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Dask merge back #2597

Merged
merged 122 commits into from
Jun 14, 2017
Merged

Dask merge back #2597

merged 122 commits into from
Jun 14, 2017

Commits on May 26, 2017

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  3. Use _lazy_data functions for cube data.

    pp-mo authored and bjlittle committed May 26, 2017
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  6. Started skipping tests.

    pp-mo authored and bjlittle committed May 26, 2017
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  8. Various skips.

    pp-mo authored and bjlittle committed May 26, 2017
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  10. dask based merge

    marqh authored and bjlittle committed May 26, 2017
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  11. skip all iris_grib tests

    marqh authored and bjlittle committed May 26, 2017
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  12. Lazy pp loading

    djkirkham authored and bjlittle committed May 26, 2017
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  15. pp_load data property fix

    marqh authored and bjlittle committed May 26, 2017
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  17. Use Dask for concatenate (#38)

    * Swap out Biggus concatenate for Dask concatenate
    
    * Re-enable passing concatenate tests
    AlexHilson authored and bjlittle committed May 26, 2017
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  18. pp unit test

    marqh authored and bjlittle committed May 26, 2017
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  21. is_lazy_data over isinstance

    marqh authored and bjlittle committed May 26, 2017
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  22. test_field_collection with dask

    marqh authored and bjlittle committed May 26, 2017
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  23. use np.dtype in mock tests

    marqh authored and bjlittle committed May 26, 2017
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  24. typo fix and fill_value guarantee (#39)

    * fixed typo lazy_array to lazy_data; give fill_value attribute to all lazy data
    corinnebosley authored and bjlittle committed May 26, 2017
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  26. remove biggus lazy data, skip netcdf save

    marqh authored and bjlittle committed May 26, 2017
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  27. fix cube pickle test

    marqh authored and bjlittle committed May 26, 2017
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  28. skip netCDF save

    marqh authored and bjlittle committed May 26, 2017
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  29. 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
    corinnebosley authored and bjlittle committed May 26, 2017
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  31. skip as fill value lost

    marqh authored and bjlittle committed May 26, 2017
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  32. Don't try and merge 0-d arrays (#42)

    AlexHilson authored and bjlittle committed May 26, 2017
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  33. biggus skippers (#43)

    corinnebosley authored and bjlittle committed May 26, 2017
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  34. plot skippers (#45)

    corinnebosley authored and bjlittle committed May 26, 2017
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  36. header dates corrected (#46)

    * header dates corrected whitespace removed
    corinnebosley authored and bjlittle committed May 26, 2017
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  37. test implementation tweaks

    marqh authored and bjlittle committed May 26, 2017
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  38. skip non lazy coord loading

    marqh authored and bjlittle committed May 26, 2017
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  39. pickling test skip

    marqh authored and bjlittle committed May 26, 2017
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  41. Data first (SciTools#2392)

    Core refactor for dask usage
    marqh authored and bjlittle committed May 26, 2017
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  42. first run at daskifying stats and maths (SciTools#2402)

    * daskifying stats and maths
    corinnebosley authored and bjlittle committed May 26, 2017
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  43. Refactor AuxCoordFactory unit tests to remove biggus references (SciT…

    …ools#2401)
    
    * Refactor AuxCoordFactory unit tests to remove biggus references
    djkirkham authored and bjlittle committed May 26, 2017
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  45. passing tests unskipped (SciTools#2408)

    * passing tests unskipped
    
    * esmpy regrid skips removed
    corinnebosley authored and bjlittle committed May 26, 2017
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  46. Dask aggs (SciTools#2406)

    * Existing lazy stats working, mean / std / var, with mdtol-action wrapper.
    * Enable and test lazy collapse over multiple dimensions.
    pp-mo authored and bjlittle committed May 26, 2017
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  47. PPfield core_data (SciTools#2410)

    * Fix FieldCollation.data; Replace uses of PPField._data outside the class with core_data or data. Fix unittests
    djkirkham authored and bjlittle committed May 26, 2017
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  48. Replace intersection (SciTools#2409)

    * daskify_intersection
    
    * removed skippers for passing tests
    corinnebosley authored and bjlittle committed May 26, 2017
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  49. Tidy dask section of dev guide

    DPeterK authored and bjlittle committed May 26, 2017
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  51. 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
    DPeterK authored and bjlittle committed May 26, 2017
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Commits on May 30, 2017

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  2. Reuse multidim_daskstack in merge + fast um loading. (SciTools#2423)

    Use multidimension dask stacks in merge and fast um loading.
    lbdreyer authored and bjlittle committed May 30, 2017
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  3. Tighten purpose of array_masked_to_nans (SciTools#2424)

    Tighten purpose of `array_masked_to_nans`
    DPeterK authored and bjlittle committed May 30, 2017
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  4. 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
    bjlittle committed May 30, 2017
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  5. Consistent check for masked array types (SciTools#2434)

    * Consistent checking for ma
    
    * License headers
    
    * Fix missed instances
    DPeterK authored and bjlittle committed May 30, 2017
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  6. 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.
    bjlittle committed May 30, 2017
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  7. Replace dask 'compute()' usage with a common realisation call. (#2) (S…

    …ciTools#2447)
    
    Replace dask 'compute()' usage with a common realisation call.
    lbdreyer authored and bjlittle committed May 30, 2017
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  8. Remove some @tests.skip_biggus that are now unnecessary (SciTools#2450

