clean up config, try install lgpio elsehwer

.github/workflows/ci.yaml

@@ -22,6 +22,7 @@ jobs:
 
       - name: Install
         run: |
+          apt-get install python3-lgpio
           pip install -e .
           pip install -r requirements/requirements_dev.txt
           pip install pyyaml

CHANGELOG.md

@@ -1,17 +1,25 @@
 ### Upcoming
- - fixed a bug where stirring DC would jump up too high when RPM measured 0.
+
+#### Enhancements
+ - Support for RPi5! To use an RPi5, we recommend not upgrading the software, but using a fresh install. Under the hood: we are using a new route to load the firmware on the HATs RP2040, which was the blocker previously.
  - new ENV variable, `HAT_PRESENT=1`, can be set to skip `is_HAT_present` checks.
  - added the RPis unique MAC addresses to the `Manage -> System` tab on the Pioreactors page.
  - added table `ir_led_intensities` to be able to be exported on the Exports page.
  - added a new `smoothing_penalizer` config option to `[od_config]`. This parameter, which has default value 700, controls how much smoothing to apply to optical density measurements. This smoothing has always been applied, but now it's a config option.
+ - Cleaned up some UI interactions
+
+#### Bug fixes
+ - Ack! I reintroduced a UI export bug. Fix is present going forward. For existing users, try the following: https://forum.pioreactor.com/t/new-pioreactor-release-23-11-18/179/2
+ - fixed a bug where stirring DC would jump up too high when RPM measured 0.
+
 
 ### 23.12.11
 
 #### Enhancements
 
  - Improvements to OD calibration and pump calibrations. Both now have a `-f` option to provide a json file with calibration data, to skip rerunning data-gathering routines. For example: `pio run pump_calibration -f pump_data.json`.
- - Ability to update via our release_archives (available on the [Github release page](https://github.com/Pioreactor/pioreactor/releases)) via the UI. To turn this feature off (which is a recommended practice when you expose your UI publically), add an empty file called `DISALLOW_UI_UPLOADS` to the `~/.pioreactor` directory.
- - A new config option to change the max volume to dose when a larger dose volume is split. For example, if your chemostat asks to dose 1.6ml, our internal algorithm will dose 0.75, 0.75 and 0.1 (this is to avoid overflow). The 0.75 was previously hardcoded, but is now a config `max_subdose` under section `[dosing_automation.config]` (default is still 0.75ml).
+ - Ability to update via our release_archives (available on the [Github release page](https://github.com/Pioreactor/pioreactor/releases)) via the UI. To turn this feature off (which is a recommended practice when you expose your UI publicly), add an empty file called `DISALLOW_UI_UPLOADS` to the `~/.pioreactor` directory.
+ - A new config option to change the max volume to dose when a larger dose volume is split. For example, if your chemostat asks to dose 1.6 ml, our internal algorithm will dose 0.75, 0.75 and 0.1 (this is to avoid overflow). The 0.75 was previously hardcoded, but is now a config `max_subdose` under section `[dosing_automation.config]` (default is still 0.75 ml).
 
 #### Breaking changes
 

config.dev.ini

@@ -57,6 +57,9 @@ ir_led_intensity=90
 # use the most recent calibration file, if available
 use_calibration=1
 
+# apply a smoothing penalizer
+smoothing_penalizer=700.0
+
 [storage]
 database=pioreactor.sqlite
 
@@ -87,18 +90,11 @@ log_display_count=65
 time_display_mode=hours
 
 
-[dosing_automation]
-pause_between_subdoses_seconds=0.1
-
 [dosing_automation.pid_morbidostat]
 Kp=5
 Ki=0
 Kd=0
 
-[dosing_automation.pid_turbidostat]
-Kp=0.05
-Ki=0.01
-Kd=0.01
 
 [temperature_automation.thermostat]
 Kp=.01
@@ -122,6 +118,10 @@ obs_std=3.0
 od_std=0.005
 rate_std=0.20
 
