XR in the UI, and hardware check when the model changes

CamDavidsonPilon · CamDavidsonPilon · commit 4190bc4ceb86 · 2026-01-17T18:43:42.000-05:00
diff --git a/core/pioreactor/calibrations/protocols/pump_duration_based.py b/core/pioreactor/calibrations/protocols/pump_duration_based.py
@@ -175,8 +175,8 @@ def render(self, ctx: SessionContext) -> CalibrationStep:
         return steps.info(
             "Pump calibration",
             (
-                "This routine calibrates the pump on this Pioreactor. You will need:\n"
-                "1. This Pioreactor.\n"
+                f"This routine calibrates the {pump_device} pump. You will need:\n"
+                "1. Pioreactor hardware.\n"
                 "2. A vial on a scale (0.1g resolution) or a graduated cylinder.\n"
                 "3. A larger container filled with water.\n"
                 f"4. {pump_device} connected to PWM channel {channel}.\n\n"
diff --git a/core/pioreactor/cli/pio.py b/core/pioreactor/cli/pio.py
@@ -714,6 +714,15 @@ def update_app(
     """
     # initialize logger and build commands based on input parameters
     logger = create_logger("update_app", unit=whoami.get_unit_name(), experiment=whoami.UNIVERSAL_EXPERIMENT)
+    logger.debug(
+        "Starting app update. branch=%s repo=%s source=%s version=%s no_deps=%s defer_web_restart=%s",
+        branch,
+        repo,
+        source,
+        version,
+        no_deps,
+        defer_web_restart,
+    )
     commands_and_priority, version_installed = get_update_app_commands(
         branch,
         repo,
@@ -722,13 +731,22 @@ def update_app(
         no_deps=no_deps,
         defer_web_restart=defer_web_restart,
     )
+    logger.debug(
+        "Prepared %s update commands. target_version=%s", len(commands_and_priority), version_installed
+    )
 
-    for command, _ in sorted(commands_and_priority, key=lambda t: t[1]):
+    for index, (command, priority) in enumerate(sorted(commands_and_priority, key=lambda t: t[1]), start=1):
         if whoami.is_testing_env():
-            logger.debug(f"DRY-RUN: {command}")
+            logger.debug("DRY-RUN (step %s, priority %s): %s", index, priority, command)
             continue
 
-        logger.debug(command)
+        logger.debug(
+            "Running update step %s/%s (priority %s): %s",
+            index,
+            len(commands_and_priority),
+            priority,
+            command,
+        )
 
         p = subprocess.run(
             command,
@@ -738,12 +756,17 @@ def update_app(
             stderr=subprocess.PIPE,
         )
         if p.returncode != 0:
-            logger.debug(p.stderr)
-            logger.error("Update failed. See logs.")
+            if p.stdout:
+                logger.debug("Update step %s stdout: %s", index, p.stdout)
+            if p.stderr:
+                logger.debug("Update step %s stderr: %s", index, p.stderr)
+            logger.debug("Update failed at step %s with returncode %s.", index, p.returncode)
             # end early
             raise click.Abort()
         elif p.stdout:
-            logger.debug(p.stdout)
+            logger.debug("Update step %s stdout: %s", index, p.stdout)
+        if p.stderr:
+            logger.debug("Update step %s stderr: %s", index, p.stderr)
 
     logger.notice(f"Updated Pioreactor app to version {version_installed}.")  # type: ignore
     # everything work? Let's publish to MQTT. This is a terrible hack, as monitor should do this.
diff --git a/core/pioreactor/hardware.py b/core/pioreactor/hardware.py
@@ -111,6 +111,23 @@ def get_layered_mod_config(mod: str) -> dict[str, Any]:
     return data
 