    )
    
    Remove some biggus skippers.
    lbdreyer authored and bjlittle committed May 30, 2017
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  10. Fix for dtype.kind (SciTools#2453)

    * Fix for dtype.kind
    bjlittle committed May 30, 2017
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  11. Only use truediv in cubes (SciTools#2458)

    Only use truediv
    DPeterK authored and bjlittle committed May 30, 2017
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  12. Remove the last bits of biggus (SciTools#2451)

    Remove biggus imports
    DPeterK authored and bjlittle committed May 30, 2017
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  13. Dask data manager (SciTools#2461)

    Add data manager with tests.
    bjlittle committed May 30, 2017
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  14. Fix test fo test_rules.py

    lbdreyer authored and bjlittle committed May 30, 2017
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  15. 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
    lbdreyer authored and bjlittle committed May 30, 2017
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  17. Bring iris_grib back into iris.

    lbdreyer authored and bjlittle committed May 30, 2017
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  18. Daskify grib loading/saving

    lbdreyer authored and bjlittle committed May 30, 2017
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  19. GribWrapper deferred data testing

    corinnebosley authored and bjlittle committed May 30, 2017
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  20. Fix import order. (#4)

    * Fix import order.
    
    * Review actions.
    bjlittle committed May 30, 2017
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  21. Dask options for Iris processing (SciTools#2511)

    Dask opts controlled by simple function
    DPeterK authored and bjlittle committed May 30, 2017
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  22. Fix iris_grib integration tests.

    Fix translation generator tool to use internal grib module.
    lbdreyer authored and bjlittle committed May 30, 2017
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  24. Fix fill value usage at grib save time

    lbdreyer authored and bjlittle committed May 30, 2017
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  25. 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.
    pp-mo authored and bjlittle committed May 30, 2017
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  26. 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.
    bjlittle committed May 30, 2017
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  27. 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.
    pp-mo authored and bjlittle committed May 30, 2017
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  28. Remove LazyArray class from coords (SciTools#2518)

    Remove `LazyArray` class
    DPeterK authored and bjlittle committed May 30, 2017
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  30. Dask core data (SciTools#2521)

    * DataManager.core_data()
    
    * Cube.core_data()
    
    * Fileformats rules core_data()
    bjlittle committed May 30, 2017
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  31. 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
    bjlittle committed May 30, 2017
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Commits on May 31, 2017

  1. 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.
    pp-mo authored and bjlittle committed May 31, 2017
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  4. Update docstring

    DPeterK authored and bjlittle committed May 31, 2017
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  5. Simplify numeric tests

    DPeterK authored and bjlittle committed May 31, 2017
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  6. Add _proportion() comment.

    bjlittle committed May 31, 2017
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  7. Update __eq__ doc-string.

    bjlittle committed May 31, 2017
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  8. Integrate DataManager with Coord, DimCoord, and AuxCoord (SciTools#2527)

    Integrate DataManager with Coord classes
    DPeterK authored and bjlittle committed May 31, 2017
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  9. 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.
    bjlittle committed May 31, 2017
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  10. Remove biggus skippers and update cml

    DPeterK authored and bjlittle committed May 31, 2017
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  11. 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.
    pp-mo authored and bjlittle committed May 31, 2017
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  12. Fix non-lazy pickle test

    DPeterK authored and bjlittle committed May 31, 2017
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  13. Unexpectedly good

    DPeterK authored and bjlittle committed May 31, 2017
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  15. 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
    djkirkham authored and bjlittle committed May 31, 2017
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  16. Update test data sha

    djkirkham authored and bjlittle committed May 31, 2017
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  17. Coord points and bounds inheritance. (SciTools#2553)

    * Refactor Coord inheritance.
    
    * Review changes.
    
    * Review change -- reword comments for clarity.
    
    * Fix Python3-specific problem.
    pp-mo authored and bjlittle committed May 31, 2017
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  18. Purge spurious imports (SciTools#2560)

    * Purge spurious imports
    DPeterK authored and bjlittle committed May 31, 2017
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  20. Fix rules test for _make_cube (SciTools#2557)

    * Fix a test resulting in a segfault
    DPeterK authored and bjlittle committed May 31, 2017
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  21. 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
    djkirkham authored and bjlittle committed May 31, 2017
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  22. 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.
    pp-mo authored and bjlittle committed May 31, 2017
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  24. 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.
    pp-mo authored and bjlittle committed May 31, 2017
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  25. Ensure cube.transpose functionality (SciTools#2580)

    * Fix cube.transpose new_order kwarg type bug
    
    * pep8: remove extraneous blank line
    DPeterK authored and bjlittle committed May 31, 2017
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  26. Reinstate doctest and extest

    DPeterK authored and bjlittle committed May 31, 2017
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  27. Reinstate deprecated Future options

    DPeterK authored and bjlittle committed May 31, 2017
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  28. Update interpolation doc example vals

    DPeterK authored and bjlittle committed May 31, 2017
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Commits on Jun 2, 2017

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  2. Backout PR SciTools#2452.

    bjlittle committed Jun 2, 2017
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Commits on Jun 5, 2017

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Commits on Jun 8, 2017

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Commits on Jun 13, 2017

  1. Review actions.

    bjlittle committed Jun 13, 2017
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