installation fixes

Makefile

@@ -1,5 +1,8 @@
-install-python:
+install-git:
 	sudo apt-get update
+	sudo apt-get install git
+
+install-python:
 	sudo apt install -y python3-pip
 	sudo apt-get install -y python3-numpy
 
@@ -76,7 +79,7 @@ logging-files:
 
 install-db:
 	sudo apt-get install -y sqlite3
-	mkdir /home/pi/db
+	mkdir -p /home/pi/db
 	touch /home/pi/db/pioreactor.sqlite
 	sqlite3 /home/pi/db/pioreactor.sqlite < sql/create_tables.sql
 
@@ -91,25 +94,37 @@ install-ui:
 
 	# get latest pioreactorUI release from Github.
 	cd /home/pi/
-	mkdir /home/pi/pioreactorui
-	curl -L https://api.github.com/repos/pioreactor/pioreactorui/tarball | tar -zxv -C /home/pi/pioreactorui --strip-components=1
+	git clone https://github.com/Pioreactor/pioreactorui.git --depth 1
+	# Use below to not have to use git
+	# mkdir /home/pi/pioreactorui
+	# curl -L https://api.github.com/repos/pioreactor/pioreactorui/tarball | tar -zxv -C /home/pi/pioreactorui --strip-components=1
 
 	# install required libraries
 	npm --prefix /home/pi/pioreactorui/client install
 	npm --prefix /home/pi/pioreactorui/backend install
 	sudo npm install pm2@latest -g
 
-install-worker: install-python configure-rpi systemd-worker install-i2c install-pioreactor-worker logging-files
+install-worker: install-git install-python configure-rpi systemd-worker install-i2c install-pioreactor-worker logging-files
 
-install-leader: install-python install-mqtt configure-mqtt-websockets configure-rpi install-db install-pioreactor-leader systemd-leader logging-files
+install-leader: install-git install-python install-mqtt configure-mqtt-websockets configure-rpi install-db install-pioreactor-leader systemd-leader logging-files install-ui
 	ssh-keygen -t rsa -N "" -f ~/.ssh/id_rsa
 	sudo apt-get install sshpass
 
-install-leader-as-worker: install-leader install-worker
+configure-hostname:
+	read -e -p "Enter new Pioreactor name: " userEnteredPioName
+	sudo hostname $$userEnteredPioName
+	hostname | sudo tee /etc/hostname
+
+	wget https://github.com/cbednarski/hostess/releases/download/v0.5.2/hostess_linux_arm
+	chmod a+x hostess_linux_arm
+	sudo ./hostess_linux_arm rm raspberry
+	sudo ./hostess_linux_arm add "$${userEnteredPioName}" 127.0.1.1
+
+install-leader-as-worker: configure-hostname install-leader install-worker
 	# I had trouble with variables, quotes and dollar signs, so https://stackoverflow.com/questions/10121182/multiline-bash-commands-in-makefile/29085684#29085684
 	{ \
 	set -e ;\
-	unitN=$$(hostname | sed "s/^pioreactor\(.*\)$$/\1/") ;\
-	touch ~/.pioreactor/config$$unitN.ini ;\
+	touch ~/.pioreactor/config_$$userEnteredPioName.ini ;\
 	cat ~/.ssh/id_rsa.pub > ~/.ssh/authorized_keys ;\
 	}
+	sudo reboot

config.ini

@@ -49,10 +49,7 @@ 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=0
-pioreactor3=1
-pioreactor4=0
-pioreactor5=0
+
 
 [ui.overview.settings]
 # changing these may require a power cycle of the leader unit.
@@ -89,6 +86,3 @@ Kd=0
 Kp=3
 Ki=0.1
 Kd=0.1
-
-[watchdog]
-email_alerts_to[email protected]

pioreactor/background_jobs/growth_rate_calculating.py

@@ -135,6 +135,7 @@ def set_od_normalization_factors(self):
         if message and not self.ignore_cache:
             return self.json_to_sorted_dict(message.payload)
         else:
+            # TODO: assert that od_reading is running
             od_normalization(unit=self.unit, experiment=self.experiment)
             return self.set_od_normalization_factors()
 

pioreactor/background_jobs/monitor.py

@@ -34,6 +34,7 @@ def __init__(self, unit, experiment):
         GPIO.add_event_detect(BUTTON_PIN, GPIO.RISING, callback=self.button_down_and_up)
 
         self.start_passive_listeners()
+        self.flicker_led()
 
     def turn_on_led(self):
         GPIO.output(LED_PIN, GPIO.HIGH)
@@ -51,10 +52,7 @@ def button_down_and_up(self, *args):
 
         self.turn_on_led()
 
-        publish(
-            f"pioreactor/{self.unit}/{self.experiment}/{self.job_name}/log",
-            "Pushed tactile button",
-        )
+        publish(f"pioreactor/{self.unit}/{self.experiment}/log", "Pushed tactile button")
 
         while GPIO.input(BUTTON_PIN) == GPIO.HIGH:
 
@@ -85,7 +83,7 @@ def publish_disk_space(self):
             disk_usage_percent,
         )
 
-    def flicker_led(self, _):
+    def flicker_led(self, *args):
         # TODO: what happens when I hear multiple msgs in quick succession?
         self.turn_on_led()
         time.sleep(0.2)

pioreactor/background_jobs/stirring.py

@@ -51,7 +51,7 @@ def on_disconnect(self):
 
     def start_stirring(self):
         self.pwm.start(100)  # get momentum to start
-        time.sleep(0.25)
+        time.sleep(0.4)
         self.pwm.ChangeDutyCycle(self.duty_cycle)
 
     def stop_stirring(self):

pioreactor/pio_cli.py

@@ -91,6 +91,10 @@ def mqtt():
 
             os.system("mosquitto_sub -v -t 'pioreactor/#'")
 
+    if not am_I_leader() and not am_I_active_worker():
+        print(
+            "Running `pio` on a non-active Pioreactor. Do you need to add this Pioreactor to `inventory` in `config.ini`?"
+        )
 
 except Exception as e:
     logger.debug(e, exc_info=True)

pioreactor/whoami.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 import sys
 import os
-import socket
 
 UNIVERSAL_IDENTIFIER = "$broadcast"
 UNIVERSAL_EXPERIMENT = "$experiment"
@@ -21,6 +20,8 @@ def get_latest_experiment_name():
 
 
 def get_hostname():
+    import socket
+
     if "pytest" in sys.modules:
         return "localhost"
     elif os.environ.get("HOSTNAME"):