 
+def get_layered_mod_config_for_model(mod: str, model_name: str, model_version: str) -> dict[str, Any]:
+    """Load one mod's YAML by layering hats -> provided model."""
+    base = Path(environ["DOT_PIOREACTOR"]) / "hardware"
+
+    if hardware_version_info is None:
+        raise exc.HardwareNotFoundError("HAT not found")
+    assert hardware_version_info is not None
+
+    model_dir = base / "models" / model_name / model_version
+    hat_dir = base / "hats" / tuple_to_text(hardware_version_info)
+
+    data: dict[str, Any] = {}
+    data = _deep_merge(data, _load_yaml_if_exists(hat_dir / f"{mod}.yaml"))
+    data = _deep_merge(data, _load_yaml_if_exists(model_dir / f"{mod}.yaml"))
+    return data
+
+
 @cache
 def determine_gpiochip() -> pt.GpioChip:
     """Return the GPIO chip index for the current Raspberry Pi."""
diff --git a/core/pioreactor/web/api.py b/core/pioreactor/web/api.py
@@ -2798,6 +2798,14 @@ def change_worker_model(pioreactor_unit: str) -> ResponseReturnValue:
             task="worker_model",
             level="INFO",
         )
+        # When new model versions are added, consider extending hardware checks here
+        # (see /unit_api/hardware/check and tasks.check_model_hardware).
+        if model_version == "1.5":
+            tasks.post_into_unit(
+                pioreactor_unit,
+                "/unit_api/hardware/check",
+                json={"model_name": model_name, "model_version": model_version},
+            )
         return {"status": "success"}, 200
     else:
         abort_with(404, f"Worker {pioreactor_unit} not found")
diff --git a/core/pioreactor/web/static/asset-manifest.json b/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.13eb0766.js",
+    "main.js": "/static/static/js/main.40638d9a.js",
     "static/media/pioreactor_cloud.webp": "/static/static/media/pioreactor_cloud.b15b29e435797dc69d76.webp",
     "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",
@@ -30,10 +30,10 @@
     "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.13eb0766.js.map": "/static/static/js/main.13eb0766.js.map"
+    "main.40638d9a.js.map": "/static/static/js/main.40638d9a.js.map"
   },
   "entrypoints": [
     "static/css/main.9c7a48b7.css",
-    "static/js/main.13eb0766.js"
+    "static/js/main.40638d9a.js"
   ]
 }
diff --git a/core/pioreactor/web/static/index.html b/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.13eb0766.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.40638d9a.js"></script><link href="/static/static/css/main.9c7a48b7.css" rel="stylesheet"></head><body><div id="root"></div></body></html>
diff --git a/core/pioreactor/web/static/static/js/main.40638d9a.js b/core/pioreactor/web/static/static/js/main.40638d9a.js
diff --git a/core/pioreactor/web/static/static/js/main.40638d9a.js.LICENSE.txt b/core/pioreactor/web/static/static/js/main.40638d9a.js.LICENSE.txt
diff --git a/core/pioreactor/web/static/static/js/main.40638d9a.js.map b/core/pioreactor/web/static/static/js/main.40638d9a.js.map
diff --git a/core/pioreactor/web/tasks.py b/core/pioreactor/web/tasks.py
@@ -31,6 +31,8 @@
 from huey.exceptions import ResultTimeout
 from huey.exceptions import TaskException
 from msgspec import DecodeError
+from pioreactor import exc
+from pioreactor import hardware
 from pioreactor import types as pt
 from pioreactor import whoami
 from pioreactor.config import config as pioreactor_config
@@ -268,6 +270,45 @@ def add_new_pioreactor(new_pioreactor_name: str, version: str, model: str) -> bo
     return True
 
 
+def _get_adc_addresses_for_model(model_name: str, model_version: str) -> set[int]:
+    adc_cfg = hardware.get_layered_mod_config_for_model("adc", model_name, model_version)
+    addresses: set[int] = set()
+    for adc_data in adc_cfg.values():
+        address = adc_data.get("address")
+        addresses.add(int(address))
+    return addresses
+
+
+@huey.task(priority=10)
+def check_model_hardware(model_name: str, model_version: str) -> None:
+    if model_version != "1.5":
+        return None
+
+    try:
+        addresses = _get_adc_addresses_for_model(model_name, model_version)
+    except exc.HardwareNotFoundError as err:
+        logger.warning(
+            f"Hardware check skipped on {get_unit_name()}: {err}",
+        )
+        return None
+
+    if not addresses:
+        logger.debug(
+            f"Hardware check found no ADC addresses for {model_name} {model_version} on {get_unit_name()}."
+        )
+        return None
+
+    missing = sorted(addr for addr in addresses if not hardware.is_i2c_device_present(addr))
+    if missing:
+        missing_hex = ", ".join(hex(addr) for addr in missing)
+        logger.warning(
+            f"Hardware check failed for {model_name} {model_version} on {get_unit_name()}: "
+            f"missing I2C devices at {missing_hex}."
+        )
+
+    return None
+
+
 @huey.task()
 def update_app_across_cluster() -> bool:
     # CPU heavy / IO heavy
diff --git a/core/pioreactor/web/unit_api.py b/core/pioreactor/web/unit_api.py
@@ -25,6 +25,7 @@
 from pioreactor import whoami
 from pioreactor.calibrations import calibration_protocols
 from pioreactor.config import get_leader_hostname
+from pioreactor.models import get_registered_models
 from pioreactor.structs import CalibrationBase
 from pioreactor.structs import subclass_union
 from pioreactor.utils import local_persistent_storage
@@ -70,6 +71,20 @@ def health_check() -> ResponseReturnValue:
     return attach_cache_control(jsonify(payload), max_age=0)
 
