more calibration stuff

pioreactor/actions/pump.py

@@ -32,7 +32,7 @@
 from pioreactor.whoami import get_unit_name
 
 DEFAULT_PWM_CALIBRATION = structs.SimplePeristalticPumpCalibration(
-    pioreactor_unit=get_unit_name(),
+    calibrated_on_pioreactor_unit=get_unit_name(),
     created_at=default_datetime_for_pioreactor(),
     hz=200.0,
     dc=100.0,

pioreactor/calibrations/od_calibration.py

@@ -468,7 +468,7 @@ def save_results(
 ) -> structs.ODCalibration:
     data_blob = structs.ODCalibration(
         created_at=current_utc_datetime(),
-        pioreactor_unit=unit,
+        calibrated_on_pioreactor_unit=unit,
         calibration_name=name,
         angle=angle,
         maximum_od600=max(od600s),

pioreactor/calibrations/pump_calibration.py

@@ -154,7 +154,7 @@ def setup(
                 hz=hz,
                 dc=dc,
                 voltage=voltage_in_aux(),
-                pioreactor_unit=unit,
+                calibrated_on_pioreactor_unit=unit,
                 recorded_data={"x": [], "y": []},
             ),
         )
@@ -233,7 +233,7 @@ def run_tests(
         dc=dc,
         created_at=current_utc_datetime(),
         voltage=voltage_in_aux(),
-        pioreactor_unit=unit,
+        calibrated_on_pioreactor_unit=unit,
         recorded_data={"x": [], "y": []},
     )
 
@@ -314,7 +314,7 @@ def save_results(
 ) -> structs.SimplePeristalticPumpCalibration:
     pump_calibration_result = structs.SimplePeristalticPumpCalibration(
         calibration_name=name,
-        pioreactor_unit=unit,
+        calibrated_on_pioreactor_unit=unit,
         created_at=current_utc_datetime(),
         curve_type="poly",
         curve_data_=[duration_, bias_],

pioreactor/calibrations/stirring_calibration.py

@@ -118,7 +118,7 @@ def run_stirring_calibration(
             pwm_hz=config.getfloat("stirring.config", "pwm_hz"),
             voltage=voltage_in_aux(),
             calibration_name=f"stirring-calibration-{current_utc_datetime().strftime('%Y-%m-%d_%H-%M-%S')}",
-            pioreactor_unit=unit,
+            calibrated_on_pioreactor_unit=unit,
             created_at=current_utc_datetime(),
             curve_data_=[rpm_coef, intercept],
             curve_type="poly",

pioreactor/cli/calibrations.py

@@ -111,6 +111,11 @@ def run_calibration(ctx, device: str, protocol_name: str | None) -> None:
         f"Do you want to set this calibration as the Active Calibration for {device}?", default=True
     ):
         calibration_struct.set_as_active_calibration_for_device(device)
+        click.echo(f"Set{calibration_struct.calibration_name} as the active calibration for {device}.")
+    else:
+        click.echo(
+            f"Okay. You can use 'pio calibration set-active --device {device} --name {calibration_struct.calibration_name}' to set this calibration as the active one."
+        )
 
     click.echo(
         f"Calibration '{calibration_struct.calibration_name}' of device '{device}' saved to {out_file} ✅"

pioreactor/structs.py

@@ -141,7 +141,7 @@ class Voltage(JSONPrintedStruct):
 
 class CalibrationBase(Struct, tag_field="calibration_type", kw_only=True):
     calibration_name: str
-    pioreactor_unit: str
+    calibrated_on_pioreactor_unit: str
     created_at: t.Annotated[datetime, Meta(tz=True)]
     curve_data_: list[float]
     curve_type: str  # ex: "poly"

pioreactor/tests/test_calibrations.py

@@ -26,7 +26,7 @@ def test_save_and_load_calibration(temp_calibration_dir) -> None:
     # 1. Create an ODCalibration object (fully valid).
     od_cal = ODCalibration(
         calibration_name="my_test_cal",
-        pioreactor_unit="unitA",
+        calibrated_on_pioreactor_unit="unitA",
         created_at=datetime.now(timezone.utc),
         curve_data_=[1.0, 2.0, 3.0],
         curve_type="poly",

