Summary

Adapts omop-graph to the oa-configurator configuration layer, replacing the previous environment-variable-based setup with a typed TOML-backed config and a first-class omop-config configure omop_graph subcommand.

Fixes: #15

Notes

Depends on the oa-configurator PR to pass.

Requires change in pyproject.toml to include the published PyPI package once changes have been approved:

dependencies = [
  "omop-alchemy>=0.6.3",
  "sqlalchemy>=2.0.45",
  "typing-extensions>=4.15.0",
  "typer",
  "oaklib",
  #"oa-configurator>=0.2.0",  # <-- uncomment and pin once on PyPI
]

Changes

• OmopGraphConfig subclasses PackageConfigBase, exposing all package settings as typed Pydantic fields backed by [tools.omop_graph] in ~/.config/omop/config.toml
• Entry point registered under omop.config so omop-config configure omop_graph prompts for package extras interactively or via named flags (--max-depth, --max-paths); omop-graph owns no database resource directly — it relies on the CDM resource configured by omop-alchemy
• OmopGraphConfig.get_config() (inherited classmethod) replaces the old standalone get_config() function; all internal call sites updated
• Resolver.from_active_config() replaces the old standalone get_resolver() function; all engine-creation helpers updated (db/session.py, oaklib_interface/omop_factory.py)
• OmopGraphConfig.configure_logging(verbosity=…) (inherited classmethod) replaces the old standalone configure_logging() wrapper; extra_logging_namespaces = ("omop_alchemy", "omop_emb") declares transitive dependencies whose logs are also configured (omop_emb is optional but harmless to include)
• docker-compose.yaml updated from --resource-set/--set flags to named flags matching the new CLI

Testing

# Interactive configure (package extras only — CDM resource comes from omop-alchemy)
omop-config configure omop_graph

# Non-interactive (Docker / CI)
omop-config configure omop_graph --max-depth 6 --max-paths 20

# Verify config loaded correctly
python -c "from omop_graph.config import OmopGraphConfig; print(OmopGraphConfig.get_config())"