24.8.22

24.8.22

Important

We highly recommend you be on version 24.7.18 before updating!

Enhancements

• pio logs now includes the UI logs (if run on leader).
• introduce a new od_reading config,turn_off_leds_during_reading, which enables / disables turning off the other LEDS during an OD snapshot. By default, it is set to 1 (enables).
• leader-only Pioreactors also have a config_<hostname>.local file now.
• a new top-level section in experiment profiles, inputs, allows you to define parameters that can be used in expressions. This is useful if you are copy the same constant over an over again, and want a quick way to change it once. Example:

inputs:
  growth_phase_temp: 37.0
  stationary_phase_temp: 30.0
  od_threshold: 1.6

common:
  jobs:
    temperature_automation:
      actions:
        ...
        - type: update
          hours_elapsed: 12.0
          if: ${{ ::od_reading:od1.od < od_threshold }}
          options:
            target_temperature: ${{ stationary_phase_temp }}
        - type: update
          hours_elapsed: 12.0
          if: ${{ ::od_reading:od1.od >= od_threshold }}
          options:
            target_temperature: ${{ growth_phase_temp }}

Bug fixes

• more resilience to "UI state" diverging from "bioreactor state". Often, this occurred when two jobs stared almost immediately (often a networking issue), and the last job would halt since it couldn't get the required resources, however any MQTT data would be overwritten by the last job. Now, multiple places in the request pipeline will reduce duplication and prevent two jobs from starting too close to each other.
• improved stirring clean up when stopped in quick succession after starting.
• if a network isn't found, the monitor job will not stall, but warn and continue.
• fixed HAT warning for HAT-less leaders.

Breaking changes

• the RP2040 firmware is now on i2c channel 0x2C (previously 0x30). This is to solve an annoying i2cdetect issue where the i2c channel would lock up.
• the web server now writes its logs to the same location as the app: /var/log/pioreactor.log. Those wishing to keep the old location can use a new configuration parameter ui_log_file to [logging] section and set it to /var/log/pioreactorui.log.
• removed psutil and zeroconf Python packages from new images. We replaced their functionality with built-in routines.
• in config.ini, the section od_config renamed to od_reading.config, and stirring is stirring.config. When you update, a script will run to automatically update these names in your config.inis.

24.8.21rc0

Upcoming

Enhancements

• pio logs now includes the UI logs (if run on leader).
• introduce a new od_reading config,turn_off_leds_during_reading, which enables / disables turning off the other LEDS during an OD snapshot. By default, it is set to 1 (enables).
• leader-only Pioreactors also have a config_<hostname>.local file now.
• a new top-level section in experiment profiles, inputs, allows you to define parameters that can be used in expressions. This is useful if you are copy the same constant over an over again, and want a quick way to change it once. Example:

inputs:
  growth_phase_temp: 37.0
  stationary_phase_temp: 30.0
  od_threshold: 1.6

common:
  jobs:
    temperature_automation:
      actions:
        ...
        - type: update
          hours_elapsed: 12.0
          if: ${{ ::od_reading:od1.od < od_threshold }}
          options:
            target_temperature: ${{ stationary_phase_temp }}
        - type: update
          hours_elapsed: 12.0
          if: ${{ ::od_reading:od1.od >= od_threshold }}
          options:
            target_temperature: ${{ growth_phase_temp }}

Bug fixes

• more resilience to "UI state" diverging from "bioreactor state". Often, this occurred when two jobs stared almost immediately (often a networking issue), and the last job would halt since it couldn't get the required resources, however any MQTT data would be overwritten by the last job. Now, multiple places in the request pipeline will reduce duplication and prevent two jobs from starting too close to each other.
• improved stirring clean up when stopped in quick succession after starting.
• if a network isn't found, the monitor job will not stall, but warn and continue.
• fixed HAT warning for HAT-less leaders.

Breaking changes

• the RP2040 firmware is now on i2c channel 0x2C (previously 0x30). This is to solve an annoying i2cdetect issue where the i2c channel would lock up.
• the web server now writes its logs to the same location as the app: /var/log/pioreactor.log. Those wishing to keep the old location can use a new configuration parameter ui_log_file to [logging] section and set it to /var/log/pioreactorui.log.
• removed psutil and zeroconf Python packages from new images. We replaced their functionality with built-in routines.
• in config.ini, the section od_config renamed to od_reading.config, and stirring is stirring.config. When you update, a script will run to automatically update these names in your config.inis.

