Preserve setpoints and embryo positions

[ceej640]

Summary

• update non-blocking temperature setpoint commands so read() and /api/temperature/set report the commanded setpoint immediately
• preserve explicit position_coarse and position_fine when saving, resuming, and writing acquisition metadata
• handle FileStore embryo calibration records whether calibration is already a dict or serialized JSON
• add regression tests for temperature setpoint reporting and coarse/fine session persistence

Stacking

This branch is stacked on #23 so the full suite can collect. Once #23 merges into 0.22-dev, this PR should reduce to the state-persistence commit.

Verification

• uv run pytest tests/test_session_manager.py tests/test_temperature_controller.py -q
• uv run pytest -q
  • 558 passed, 4 skipped

[pskeshu]

Can this be tested against the MQTT digital twin of Roland's thermostat?

…

On Sat, 30 May 2026 at 21:00, ceej640 ***@***.***> wrote: Summary - update non-blocking temperature setpoint commands so read() and /api/temperature/set report the commanded setpoint immediately - preserve explicit position_coarse and position_fine when saving, resuming, and writing acquisition metadata - handle FileStore embryo calibration records whether calibration is already a dict or serialized JSON - add regression tests for temperature setpoint reporting and coarse/fine session persistence Stacking This branch is stacked on #23 <https://github.com/pskeshu/gently/pull/23> so the full suite can collect. Once #23 <https://github.com/pskeshu/gently/pull/23> merges into 0.22-dev, this PR should reduce to the state-persistence commit. Verification - uv run pytest tests/test_session_manager.py tests/test_temperature_controller.py -q - uv run pytest -q - 558 passed, 4 skipped ------------------------------ You can view, comment on, or merge this pull request online at: https://github.com/pskeshu/gently/pull/26 Commit Summary - cb1ac02 <pskeshu@cb1ac02> Fix test suite collection and stale expectations - 437d115 <pskeshu@437d115> Preserve setpoints and embryo positions File Changes (10 files <https://github.com/pskeshu/gently/pull/26/files>) - *M* gently/app/tools/acquisition_tools.py <https://github.com/pskeshu/gently/pull/26/files#diff-817f25dfca322932eaaf0a998b317174e5e4a91b3086664a96ded43e51109882> (4) - *M* gently/hardware/dispim/device_layer.py <https://github.com/pskeshu/gently/pull/26/files#diff-32453f9e1c11ad0aed9faa140e3530652fdb0def740d17e6dd56958ae39f5324> (1) - *M* gently/hardware/temperature.py <https://github.com/pskeshu/gently/pull/26/files#diff-1a2119dda75234d5b1ba80f33486db655642957e149c82dd320ed1a0235a2bee> (8) - *M* gently/harness/conversation.py <https://github.com/pskeshu/gently/pull/26/files#diff-632feaa216b8cc24e32645b92dc64a0783b6c9f26baeb7b4d8c7f5643930ee88> (41) - *M* gently/harness/session/manager.py <https://github.com/pskeshu/gently/pull/26/files#diff-945d838e526f9cc869f7b3f10a5ab7f46fd4127f01d452766355f67ca042464b> (29) - *M* gently/mesh/mesh_service.py <https://github.com/pskeshu/gently/pull/26/files#diff-73595f2a2a804444d1374305a1b1e2a55774e2ccbe20bfa23a5a72a462791d4e> (20) - *M* tests/test_campaign_coordination.py <https://github.com/pskeshu/gently/pull/26/files#diff-a1bfd6d13f647b1bbfb7650d9b2c4a89560b01a96a56b8191de8d5b7831a7429> (8) - *M* tests/test_dispim_device_safety.py <https://github.com/pskeshu/gently/pull/26/files#diff-e3bc17744c2f44923aea78a254b613462a99a1307f2c6a5c04c94efdf45ce66e> (33) - *M* tests/test_session_manager.py <https://github.com/pskeshu/gently/pull/26/files#diff-8025b5e4147c32f9f4ed5f1686b098712f0c275f457c6d9e1b807a033f14e921> (43) - *A* tests/test_temperature_controller.py <https://github.com/pskeshu/gently/pull/26/files#diff-8323a8c1f8b6748ab7f172b165195809a78fec8f493b0b4682fce99f84fd29a0> (21) Patch Links: - https://github.com/pskeshu/gently/pull/26.patch - https://github.com/pskeshu/gently/pull/26.diff — Reply to this email directly, view it on GitHub <https://github.com/pskeshu/gently/pull/26?email_source=notifications&email_token=ABVNN4G6ZIE7CD2QMJJFZWL45N7ZTA5CNFSNUABEM5UWIORPF5TWS5BNNB2WEL2QOVWGYUTFOF2WK43UF4ZTONZVGI4TONRRGSTHEZLBONXW5KTTOVRHGY3SNFRGKZFFMV3GK3TUVRTG633UMVZF6Y3MNFRWW>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABVNN4HUQWNMMZWZYBM45IL45N7ZTAVCNFSM6AAAAACZUBL5Z6VHI2DSMVQWIX3LMV43ASLTON2WKOZUGU2TMMJYGEYTKMQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Kesavan

[ceej640]

Yes, that is the right integration test, but I cannot run it from this environment unless the MQTT digital twin endpoint, topic schema, and credentials are available.

The current PR only tests the controller contract locally: after a non-blocking setpoint command, read() and the API report the commanded setpoint immediately. It does not prove the MQTT transport or Roland thermostat twin behavior.

A good follow-up would be a skipped-by-default integration test, gated behind something like --run-mqtt-digital-twin and environment variables for broker URL/topics. The test should:

• connect to the thermostat digital twin
• issue a temperature setpoint through the same Gently path used at runtime
• verify the commanded setpoint is reflected immediately
• observe the twin's reported state converge, or time out cleanly
• verify the setpoint survives session save/resume metadata paths

That should stay out of the default suite, but it would be the right confirmation before relying on this against the real hardware-facing path.

[ceej640]

Follow-up implemented from this thread in commit df8dd77.

I added an opt-in MQTT thermostat digital-twin test hook. It is skipped by default and runs only when GENTLY_MQTT_THERMOSTAT_CONFIG is supplied as JSON or a config-file path. The test commands the same non-blocking setpoint path, verifies immediate setpoint readback, then waits for convergence or lock from the digital twin.

I could not run it against Roland's actual MQTT twin here because I do not have the endpoint/topic/credential config, but the test hook is now present.

Verification:

• pytest tests/test_temperature_controller.py -q -p no:cacheprovider

[ceej640]

Follow-up added for the MQTT thermostat digital-twin request in commit dfdfc98.

What changed:

• Added docs/mqtt-thermostat-digital-twin.md documenting the opt-in test hook configuration, topic expectations, run command, and the pass/fail contract.
• The doc makes explicit that the default suite remains offline, and the MQTT test runs only when GENTLY_MQTT_THERMOSTAT_CONFIG is supplied.
• It also states what I still could not verify here: Roland's actual MQTT broker endpoint, topics, and credentials were not available in this environment.

Verification:

• pytest tests/test_temperature_controller.py -q -p no:cacheprovider