-[motor_driver]
-initial_duty_cycle=10
-hz=20
+
+[dosing_automation.config]
+pause_between_subdoses_seconds=5
+waste_removal_multiplier=2
+max_volume_to_warn=17.0
+max_volume_to_stop=18.0
+max_subdose=0.75

pioreactor/utils/pwm.py

@@ -36,23 +36,21 @@
 
 class HardwarePWMOutputDevice(HardwarePWM):
     HARDWARE_PWM_CHANNELS: dict[GpioPin, int] = {12: 0, 13: 1}
+    _started = False
 
     def __init__(
         self, pin: GpioPin, initial_dc: pt.FloatBetween0and100 = 0.0, frequency: float = 100
     ) -> None:
-        if (
-            pin not in self.HARDWARE_PWM_CHANNELS
-        ):  # Only GPIO pins 18 and 19 are supported for hardware PWM
-            raise ValueError(
-                "Only GPIO pins 12 (PWM channel 0) and 13 (PWM channel 1) are supported."
-            )
+        if pin not in self.HARDWARE_PWM_CHANNELS:  # Only GPIO pins 18 and 19 are supported for hardware PWM
+            raise ValueError("Only GPIO pins 12 (PWM channel 0) and 13 (PWM channel 1) are supported.")
 
         pwm_channel = self.HARDWARE_PWM_CHANNELS[pin]
         super().__init__(pwm_channel, hz=frequency)
         self._dc = initial_dc
 
     def start(self) -> None:
         super().start(self.dc)
+        self._started = True
 
     def off(self) -> None:
         self.dc = 0.0
@@ -63,20 +61,24 @@ def dc(self) -> pt.FloatBetween0and100:
 
     @dc.setter
     def dc(self, dc: pt.FloatBetween0and100) -> None:
-        dc = clamp(0.0, dc, 100.0)
-        self.change_duty_cycle(dc)
-        self._dc = dc
+        if self._started:
+            dc = clamp(0.0, dc, 100.0)
+            self.change_duty_cycle(dc)
+            self._dc = dc
+        else:
+            raise ValueError("must call .start() first!")
 
     def close(self) -> None:
         pass
 
 
 class SoftwarePWMOutputDevice:
+    _started = False
+
     def __init__(self, pin: GpioPin, initial_dc: pt.FloatBetween0and100 = 0.0, frequency=100):
         self.pin = pin
         self._dc = initial_dc
         self.frequency = frequency
-        self._started = False
         self._handle = lgpio.gpiochip_open(0)
 
         lgpio.gpio_claim_output(self._handle, self.pin)
@@ -103,6 +105,8 @@ def dc(self, dc: pt.FloatBetween0and100) -> None:
         self._dc = dc
         if self._started:
             lgpio.tx_pwm(self._handle, self.pin, self.frequency, self.dc)
+        else:
+            raise ValueError("must call .start() first!")
 
     def close(self):
         lgpio.gpiochip_close(self._handle)
@@ -173,9 +177,7 @@ def __init__(
             self.pubsub_client = pubsub_client
 
         if logger is None:
-            self.logger = create_logger(
-                f"PWM@GPIO-{pin}", experiment=self.experiment, unit=self.unit
-            )
+            self.logger = create_logger(f"PWM@GPIO-{pin}", experiment=self.experiment, unit=self.unit)
         else:
             self.logger = logger
 

requirements/requirements.txt

@@ -8,4 +8,4 @@ msgspec==0.18.4
 diskcache==5.6.3
 wheel==0.41.2
 crudini==0.9.5
-lgpio; platform_machine!='armv7l' and platform_machine!='armv6l'
+# lgpio; platform_machine!='armv7l' and platform_machine!='armv6l'

setup.py

@@ -18,7 +18,7 @@
     "diskcache==5.6.3",
     "wheel==0.41.2",
     "crudini==0.9.5",
-    "lgpio; platform_machine!='armv7l' and platform_machine!='armv6l'",
+    # "lgpio; platform_machine!='armv7l' and platform_machine!='armv6l'", # primarily available via apt-get install python3-lgpio
 ]