Functionality enhancements to address lazy loading of chunked data, variable length strings, and other minor bug fixes#68

Merged

valeriupredoi merged 130 commits intomasterfrom

Jun 3, 2025

Commits on Feb 22, 2024

Using s3 to get at some real data for testing
Bryan Lawrence
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Getting the address as well as size into the index
Bryan Lawrence
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With timer
Bryan Lawrence
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Commits on Feb 23, 2024

Not working yet. Don't reckon I have the arguments to OrthogonalIndexer right yet.
Bryan Lawrence
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A few more notes in the code so I can come back to it anon.
Bryan Lawrence
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Woops. Need this.
Bryan Lawrence
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Commits on Feb 24, 2024

First working lazy read (only reads chunks needed for selection)
Bryan Lawrence
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Woops didnt' commit the real oil
Bryan Lawrence
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Should now support filtering chunks in the partical chunk loading. Haven't got any tests around this yet.
Bryan Lawrence
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Commits on Feb 25, 2024

Some additional documentation
Bryan Lawrence
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Commits on Feb 29, 2024

Seems to work, prior to re-integration
Bryan Lawrence
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Commits on Mar 1, 2024

Moved chunk support into standard API
Bryan Lawrence
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removing playing code
Bryan Lawrence
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Merge branch 'jjhelmus:master' into issue6
bnlawrence
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Commits on Mar 3, 2024

Commits on Mar 5, 2024

Remove obsolete function
Bryan Lawrence
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Support for third party access to contiguous data address and size. Also remove list definition which breaks references.
Bryan Lawrence
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Commits on Mar 7, 2024

Commits on Apr 21, 2024

First cut, no tests yet
Bryan Lawrence
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Commits on Apr 22, 2024

Improvements
Bryan Lawrence
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With some failing tests
Bryan Lawrence
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Fixed one test
Bryan Lawrence
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All tests for new functionality pass, but I've broken something old
Bryan Lawrence
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Now passing all tests
Bryan Lawrence
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Checking coverage of get_chunk_info_by_coord(method)
Bryan Lawrence
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Missing docstring
Bryan Lawrence
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Commits on Apr 26, 2024

Cleaning up
Bryan Lawrence
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Commits on Jul 9, 2024

Merge pull request #5 from bnlawrence/h5pyapi
bnlawrence
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Ok, these were the pull request fixes that I thought I'd merged
Bryan Lawrence
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Merge branch 'h5pyapi'
Bryan Lawrence
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Commits on Jul 10, 2024

Adding Datatype and check_enum_dtype in a minimal manner - closes #8
Bryan Lawrence
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Commits on Jul 12, 2024

Commits on Jul 14, 2024

Committing to the dtype returned as a numpy dtype, and the extra h5t interface.
Bryan Lawrence
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Commits on Jul 19, 2024

Test for reference_list
Bryan Lawrence
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Commits on Dec 19, 2024

(New reference list test still broken) H5D has been disconnected from the parent dataobjects so once instantiated it does not need to touch the file metadata.
Bryan Lawrence
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Commits on Dec 20, 2024

Interim commit so we have something to point to in a discussion around the problem with references and caching everything we need in a variable.
Bryan Lawrence
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Commits on Dec 21, 2024

Transition to H5D cached backend is complete, though we still have the test_reference_list fail
Bryan Lawrence
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Removed obsolete DatasetDataObjects
Bryan Lawrence
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Commits on Dec 22, 2024

Expose package version in code, and separate testing requirements out in package metadata.
Bryan Lawrence
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Attempt to get b-tree logging in h5d
Bryan Lawrence
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Commits on Dec 28, 2024

Cleared a few bugs and misunderstandings which arose from workign with h5netcdf (closed #15)
Bryan Lawrence
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Commits on Dec 30, 2024

Continue to use open file in h5d, closes #18
Bryan Lawrence
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Commits on Jan 1, 2025

Test for true bytes-io testing (needed for h5netcdf test compatability)
Bryan Lawrence
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Commits on Jan 2, 2025

Commits on Jan 3, 2025

Fix location of files so tests run properly from parent directory.
Bryan Lawrence
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Commits on Jan 7, 2025

Well, I think this is a fix for #23, and it's so complex I'm committing it now in case my laptop dies and I can't repeat this :-)
Bryan Lawrence
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Commits on Jan 8, 2025

Cleaned up issue23 fixes, all tests pass
Bryan Lawrence
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Test localisation, and a new test for laziness outside a context manager
Bryan Lawrence
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Changes to support out of context variable access as described in #24
Bryan Lawrence
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Removing the pseudo chunking stuff that snuck into the last commit
Bryan Lawrence
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catching up to the main trunk in h5netcdf
Bryan Lawrence
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Starting to sketch out the pseudo chunking
Bryan Lawrence
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threadsafe data access
davidhassell
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merge from h5netcdf
davidhassell
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Commits on Jan 9, 2025

Commits on Jan 10, 2025

Commits on Jan 13, 2025

Commits on Jan 15, 2025

Commits on Jan 16, 2025

Using context manager for threadsafe test
Bryan Lawrence
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Commits on Jan 20, 2025

no returned memory maps
davidhassell
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Test for #16 and #29
Bryan Lawrence
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More versions of the #29 tests
Bryan Lawrence
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Better .gitignore
Bryan Lawrence
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Giving up on in-memory netcdf tests for #29
Bryan Lawrence
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explicitly close POSIX files
davidhassell
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Commits on Jan 21, 2025

vlen strings data test case, vanilla version, and version with missing defined. tests fail.
Bryan Lawrence
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add extra posix test for file closure
davidhassell
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Merge branch 'h5netcdf' into fix-memmap
davidhassell
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More on h5d and testing. The iter_chunks method is broken and we now have a test which shows that.
Bryan Lawrence
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Support for pyactivestorage via a bespoke `get_chunk_info_from_chunk_coord` method
Bryan Lawrence
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better ignore
Bryan Lawrence
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The first vlen data test passes with this code
Bryan Lawrence
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closer to a solution for #29. These tests pass, but we need to deal with multidimensional arrays as well.
Bryan Lawrence
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Commits on Jan 22, 2025

Partially working vlen string support, issues with global heap usage and dtypes remain
Bryan Lawrence
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Passing all vlen tests for #29, though we are ignoreing the dtype of the dataset itself, which needs to be a new issue. Also the caching stuff needs to be a new issue.
Bryan Lawrence
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Merge pull request #33 from NCAS-CMS/vlen
bnlawrence
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Merge remote-tracking branch 'refs/remotes/origin/h5netcdf' into h5netcdf
Bryan Lawrence
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Merge branch 'fix-memmap' into h5netcdf
Bryan Lawrence
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Remaining tests for vlen and iterchunks, support for vlen dtypes (closes #34)
Bryan Lawrence
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Commits on Jan 23, 2025

Commits on Jan 24, 2025

vlen related fixes
davidhassell
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Commits on Jan 28, 2025

Commits on Jan 30, 2025

Merge branch 'master' into wacasoft
Bryan Lawrence
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install only in test mode
valeriupredoi
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actual correct name for testing regime
valeriupredoi
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Commits on Mar 17, 2025

fix h5py attribute compatibility
davidhassell
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Commits on Mar 19, 2025

dev
davidhassell
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Commits on Jun 3, 2025