Add item access support for non-identifier subject/surface/transform names

[alexhuth]

Summary

This PR adds __getitem__ support throughout the database access hierarchy, enabling users to access subjects, surfaces, and transforms by name using bracket notation (e.g., db['S1-test']). This is essential for names that are not valid Python identifiers and cannot be accessed via attribute notation.

Key Changes

• Database class: Added __getitem__, __contains__, and __iter__ methods to support item access for subjects. Improved __getattr__ to provide helpful error messages directing users to use item access for non-identifier names.

• SubjectDB.surfaces (Surfaces class): Added __getitem__ method with informative KeyError messages listing available surfaces. Updated __getattr__ to avoid recursion issues with dunder attributes.

• SubjectDB.transforms (Transforms class): Added __getitem__ method, __dir__ method, and improved __getattr__ to support both item and attribute access patterns.

• XfmSet class: Added __getitem__ method for accessing transform types (e.g., 'coord', 'magnet'), __dir__ method, and improved __getattr__ with better error handling.

• Error handling: All __getitem__ implementations now raise KeyError (not AttributeError) with helpful messages listing available options. Dunder attributes are explicitly excluded from filestore lookups to prevent recursion during object construction, copying, or pickling.

• Documentation: Updated docs/database.rst with examples and explanation of item access for non-identifier names, including usage of in operator and iteration.

• Tests: Added comprehensive test suite (cortex/tests/test_database.py) covering item access, attribute access, error messages, dunder attribute handling, and warning behavior.

Notable Implementation Details

• Dunder attributes (__*__) are explicitly checked and raise AttributeError before attempting filestore lookups, preventing infinite recursion during object operations.
• Error messages consistently list available options to help users discover valid names.
• The implementation maintains backward compatibility with existing attribute-based access while adding the new item-based access pattern.

https://claude.ai/code/session_01XvzkAD2Fu6irNYq4uKyfRT