Fix generate-embeddings row payload shape for CurateGPT insertion

[Copilot]

generate-embeddings was passing each CSV row to CurateGPT in a shape that caused dict keys to be treated as strings during embedding insertion, producing 'str' object has no attribute 'items' and resulting in zero embedded rows. This update aligns the CLI embedding path with CurateGPT’s expected document input structure.

• Embedding insertion contract

  • Updated embedding generation to pass each row as a single-document list when calling CurateGPT store insertion.
  • This prevents per-row dicts from being interpreted as iterables of string keys.

• Focused test updates

  • Adjusted embedding generation tests to assert the inserted payload shape ([row]).
  • Kept existing skip/ordering assertions, updated for the new call structure.

# before
store.insert(row, collection=collection_name)

# after
store.insert([row], collection=collection_name)

Original prompt

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This section details on the original issue you should resolve

<issue_title>type error when generating embeddings with trowel CLI</issue_title>
<issue_description>Trying to generate embeddings with generate-embeddings gives a 'str' object has no attribute 'items' WARNING and leads to no embedding generation. Seems like at some point, strings aren't digested into a dictionary. Same file runs fine with curategpt.

trowel embeddings generate-embeddings -i bervo_prepared_small.csv
INFO: Starting embedding generation...
/Users/ukaraoz/Work/bioepic/ldrd/trowel/.venv/lib/python3.11/site-packages/eutils/init.py:4: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
INFO: Initializing CurateGPT store with DuckDB at ./backup/db.duckdb...
INFO: Loading data from bervo_prepared_small.csv...
WARNING: Failed to embed row 0: 'str' object has no attribute 'items'
WARNING: Failed to embed row 1: 'str' object has no attribute 'items'
WARNING: Failed to embed row 2: 'str' object has no attribute 'items'
INFO: Successfully embedded 0 rows from bervo_prepared_small.csv
INFO: Embeddings stored in collection 'embeddings' at ./backup/db.duckdb
INFO: Successfully generated 0 embeddings
INFO: Database saved at: ./backup/db.duckdb
</issue_description>

Comments on the Issue (you are @copilot in this section)

@caufieldjh Thanks @ukaraoz - I'll take a look

• Fixes type error when generating embeddings with trowel CLI #12

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