24.3.6rc1

Upcoming

Highlights

• For better consistency between Pioreactors, we've introduced a new configuration option that will automatically vary the IR LED intensity to match a target value in the reference. This means that if your IR LED is slightly different between Pioreactors, the intensity % will be adjusted to match an internal value. To enable this feature, change the [od_config] config parameter ir_led_intensity value to auto

Bug fixes

• Fixes updating automations in experiment profiles

24.3.4

24.3.4

Enhancements

• reusing more MQTT clients internally => faster job startup and less network overhead

Bug fixes

• using the archive upload method to update Pioreactors had a bug when distributing the archive to workers on the cluster. That has been fixed. The first time, you archive update may fail. But it should succeed the second time.
• fix UI bug that was preventing real-time data from showing up in some custom charts.
• fix UI bug that was causing a stale datum to appear in charts.
• To avoid downstream permission issues, pio can't be run as root. That is, sudo pio ... will fail.
• a typo prevented od_config.smoothing_penalizer from being used internally. This is fixed.
• some retry logic for fixing "lost" state in the UI.
• fixed numerous MQTT connections from accumulating in the UI

24.2.27rc0

This is a release to test some release changes.

24.2.26

24.2.26

Highlights

• Experimental introducing outlier filtering in growth rate calculations. This is tunable with the new ekf_outlier_std_threshold parameter under [growth_rate_calculating.config]. To turn off outlier filtering, set this parameter to some very large number (1000s). Don't put it less than 3.0 - that's silly.
• With this new filtering, we can provide more reasonable values for the parameters of the growth rate Kalman filter. We previously had to artificially increase the measurement std. deviation (obs_std) to allow for some outliers. This had the knock-on effect of hiding growth-rate changes, so we had to also increase that parameter rate_std. With better outlier protection in the model, we can move these values back. New installs will have the following parameters, and we encourage existing users to try these values if you plan to use the outlier filtering.

[growth_rate_kalman]
acc_std=0.0008
obs_std=1.5
od_std=0.0025
rate_std=0.1

• added configuration for alternative mqtt brokers with the new configuration

  [mqtt]
  username=pioreactor
  password=raspberry
  broker_address=
  broker_ws_port=9001
  broker_port=1883
  ws_protocol=ws
  use_tls=0
  

Enhancements

• clear the growth-rate cache with pio run growth_rate_cacluating clear_cache
• added Pioreactor specific software version to the UI: Page Pioreactors -> Manage -> System -> Version. this requires a restart to display correctly
• new UI MQTT library. Is it faster? Maybe!
• increased the default max_subdose to 1.0.

Bug fixes

• fixed a case where dosing automation IO execution would not run due to a floating point rounding error. Sorry!
• fixed a memory leak in long running dosing automations that had thousands of dosing events. Sorry!
• fixed a race condition that caused an error to occur when a software PWM channel was closed too quickly. Sorry!
• fixed bug that was partially crashing the UI if some bad syntax was entered into a custom yaml file. Sorry!
• fixed bug that was causing bad json from the server, causing empty / non-loading areas in the UI. Sorry!
• fixed datum bug in the Overview that was crashing the UI. Sorry!

24.2.25rc0

Upcoming

Highlights

• Experimental introducing outlier filtering in growth rate calculations. This is tunable with the new ekf_outlier_std_threshold parameter under [growth_rate_calculating.config]. To turn off outlier filtering, set this parameter to some very large number (1000s). Don't put it less than 3.0 - that's silly.
• With this new filtering, we can provide more reasonable values for the parameters of the growth rate Kalman filter. We previously had to artificially increase the measurement std. deviation (obs_std) to allow for some outliers. This had the knock-on effect of hiding growth-rate changes, so we had to also increase that parameter rate_std. With better outlier protection in the model, we can move these values back. New installs will have the following parameters, and we encourage existing users to try these values if you plan to use the outlier filtering.

[growth_rate_kalman]
acc_std=0.0008
obs_std=1.0
od_std=0.005
rate_std=0.10

• added configuration for alternative mqtt brokers with the new configuration

[mqtt]
username=pioreactor
password=raspberry
broker_address=
broker_ws_port=9001
broker_port=1883
ws_protocol=ws
tls=0

#### Enhancements
- clear the growth-rate cache with `pio run growth_rate_cacluating clear_cache`
- added Pioreactor specific software version to the UI: Page *Pioreactors -> Manage -> System -> Version*
- new UI MQTT library. Is it faster? Maybe!
- increased the default `max_subdose` to 1.0.

#### Bug fixes
- fixed a case where dosing automation IO execution would not run due to a floating point rounding error.
- fixed a memory leak in long running dosing automations that had thousands of dosing events.
- fixed a race condition that caused an error to occur when a software PWM channel was closed too quickly.
- fixed bug that was partially crashing the UI if some bad syntax was entered into a custom yaml file. Sorry!
- fixed bug that was causing bad json from the server, causing empty / non-loading areas in the UI. Sorry!
- fixed `datum` bug in the Overview that was crashing the UI. Sorry!

24.2.11

24.2.11

• boot-up performance improvements
• job start performance improvements
• improved RPM calculation for lower RPMs.
• Added buttons to the Overview UI to change common settings.

Area.mp4

24.2.10rc0

24.2.10rc0

• boot-up performance improvements
• job start performance improvements
• improved RPM calculation for lower RPMs.
• Added buttons to the Overview UI to change common settings.

