Add download simulation dataset feature

[remy-rabideau]

Summary

Adds a new aerie-cli plans download-simulation-full-results command that downloads simulated activities, resource timelines, simulation configuration arguments, and simulation events for a simulation dataset, converts them into the PlanDev SimulationResultsWriter upload format, and writes the result to a single JSON file — all in one step.

Motivation

Previously, producing a simulation upload JSON required three manual steps:

1. aerie-cli plans download-simulation → sim_results.json
2. aerie-cli plans download-resources → res_results.json
3. Running a standalone conversion script to merge and reformat both outputs

This PR integrates all three steps into a single CLI command. The output JSON matches the format expected by PlanDev's uploadSimulationDataset endpoint. See the PlanDev repository for more information.

Changes

• src/aerie_cli/utils/simulation_convert.py (new) — conversion logic extracted into a proper importable module:

  • build_simulation_upload(activities, resources, resource_schemas, profile_types, ...) — top-level entry point
  • convert_activities — renames fields, derives childIds from parent_id back-references, normalizes durations to 6 fractional digits, and folds the day component of Postgres intervals (e.g. 9 days 21:55:18.272000) into hours, since Duration.fromString on the upload side only accepts HH:MM:SS.ssssss
  • convert_resources — classifies profiles as real ({initial, rate} dynamics) or discrete (raw value dynamics), reconstructs segments from aerie-cli's flattened sample points
  • infer_window — infers simulation start/end from activity timestamps and resource sample offsets
  • _convert_topics / _convert_events — converts simulation event topics and event rows into the writer format
  • Time helpers: iso_to_doy, micros_to_extent, dt_to_doy

• src/aerie_cli/commands/plans.py — adds download-simulation-full-results command:

  aerie-cli plans download-simulation-full-results --sim-id <ID> --output <FILE>
  

• src/aerie_cli/aerie_client.py — three new client methods, plus one new optional argument:

  • get_profile_types(simulation_dataset_id, state_names=None) (new) — returns a mapping of resource name to "real" or "discrete" as recorded in the database. This distinction cannot be recovered from sample points alone: a real profile whose values never change is indistinguishable from a discrete one, which caused profiles to be misclassified on re-upload.
  • get_simulation_dataset_arguments(sim_dataset_id) (new) — returns the simulation configuration arguments snapshot.
  • get_simulation_events(sim_dataset_id) (new) — returns {"topics": [...], "events": [...]}, flattening the nested topic→events GraphQL response into a flat event list.
  • get_resource_samples(...) gains an optional deduplicate argument, defaulting to True. The default preserves existing behavior of collapsing points at segment boundaries when the value is unchanged, which is correct for plotting but merges adjacent segments and loses one segment per continuous boundary. The round-trip path passes False to keep segment counts intact (e.g. 573→573 rather than 573→572). The return shape is unchanged — existing callers are unaffected.

• tests/unit_tests/test_simulation_convert.py (new) — 65 unit tests covering all helpers and the full build_simulation_upload pipeline, including simulation events, day-component intervals, zero-extent segments, and same-value boundaries. All pass without a running PlanDev instance.

• tests/unit_tests/test_aerie_client.py — adds test_get_profile_types, with new fixtures under files/expected_results/ and files/mock_responses/. Existing tests and fixtures are unmodified.

• pyproject.toml — constrains python to >=3.6.8,<4.0, migrates [tool.poetry.dev-dependencies] to the [tool.poetry.group.dev.dependencies] form, and scopes flake8 ^6.0.0 to python >=3.8.1. Required for poetry lock to resolve; poetry.lock is regenerated accordingly.

• .gitignore — ignores config.json and out/.

Design note

An earlier revision of this branch returned profile types as a second "profileTypes" key from get_resource_samples(). That changed the method's return shape for every caller in order to serve one of them, and it broke get_resource_timelines() — ApiResourceSampleResults declares only resourceSamples, so the extra key raised a TypeError in from_dict(). That method has no unit test, so the suite stayed green while it was broken.

Profile types now live in their own get_profile_types() method, which queries name and type only — no segments, no plan-duration lookup. get_resource_samples() keeps its original return shape. The deduplicate flag stays on get_resource_samples(), since it changes how sampling itself works and belongs there.

Output format

The JSON produced matches the SimulationResultsWriter format expected by PlanDev's uploadSimulationDataset endpoint. topics and events are omitted when the simulation dataset has no events. simulationArguments is omitted when empty.

Testing

Unit tests only (no live server required):

pytest tests/unit_tests/ -v

End-to-end, with an active session:

aerie-cli plans download-simulation-full-results --sim-id <ID> --output simulation_upload.json