some small updateS

Author: CamDavidsonPilon

core/pioreactor/background_jobs/od_reading.py

@@ -1127,9 +1127,6 @@ def __init__(
         else:
             self.estimator_transformer = estimator_transformer  # type: ignore
 
-        if self.estimator_transformer.estimator is not None:
-            self.add_to_published_settings("od_fused", {"datatype": "ODFused", "settable": False})
-
         self.adc_reader.add_external_logger(self.logger)
         self.calibration_transformer.add_external_logger(self.logger)
         self.ir_led_reference_transformer.add_external_logger(self.logger)

core/pioreactor/calibrations/protocols/README.md

@@ -14,42 +14,10 @@ the saved artifact differs.
 
 ## How protocols produce artifacts
 
-Protocols define a step registry and are executed through a `CalibrationSession`. During the flow,
-protocol steps call one of:
-
-- `ctx.store_calibration(...)` to persist a calibration artifact, or
-- `ctx.store_estimator(...)` to persist an estimator artifact.
-
-Both run through the same session engine and UI, but they store into different backends and are
-surfaced differently:
 
 - Calibrations are saved under `.../storage/calibrations/` and are listed in calibration APIs/CLI.
 - Estimators are saved under `.../storage/estimators/` and are not listed in calibration APIs/CLI.
 
-## Field builders
-
-Protocol steps build forms using `fields.*` helpers from `session_flow.py`. These correspond to
-`SessionInputs.*` accessors used in `advance()` methods.
-
-- `fields.str(name, label=None, default=None)` -> `ctx.inputs.str(name, default=..., required=...)`
-  - `field_type`: `string`
-  - Use for names, labels, and free-form text.
-- `fields.float(name, label=None, minimum=None, maximum=None, default=None)` -> `ctx.inputs.float(...)`
-  - `field_type`: `float`
-  - Enforces numeric bounds when provided.
-- `fields.int(name, label=None, minimum=None, maximum=None, default=None)` -> `ctx.inputs.int(...)`
-  - `field_type`: `int`
-  - Enforces integer bounds when provided.
-- `fields.choice(name, options, label=None, default=None)` -> `ctx.inputs.choice(...)`
-  - `field_type`: `choice`
-  - Validates input against the provided options.
-- `fields.bool(name, label=None, default=None)` -> `ctx.inputs.bool(...)`
-  - `field_type`: `bool`
-  - Accepts true/false and common yes/no string inputs.
-- `fields.float_list(name, label=None, default=None)` -> `ctx.inputs.float_list(...)`
-  - `field_type`: `float_list`
-  - Accepts a list of numbers or a comma-separated string.
-
 ## Example
 
 The `od_fusion_standards` protocol uses the calibration session UI, but saves an estimator:

core/pioreactor/cli/calibrations.py

@@ -103,7 +103,7 @@ def run_calibration(ctx, device: str, protocol_name: str | None, y: bool) -> Non
             raise click.Abort()
         protocols_sorted = sorted(
             protocols_by_device.values(),
-            key=lambda protocol: (getattr(protocol, "priority", 99), protocol.protocol_name),
+            key=lambda protocol: protocol.priority,
         )
         protocol_names_sorted = [protocol.protocol_name for protocol in protocols_sorted]
         if len(protocol_names_sorted) == 1:
@@ -192,10 +192,7 @@ def list_protocols() -> None:
     List available protocols for device calibrations.
     """
     for device, protocols in get_calibration_protocols().items():
-        sorted_protocols = sorted(
-            protocols.values(),
-            key=lambda protocol: (getattr(protocol, "priority", 99), protocol.protocol_name),
-        )
+        sorted_protocols = sorted(protocols.values(), key=lambda protocol: protocol.priority)
         protocol_names = [protocol.protocol_name for protocol in sorted_protocols]
         click.echo(f"{bold(device)}: {', '.join(protocol_names)}")
 