 
+@unit_api_bp.route("/hardware/check", methods=["POST", "PATCH"])
+def check_hardware_for_model() -> DelayedResponseReturnValue:
+    data = request.get_json(silent=True) or {}
+    model_name = data.get("model_name")
+    model_version = data.get("model_version")
+    if not model_name or not model_version:
+        abort_with(400, "Missing model_name or model_version")
+    if (model_name, model_version) not in get_registered_models():
+        abort_with(400, "Model name or version not found in available models.")
+
+    task = tasks.check_model_hardware(model_name, model_version)
+    return create_task_response(task)
+
+
 # Endpoint to check the status of a background task. unit_api is required to ping workers (who only expose unit_api)
 @unit_api_bp.route("/task_results/<task_id>", methods=["GET"])
 def task_status(task_id: str):
diff --git a/core/tests/web/test_app.py b/core/tests/web/test_app.py
@@ -137,6 +137,39 @@ def test_change_worker_status(client) -> None:
     assert data["is_active"] == 0
 
 
+def test_change_worker_model_triggers_hardware_check_for_v1_5(client, monkeypatch) -> None:
+    captured: dict[str, object] = {}
+
+    def fake_post_into_unit(unit: str, endpoint: str, json: dict | None = None) -> None:
+        captured["unit"] = unit
+        captured["endpoint"] = endpoint
+        captured["json"] = json
+
+    monkeypatch.setattr("pioreactor.web.api.tasks.post_into_unit", fake_post_into_unit)
+
+    response = client.put(
+        "/api/workers/unit1/model",
+        json={"model_name": "pioreactor_20ml", "model_version": "1.5"},
+    )
+    assert response.status_code == 200
+    assert captured["unit"] == "unit1"
+    assert captured["endpoint"] == "/unit_api/hardware/check"
+    assert captured["json"] == {"model_name": "pioreactor_20ml", "model_version": "1.5"}
+
+
+def test_change_worker_model_does_not_trigger_hardware_check_for_non_v1_5(client, monkeypatch) -> None:
+    def fake_post_into_unit(*_args, **_kwargs) -> None:
+        raise AssertionError("hardware check should not be triggered")
+
+    monkeypatch.setattr("pioreactor.web.api.tasks.post_into_unit", fake_post_into_unit)
+
+    response = client.put(
+        "/api/workers/unit1/model",
+        json={"model_name": "pioreactor_20ml", "model_version": "1.1"},
+    )
+    assert response.status_code == 200
+
+
 def test_get_unit_labels(client) -> None:
     response = client.get("/api/experiments/exp1/unit_labels")
     assert response.status_code == 200
diff --git a/core/tests/web/test_unit_api.py b/core/tests/web/test_unit_api.py
@@ -67,6 +67,30 @@ def test_get_versions_endpoints(client) -> None:
     assert "version" in v_app and isinstance(v_app["version"], str)
 
