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Pioreactor · Jun 21, 2023 · 6d06c6d · 6d06c6d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,12 +1,17 @@
 ### Upcoming
 
 #### Highlights
- -
+ - The UI now offers a way to upgrade to the bleeding-edge Pioreactor app and UI software, called "development". This software is unstable (and fun!).
 
 #### Everything else
  - Fixed `source` in `BackgroundJobContrib` - thanks @odcambc!
  - `pio add-pioreactor` will now accept an option that is the password of the RPi being added (default: `raspberry`). Ex: `pio add-pioreactor worker1 -p mypass`
  - Improved some warning and error messages.
+ - Improved watchdog detecting and fixing "lost" Pioreactors.
+ - Improved temperature inference accuracy.
+ - Starting to test software against Python 3.11, in anticipation of a Python 3.11 coming to Raspberry Pi OS.
+ - Improvements to bash scripts to make them more robust.
+
 
 
 ### 23.6.7

diff --git a/pioreactor/background_jobs/base.py b/pioreactor/background_jobs/base.py
@@ -468,6 +468,14 @@ def _callback(client, userdata, message: pt.MQTTMessage) -> t.Optional[T]:
         return
 
     def set_state(self, new_state: pt.JobState) -> None:
+        """
+        The preferred way to change states is to use this function (instead of self.state = state). Note:
+
+         - no-op if in the same state
+         - will call the transition callback
+
+        """
+
         if new_state not in {self.INIT, self.READY, self.DISCONNECTED, self.SLEEPING, self.LOST}:
             self.logger.error(f"saw {new_state}: not a valid state")
             return

diff --git a/pioreactor/background_jobs/dosing_control.py b/pioreactor/background_jobs/dosing_control.py
@@ -163,7 +163,6 @@ def start_dosing_control(
 )
 @click.option(
     "--automation-name",
-    default="silent",
     help="set the automation of the system: turbidostat, morbidostat, silent, etc.",
     show_default=True,
 )

diff --git a/pioreactor/background_jobs/leader/watchdog.py b/pioreactor/background_jobs/leader/watchdog.py
@@ -60,9 +60,16 @@ def watch_for_lost_state(self, state_message: MQTTMessage) -> None:
                 # let's return early.
                 return
 
+            # this is a hack! If the monitor job is in state READY, it will no op any transition.
+            # so we set to sleeping for a second, and the back to ready.
+            self.pub_client.publish(
+                f"pioreactor/{unit}/{UNIVERSAL_EXPERIMENT}/monitor/$state/set", self.SLEEPING
+            )
+            time.sleep(1)
             self.pub_client.publish(
                 f"pioreactor/{unit}/{UNIVERSAL_EXPERIMENT}/monitor/$state/set", self.READY
             )
+            ###
             time.sleep(20)
 
             if self.state != self.READY:

diff --git a/pioreactor/background_jobs/led_control.py b/pioreactor/background_jobs/led_control.py
@@ -122,7 +122,6 @@ def start_led_control(
 )
 @click.option(
     "--automation-name",
-    default="silent",
     help="set the automation of the system: silent, etc.",
     show_default=True,
 )

diff --git a/pioreactor/background_jobs/monitor.py b/pioreactor/background_jobs/monitor.py
@@ -225,22 +225,42 @@ def check_for_webserver(self):
                 if status == "failed" or status == "inactive":
                     self.logger.error("lighttpd is not running. Check `systemctl status lighttpd`.")
                     self.flicker_led_with_error_code(error_codes.WEBSERVER_OFFLINE)
-
                 elif status == "activating":
                     # try again
                     pass
-
                 elif status == "active":
                     # okay
                     break
-
                 else:
                     raise ValueError(status)
-
         except Exception as e:
             self.logger.debug(f"Error checking lighttpd status: {e}", exc_info=True)
             self.logger.error(f"Error checking lighttpd status: {e}")
 
+        try:
+            while True:
+                # Run the command 'systemctl is-active huey' and capture the output
+                result = subprocess.run(
+                    ["systemctl", "is-active", "huey"], capture_output=True, text=True
+                )
+                status = result.stdout.strip()
+
+                # Check if the output is okay
+                if status == "failed" or status == "inactive":
+                    self.logger.error("huey is not running. Check `systemctl status huey`.")
+                    self.flicker_led_with_error_code(error_codes.WEBSERVER_OFFLINE)
+                elif status == "activating":
+                    # try again
+                    pass
+                elif status == "active":
+                    # okay
+                    break
+                else:
+                    raise ValueError(status)
+        except Exception as e:
+            self.logger.debug(f"Error checking huey status: {e}", exc_info=True)
+            self.logger.error(f"Error checking huey status: {e}")
+
         try:
             # can we ping ourselves? should have a response
             res = get("http://localhost")

diff --git a/pioreactor/background_jobs/temperature_control.py b/pioreactor/background_jobs/temperature_control.py
@@ -71,8 +71,10 @@ class TemperatureController(BackgroundJob):
         True if supplying an external thermometer that will publish to MQTT.
     """
 
-    MAX_TEMP_TO_REDUCE_HEATING = 61.5  # ~PLA glass transition temp
-    MAX_TEMP_TO_DISABLE_HEATING = 63.5
+    MAX_TEMP_TO_REDUCE_HEATING = (
+        63.0  # ~PLA glass transition temp, and I've gone safely above this an it's not a problem.
+    )
+    MAX_TEMP_TO_DISABLE_HEATING = 65.0
     MAX_TEMP_TO_SHUTDOWN = 66.0
 
