add metadata/copy_modality_slots component

[jakubmajercik]

Changelog

Adds a new metadata/copy_modality_slots component, consolidating PR #1166 (originally dataflow/insert_partial_items) and PR #1163 (dataflow/move_anndata_slots) into a single component covering both use cases.

What it does

Copies items (.obs, .var, .layers, .obsm, .varm, .obsp, .varp, .uns) from a modality in a source MuData file into a modality in a target MuData file. Cross-modality transfers are supported via --source_modality / --target_modality.

Behavior

• Strict mode (default): source and target .obs/.var index sets must match. Source is reindexed to target order if needed.
• --allow_partial: source's indices may be a strict subset of target's. Missing rows/cols are NaN-filled (with the appropriate sentinel for nullable DataFrame columns).
• --allow_overwrite: opt-in; by default the component errors if a key already exists in the target.
• __auto__ token: per slot, automatically include items present in source but missing from target.
• --var_match_column: rewrite source .var index from a named column before matching — useful when an upstream step has sanitised gene names.

PR #1163 will be closed.

Checklist before requesting a review

• I have performed a self-review of my code

• Conforms to the Contributor's guide

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Documentation
  • Bug fixes

• Proposed changes are described in the CHANGELOG.md

• CI tests succeed!

[DriesSchaumont]

This PR and #1163 look very similar. Are separete components required?

[lazappi]

How would this be used to replicate the move_layer component which moves or copies a single layer/X in one MuData? I guess you could input the same file twice and set the arguments correctly? I don't think this has any way of handling X though which is the main use of move_layer.

[jakubmajercik]

How would this be used to replicate the move_layer component which moves or copies a single layer/X in one MuData? I guess you could input the same file twice and set the arguments correctly? I don't think this has any way of handling X though which is the main use of move_layer.

The aim here wasn't to replace move_layer — just #1166 insert_partial_items and #1163 move_anndata_slots

[lazappi]

This looks good to me but Dries should check to see it matches OP