@@ -211,7 +208,7 @@ def display_calibration(device: str, calibration_name: str) -> None:
         data = load_calibration(device, calibration_name)
     except (FileNotFoundError, ValidationError) as exc:
         click.echo(f"Error: {exc}", err=True)
-        raise SystemExit(1) from exc
+        raise click.Abort()
 
     click.echo()
     curve = curve_to_callable(data.curve_data_)

core/pioreactor/cli/estimators.py

@@ -92,10 +92,7 @@ def list_protocols() -> None:
         protocols = get_calibration_protocols().get(device, {})
         if not protocols:
             continue
-        sorted_protocols = sorted(
-            protocols.values(),
-            key=lambda protocol: (getattr(protocol, "priority", 99), protocol.protocol_name),
-        )
+        sorted_protocols = sorted(protocols.values(), key=lambda protocol: protocol.priority)
         protocol_names = [protocol.protocol_name for protocol in sorted_protocols]
         click.echo(f"{bold(device)}: {', '.join(protocol_names)}")
         shown = True
@@ -210,26 +207,26 @@ def analyze_estimator(device: str, estimator_name: str, fit: str) -> None:
     target_file = ESTIMATOR_PATH / device / f"{estimator_name}.yaml"
     if not target_file.exists():
         click.echo(f"No such estimator file: {target_file}", err=True)
-        raise SystemExit(1)
+        raise click.Abort()
 
     try:
         estimator = load_estimator(device, estimator_name)
     except Exception as exc:
         click.echo(f"Unable to load estimator: {exc}", err=True)
-        raise SystemExit(1) from exc
+        raise click.Abort()
 
     if not isinstance(estimator, structs.ODFusionEstimator):
         click.echo("Only od_fused estimators are supported for analyze.", err=True)
-        raise SystemExit(1)
+        raise click.Abort()
 
     if fit != "akima":
         click.echo("Only akima fits are supported for od_fused estimators.", err=True)
-        raise SystemExit(1)
+        raise click.Abort()
 
     by_angle = _extract_fusion_by_angle_records(estimator)
     if not by_angle:
         click.echo("No recorded fusion data available to analyze.", err=True)
-        raise SystemExit(1)
+        raise click.Abort()
 
     click.echo(f"Estimator: {estimator.estimator_name}")
     click.echo(f"Device: {device}")
@@ -257,15 +254,15 @@ def analyze_estimator(device: str, estimator_name: str, fit: str) -> None:
             mu_rmse = _rmse_for_fit(mu_curve, x_vals, y_vals)
         except Exception as exc:
             click.echo(f"{angle}°: unable to fit mu curve: {exc}", err=True)
-            raise SystemExit(1) from exc
+            raise click.Abort()
 
         sigma_reference = [akima_eval(estimator.sigma_splines_log[angle], float(x_val)) for x_val in x_vals]
         try:
             sigma_curve = _fit_curve_data_from_points(fit=fit, x=x_vals, y=sigma_reference)
             sigma_rmse = _rmse_for_fit(sigma_curve, x_vals, sigma_reference)
         except Exception as exc:
             click.echo(f"{angle}°: unable to fit sigma curve: {exc}", err=True)
-            raise SystemExit(1) from exc
+            raise click.Abort()
 
         click.echo(f"{angle}° mu: {curve_to_functional_form(mu_curve)}")
         click.echo(f"{angle}° mu rmse: {mu_rmse:0.4f}")

core/pioreactor/web/unit_api.py

@@ -132,7 +132,7 @@ def _build_calibration_protocol_payloads() -> list[dict[str, Any]]:
             title = getattr(protocol, "title", "") or f"{protocol_name.replace('_', ' ').title()} calibration"
             description = getattr(protocol, "description", "")
             requirements = list(getattr(protocol, "requirements", ()))
-            priority = int(getattr(protocol, "priority", 99))
+            priority = int(protocol.priority)
             protocols.append(
                 {
                     "id": f"{device}_{protocol_name}",