     INFERENCE_SAMPLES_EVERY_T_SECONDS: float = 5.0
@@ -579,7 +581,6 @@ def start_temperature_control(
 )
 @click.option(
     "--automation-name",
-    default="only_record_temperature",
     help="set the automation of the system",
     show_default=True,
 )

diff --git a/pioreactor/cli/pio.py b/pioreactor/cli/pio.py
@@ -535,7 +535,7 @@ def update_app(branch: Optional[str], source: Optional[str], version: Optional[s
         else:
             logger.debug(p.stdout)
 
-    logger.notice(f"Updated Pioreactor to version {version_installed}.")  # type: ignore
+    logger.notice(f"Updated {whoami.get_unit_name()} to version {version_installed}.")  # type: ignore
 
 
 @update.command(name="firmware")

diff --git a/pioreactor/cli/pios.py b/pioreactor/cli/pios.py
@@ -101,7 +101,7 @@ def sync_config_files(unit: str, shared: bool, specific: bool) -> None:
 
         # move the global config.ini
         # there was a bug where if the leader == unit, the config.ini would get wiped
-        if (get_leader_hostname() != unit) and shared:
+        if shared and unit != get_leader_hostname():
             localpath = "/home/pioreactor/.pioreactor/config.ini"
             remotepath = "/home/pioreactor/.pioreactor/config.ini"
             cp_file_across_cluster(unit, localpath, remotepath)

diff --git a/pioreactor/tests/test_temperature_approximation.py b/pioreactor/tests/test_temperature_approximation.py
@@ -980,3 +980,97 @@ def test_temperature_approximation15() -> None:
         "only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 28.815 <= t.approximate_temperature(features) <= 29.119
+
+
+@pytest.mark.xfail
+def test_temperature_approximation16() -> None:
+    unit = get_unit_name()
+
+    experiment = "test_temperature_approximation16"
+    features = {
+        "previous_heater_dc": 18.156877790712812,
+        "room_temp": 22.0,
+        "time_series_of_temp": [
+            29.625,
+            29.0625,
+            28.6125,
+            28.225,
+            27.8875,
+            27.625,
+            27.375,
+            27.1875,
+            27.0,
+            26.825,
+            26.6875,
+            26.5625,
+            26.4375,
+            26.325,
+            26.25,
+            26.1875,
+            26.125,
+            26.05,
+            26.0,
+            25.9375,
+            25.8875,
+            25.875,
+            25.8125,
+            25.7875,
+            25.75,
+            25.725,
+            25.6875,
+            25.6875,
+            25.625,
+        ],
+    }
+
+    with temperature_control.TemperatureController(
+        "only_record_temperature", unit=unit, experiment=experiment
+    ) as t:
+        assert 25.261 <= t.approximate_temperature(features) <= 25.430
+
+
+@pytest.mark.xfail
+def test_temperature_approximation17() -> None:
+    unit = get_unit_name()
+
+    experiment = "test_temperature_approximation17"
+    features = {
+        "previous_heater_dc": 18.518440157554934,
+        "room_temp": 22.0,
+        "time_series_of_temp": [
+            29.75,
+            29.1875,
+            28.7125,
+            28.3125,
+            28.0,
+            27.6875,
+            27.475,
+            27.25,
+            27.0625,
+            26.925,
+            26.7625,
+            26.625,
+            26.55,
+            26.4375,
+            26.3125,
+            26.25,
+            26.1875,
+            26.125,
+            26.0625,
+            26.0,
+            25.9875,
+            25.9375,
+            25.875,
+            25.8625,
+            25.8125,
+            25.8125,
+            25.75,
+            25.725,
+            25.6875,
+        ],
+    }
+
+    with temperature_control.TemperatureController(
+        "only_record_temperature", unit=unit, experiment=experiment
+    ) as t:
+        assert 25.295 <= t.approximate_temperature(features) <= 25.430
diff --git a/pioreactor/version.py b/pioreactor/version.py
@@ -5,7 +5,7 @@
 
 # Append "dev" if a dev version
 # Append "rc0" if a rc version
-__version__ = "23.6.7"
+__version__ = "23.6.7.dev"
 
 
 def _get_hardware_version() -> tuple[int, int] | tuple[int, int, str]:

diff --git a/update_scripts/README.md b/update_scripts/README.md
@@ -11,11 +11,12 @@ Possible update scripts and their sequence:
 
 It's very important that update scripts are idempotent. Some tips:
 
- - Use ChatGPT to assist psuedo-check if a script is idempotent, or making suggestions.
+> Use ChatGPT to assist psuedo-check if a script is idempotent, or making suggestions.
 
 ### bash specific tips
+ - use `|| true` if a command may fail, but you want to continue anyways
+ - use `trap` and `EXIT` semantics (like try / expect) to force some code block to always run.
  - https://arslan.io/2019/07/03/how-to-write-idempotent-bash-scripts/
- - use `|| true` if a command may fail, but you want to continue
 
 
 ### SQL specific tips

diff --git a/update_scripts/upcoming/update.sh b/update_scripts/upcoming/update.sh
@@ -5,7 +5,6 @@ set -e
 
 export LC_ALL=C
 
-
-# new naming for python install dirs/
 wget -O /usr/local/bin/install_pioreactor_plugin.sh https://raw.githubusercontent.com/Pioreactor/CustoPiZer/pioreactor/workspace/scripts/files/bash/install_pioreactor_plugin.sh
 wget -O /usr/local/bin/uninstall_pioreactor_plugin.sh https://raw.githubusercontent.com/Pioreactor/CustoPiZer/pioreactor/workspace/scripts/files/bash/uninstall_pioreactor_plugin.sh
+wget -O /usr/local/bin/add_new_pioreactor_worker_from_leader.sh https://raw.githubusercontent.com/Pioreactor/CustoPiZer/pioreactor/workspace/scripts/files/bash/add_new_pioreactor_worker_from_leader.sh