Root attributes

[Claptar]

PR: Enforce AnnData root attrs and make subset outputs concat-friendly

Title

Enforce AnnData root attrs and make subset outputs concat-friendly

Summary

This PR updates subset/store behavior to improve AnnData schema compliance and downstream compatibility with disk-based concat workflows.

• Root AnnData metadata is now enforced on writable store opens and copy operations.
• Read mode emits a warning (not an error) when root attrs are missing.
• Subset outputs now always include optional empty AnnData groups (layers, obsm, obsp, varm, varp) so generated files are structurally closer to full AnnData outputs.
• Regression coverage added for root-attr handling and optional-group creation.

Files Changed

• src/h5ad/storage/__init__.py
• src/h5ad/core/subset.py
• tests/test_storage_root_attrs.py
• tests/test_subset.py
• uv.lock

Validation

Targeted tests run:

/lustre/scratch124/cellgen/cellgeni/aljes/h5ad/.venv/bin/python -m pytest tests/test_storage_root_attrs.py tests/test_zarr.py -q
/lustre/scratch124/cellgen/cellgeni/aljes/h5ad/.venv/bin/python -m pytest tests/test_subset.py tests/test_zarr.py -q

Both passed.

Commits in this PR (dev..root_attributes)

• 2bce366 Add function to ensure optional anndata groups in subset operations
• 8553664 Add functions to ensure and validate AnnData root attributes in store operations
• 796e74c Add tests for AnnData root encoding attributes enforcement and warnings
• 4d44e46 Add test for optional empty groups in subset_h5ad function
• 1911cdc Refactor test_subset_h5ad to improve readability and ensure optional empty groups are included in the subset output
• a62f6e0 Bump h5ad package version to 0.3.1

[Copilot]

Pull request overview

This PR strengthens AnnData schema compliance by enforcing required root-level encoding attributes on writable store opens/copies, while keeping read-mode tolerant via warnings, and makes subset outputs more compatible with downstream concat workflows by always materializing optional empty AnnData groups.

Changes:

• Enforce encoding-type / encoding-version root attributes on writable open_store(...) and in copy_store_contents(...); emit a warning (not an error) on read when missing/invalid.
• Ensure subset outputs always contain optional empty AnnData groups: layers, obsm, obsp, varm, varp.
• Add regression tests for root-attr enforcement/warnings and optional-group creation in subset output; bump locked package version.

Reviewed changes

Copilot reviewed 4 out of 5 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/h5ad/storage/__init__.py	Adds root AnnData attr validation/enforcement and warning behavior; ensures copied stores include enforced root attrs.
src/h5ad/core/subset.py	Creates optional empty AnnData groups in subset outputs to be more concat-friendly.
tests/test_storage_root_attrs.py	New tests covering read-mode warning and writable-mode enforcement for root attrs.
tests/test_subset.py	Adds integration test asserting optional empty groups exist in subset outputs; minor formatting tweaks.
uv.lock	Updates locked editable project version to 0.3.1.

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[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Set mapping attrs when creating optional AnnData groups

subset_h5ad now always creates layers/obsm/obsp/varm/varp when absent, but these groups are created without any encoding-type/encoding-version metadata. In this codebase’s AnnData element docs, those members are mappings and mappings must carry encoding-type="dict" and encoding-version="0.1.0"; creating the groups without attrs turns previously-valid “absent optional member” outputs into malformed mapping groups, which can break schema-aware downstream readers/concat workflows.

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