Fix ItemizedResource item ordering

[rickwierenga]

This PR refactors the ItemizedResource class (and its subclasses like Plate and TipRack) to store item ordering as an OrderedDict[str, str] mapping from identifier (e.g. “A1”) to child name (e.g. “plate_A1”) instead of a List[str]. This enables unambiguous conversion between indices and identifiers, resolving issues where get_item() and other methods could retrieve the wrong child due to reordered and/or extra children. The example that inspired this is a Lid as a child of Plate in front of Wells, messing up the well indexing. See #565.

Key Changes:

• ItemizedResource._ordering is now an OrderedDict[str, str] mapping identifier to item name.
• All usages of self._ordering that previously relied on list indexing have been updated to use the mapping correctly.
• index_of_item() and get_child_identifier() have been updated to work with item names via _ordering.values(). No API change.
• Constructors for Plate, TipRack, and NestedTipRack now accept an OrderedDict for ordering.

Why:

Previously, child retrieval methods relied on a flat list of identifiers without a stable mapping to actual child names. This was fragile in cases where there are other children (such as a Lid on a Plate). By tracking the mapping explicitly, we can safely reference children by both identifier and name without relying on implicit positional assumptions.

[Copilot]

Pull Request Overview

This PR refactors how ItemizedResource and its subclasses track item order by switching from a List[str] to an OrderedDict[str, str] mapping identifiers to child names, and updates all lookup and indexing methods to use this mapping.

• Constructors in ItemizedResource, Plate, and TipRack now accept an OrderedDict for ordering instead of a list.
• Methods like __getitem__, get_item, index_of_item, and get_child_identifier have been updated to work with the new _ordering mapping.
• Imported OrderedDict where needed and adjusted assignment of _ordering in the base class initializer.

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
pylabrobot/resources/tip_rack.py	Changed ordering parameter type to OrderedDict in constructors (TipRack/NestedTipRack).
pylabrobot/resources/plate.py	Updated ordering parameter type to OrderedDict in Plate constructor.
pylabrobot/resources/itemized_resource.py	Switched _ordering from list to OrderedDict, updated slicing and lookup methods.

Comments suppressed due to low confidence (4)

pylabrobot/resources/tip_rack.py:124

• The docstring for the ordering parameter in these constructors still describes a List[str]. Please update it to explain that it now expects an OrderedDict[str, str] mapping identifiers to child names.

ordering: Optional[OrderedDict[str, str]] = None,

pylabrobot/resources/plate.py:77

• The docstring above this signature still refers to ordering as a list of identifiers. It should be updated to reflect that ordering is now an OrderedDict from identifier to child name.

ordering: Optional[OrderedDict[str, str]] = None,

pylabrobot/resources/itemized_resource.py:158

• [nitpick] Converting self._ordering.keys() to a list and calling index() on every lookup may be inefficient for large resources. Consider caching the list of keys or maintaining a reverse mapping from identifier to index for faster lookups.

start = list(self._ordering.keys()).index(identifier)

pylabrobot/resources/itemized_resource.py:158

• New behavior for identifier-based slicing in __getitem__ (and similar string‐based index lookups) should be covered by unit tests to ensure that slices using string identifiers return the expected items.

start = list(self._ordering.keys()).index(identifier)