24.1.30

24.1.30

Enhancements

• profiles in the UI are sorted by their last edit time.
• Jobs can't run if self_test is running
• exporting pioreactor_unit_activity_data no longer requires an experiment name to be included.
• new config option: samples_for_od_statistics in [growth_rate_calculating.config] for specifying the number of OD samples to take for initial statistics.
• $ can be used in expressions (this is used to specify the $state setting).
• repeat directive in experiment profiles.

  experiment_profile_name: demo_stirring_repeat
  
  common:
    jobs:
      stirring:
        actions:
          - type: start
            hours_elapsed: 0.0
            options:
              target_rpm: 400.0
          - type: repeat
            hours_elapsed: 0.001
            while: ::stirring:target_rpm <= 1000
            repeat_every_hours: 12
            max_hours: 10
            actions:
              - type: update
                hours_elapsed: 0.0
                options:
                  target_rpm: ${{::stirring:target_rpm + 100}}

• use expressions in common block. Instead of the usual unit:job:setting syntax, use ::job:setting. For example:

  common:
    jobs:
      stirring:
        actions:
          - type: update
            hours_elapsed: 0.002
            if: ::stirring:target_rpm > 600
            options:
              target_rpm: ${{::stirring:target_rpm - 100}}

Bug fixes

• fixed a bug in the chart of OD reading that was causing historical and realtime data to be different lines.
• fixed bug where a PWM wouldn't clean up correctly if the job was canceled too early.
• fix for self-test test_REF_is_in_correct_position
• accidentally appended text to the end of an old experiment profile in the last update. We've fixed that in this update.

24.1.26

24.1.26

Conditionals and expressions in experiment profiles!

• adding if directives to experiment_profiles, with dynamic expressions. See full docs here

...
   stirring:
     actions:
       ...
       - type: update
         hours_elapsed: 12.0
         if: pio1:od_reading:od1.od > 2.0
         options:
           - target_rpm: 600

• adding dynamic options via expressions, see full docs here

...
   stirring:
     actions:
       ...
       - type: update
         hours_elapsed: 12.0
         options:
           - target_rpm: ${{ pio1:stirring:target_rpm * 1.1 }}

Breaking changes

Breaking changes to experiment profiles:

1. the common block requires a jobs block. Previously:

   experiment_profile_name: demo_stirring_example
   
   metadata:
     author: Cam Davidson-Pilon
     description:
   
   common:
     stirring:
       actions:
         - type: start
           hours_elapsed: 0.0
           options:
             target_rpm: 400.0
   

   Now:

   experiment_profile_name: demo_stirring_example
   
   metadata:
     author: Cam Davidson-Pilon
     description:
   
   common:
    jobs:            # this text is required
      stirring:
        actions:
          - type: start
            hours_elapsed: 0.0
            options:
              target_rpm: 400.0
   

2. labels has moved into the pioreactors block. Previously,

   experiment_profile_name: simple_stirring_example
   
   labels:
    worker1: PR-001
   
   metadata:
     author: John Doe
     description:
   
   pioreactors:
     worker1:
       jobs: {}
   

   Now,

   experiment_profile_name: simple_stirring_example
   
   metadata:
     author: John Doe
     description:
   
   pioreactors:
     worker1:
       label: PR-001
       jobs: {}
   

   Related, you can't use the label as an alias in the pioreactor block.

   Need a hand updating your profiles? Let us know, [email protected]!

• removing ODReadings.latest_od_reading and it's replaced by ODReadings.ods.
• removed the topic pioreactor/{unit}/.../od_readings/od/{channel}. Use pioreactor/{unit}/.../od_readings/od1 or pioreactor/{unit}/.../od_readings/od2. This change was made to fit more and more published data into the same format (and it makes od1 and od2 published settings on ODReader)

Enhancements

• ods, od1, od2 now a published settings of ODReadings.
• when a worker is first turned on, and pre-connected to a cluster, the LED is turned on to give some feedback to the user.
• using the 2023-12-11 RPi base image

Bug fixes

• fixed the UI crashing if trying to edit a blank experiment profile

Experimental builds

We've released new 64 bit builds, and a 64 bit "headful" build. These builds are experimental, and require a RPi4, RPi5, or RPi400 due to their larger memory requirements.

• 64 bit leader-worker and worker builds will be marginally more performant, at the cost of some additional memory consumption.
• The "headful" leader-worker build allows you to attach a monitor, keyboard, mouse, etc. to the Raspberry Pi and use it as an interface for your cluster.

These builds are available only on our nightly page.

24.1.25rc0

Upcoming

Conditionals and expressions in experiment profiles!

• adding if directives to experiment_profiles, with dynamic expressions. See full docs here

...
   stirring:
     actions:
       ...
       - type: update
         hours_elapsed: 12.0
         if: pio1:od_reading:od1.od > 2.0
         options:
           - target_rpm: 600

• adding dynamic options via expressions, see full docs here

...
   stirring:
     actions:
       ...
       - type: update
         hours_elapsed: 12.0
         options:
           - target_rpm: ${{ pio1:stirring:target_rpm * 1.1 }}

Breaking changes

• removing ODReadings.latest_od_reading and it's replaced by ODReadings.ods.
• removed the topic pioreactor/{unit}/.../od_readings/od/{channel}. Use pioreactor/{unit}/.../od_readings/od1 or pioreactor/{unit}/.../od_readings/od2. This change was made to fit more and more published data into the same format (and it makes od1 and od2 published settings on ODReader)

Enhancements

• ods, od1, od2 now a published settings of ODReadings.
• when a worker is first turned on, and pre-connected to a cluster, the LED is turned on to give some feedback to the user.
• using the 2023-12-11 RPi base image

Bug fixes

• fixed the UI crashing if trying to edit a blank experiment profile