new svgs

Author: CamDavidsonPilon

core/pioreactor/calibrations/protocols/od_reference_standard.py

@@ -261,11 +261,7 @@ class ODReferenceStandardProtocol(CalibrationProtocol[pt.ODCalibrationDevices]):
     protocol_name = "od_reference_standard"
     title = "Optics Calibration Jig"
     description = "Calibrate OD using the Pioreactor Optical Reference Standard."
-    requirements = (
-        "OD reading must be off before starting.",
-        "Insert the Optics Calibration Jig.",
-        "Set ir_led_intensity in [od_reading.config] to a numeric value.",
-    )
+    requirements = ("Optics Calibration Jig", "2x tubes from the Vial Cap S")
     step_registry: ClassVar[StepRegistry] = _REFERENCE_STANDARD_STEPS
 
     @classmethod

core/pioreactor/calibrations/protocols/od_standards.py

@@ -349,7 +349,12 @@ class ChannelConfirm(SessionStep):
 
     def render(self, ctx: SessionContext) -> CalibrationStep:
         channel_summary = ctx.data.get("channel_summary", "")
-        return steps.info("Confirm channels", f"Using channels {channel_summary}.")
+        channel_lines = channel_summary.split(", ") if channel_summary else []
+        if channel_lines:
+            message = "Using channels:\n" + "\n".join(channel_lines)
+        else:
+            message = "Using channels."
+        return steps.info("Confirm channels", message)
 
     def advance(self, ctx: SessionContext) -> SessionStep | None:
         if ctx.inputs.has_inputs:
@@ -389,7 +394,15 @@ def render(self, ctx: SessionContext) -> CalibrationStep:
             _get_channel_angle_map(ctx),
         )
         if chart:
-            step.metadata = {"chart": chart}
+            step.metadata["chart"] = chart
+        else:
+            step.metadata = {
+                "image": {
+                    "src": "/static/svgs/place-standard-arrow-pioreactor.svg",
+                    "alt": "Place a non-blank standard vial with a stir bar into the Pioreactor.",
+                    "caption": "Place a non-blank standard vial with a stir bar into the Pioreactor.",
+                }
+            }
         return step
 
     def advance(self, ctx: SessionContext) -> SessionStep | None:
@@ -436,7 +449,7 @@ def render(self, ctx: SessionContext) -> CalibrationStep:
             [
                 fields.choice(
                     "next_action",
-                    ["record another standard", "continue to blank"],
+                    ["record another standard", "finish, and continue to blank"],
                     label="Next action",
                     default="record another standard",
                 )
@@ -469,7 +482,7 @@ def advance(self, ctx: SessionContext) -> SessionStep | None:
             return PlaceStandard()
         next_action = ctx.inputs.choice(
             "next_action",
-            ["record another standard", "continue to blank"],
+            ["record another standard", "finish, and continue to blank"],
             default="record another standard",
         )
         if next_action == "record another standard":
@@ -485,13 +498,14 @@ def render(self, ctx: SessionContext) -> CalibrationStep:
             "Place blank",
             "Place the blank (media only) standard vial into the Pioreactor.",
         )
-        chart = _build_standards_chart_metadata(
-            ctx.data.get("od600_values", []),
-            ctx.data.get("voltages_by_channel", {}),
-            _get_channel_angle_map(ctx),
-        )
-        if chart:
-            step.metadata = {"chart": chart}
+        step.metadata = {
+            "image": {
+                "src": "/static/svgs/place-blank-arrow-pioreactor.svg",
+                "alt": "Place the blank (media only) standard vial into the Pioreactor.",
+                "caption": "Place the blank (media only) standard vial into the Pioreactor.",
+            }
+        }
+
         return step
 
     def advance(self, ctx: SessionContext) -> SessionStep | None:
@@ -582,9 +596,9 @@ class StandardsODProtocol(CalibrationProtocol[pt.ODCalibrationDevices]):
     title = "OD standards calibration"
     description = "Calibrate OD channels using a series of OD600 standards and a blank."
     requirements = (
-        "OD reading and stirring must be off before starting.",
-        "Have OD600 standards ready (including a blank).",
-        "Each vial should include a stir bar.",
+        "OD600 standards (including a blank)",
+        "Vials",
+        "Stir bars",
     )
     step_registry: ClassVar[StepRegistry] = _OD_STANDARDS_STEPS
 