 
+def test_hardware_check_requires_model_payload(client) -> None:
+    resp = client.post("/unit_api/hardware/check", json={})
+    assert resp.status_code == 400
+    data = resp.get_json()
+    assert data["error"] == "Missing model_name or model_version"
+
+
+def test_hardware_check_queues_task(client, monkeypatch) -> None:
+    import pioreactor.web.unit_api as mod
+
+    class DummyTask:
+        id = "task-456"
+
+    monkeypatch.setattr(mod.tasks, "check_model_hardware", lambda *_args, **_kwargs: DummyTask())
+
+    resp = client.post(
+        "/unit_api/hardware/check",
+        json={"model_name": "pioreactor_20ml", "model_version": "1.5"},
+    )
+    assert resp.status_code == 202
+    data = resp.get_json()
+    assert data["task_id"] == "task-456"
+
+
 @pytest.mark.xfail
 def test_install_plugin_rejects_without_allowlist(client, monkeypatch, tmp_path) -> None:
     """API install should fail closed if allowlist is missing."""
diff --git a/frontend/src/Pioreactor.jsx b/frontend/src/Pioreactor.jsx
@@ -759,6 +759,7 @@ function SettingsActionsDialog(props) {
   const ipInfo = props.jobs.monitor.publishedSettings.ipv4.value
   const macInfoWlan = props.jobs.monitor.publishedSettings.wlan_mac_address.value
   const macInfoEth = props.jobs.monitor.publishedSettings.eth_mac_address.value
+  const isXrModel = Boolean(props.modelDetails?.model_name?.toLowerCase().includes("xr"));
 
   const isLargeScreen = useMediaQuery(theme => theme.breakpoints.down('xl'));
   const dosingControlJob = props.jobs.dosing_automation
@@ -819,6 +820,14 @@ function SettingsActionsDialog(props) {
               <div style={{justifyContent: "space-between", display: "flex"}}>
                 <Typography display="block">
                   {job.metadata.display_name}
+                  {(job.metadata.display_name === "Optical density" && isXrModel) ? (
+                    <Chip
+                      size="small"
+                      variant="outlined"
+                      label="XR"
+                      sx={{ ml: 0.5, height: 18, fontSize: "0.65rem" }}
+                    />
+                  ) : null}
                 </Typography>
                 <StateTypography state={job.state}/>
               </div>
@@ -1580,6 +1589,7 @@ function PioreactorCard({ unit, modelDetails, isUnitActive, experiment, config,
   const [jobFetchComplete, setJobFetchComplete] = useState(false)
   const [label, setLabel] = useState(initialLabel || "")
   const {client, subscribeToTopic } = useMQTT();
+  const isXrModel = Boolean(modelDetails.model_name?.toLowerCase().includes("xr"));
 
   const [jobs, setJobs] = useState({
     monitor: {
@@ -1830,6 +1840,14 @@ function PioreactorCard({ unit, modelDetails, isUnitActive, experiment, config,
             <Box sx={{width: "130px", mt: "10px", mr: "2px", px: "3px"}} key={job.metadata.key}>
               <Typography variant="body2" style={{fontSize: "0.84rem"}} sx={{ color: !isUnitActive ? disabledColor : 'inherit' }}>
                 {job.metadata.display_name}
+                {(job.metadata.display_name === "Optical density" && isXrModel) ? (
+                  <Chip
+                    size="small"
+                    variant="outlined"
+                    label="XR"
+                    sx={{ ml: 0.5, height: 18, fontSize: "0.65rem" }}
+                  />
+                ) : null}
               </Typography>
               <UnitSettingDisplay
                 value={job.state}
@@ -1869,6 +1887,14 @@ function PioreactorCard({ unit, modelDetails, isUnitActive, experiment, config,
                   <Box sx={{width: "130px", mt: "10px", mr: "2px", px: "3px"}} key={job_key + setting_key}>
                     <Typography variant="body2" style={{fontSize: "0.84rem"}} sx={{ color: !isUnitActive ? disabledColor : 'inherit' }}>
                       {setting.label}
+                      {(setting.label === "Optical density" && isXrModel) ? (
+                        <Chip
+                          size="small"
+                          variant="outlined"
+                          label="XR"
+                          sx={{ ml: 0.5, height: 18, fontSize: "0.65rem" }}
+                        />
+                      ) : null}
                     </Typography>
                     <UnitSettingDisplay
                       value={setting.value}
diff --git a/frontend/src/Pioreactors.jsx b/frontend/src/Pioreactors.jsx

Original file line number	Diff line number	Diff line change
`@@ -1 +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.13eb0766.js"></script><link href="/static/static/css/main.9c7a48b7.css" rel="stylesheet"></head><body><div id="root"></div></body></html>
	`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.40638d9a.js"></script><link href="/static/static/css/main.9c7a48b7.css" rel="stylesheet"></head><body><div id="root"></div></body></html>