vial icon

Author: CamDavidsonPilon

CHANGELOG.md

@@ -1,32 +1,38 @@
 ### Upcoming
 
-#### Highligts
+#### Highlights
 
- - Perform calibrations in the UI!
+ - Run calibrations from the UI.
+ - New Protocols page with guided calibration sessions, including step-by-step instructions and live charts.
 
 #### Enhancements
 
- - Support for Pioreactor XR
- - Support for Optics calibration jig
- - faster Stop commands in the UI, listing plugins, and exporting data
- - new events in the dosing_automation_events table & export detailing when dosing starts and stops.
- - new query pattern for faster Experiment Overview chart loading. However, there is a random element to what data is displayed in a time series for large datasets. Let us know if this is too distracting.
+ - Support for Pioreactor XR.
+ - Support for the optics calibration jig.
+ - Faster Stop commands in the UI, plugin listing, and data exports.
+ - Added dosing start/stop events to `dosing_automation_events`, including exports.
+ - New query pattern for faster Experiment Overview chart loading; large datasets may show randomized sampling in time series. Let us know if this is too distracting. Max point targets per series increased to 1400.
  - OD calibrations now support multiple photodiode angles; `pio calibrations run --device od` can emit per-angle calibrations for 45/90/135.
    - Added an update helper to migrate legacy OD calibrations into per-angle devices.
- - reorganized calibration protocol modules into `core/pioreactor/calibrations/protocols/` and extracted a `registry.py` for protocol registration.
+ - Reorganized calibration protocol modules into `core/pioreactor/calibrations/protocols/` and extracted a `registry.py` for protocol registration.
+ - Calibration protocols are now exposed via API for the UI and CLI, with session IDs that can be advanced or aborted.
+ - Self-test results now surface per-check pass/fail status in the Inventory page and support retrying failed checks.
+ - Removed redundant `from __future__ import annotations` usage now that we run on Python 3.13.
 
 #### Breaking changes
- - Moved Self-test to Inventory page. Pioreactors no longer need to be assigned to an experiment to run self-test.
+ - Moved Self-test to the Inventory page. Pioreactors no longer need to be assigned to an experiment to run self-test.
  - Removed `/api/workers/<pioreactor_unit>/configuration`; use `/api/units/<pioreactor_unit>/configuration`.
- - self-test logs are now part of "$experiment"
- - calibration flow modules were merged into protocol modules; old import paths like `pioreactor.calibrations.pump_calibration` and `pioreactor.calibrations.od_calibration_*` are removed.
- - removed experimental pump-detection failure from chemostat and turbidostat
+ - Self-test logs are now part of `$experiment`.
+ - Calibration flow modules were merged into protocol modules; old import paths like `pioreactor.calibrations.pump_calibration` and `pioreactor.calibrations.od_calibration_*` are removed.
+ - Removed experimental pump-detection failure handling from chemostat and turbidostat.
  - OD calibration devices are now per-angle (`od45`, `od90`, `od135`) instead of just `od`. Physically, this changes the calibration directory in `~/.pioreactor/storage/calibrations/od` to  `~/.pioreactor/storage/calibrations/{od45,od90,od135}`. Existing `od` calibration files and active calibrations are migrated during the update.
+ - Self-test no longer creates a stirring calibration.
 
-#### Bug Fixes
+#### Bug fixes
 
- - Fix logging prematurely closing for self-tests
- - Fix floating point error at the boundary of OD calibrations
+ - Fix self-test logging closing prematurely.
+ - Fix floating point error at the boundary of OD calibrations.
+ - Fix runtime forward-reference errors in type annotations after dropping `__future__` imports.
 
 ### 25.12.10
 

core/tests/test_calibration_sessions.py

@@ -145,7 +145,7 @@ def test_read_voltage_requires_executor_in_ui() -> None:
     session = _build_session()
 
     def executor(action: str, payload: dict[str, object]) -> dict[str, object]:
-        assert action == "read_voltage"
+        assert action == "read_aux_voltage"
         return {"voltage": "3.3"}
 
     class Dummy(SessionStep):

core/tests/test_od_reading.py

@@ -1438,6 +1438,8 @@ def test_can_pass_config_section_directly() -> None:
         [
             ("od_config.photodiode_channel", "1", "90"),
             ("od_config.photodiode_channel", "2", "REF"),
+            ("od_config.photodiode_channel", "3", None),
+            ("od_config.photodiode_channel", "4", None),
         ],
     ):
         section = config["od_config.photodiode_channel"]

frontend/src/Protocols.jsx

@@ -18,6 +18,7 @@ import PlayArrowIcon from "@mui/icons-material/PlayArrow";
 import CalibrationSessionDialog from "./components/CalibrationSessionDialog";
 import { fetchTaskResult } from "./utilities";
 import CircularProgress from "@mui/material/CircularProgress";
+import RequirementsAlert from "./components/RequirementsAlert";
 
 function ProtocolCard({
   protocol,
@@ -40,16 +41,19 @@ function ProtocolCard({
         </Typography>
 
