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Lazy netcdf saves #5191

Merged
merged 92 commits into from
Apr 21, 2023
Merged

Lazy netcdf saves #5191

merged 92 commits into from
Apr 21, 2023

Commits on Mar 10, 2023

  1. Basic functional lazy saving.

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  2. Simplify function signature which upsets Sphinx.

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  3. Non-lazy saves return nothing.

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  4. Now fixed to enable use with process/distributed scheduling.

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  5. Remove dask.utils.SerializableLock, which I think was a mistake.

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  6. Make DefferedSaveWrapper use _thread_safe_nc.

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  7. Fixes for non-lazy save.

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  8. Avoid saver error when no deferred writes.

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  9. Reorganise locking code, ready for shareable locks.

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  10. Remove optional usage of 'filelock' for lazy saves.

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  11. Document dask-specific locking; implement differently for threads or … 

    …distributed schedulers.
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  12. Minor fix for unit-tests.

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  13. Pin libnetcdf to avoid problems -- see SciTools#5187.

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  14. Minor test fix.

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Commits on Mar 13, 2023

  1. Move DeferredSaveWrapper into _thread_safe_nc; replicate the NetCDFDa… 

    …taProxy fix; use one lock per Saver; add extra up-scaled test
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Commits on Mar 16, 2023

  1. Update lib/iris/fileformats/netcdf/saver.py 

    Co-authored-by: Bouwe Andela <bouweandela@gmail.com>
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  2. Update lib/iris/fileformats/netcdf/_dask_locks.py 

    Co-authored-by: Bouwe Andela <bouweandela@gmail.com>
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  3. Update lib/iris/fileformats/netcdf/saver.py 

    Co-authored-by: Bouwe Andela <bouweandela@gmail.com>
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Commits on Mar 17, 2023

  1. Small rename + reformat.

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Commits on Mar 18, 2023

  1. Remove Saver lazy option; all lazy saves are delayed; factor out fill… 

    …value checks and make them delayable.
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  2. Merge branch 'main' into lazy_save_2

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Commits on Mar 20, 2023

  1. Merge remote-tracking branch 'upstream/main' into lazy_save_2

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  2. Repurposed 'test__FillValueMaskCheckAndStoreTarget' to 'test__data_fi… 

    …llvalue_check', since old class is gone.
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  3. Disable (temporary) saver debug printouts.

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  4. Fix test problems; Saver automatically completes to preserve existing… 

    … direct usage (which is public API).
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  5. Fix docstring error.

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  6. Fix spurious error in old saver test.

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  7. Fix Saver docstring.

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  8. More robust exit for NetCDFWriteProxy operation.

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Commits on Mar 21, 2023

  1. Fix doctests by making the Saver example functional.

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Commits on Mar 23, 2023

  1. Improve docstrings; unify terminology; simplify non-lazy save call.

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Commits on Mar 27, 2023

  1. Moved netcdf cell-method handling into nc_load_rules.helpers, and var… 

    …ious tests into more specific test folders.
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  2. Merge branch 'latest' into lazy_save_2

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  3. Fix lockfiles and Makefile process.

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  4. Add unit tests for routine _fillvalue_report().

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  5. Remove debug-only code.

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Commits on Mar 28, 2023

  1. Added tests for what the save function does with the 'compute' keyword.

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  2. Fix mock-specific problems, small tidy.

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Commits on Mar 29, 2023

  1. Restructure hierarchy of tests.unit.fileformats.netcdf

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  2. Tidy test docstrings.

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  3. Correct test import.

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  4. Avoid incorrect checking of byte data, and a numpy deprecation warning.

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  5. Alter parameter names to make test reports clearer.

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Commits on Mar 30, 2023

  1. Test basic behaviour of _lazy_stream_data; make 'Saver._delayed_write… 

    …s' private.
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  2. Add integration tests, and distributed dependency.

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Commits on Mar 31, 2023

  1. Docstring fixes.

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Commits on Apr 4, 2023

  1. Documentation section and whatsnew entry.

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  2. Merge branch 'main' into lazy_save_2

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  3. Various fixes to whatsnew, docstrings and docs.

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Commits on Apr 11, 2023

  1. Minor review changes, fix doctest.

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  2. Arrange tests + results to organise by package-name alone.

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  3. Review changes.

