Adds support for more types of FractalHeap (used for storing attributes)

[bnlawrence]

Description

This pull request includes implementation and tests for two types of FractalHeap which we had not previously encountered (as described in #243).

In practice we have added some more code within the implementation of the Fractal_Heap class, which replaces some "NotImplementedError" branches, and support for the particular kind of b-tree used in the fractal heaps. One large test file which requires one of the two new branches is included - we couldn't shrink it as any attempt to rewrite it invoked a differnt kind of FractalHeap. We have not been able to generate a real file using the other branch, so some synthetic testing has been included.

Closes #243

Checklist

• This pull request has a descriptive title and labels
• This pull request has a minimal description (most was discussed in the issue, but a two-liner description is still desirable)
• Unit tests have been added (if codecov test fails)
• Any changed dependencies have been added or removed correctly (if need be)
• If you are working on the documentation, please ensure the current build passes
• All tests pass

[codecov]

Codecov Report

❌ Patch coverage is 65.78947% with 26 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.48%. Comparing base (b9e3df5) to head (ba4a18a).

Files with missing lines	Patch %	Lines
pyfive/misc_low_level.py	58.18%	16 Missing and 7 partials ⚠️
pyfive/btree.py	85.71%	2 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #244      +/-   ##
==========================================
- Coverage   78.65%   78.48%   -0.18%     
==========================================
  Files          15       15              
  Lines        3345     3416      +71     
  Branches      534      546      +12     
==========================================
+ Hits         2631     2681      +50     
- Misses        579      593      +14     
- Partials      135      142       +7     

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[Copilot]

Pull request overview

This PR extends pyfive’s Fractal Heap support to handle additional huge/tiny object encodings encountered in real-world netCDF/HDF5 files (notably CMIP6), including huge-object lookup through a v2 B-tree, and adds tests/fixtures to exercise these branches.

Changes:

• Implement decoding for tiny heap IDs and huge heap IDs (direct + indirect via v2 B-tree) in FractalHeap.get_data().
• Add BTreeV2HugeObjectsIndirect to parse/iterate huge-object records stored in HDF5 v2 B-trees.
• Add tests including a real CMIP6 fixture-based test and synthetic tiny-object decoding tests; update pre-commit config to allow the large fixture file.

Reviewed changes

Copilot reviewed 4 out of 5 changed files in this pull request and generated 2 comments.

File	Description
pyfive/misc_low_level.py	Adds huge/tiny Fractal Heap ID decoding and indirect huge-object lookup via a v2 B-tree.
pyfive/btree.py	Introduces a v2 B-tree reader for indirectly accessed huge objects.
tests/test_fractal_heap.py	Adds coverage for tiny IDs and a real CMIP6 huge-object case; updates huge-object expectations.
.pre-commit-config.yaml	Excludes the large CMIP fixture from the “added large files” pre-commit hook.

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[davidhassell]

Looks good, as far as I can tell (I've eyeballed the code and tests, and run the test, and played on the command line)

[valeriupredoi]

bit more testing would be nice though; RTD fails unrelated to here see #245

[bnlawrence]

Can't test half of this because we can't create synthetic data with these properties. At some point mocking it becomes pointless ...

[valeriupredoi]

Can't test half of this because we can't create synthetic data with these properties. At some point mocking it becomes pointless ...

no probs, cov hit is not big 😃

[valeriupredoi]

docs build issue sorted, this is ready for merge when @bnlawrence is happy to 🍺