pioreactor/tests/test_dosing_automation.py

@@ -51,7 +51,7 @@ def setup_function() -> None:
         hz=100,
         created_at=datetime(2010, 1, 1, tzinfo=timezone.utc),
         voltage=-1.0,
-        pioreactor_unit=unit,
+        calibrated_on_pioreactor_unit=unit,
     )
     cal.set_as_active_calibration_for_device("media_pump")
     cal.set_as_active_calibration_for_device("alt_media_pump")

pioreactor/tests/test_mqtt_to_db_streaming.py

@@ -134,7 +134,7 @@ def test_dosing_events_land_in_db() -> None:
                 hz=100,
                 created_at=current_utc_datetime(),
                 voltage=-1.0,
-                pioreactor_unit=unit,
+                calibrated_on_pioreactor_unit=unit,
             ),
         )
 

pioreactor/tests/test_od_reading.py

@@ -638,7 +638,7 @@ def test_calibration_simple_linear_calibration_positive_slope() -> None:
         x="voltage",
         y="od600s",
         pd_channel="2",
-        pioreactor_unit=get_unit_name(),
+        calibrated_on_pioreactor_unit=get_unit_name(),
     )
 
     cal.set_as_active_calibration_for_device("od")
@@ -692,7 +692,7 @@ def test_calibration_simple_linear_calibration_negative_slope() -> None:
         x="voltage",
         y="od600s",
         pd_channel="2",
-        pioreactor_unit=get_unit_name(),
+        calibrated_on_pioreactor_unit=get_unit_name(),
     )
 
     cal.set_as_active_calibration_for_device("od")
@@ -737,7 +737,7 @@ def test_calibration_simple_quadratic_calibration() -> None:
         x="voltage",
         y="od600s",
         pd_channel="2",
-        pioreactor_unit=get_unit_name(),
+        calibrated_on_pioreactor_unit=get_unit_name(),
     )
 
     cal.set_as_active_calibration_for_device("od")
@@ -770,7 +770,7 @@ def test_calibration_multi_modal() -> None:
         x="voltage",
         y="od600s",
         pd_channel="2",
-        pioreactor_unit=get_unit_name(),
+        calibrated_on_pioreactor_unit=get_unit_name(),
     )
 
     cal.set_as_active_calibration_for_device("od")
@@ -801,7 +801,7 @@ def test_calibration_errors_when_ir_led_differs() -> None:
             x="voltage",
             y="od600s",
             pd_channel="2",
-            pioreactor_unit=get_unit_name(),
+            calibrated_on_pioreactor_unit=get_unit_name(),
         )
 
         cal.set_as_active_calibration_for_device("od")
@@ -846,7 +846,7 @@ def test_calibration_with_irl_data1() -> None:
         x="voltage",
         y="od600s",
         pd_channel="2",
-        pioreactor_unit=get_unit_name(),
+        calibrated_on_pioreactor_unit=get_unit_name(),
     )
 
     cal.set_as_active_calibration_for_device("od")
@@ -929,7 +929,7 @@ def test_calibration_data_from_user1() -> None:
         x="voltage",
         y="od600s",
         pd_channel="2",
-        pioreactor_unit=get_unit_name(),
+        calibrated_on_pioreactor_unit=get_unit_name(),
     )
 
     calibration.set_as_active_calibration_for_device("od")
@@ -971,7 +971,7 @@ def test_calibration_data_from_user2() -> None:
         x="voltage",
         y="od600s",
         pd_channel="2",
-        pioreactor_unit=get_unit_name(),
+        calibrated_on_pioreactor_unit=get_unit_name(),
     )
 
     cal.set_as_active_calibration_for_device("od")
@@ -1047,7 +1047,7 @@ def test_CachedCalibrationTransformer_with_real_calibration() -> None:
         ir_led_intensity=50,
         pd_channel="2",
         created_at=current_utc_datetime(),
-        pioreactor_unit="pio1",
+        calibrated_on_pioreactor_unit="pio1",
         recorded_data={
             "x": [
                 1.359234153183015,

