some updateS

Author: CamDavidsonPilon

.github/workflows/test-deploy.yml

@@ -15,7 +15,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-node@v3
         with:
-          node-version: 16.x
+          node-version: 18.x
           cache: npm
 
       - name: Install dependencies

developer-guide/03-Background jobs/03-avoiding-od.md

@@ -21,7 +21,8 @@ class JustPause(BackgroundJobWithDodgingContrib):
 ```python
 class JustPause(BackgroundJobWithDodgingContrib):
 
-    ...
+    def __init__(self, ...):
+        super().__init__(..., enable_dodging_od=True or False) # set to True if you want the dodging behaviour right away.
 
 
     def action_to_do_before_od_reading(self):
@@ -43,6 +44,9 @@ You can handle the "dodging" case and "continuous" with the `initialize_*` metho
 ```python
 class JustPause(BackgroundJobWithDodgingContrib):
 
+    def __init__(self, ...):
+        super().__init__(..., enable_dodging_od=True or False) # set to True if you want the dodging behaviour right away.
+
     ...
 
     def initialize_dodging_operation(self):
@@ -68,7 +72,7 @@ class JustPause(BackgroundJobWithDodgingContrib):
 [<job_name>]
 pre_delay_duration=<float>
 post_delay_duration=<float>
-enable_dodging_od=1 # 1 if you want the behaviour, 0 to disable it.
+enable_dodging_od=1
 ```
 
 The diagram of timing, actions, and OD reading, looks like the following:

developer-guide/08-Custom pumps/20-writing-pump-software.md

@@ -14,7 +14,7 @@ may be provided via another system, for example an Arduino.
 The first thing to do is to add a hook to your custom pump into Pioreactor's software. To do this, we attach new functions to a dosing automation that are invoked when `execute_io_action` is called. These functions will call your logic that runs the external pump. Specifically, if we wish to overwrite the `media` pump, we create a function called `add_media_to_bioreactor`, with signature
 
 ```
-(cls, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client: pioreactor.pubsub.Client) -> float)
+(cls, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client: pioreactor.pubsub.Client, logger: logger) -> float)
 ```
 
 To see this in an example:
@@ -30,12 +30,12 @@ class CustomPumper(DosingAutomationJob):
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
 
-    def add_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float:
+    def add_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client, logger) -> float:
         # overrides the built in add_media_to_bioreactor
         # add your custom logic here. Example could be interfacing with i2c, serial, PWM, etc.
         ...
         pwm = PWM(...)
-        self.logger.info(f"pumping {ml}")
+        logger.info(f"pumping {ml}")
         return ml
 
     def execute(self):
@@ -49,17 +49,17 @@ class CustomPumper(DosingAutomationJob):
 
     automation_name = "custom_pumper"
 
-    def add_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float:
+    def add_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client, logger) -> float:
         # overrides the built in add_media_to_bioreactor
         ...
         return ml
 
-    def add_alt_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float:
+    def add_alt_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client, logger) -> float:
         # overrides the built in remove_waste_from_bioreactor
         ...
         return ml
 
-    def remove_waste_from_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float:
+    def remove_waste_from_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client, logger) -> float:
         # overrides the built in remove_waste_from_bioreactor
         ...
         return ml
@@ -83,7 +83,7 @@ class ThreePumps(DosingAutomationJob):
 
     automation_name = "three_pumps"
 
-    def add_salty_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client) -> float:
+    def add_salty_media_to_bioreactor(self, ml: float, unit: str, experiment: str, source_of_event: str, mqtt_client, logger) -> float:
         # call an external pump, via i2c, serial, GPIO, etc.,
         # or pumping_functions.add_salt_media
         ...