MAINT: Standardize JSON serialization in models

[romanlutz]

Description

Cleanup pass that standardizes how models do JSON (de)serialization. Two parts.

Part A — Pydantic models: forward to Pydantic built-ins, deprecate the wrappers

ChatMessage and EmbeddingResponse are both pydantic.BaseModel subclasses, but each defined a to_json (and ChatMessage also a from_json) that was a one-line passthrough to model_dump_json() / model_validate_json(). The wrappers add no value over the Pydantic built-ins.

• Migrated 5 in-tree call sites across 3 files to the Pydantic API directly:
  • tests/unit/models/test_chat_message.py (4 call sites in 3 tests; test names renamed to reflect the Pydantic API they exercise)
  • doc/code/memory/embeddings.py and doc/code/memory/embeddings.ipynb (1 call site each, kept in sync per the docs sync rule)
• Kept the 3 methods as deprecated shims (ChatMessage.to_json, ChatMessage.from_json, EmbeddingResponse.to_json) so external callers get a soft migration window. Each shim now emits DeprecationWarning via print_deprecation_message with removed_in="0.15.0" and forwards to the underlying Pydantic method. Tests added to assert each shim still works and emits the warning.

Part B — ScorerMetrics: stop misnaming the file-based loader

ScorerMetrics is a plain @dataclass (not Pydantic) and its serialization helpers have real behavior beyond json.dumps(asdict(...)):

• from_json accepted a file path, opened the file, unwrapped a top-level "metrics" key (used by evaluation result files), and filtered out internal underscore-prefixed fields (e.g., init=False cached attrs like _harm_definition_obj).

The name from_json strongly suggested a JSON string argument, which it never accepted. Changes:

• Renamed ScorerMetrics.from_json → ScorerMetrics.from_json_file to honestly reflect what it does (kept to_json as-is — it correctly returns a string).
• Kept from_json as a deprecated shim that forwards to from_json_file and emits DeprecationWarning via print_deprecation_message with removed_in="0.15.0".
• Clarified docstrings on both to_json and from_json_file — they're now documented as the canonical (de)serialization entry points for ScorerMetrics subclasses, and from_json_file calls out that it takes a file path and unwraps the "metrics" key plus filters underscore fields.
• Updated 2 in-tree call sites in tests/unit/score/test_scorer_metrics.py to use the new name, and added a test that asserts the deprecated alias still works and emits the warning.
• Verified there are no other places in pyrit/score/ that hand-roll json.dumps(asdict(metrics)) or json.load(...) plus ScorerMetrics(**...) outside these methods themselves. (scorer_metrics_io.py parses JSONL with wrapper metadata, which is a different abstraction and unchanged.)
• Did not add from_json_str — no caller needs a string-only round trip today.

Verification

• uv run pytest tests/unit -x -q — full unit suite passes (8049+ tests); new deprecation tests pass too
• uv run pre-commit run --all-files — clean
• grep confirms zero remaining non-deprecation in-tree callers of the old to_json/from_json symbols on ChatMessage / EmbeddingResponse / ScorerMetrics.