Finalises Lazy Data documentation #5137
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Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## main #5137 +/- ##
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- Coverage 89.28% 89.27% -0.01%
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Files 88 88
Lines 22269 22261 -8
Branches 4870 4873 +3
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- Hits 19882 19874 -8
Misses 1641 1641
Partials 746 746
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bjlittle
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Apr 4, 2023
bjlittle
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bjlittle
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Apr 12, 2023
tkknight
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Apr 13, 2023
* upstream/main: (59 commits) Updated environment lockfiles (SciTools#5211) update ci locks location (SciTools#5228) Fixes to _discontiguity_in_bounds (attempt 2) (SciTools#4975) Finalises Lazy Data documentation (SciTools#5137) Modernize and simplify iris.analysis._Groupby (SciTools#5015) clarity on whatsnew entry contributors (SciTools#5240) Handle derived coordinates correctly in `concatenate` (SciTools#5096) Use real array for data of of small netCDF variables. (SciTools#5229) Bump scitools/workflows from 2023.04.1 to 2023.04.2 (SciTools#5236) fixing whatsnew entry remove results creation commit from blame configure codecov adding a whatsnew entry Replacing numpy legacy printing with array2string and remaking results for dependent tests Adding a whatsnew entry for 5224 (SciTools#5234) Cf cell method (SciTools#5224) Bump scitools/workflows from 2023.03.3 to 2023.04.1 (SciTools#5231) [pre-commit.ci] pre-commit autoupdate (SciTools#5230) Bump scitools/workflows from 2023.03.2 to 2023.03.3 (SciTools#5227) raise dask min pin (SciTools#5225) ...
pp-mo
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Apr 13, 2023
* 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>
tkknight
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Apr 18, 2023
* upstream/main: (29 commits) review actions update .git-blame-ignore-revs adopt codespell Adopt sphinx design (SciTools#5127) Bump scitools/workflows from 2023.04.2 to 2023.04.3 (SciTools#5253) refresh manual pypi publish instructions (SciTools#5252) Updated environment lockfiles (SciTools#5250) removed bugfix section Make bm_runner location agnostic and include debugging. (SciTools#5247) Restore latest Whats New files. SciTools#5220 typo github.repository_owner. (SciTools#5248) Whats new updates for v3.5.0rc0. (SciTools#5246) libnetcdf <4.9 pin (SciTools#5242) update cf standard units (SciTools#5244) Updated environment lockfiles (SciTools#5211) update ci locks location (SciTools#5228) Fixes to _discontiguity_in_bounds (attempt 2) (SciTools#4975) Finalises Lazy Data documentation (SciTools#5137) Modernize and simplify iris.analysis._Groupby (SciTools#5015) clarity on whatsnew entry contributors (SciTools#5240) ...
lbdreyer
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Apr 21, 2023
* Basic functional lazy saving. * Simplify function signature which upsets Sphinx. * Non-lazy saves return nothing. * Now fixed to enable use with process/distributed scheduling. * Remove dask.utils.SerializableLock, which I think was a mistake. * Make DefferedSaveWrapper use _thread_safe_nc. * Fixes for non-lazy save. * Avoid saver error when no deferred writes. * Reorganise locking code, ready for shareable locks. * Remove optional usage of 'filelock' for lazy saves. * Document dask-specific locking; implement differently for threads or distributed schedulers. * Minor fix for unit-tests. * Pin libnetcdf to avoid problems -- see #5187. * Minor test fix. * Move DeferredSaveWrapper into _thread_safe_nc; replicate the NetCDFDataProxy fix; use one lock per Saver; add extra up-scaled test * Update lib/iris/fileformats/netcdf/saver.py Co-authored-by: Bouwe Andela <bouweandela@gmail.com> * Update lib/iris/fileformats/netcdf/_dask_locks.py Co-authored-by: Bouwe Andela <bouweandela@gmail.com> * Update lib/iris/fileformats/netcdf/saver.py Co-authored-by: Bouwe Andela <bouweandela@gmail.com> * Small rename + reformat. * Remove Saver lazy option; all lazy saves are delayed; factor out fillvalue checks and make them delayable. * Repurposed 'test__FillValueMaskCheckAndStoreTarget' to 'test__data_fillvalue_check', since old class is gone. * Disable (temporary) saver debug printouts. * Fix test problems; Saver automatically completes to preserve existing direct usage (which is public API). * Fix docstring error. * Fix spurious error in