ipv4 to pulbished settings

.pre-commit-config.yaml

@@ -36,7 +36,7 @@ repos:
     hooks:
     -   id: mypy
         additional_dependencies: [
-            msgspec==0.17.0,
+            msgspec==0.18.0,
             types-pkg_resources==0.1.3,
             types-paho-mqtt==1.6.0.6
         ]

pioreactor/actions/od_blank.py

@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+# -*- coding: utf-8 -*-
 from __future__ import annotations
 
 from collections import defaultdict

pioreactor/automations/dosing/base.py

@@ -455,7 +455,10 @@ def execute_io_action(
                 self.remove_waste_from_bioreactor(
                     unit=self.unit,
                     experiment=self.experiment,
-                    ml=waste_ml * 2,
+                    ml=waste_ml
+                    * config.getfloat(
+                        "dosing_automation", "waste_removal_multiplier", fallback=2.0
+                    ),
                     source_of_event=source_of_event,
                 )
                 briefer_pause()

pioreactor/background_jobs/monitor.py

@@ -16,6 +16,7 @@
 from pioreactor import version
 from pioreactor import whoami
 from pioreactor.background_jobs.base import BackgroundJob
+from pioreactor.hardware import is_HAT_present
 from pioreactor.hardware import PCB_BUTTON_PIN as BUTTON_PIN
 from pioreactor.hardware import PCB_LED_PIN as LED_PIN
 from pioreactor.hardware import TEMP
@@ -77,6 +78,7 @@ def off(): # functions don't take any arguments, nothing is passed in
         "button_down": {"datatype": "boolean", "settable": False},
         "versions": {"datatype": "json", "settable": False},
         "voltage_on_pwm_rail": {"datatype": "Voltage", "settable": False},
+        "ipv4": {"datatype": "string", "settable": False},
     }
     computer_statistics: Optional[dict] = None
     led_in_use: bool = False
@@ -178,12 +180,19 @@ def _setup_GPIO(self) -> None:
         self.logger.warning("Failed to add button detect.")
 
     def check_for_network(self) -> None:
-        ip = get_ip()
-        while (not whoami.is_testing_env()) and ((ip == "127.0.0.1") or (ip is None)):
-            # no wifi connection? Sound the alarm.
-            self.logger.warning("Unable to connect to network...")
-            self.flicker_led_with_error_code(error_codes.NO_NETWORK_CONNECTION)
-            ip = get_ip()
+        if whoami.is_testing_env():
+            self.ipv4 = "127.0.0.1"
+        else:
+            ipv4 = get_ip()
+            while ipv4 == "127.0.0.1" or ipv4 is None:
+                # no wifi connection? Sound the alarm.
+                self.logger.warning("Unable to connect to network...")
+                self.flicker_led_with_error_code(error_codes.NO_NETWORK_CONNECTION)
+                ipv4 = get_ip()
+
+            self.ipv4 = ipv4
+
+        self.logger.debug(f"IPv4 address: {self.ipv4}")
 
     def self_checks(self) -> None:
         # check active network connection
@@ -202,6 +211,7 @@ def self_checks(self) -> None:
             self.check_for_webserver()
 
         if whoami.am_I_active_worker():
+            self.check_for_HAT()
             # check the PCB temperature
             self.check_heater_pcb_temperature()
 
@@ -276,6 +286,10 @@ def check_for_required_jobs_running(self):
                 "watchdog and mqtt_to_db_streaming should be running on leader. Double check."
             )
 
+    def check_for_HAT(self) -> None:
+        if not is_HAT_present():
+            self.logger.warning("HAT is not detected.")
+
     def check_heater_pcb_temperature(self) -> None:
         """
         Originally from #220
@@ -296,6 +310,7 @@ def check_heater_pcb_temperature(self) -> None:
             tmp_driver = TMP1075(address=TEMP)
         except ValueError:
             # No PCB detected using i2c - fine to exit.
+            self.logger.warning("Heater PCB is not detected.")
             return
 
         observed_tmp = tmp_driver.get_temperature()

pioreactor/background_jobs/stirring.py

@@ -22,6 +22,7 @@
 from pioreactor.utils import clamp
 from pioreactor.utils import is_pio_job_running
 from pioreactor.utils import local_persistant_storage
+from pioreactor.utils import retry
 from pioreactor.utils.gpio_helpers import set_gpio_availability
 from pioreactor.utils.pwm import PWM
 from pioreactor.utils.streaming_calculations import PID
@@ -73,9 +74,11 @@ def setup(self) -> None:
 