pioreactor/tests/test_pumps.py

@@ -42,7 +42,7 @@ def setup_function():
         hz=100,
         created_at=datetime(2010, 1, 1, tzinfo=timezone.utc),
         voltage=-1.0,
-        pioreactor_unit=unit,
+        calibrated_on_pioreactor_unit=unit,
     )
     cal.set_as_active_calibration_for_device("media_pump")
     cal.set_as_active_calibration_for_device("alt_media_pump")
@@ -189,7 +189,7 @@ def test_pump_can_be_interrupted() -> None:
         hz=100,
         created_at=datetime(2010, 1, 1, tzinfo=timezone.utc),
         voltage=-1.0,
-        pioreactor_unit=unit,
+        calibrated_on_pioreactor_unit=unit,
     )
 
     with PWMPump(unit=unit, experiment=experiment, pin=13, calibration=calibration) as p:
@@ -236,7 +236,7 @@ def test_pumps_can_run_in_background() -> None:
         hz=100,
         created_at=datetime(2010, 1, 1, tzinfo=timezone.utc),
         voltage=-1.0,
-        pioreactor_unit=unit,
+        calibrated_on_pioreactor_unit=unit,
     )
     with PWMPump(unit=unit, experiment=experiment, pin=13, calibration=calibration) as p:
         with local_intermittent_storage("pwm_dc") as cache:
@@ -298,7 +298,7 @@ def test_media_circulation_will_control_media_pump_if_it_has_a_higher_flow_rate(
         hz=100,
         created_at=datetime(2010, 1, 1, tzinfo=timezone.utc),
         voltage=-1.0,
-        pioreactor_unit=unit,
+        calibrated_on_pioreactor_unit=unit,
     ).set_as_active_calibration_for_device("media_pump")
 
     structs.SimplePeristalticPumpCalibration(
@@ -310,7 +310,7 @@ def test_media_circulation_will_control_media_pump_if_it_has_a_higher_flow_rate(
         hz=100,
         created_at=datetime(2010, 1, 1, tzinfo=timezone.utc),
         voltage=-1.0,
-        pioreactor_unit=unit,
+        calibrated_on_pioreactor_unit=unit,
     ).set_as_active_calibration_for_device("waste_pump")
 
     media_added, waste_removed = circulate_media(5.0, unit, exp)
@@ -329,7 +329,7 @@ def test_media_circulation_will_control_media_pump_if_it_has_a_lower_flow_rate()
         hz=100,
         created_at=datetime(2010, 1, 1, tzinfo=timezone.utc),
         voltage=-1.0,
-        pioreactor_unit=unit,
+        calibrated_on_pioreactor_unit=unit,
     ).set_as_active_calibration_for_device("media_pump")
 
     structs.SimplePeristalticPumpCalibration(
@@ -341,7 +341,7 @@ def test_media_circulation_will_control_media_pump_if_it_has_a_lower_flow_rate()
         hz=100,
         created_at=datetime(2010, 1, 1, tzinfo=timezone.utc),
         voltage=-1.0,
-        pioreactor_unit=unit,
+        calibrated_on_pioreactor_unit=unit,
     ).set_as_active_calibration_for_device("waste_pump")
 
     media_added, waste_removed = circulate_media(5.0, unit, exp)

pioreactor/tests/test_stirring.py

@@ -163,7 +163,7 @@ def clean_up(self):
     linear_term, constant_term = 10, -5
     cal = SimpleStirringCalibration(
         calibration_name="test_stirring_with_calibration",
-        pioreactor_unit=unit,
+        calibrated_on_pioreactor_unit=unit,
         created_at=current_utc_datetime(),
         curve_data_=[linear_term, constant_term],
         curve_type="poly",

update_scripts/upcoming/update.sh

@@ -16,4 +16,4 @@ touch $DB
 touch $DB-shm
 touch $DB-wal
 
-chown -R $USERNAME:www-data $DB*
+chown -R $USERNAME:www-data $DB*