old saver test. * Fix Saver docstring. * More robust exit for NetCDFWriteProxy operation. * Fix doctests by making the Saver example functional. * Improve docstrings; unify terminology; simplify non-lazy save call. * Moved netcdf cell-method handling into nc_load_rules.helpers, and various tests into more specific test folders. * Fix lockfiles and Makefile process. * Add unit tests for routine _fillvalue_report(). * Remove debug-only code. * Added tests for what the save function does with the 'compute' keyword. * Fix mock-specific problems, small tidy. * Restructure hierarchy of tests.unit.fileformats.netcdf * Tidy test docstrings. * Correct test import. * Avoid incorrect checking of byte data, and a numpy deprecation warning. * Alter parameter names to make test reports clearer. * Test basic behaviour of _lazy_stream_data; make 'Saver._delayed_writes' private. * Add integration tests, and distributed dependency. * Docstring fixes. * Documentation section and whatsnew entry. * Various fixes to whatsnew, docstrings and docs. * Minor review changes, fix doctest. * Arrange tests + results to organise by package-name alone. * Review changes. * Review changes. * Enhance tests + debug. * Support scheduler type 'single-threaded'; allow retries on delayed-save test. * Improve test. * Adding a whatsnew entry for 5224 (#5234) * Adding a whatsnew entry explaining 5224 * Fixing link and format error * Replacing numpy legacy printing with array2string and remaking results for dependent tests * adding a whatsnew entry * configure codecov * remove results creation commit from blame * fixing whatsnew entry * Bump scitools/workflows from 2023.04.1 to 2023.04.2 (#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> * Use real array for data of of small netCDF variables. (#5229) * Small netCDF variable data is real. * Various test fixes. * More test fixing. * Fix printout in Mesh documentation. * Whatsnew + doctests fix. * Tweak whatsnew. * Handle derived coordinates correctly in `concatenate` (#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 * clarity on whatsnew entry contributors (#5240) * Modernize and simplify iris.analysis._Groupby (#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> * Finalises Lazy Data documentation (#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> * Fixes to _discontiguity_in_bounds (attempt 2) (#4975) * update ci locks location (#5228) * Updated environment lockfiles (#5211) Co-authored-by: Lockfile bot <noreply@github.com> * Increase retries. * Change debug to show which elements failed. * update cf standard units (#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> * libnetcdf <4.9 pin (#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. * Avoid possible same-file crossover between tests. * Ensure all-different testfiles; load all vars lazy. * Revert changes to testing framework. * Remove repeated line from requirements/py*.yml (?merge error), and re-fix lockfiles. * Revert some more debug changes. * Reorganise test for better code clarity. * Use public 'Dataset.isopen()' instead of '._isopen'. * Create output files in unique temporary directories. * Tests for fileformats.netcdf._dask_locks. * Fix attribution names. * Fixed new py311 lockfile. * Fix typos spotted by codespell. * Add distributed test dep for python 3.11 * Fix lockfile for python 3.11 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Bouwe Andela <bouweandela@gmail.com> Co-authored-by: Henry Wright <84939917+HGWright@users.noreply.github.com> Co-authored-by: Henry Wright <henrywright@sky.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Manuel Schlund <32543114+schlunma@users.noreply.github.com> Co-authored-by: Bill Little <bill.james.little@gmail.com> Co-authored-by: Bouwe Andela <b.andela@esciencecenter.nl> Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com> Co-authored-by: Elias <110238618+ESadek-MO@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: stephenworsley <49274989+stephenworsley@users.noreply.github.com> Co-authored-by: scitools-ci[bot] <107775138+scitools-ci[bot]@users.noreply.github.com> Co-authored-by: Lockfile bot <noreply@github.com>
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🚀 Pull Request
Closes #3293.
Description
(Hopefully) Finalises the documentation of Lazy Data within Iris docstrings.
Certain files were decided to be excluded due to them being either entirely irrelevant, or existing documentation seemed clear.
There were a couple issues with merge conflicts where I ended up using a git-reset, which means there's a slight possibility some of my changes were rolled back unintentionally.