         # ignore any changes that occur within 15ms - at 1000rpm (very fast), the
         # delta between changes is ~60ms, so 15ms is good enough.
-        # TODO: sometimes this fails with `RuntimeError: Failed to add edge detection`
-        self.GPIO.add_event_detect(
-            self.hall_sensor_pin, self.GPIO.FALLING, callback=self.callback, bouncetime=15
+        # sometimes this fails with `RuntimeError: Failed to add edge detection`, so we retry.
+        retry(
+            self.GPIO.add_event_detect,
+            args=(self.hall_sensor_pin, self.GPIO.FALLING),
+            kwargs={"callback": self.callback, "bouncetime": 15},
         )
         self.turn_off_collection()
 

pioreactor/cli/pio.py

@@ -141,11 +141,6 @@ def log(message: str, level: str, name: str, local_only: bool):
         )
         getattr(logger, level)(message)
 
-        # flush and close handlers
-        for handler in logger.logger.handlers:
-            handler.flush()
-            handler.close()
-
     except Exception as e:
         # don't let a logging error bring down a script...
         print(e)
@@ -465,7 +460,9 @@ def update_app(
 
     if source is not None:
         version_installed = source
-        commands_and_priority.append((f"sudo pip3 install -U --force-reinstall {source}", 1))
+        commands_and_priority.append(
+            (f"sudo pip3 install --force-reinstall --no-index {source}", 1)
+        )
 
     elif branch is not None:
         version_installed = quote(branch)

pioreactor/utils/__init__.py

@@ -4,7 +4,9 @@
 import os
 import signal
 import tempfile
+import time
 from contextlib import contextmanager
+from functools import wraps
 from threading import Event
 from typing import Callable
 from typing import cast
@@ -375,3 +377,46 @@ def __getitem__(self, key):
             return 0
         else:
             return dict.__getitem__(self, key)
+
+
+def retry(func: Callable, retries=3, delay=0.5, args=(), kwargs={}):
+    """
+    Retries a function upon encountering an exception until it succeeds or the maximum number of retries is exhausted.
+
+    This function executes the provided function and handles any exceptions it raises. If an exception is raised,
+    the function will wait for a specified delay before attempting to execute the function again. This process repeats
+    until either the function execution is successful or the specified maximum number of retries is exhausted.
+    On the final attempt, if the function still raises an exception, that exception will be re-raised to the caller.
+
+    Parameters
+    -----------
+    func (callable): The function to be retried.
+    retries (int, optional): The maximum number of times to retry the function. Defaults to 3.
+    delay (float, optional): The number of seconds to wait between retries. Defaults to 0.5.
+    args (tuple, optional): The positional arguments to pass to the function. Defaults to an empty tuple.
+    kwargs (dict, optional): The keyword arguments to pass to the function. Defaults to an empty dictionary.
+
+    Returns
+    --------
+    The return value of the function call, if the function call is successful.
+
+    Raises
+    --------
+    Exception: The exception raised by the function call if the function call is unsuccessful after the specified number of retries.
+
+    Example
+    --------
+
+    > def risky_function(x, y):
+    >     return x / y
+    >
+    > # Call the function with retry
+    > result = retry(risky_function, retries=5, delay=1, args=(10, 0))
+    """
+    for i in range(retries):
+        try:
+            return func(*args, **kwargs)
+        except Exception as e:
+            if i == retries - 1:  # If this was the last attempt
+                raise e
+            time.sleep(delay)

pioreactor/utils/networking.py

@@ -79,6 +79,7 @@ def is_connected_to_network() -> bool:
 
 
 def get_ip() -> Optional[str]:
+    # TODO: is this always ipv4??
     from psutil import net_if_addrs  # type: ignore
 
     # Check for IP address of wireless network interface 'wlan0'

requirements/requirements.txt

@@ -5,5 +5,5 @@ sh==1.14.2
 JSON-log-formatter==0.4.0
 rpi_hardware_pwm==0.1.3
 colorlog==6.6.0
-msgspec==0.17.0
+msgspec==0.18.0
 diskcache==5.6.1

setup.py

@@ -14,7 +14,7 @@
     "sh==1.14.3",
     "JSON-log-formatter==0.5.1",
     "colorlog==6.7.0",
-    "msgspec==0.17.0",
+    "msgspec==0.18.0",
     "diskcache==5.6.1",
     "wheel==0.38.4",
     "crudini==0.9.4",