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Commits on Apr 12, 2023

  1. Review changes.

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Commits on Apr 13, 2023

  1. Enhance tests + debug.

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  2. Support scheduler type 'single-threaded'; allow retries on delayed-sa… 

    …ve test.
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  3. Improve test.

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  4. Adding a whatsnew entry for 5224 (SciTools#5234) 

    * Adding a whatsnew entry explaining 5224

* Fixing link and format error
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  5. Replacing numpy legacy printing with array2string and remaking result… 

    …s for dependent tests
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  6. adding a whatsnew entry

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  7. configure codecov

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  8. remove results creation commit from blame

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  9. fixing whatsnew entry

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  10. Bump scitools/workflows from 2023.04.1 to 2023.04.2 (SciTools#5236) 

    Bumps [scitools/workflows](https://github.com/scitools/workflows) from 2023.04.1 to 2023.04.2.
- [Release notes](https://github.com/scitools/workflows/releases)
- [Commits](SciTools/workflows@2023.04.1...2023.04.2)

---
updated-dependencies:
- dependency-name: scitools/workflows
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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  11. Use real array for data of of small netCDF variables. (SciTools#5229) 

    * Small netCDF variable data is real.

* Various test fixes.

* More test fixing.

* Fix printout in Mesh documentation.

* Whatsnew + doctests fix.

* Tweak whatsnew.
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  12. Handle derived coordinates correctly in concatenate (SciTools#5096) 

    * First working prototype of concatenate that handels derived coordinates correctly

* Added checks for derived coord metadata during concatenation

* Added tests

* Fixed defaults

* Added what's new entry

* Optimized test coverage
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  13. clarity on whatsnew entry contributors (SciTools#5240)

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  14. Modernize and simplify iris.analysis._Groupby (SciTools#5015) 

    * Modernize and simplify _Groupby

* Rename variable to improve readability

Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com>

* Add a whatsnew entry

* Add a type hint to _add_shared_coord

* Add a test for iris.analysis._Groupby.__repr__

---------

Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com>
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  15. Finalises Lazy Data documentation (SciTools#5137) 

    * cube and io lazy data notes added

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Added comments within analysis, as well as palette and iterate, and what's new

* fixed docstrings as requested in @trexfeathers review

* reverted cube.py for time being

* fixed flake8 issue

* Lazy data second batch

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* updated lastest what'snew

* I almost hope this wasn't the fix, I'm such a moron

* adressed review changes

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Bill Little <bill.james.little@gmail.com>
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  16. Fixes to _discontiguity_in_bounds (attempt 2) (SciTools#4975)

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  17. update ci locks location (SciTools#5228)

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  18. Updated environment lockfiles (SciTools#5211) 

    Co-authored-by: Lockfile bot <noreply@github.com>
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  19. Increase retries.

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  20. Change debug to show which elements failed.

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  21. update cf standard units (SciTools#5244) 

    * update cf standard units

* added whatsnew entry

* Correct pull number

Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com>

---------

Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com>
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  22. libnetcdf <4.9 pin (SciTools#5242) 

    * Pin libnetcdf<4.9 and update lock files.

* What's New entry.

* libnetcdf not available on PyPI.

* Fix for Pandas v2.0.

* Fix for Pandas v2.0.
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  23. Avoid possible same-file crossover between tests.

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  24. Ensure all-different testfiles; load all vars lazy.

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  25. Revert changes to testing framework.

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  26. Remove repeated line from requirements/py*.yml (?merge error), and re… 

    …-fix lockfiles.
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  27. Revert some more debug changes.

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  28. Merge branch 'latest' into lazy_save_2

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Commits on Apr 14, 2023

  1. Reorganise test for better code clarity.

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  2. Use public 'Dataset.isopen()' instead of '._isopen'.

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  3. Create output files in unique temporary directories.

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  4. Tests for fileformats.netcdf._dask_locks.

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Commits on Apr 21, 2023

  1. Merge branch 'latest' into lazy_save_2

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  2. Fix attribution names.

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  3. Merge branch 'latest' into lazy_save_2

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  4. Fixed new py311 lockfile.

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  5. Fix typos spotted by codespell.

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  6. Add distributed test dep for python 3.11

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  7. Fix lockfile for python 3.11

    @pp-mo
    pp-mo committed Apr 21, 2023
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