turbidostat now dynamically chooses the biomass signal; some UI updates

Author: CamDavidsonPilon

CHANGELOG.md

@@ -2,6 +2,15 @@
 
 #### Breaking changes
 
+ - Turbidostat biomass signal behavior has changed in a user-visible way:
+   - The setting key is now `biomass_signal` (renamed from `biomass_signal_override`).
+   - The config moved from `[turbidostat.config]` to `[dosing_automation.turbidostat]`.
+   - Default behavior is now `biomass_signal=auto`, with selection order:
+     1. active `od_fused` estimator
+     2. active OD calibration for the configured angle (`od`)
+     3. normalized OD
+   - Users can still explicitly override `biomass_signal` in config (including via profiles), but Turbidostat now defaults to `auto`.
+   - Update scripts migrate existing values from the legacy section/key when present.
  - Renamed `/api/is_local_access_point_active` to `/api/local_access_point` (now returns `{active: <bool>}`).
  - Consolidated experiment profile routes under `/api/experiment_profiles` and `/api/experiments/<experiment>/experiment_profiles/*`. Removed `/api/contrib/experiment_profiles` and `/api/experiment_profiles/running/experiments/<experiment>`. `PATCH` now targets `/api/experiment_profiles/<filename>`.
  - Consolidated config API routes under `/api/config/*`: `/api/units/<pioreactor_unit>/configuration` is now `/api/config/units/<pioreactor_unit>`, and `/api/configs` + `/api/configs/<filename>` + `/api/configs/<filename>/history` are now `/api/config/files` + `/api/config/files/<filename>` + `/api/config/files/<filename>/history`.
@@ -18,6 +27,8 @@
  - Added a new calibration coverage matrix page in the UI (linked from Calibrations) to show cluster-wide per-unit/per-device coverage and quick actions: open active calibration details, view available calibrations for a device, or create missing calibrations via `/protocols/<unit>/<device>`.
  - Added card-level quick controls to both `/pioreactors` and `/pioreactor/<unit>`: clicking an activity state now runs contextual actions (start, stop, pause, resume), and shows an in-place spinner until MQTT reports the expected state transition.
  - Added inline quick-edit popovers for card settings values.
+ - Automation advanced config now discovers and displays both `[<x>_automation.config]` and per-automation sections like `[<x>_automation.<automation_name>]`, enabling section-specific overrides from the UI.
+
 
 #### Bug fixes
 
@@ -28,6 +39,7 @@
  - Fixed Inventory model updates and active/inactive toggles to show success only after confirmed backend `2xx` responses, with explicit error feedback on failure.
 
 
+
 ### 26.2.3
 
 #### Enhancements

config.dev.ini

@@ -38,9 +38,8 @@ target_rpm_outside_od_reading=500
 
 
 
-[turbidostat.config]
-signal_channel=2
-od_smoothing_ema=0.5
+[dosing_automation.turbidostat]
+biomass_signal=auto
 
 [stirring.pid]
 Kp=0.007

core/pioreactor/automations/dosing/turbidostat.py

@@ -34,7 +34,7 @@ def __init__(
         self,
         exchange_volume_ml: float | str,
         target_biomass: Optional[float | str] = None,
-        biomass_signal: str = "auto",
+        biomass_signal: str | None = None,
         **kwargs,
     ) -> None:
         super().__init__(**kwargs)
@@ -48,6 +48,13 @@ def __init__(
         if target_biomass is None:
             raise ValueError("Provide a target biomass.")
 
+        if biomass_signal is None:
+            biomass_signal = config.get(
+                "dosing_automation.turbidostat",
+                "biomass_signal",
+                fallback="auto",
+            )
+
         self._set_biomass_signal(biomass_signal)
         self.target_biomass = float(target_biomass)
 

core/pioreactor/web/static/asset-manifest.json

@@ -1,7 +1,7 @@
 {
   "files": {
     "main.css": "/static/static/css/main.9c7a48b7.css",
-    "main.js": "/static/static/js/main.45157214.js",
+    "main.js": "/static/static/js/main.c87c24a5.js",
     "static/media/roboto-all-500-normal.woff": "/static/static/media/roboto-all-500-normal.0ab669b7a0d19b178f57.woff",
     "static/media/roboto-all-700-normal.woff": "/static/static/media/roboto-all-700-normal.a457fde362a540fcadff.woff",
     "static/media/roboto-all-400-normal.woff": "/static/static/media/roboto-all-400-normal.c5d001fa922fa66a147f.woff",
@@ -28,10 +28,10 @@
     "static/media/roboto-greek-ext-700-normal.woff2": "/static/static/media/roboto-greek-ext-700-normal.bd9854c751441ccc1a70.woff2",
     "index.html": "/static/index.html",
     "main.9c7a48b7.css.map": "/static/static/css/main.9c7a48b7.css.map",
-    "main.45157214.js.map": "/static/static/js/main.45157214.js.map"
+    "main.c87c24a5.js.map": "/static/static/js/main.c87c24a5.js.map"
   },
   "entrypoints": [
     "static/css/main.9c7a48b7.css",
-    "static/js/main.45157214.js"
+    "static/js/main.c87c24a5.js"
   ]
 }