         <Box sx={{ mt: 2 }}>
-          <Typography variant="subtitle2">Requirements</Typography>
-          <Box component="ul" sx={{ mt: 1, mb: 0, pl: 2 }}>
-            {requirements.map((item) => (
-              <li key={item}>
-                <Typography variant="body2" >
-                  {item}
-                </Typography>
-              </li>
-            ))}
-          </Box>
+          <RequirementsAlert>
+            <Box>
+              <Box component="ul" sx={{ mt: 0, mb: 0, pl: 2 }}>
+              {requirements.map((item) => (
+                <li key={item}>
+                  <Typography variant="body2">
+                    {item}
+                  </Typography>
+                </li>
+              ))}
+              </Box>
+            </Box>
+          </RequirementsAlert>
         </Box>
         <Box
           sx={{

frontend/src/components/RequirementsAlert.jsx

@@ -0,0 +1,29 @@
+import React from "react";
+import Alert from "@mui/material/Alert";
+import AlertTitle from "@mui/material/AlertTitle";
+import VialIcon from "./VialIcon";
+
+function RequirementsAlert(props) {
+  const { sx, children, ...rest } = props;
+  const baseSx = {
+    backgroundColor: "grey.100",
+    borderColor: "grey.300",
+    borderStyle: "solid",
+    borderWidth: "1px",
+    color: "grey.700",
+    mt: 1,
+    mb: 1,
+    "& .MuiAlert-icon": {
+      color: "grey.600",
+    },
+  };
+  const combinedSx = Array.isArray(sx) ? [baseSx, ...sx] : [baseSx, sx];
+
+  return (
+    <Alert icon={<VialIcon sx={{ color: "grey.600" }} />} severity="info" sx={combinedSx} {...rest}>
+      {children}
+    </Alert>
+  );
+}
+
+export default RequirementsAlert;

frontend/src/components/SelfTestDialog.jsx

@@ -25,6 +25,7 @@ import PlayArrowIcon from "@mui/icons-material/PlayArrow";
 
 
 import PioreactorIcon from "./PioreactorIcon"
+import RequirementsAlert from "./RequirementsAlert"
 import {runPioreactorJob} from "../utilities"
 
 
@@ -150,9 +151,9 @@ export default function SelfTestDialog({client, disabled, experiment, unit, labe
           <Typography variant="body2" component="p" gutterBottom>
             Perform a check of the heating & temperature sensor, LEDs & photodiodes, and stirring.
           </Typography>
-          <Typography variant="body2" component="p" gutterBottom>
+          <RequirementsAlert>
             Add a closed vial, half-filled with water, and stirbar into the Pioreactor.
-          </Typography>
+          </RequirementsAlert>
 
             <Box>
 

frontend/src/components/VialIcon.jsx

@@ -0,0 +1,29 @@
+import React from 'react'
+import SvgIcon from '@mui/material/SvgIcon'
+
+function VialIcon(props) {
+  return (
+    <SvgIcon viewBox="-1 -2 13 23" strokeWidth="1.9" {...props}>
+      <rect
+        x="0.56"
+        y="0.59"
+        width="10.21"
+        height="2.72"
+        fill="currentColor"
+        stroke="currentColor"
+        strokeLinejoin="round"
+      />
+      <path
+        d="M0.17 5.96L0.14 19.44H11.17V5.81L0.18 5.97Z"
+        fill={props.fillColor || 'none'}
+        stroke="currentColor"
+        strokeLinecap="round"
+        strokeLinejoin="round"
+      />
+      <line fill={props.fillColor || 'none'} id="svg_15" stroke="currentColor" strokeLinejoin="round" x1="7.14" x2="7.14" y1="-1.00" y2="12.94"/>
+      <line fill={props.fillColor || 'none'} id="svg_15" stroke="currentColor" strokeLinejoin="round" x1="4" x2="4" y1="0.00" y2="14.94"/>
+    </SvgIcon>
+  )
+}
+
+export default VialIcon