rename some files; add docs

config.ini

@@ -42,7 +42,9 @@ pioreactor1=192.168.0.1
 # a 1 means available, and a 0 means not available.
 # See docs: https://github.com/Pioreactor/pioreactor/wiki/Leaders,-workers-and-inventory
 pioreactor1=1
-
+pioreactor2=1
+pioreactor3=1
+pioreactor4=0
 
 [dashboard.settings]
 # changing these requires a power cycle of the leader unit.
@@ -51,6 +53,8 @@ raw_od_lookback_minutes=240
 log_display_count=65
 
 [dashboard.charts]
+# show/hide charts on the PioreactorUI dashboard
+# 1 is show, 0 is hide
 implied_growth_rate=1
 fraction_of_volume_that_is_alternative_media=1
 normalized_135_optical_density=1
@@ -66,6 +70,10 @@ Kp=5
 Ki=0
 Kd=0
 
+[pid_turbidostat]
+Kp=3
+Ki=0.1
+Kd=0.1
 
 [watchdog]
 email_alerts_to[email protected]

pioreactor/actions/add_alt_media.py

@@ -104,6 +104,9 @@ def cleanUpGPIO():
     help="who is calling this function - data goes into database and MQTT",
 )
 def click_add_alt_media(ml, duration, duty_cycle, source_of_event):
+    """
+    Add alt. media to unit
+    """
     unit = get_unit_name()
     experiment = get_latest_experiment_name()
 

pioreactor/actions/add_media.py

@@ -106,6 +106,9 @@ def cleanUpGPIO():
     help="who is calling this function - data goes into database and MQTT",
 )
 def click_add_media(ml, duration, duty_cycle, source_of_event):
+    """
+    Add media to unit
+    """
     unit = get_unit_name()
     experiment = get_latest_experiment_name()
 

pioreactor/actions/od_normalization.py

@@ -96,6 +96,9 @@ def yield_from_mqtt():
 """,
 )
 def click_od_normalization(od_angle_channel):
+    """
+    Compute statistics about the OD timeseries
+    """
     unit = get_unit_name()
     experiment = get_latest_experiment_name()
     od_normalization(od_angle_channel, unit, experiment)

pioreactor/actions/remove_waste.py

@@ -105,7 +105,9 @@ def cleanUpGPIO():
     help="who is calling this function - data goes into database and MQTT",
 )
 def click_remove_waste(ml, duration, duty_cycle, source_of_event):
-
+    """
+    Remove waste/media from unit
+    """
     unit = get_unit_name()
     experiment = get_latest_experiment_name()
     signal.signal(signal.SIGTERM, cleanUpGPIO)

pioreactor/background_jobs/io_controlling.py

@@ -353,10 +353,14 @@ def __init__(self, target_od=None, volume=None, **kwargs):
         self.volume = float(volume)
 
         # PID%20controller%20turbidostat.ipynb
+        Kp = config.getFloat("pid_turbidostat", "Kp")
+        Ki = config.getFloat("pid_turbidostat", "Ki")
+        Kd = config.getFloat("pid_turbidostat", "Kd")
+
         self.pid = PID(
-            -3.0,
-            -0.1,
-            -0.1,
+            -Kp,
+            -Ki,
+            -Kd,
             setpoint=self.target_od,
             output_limits=(0, 1),
             sample_time=None,

pioreactor/background_jobs/monitor.py

@@ -38,7 +38,7 @@ def get_and_publish_disk_space(self):
 @click.command(name="monitor")
 def click_monitor():
     """
-    Start the watchdog on a unit. Reports back to the leader.
+    Monitor and report metadata on the unit.
     """
     heidi = Monitor(unit=get_unit_name(), exp=UNIVERSAL_EXPERIMENT)  # noqa: F841
 

pioreactor/command_line_worker.py → pioreactor/pio_cli.py

@@ -7,7 +7,7 @@
 > pio log
 """
 import click
-from pioreactor.whoami import am_I_leader
+from pioreactor.whoami import am_I_leader, am_I_active_worker
 from pioreactor.config import config
 from pioreactor import background_jobs as jobs
 from pioreactor import actions
@@ -50,21 +50,22 @@ def kill(process):
         pass
 
 
-@pio.group()
-def run(short_help="run a job"):
+@pio.group(short_help="run a job")
+def run():
     pass
 
 
-run.add_command(jobs.growth_rate_calculating.click_growth_rate_calculating)
-run.add_command(jobs.stirring.click_stirring)
-run.add_command(jobs.od_reading.click_od_reading)
-run.add_command(jobs.io_controlling.click_io_controlling)
-run.add_command(jobs.monitor.click_monitor)
+if am_I_active_worker():
+    run.add_command(jobs.growth_rate_calculating.click_growth_rate_calculating)
+    run.add_command(jobs.stirring.click_stirring)
+    run.add_command(jobs.od_reading.click_od_reading)
+    run.add_command(jobs.io_controlling.click_io_controlling)
+    run.add_command(jobs.monitor.click_monitor)
 
-run.add_command(actions.add_alt_media.click_add_alt_media)
-run.add_command(actions.add_media.click_add_media)
-run.add_command(actions.remove_waste.click_remove_waste)
-run.add_command(actions.od_normalization.click_od_normalization)
+    run.add_command(actions.add_alt_media.click_add_alt_media)
+    run.add_command(actions.add_media.click_add_media)
+    run.add_command(actions.remove_waste.click_remove_waste)
+    run.add_command(actions.od_normalization.click_od_normalization)
 
 if am_I_leader():
     run.add_command(jobs.log_aggregating.click_log_aggregating)

pioreactor/whoami.py

@@ -48,4 +48,10 @@ def get_unit_name():
 def am_I_leader():
     from pioreactor.config import leader_hostname
 
-    return get_hostname() == leader_hostname
+    return get_unit_name() == leader_hostname
+
+
+def am_I_active_worker():
+    from pioreactor.config import get_active_worker_units_and_ips
+
+    return get_unit_name() in get_active_worker_units_and_ips().keys()

setup.py

@@ -16,7 +16,7 @@
     packages=find_packages(exclude=["*.tests", "*.tests.*", "*benchmarks*"]),
     entry_points="""
         [console_scripts]
-        pio=pioreactor.command_line_worker:pio
-        pios=pioreactor.command_line_leader:pios
+        pio=pioreactor.pio_cli:pio
+        pios=pioreactor.pios_cli:pios
     """,
 )