cube tidy. * Update test case comment. * Update iris.cube.Cube doc-string. * Align data & cube fill-value + supporting tests. * Fix replace corner case. * Added cube.__getitem__ test. * Fix merge + merge fill-value promote. * Fix concatenate + concatenate fill-value promote. * Add dask issue reference + use np.promote_types. * Added extra review action tests.
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Prevent sliced coords sharing data with their parent coord. (SciTools…
…#2517) * Prevent sliced coords sharing data with their parent coord. * Fix (and test) null slicing [:, :, ...] specifically. * Simplify coord getitem code. * Review changes.
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Remove
LazyArray
class from coords (SciTools#2518)Remove `LazyArray` class
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Dask core data (SciTools#2521)
* DataManager.core_data() * Cube.core_data() * Fileformats rules core_data()
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Dask merge concat fill value (SciTools#2520)
* Fix concatenate fill value. * Fix merge fill value. * Added merge invariant tests. * Added concatenate invariant tests. * Review actions. * Simplify merge/concatenate match condition. * expected_fill_value
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Commits on May 31, 2017
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Unify getitem code between Cube, Coord and CellMeasures. (SciTools#2519)
* Some changes on the way to getting lazy AuxCoords in an actual load. * Unify getitem code between Cube, Coord and CellMeasures. * Review changes: Simplify + document '_slice_data_with_keys' function. * Further review changes; functional tests for iris.util._slice_data_with_keys. * Added purely results-based tests.
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Integrate DataManager with Coord, DimCoord, and AuxCoord (SciTools#2527)
Integrate DataManager with Coord classes
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Dask data manager propagate (SciTools#2548)
* Propogate masked fill-value to dm. * Fix existing CML. * __init__ fill-value 'none' and None * Fix broken DataManager tests. * Add propogate test coverage + minor refactor * Fix typo * Review actions.
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More Coordinate tests for variously lazy/real points and bounds (SciT…
…ools#2547) * Enhanced Coord tests including new dask+lazy functionality. * Review changes: remove skips, legacy support and debug code. * Factor out common test code. * Test init on all combinations; test with bounds dtype different from points. * Review changes to tests.unit.coords module. * Pep8 fix. * Review changes.
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Ensure declared dtype of data proxy objects matches returned dtype (S…
…ciTools#2543) * Make NetCDFDataProxy dtype equal nan_array dtype * Handle PPDataProxy. Require correct dtype to be passed to BetCDFProxy initialiser * Update cml files * Always return array of specified dtype, even if the type would be promotable * Add data_dtype property to field classes * Add test for partial mask in pp file * Update test data sha * Use data_dtype to construct grib proxy * Minor tweaks * data_dtype -> realised_dtype
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Coord points and bounds inheritance. (SciTools#2553)
* Refactor Coord inheritance. * Review changes. * Review change -- reword comments for clarity. * Fix Python3-specific problem.
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Purge spurious imports (SciTools#2560)
* Purge spurious imports
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Fix rules test for _make_cube (SciTools#2557)
* Fix a test resulting in a segfault
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Handle MaskedConstant in cube maths (SciTools#2526)
* Handle MaskedConstant in cube maths * np.ma -> ma * Remove fill_value from tests. Fix comment typo * Refactor _inplace_common_checks * Refactor _output_dtype. Modify _get_dtype * Add unit tests * Fix fill_value issue * Fix docstrings and add clarifying comment * Fix Python 3 div issue * Refactor, and add docstring fro _output_dtype
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Fix PP bmdi handling (SciTools#2564)
* Various un-skips. * Checked new result for PPfields repr. * Fix mock field data in TestVertical. * Fix usage of BMDI in pp load and save. * Fix test problem. * Tidy out old comments. * Use new field.realised_dtype where appropriate. * More test fixes. * Review changes, mostly cosmetic.
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Use six.assertRegex to avoid Python 3 test method deprecation. (SciTo…
…ols#2565) * Use six.assertRegex to avoid Python 3 test method deprecation. * Review changes.
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Ensure cube.transpose functionality (SciTools#2580)
* Fix cube.transpose new_order kwarg type bug * pep8: remove extraneous blank line
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Commits on Jun 2, 2017
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Commits on Jun 5, 2017
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