core/pioreactor/web/static/index.html

@@ -1 +1 @@
-<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/static/favicon.ico"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="Pioreactor"/><link rel="apple-touch-icon" href="/static/logo192.png"/><link rel="manifest" href="/static/manifest.json"/><script defer="defer" src="/static/static/js/main.45157214.js"></script><link href="/static/static/css/main.9c7a48b7.css" rel="stylesheet"></head><body><div id="root"></div></body></html>
+<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/static/favicon.ico"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="Pioreactor"/><link rel="apple-touch-icon" href="/static/logo192.png"/><link rel="manifest" href="/static/manifest.json"/><script defer="defer" src="/static/static/js/main.c87c24a5.js"></script><link href="/static/static/css/main.9c7a48b7.css" rel="stylesheet"></head><body><div id="root"></div></body></html>

…or/web/static/static/js/main.45157214.js …or/web/static/static/js/main.c87c24a5.jscore/pioreactor/web/static/static/js/main.45157214.js renamed to core/pioreactor/web/static/static/js/main.c87c24a5.js core/pioreactor/web/static/static/js/main.45157214.js renamed to core/pioreactor/web/static/static/js/main.c87c24a5.js

@@ -24,6 +24,8 @@
 from pioreactor.background_jobs.dosing_automation import DosingAutomationJob
 from pioreactor.background_jobs.dosing_automation import start_dosing_automation
 from pioreactor.background_jobs.dosing_automation import VolumeCalculator
+from pioreactor.config import config
+from pioreactor.config import temporary_config_change
 from pioreactor.structs import DosingEvent
 from pioreactor.utils import local_persistent_storage
 from pioreactor.utils import SummableDict
@@ -315,6 +317,20 @@ def test_rejects_invalid_biomass_signal_in_turbidostat() -> None:
             pass
 
 
+def test_turbidostat_uses_config_default_biomass_signal() -> None:
+    experiment = "test_turbidostat_uses_config_default_biomass_signal"
+    with temporary_config_change(config, "dosing_automation.turbidostat", "biomass_signal", "od"):
+        with Turbidostat(
+            target_biomass=0.5,
+            duration=60,
+            exchange_volume_ml=0.25,
+            unit=unit,
+            experiment=experiment,
+            skip_first_run=True,
+        ) as algo:
+            assert algo.biomass_signal == "od"
+
+
 def test_turbidostat_auto_prefers_active_od_fused_estimator(monkeypatch) -> None:
     experiment = "test_turbidostat_auto_prefers_active_od_fused_estimator"
 

…c/static/js/main.45157214.js.LICENSE.txt …c/static/js/main.c87c24a5.js.LICENSE.txtcore/pioreactor/web/static/static/js/main.45157214.js.LICENSE.txt renamed to core/pioreactor/web/static/static/js/main.c87c24a5.js.LICENSE.txt core/pioreactor/web/static/static/js/main.45157214.js.LICENSE.txt renamed to core/pioreactor/web/static/static/js/main.c87c24a5.js.LICENSE.txt

@@ -10,6 +10,17 @@ SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 HOSTNAME=$(hostname)
 LEADER_HOSTNAME=$(/opt/pioreactor/venv/crudini --get "$CONFIG" cluster.topology leader_hostname)
 
+# Migrate / seed turbidostat config namespace:
+# [turbidostat.config] -> [dosing_automation.turbidostat]
+biomass_signal=$(/opt/pioreactor/venv/crudini --get "$CONFIG" dosing_automation.turbidostat biomass_signal 2>/dev/null || true)
+if [ -z "$biomass_signal" ]; then
+    biomass_signal=$(/opt/pioreactor/venv/crudini --get "$CONFIG" turbidostat.config biomass_signal 2>/dev/null || true)
+fi
+if [ -z "$biomass_signal" ]; then
+    biomass_signal="auto"
+fi
+/opt/pioreactor/venv/crudini --set "$CONFIG" dosing_automation.turbidostat biomass_signal "$biomass_signal"
+
 # UI automation definitions are leader-facing, so only install on the leader.
 if [ "$HOSTNAME" = "$LEADER_HOSTNAME" ]; then
     install -d -o pioreactor -g pioreactor -m 0755 "$DOT_PIOREACTOR/ui/automations/dosing"