core/pioreactor/calibrations/protocols/pump_duration_based.py

@@ -220,7 +220,7 @@ class IntroConfirm3(SessionStep):
     def render(self, ctx: SessionContext) -> CalibrationStep:
         step = steps.info(
             "Keep hardware safe",
-            "Keep the vial and tubing away from the Pioreactor hardware during this protocol",
+            "Make space between the vial and Pioreactor hardware",
         )
         step.metadata = {
             "image": {
@@ -332,8 +332,8 @@ class TubingIntoWater(SessionStep):
     def render(self, ctx: SessionContext) -> CalibrationStep:
         pump_device = _get_pump_device(ctx)
         step = steps.info(
-            f"Place tubing ends in water ({pump_device})",
-            "Place both ends of the tubing into the larger container of water before priming.",
+            f"Place tubing ends of {pump_device} in water",
+            f"Place both ends of the {pump_device} tubing into the larger container of water to prime.",
         )
         step.metadata = {
             "image": {
@@ -356,8 +356,8 @@ class PrimePumpDuration(SessionStep):
     def render(self, ctx: SessionContext) -> CalibrationStep:
         return steps.form(
             "Prime pump",
-            "Prime the pump by filling the tubes completely with water.",
-            [fields.float("prime_duration_s", label="Prime duration (seconds)", default=10.0, minimum=0.1)],
+            "Prime the pump by filling the tubes completely with water. There should be no air pockets by the end.",
+            [fields.float("prime_duration_s", label="Prime duration (seconds)", default=15.0, minimum=5)],
         )
 
     def advance(self, ctx: SessionContext) -> SessionStep | None:
@@ -375,7 +375,11 @@ def render(self, ctx: SessionContext) -> CalibrationStep:
         tracer_duration = float(ctx.data.get("tracer_duration_s", 1.0))
         step = steps.action(
             "Tracer run",
-            f"Running the pump for {tracer_duration:.2f} seconds. While running, hold the tube above the vial. Please measure the volume expelled. Ready?",
+            (
+                f"Running the pump for {tracer_duration:.2f} seconds.\n\n"
+                "While running, hold the tube above the vial. Please measure the volume expelled.\n\n"
+                "Ready?"
+            ),
         )
         step.metadata = {
             "image": {
@@ -428,7 +432,7 @@ def render(self, ctx: SessionContext) -> CalibrationStep:
         duration = float(durations[test_index])
         step = steps.action(
             "Dispense",
-            f"Next: running the pump for {duration:.2f} seconds. Please measure the volume expelled. Ready?",
+            f"Next: running the pump for {duration:.2f} seconds. Please measure the volume expelled. \n\nReady?",
         )
         if results:
             step.metadata = {
@@ -581,8 +585,10 @@ class DurationBasedPumpProtocol(CalibrationProtocol[pt.PumpCalibrationDevices]):
     title = "Duration-based pump calibration"
     description = "Build a duration-to-volume curve for the {device} pump using a simple multi-step flow."
     requirements = (
-        "Place the outflow tube into a measuring container or scale.",
-        "Have clean water available for priming and tests.",
+        "Peristaltic pump",
+        "Pioreactor vial",
+        "Container of clean water",
+        "Measuring container or scale",
     )
     step_registry: ClassVar[StepRegistry] = _PUMP_DURATION_STEPS
 

core/pioreactor/calibrations/protocols/stirring_dc_based.py

@@ -278,8 +278,9 @@ class DCBasedStirringProtocol(CalibrationProtocol[Literal["stirring"]]):
     title = "Stirring DC-based calibration"
     description = "Maps duty cycle to RPM for the current stirrer configuration."
     requirements = (
-        "Stirring must be off before starting.",
-        "Insert a vial with a stir bar and the liquid volume you plan to use (water is fine).",
+        "Vial",
+        "Stir bar",
+        "Liquid (water is fine)",
     )
     step_registry: ClassVar[StepRegistry] = _DC_BASED_STEPS