24.8.19rc0

Upcoming

Enhancements

• pio logs now includes the UI logs (if run on leader).
• introduce a new od_reading config,turn_off_leds_during_reading, which enables / disables turning off the other LEDS during an OD snapshot. By default, it is set to 1 (enables).
• leader-only Pioreactors also have a config_<hostname>.local file now.
• a new top-level section in experiment profiles, inputs, allows you to define parameters that can be used in expressions. This is useful if you are copy the same constant over an over again, and want a quick way to change it once. Example:

inputs:
  growth_phase_temp: 37.0
  stationary_phase_temp: 30.0
  od_threshold: 1.6

common:
  jobs:
    temperature_automation:
      actions:
        ...
        - type: update
          hours_elapsed: 12.0
          if: ${{ ::od_reading:od1.od < od_threshold }}
          options:
            target_temperature: ${{ stationary_phase_temp }}
        - type: update
          hours_elapsed: 12.0
          if: ${{ ::od_reading:od1.od >= od_threshold }}
          options:
            target_temperature: ${{ growth_phase_temp }}

Bug fixes

• more resilience to "UI state" diverging from "bioreactor state". Often, this occurred when two jobs stared almost immediately (often a networking issue), and the last job would halt since it couldn't get the required resources, however any MQTT data would be overwritten by the last job. Now, multiple places in the request pipeline will reduce duplication and prevent two jobs from starting too close to each other.
• improved stirring clean up when stopped in quick succession after starting.
• if a network isn't found, the monitor job will not stall, but warn and continue.
• fixed HAT warning for HAT-less leaders.

Breaking changes

• the RP2040 firmware is now on i2c channel 0x2C (previously 0x30). This is to solve an annoying i2cdetect issue where the i2c channel would lock up.
• the web server now writes its logs to the same location as the app: /var/log/pioreactor.log. Those wishing to keep the old location can use a new configuration parameter ui_log_file to [logging] section and set it to /var/log/pioreactorui.log.
• removed psutil and zeroconf Python packages from new images. We replaced their functionality with built-in routines.
• in config.ini, the section od_config renamed to od_reading.config, and stirring is stirring.config. When you update, a script will run to automatically update these names in your config.inis.

24.8.16rc0

Upcoming

Enhancements

• pio logs now includes the UI logs (if run on leader).
• introduce a new od_reading config,turn_off_leds_during_reading, which enables / disables turning off the other LEDS during an OD snapshot. By default, it is set to 1 (enables).
• leader-only Pioreactors also have a config_<hostname>.local file now.
• a new top-level section in experiment profiles, inputs, allows you to define parameters that can be used in expressions. This is useful if you are copy the same constant over an over again, and want a quick way to change it once. Example:

inputs:
  growth_phase_temp: 37.0
  stationary_phase_temp: 30.0
  od_threshold: 1.6

common:
  jobs:
    temperature_automation:
      actions:
        ...
        - type: update
          hours_elapsed: 12.0
          if: ${{ ::od_reading:od1.od < od_threshold }}
          options:
            target_temperature: ${{ stationary_phase_temp }}
        - type: update
          hours_elapsed: 12.0
          if: ${{ ::od_reading:od1.od >= od_threshold }}
          options:
            target_temperature: ${{ growth_phase_temp }}

Bug fixes

• more resilience to "UI state" diverging from "bioreactor state". Often, this occurred when two jobs stared almost immediately (often a networking issue), and the last job would halt since it couldn't get the required resources, however any MQTT data would be overwritten by the last job. Now, multiple places in the request pipeline will reduce duplication and prevent two jobs from starting too close to each other.
• improved stirring clean up when stopped in quick succession after starting.
• if a network isn't found, the monitor job will not stall, but warn and continue.
• fixed HAT warning for HAT-less leaders.

Breaking changes

• the web server now writes its logs to the same location as the app: /var/log/pioreactor.log. Those wishing to keep the old location can use a new configuration parameter ui_log_file to [logging] section and set it to /var/log/pioreactorui.log.
• removed psutil and zeroconf Python packages from new images. We replaced their functionality with built-in routines.
• in config.ini, the section od_config renamed to od_reading.config, and stirring is stirring.config. When you update, a script will run to automatically update these names in your config.inis.

24.7.18

24.7.18

Important

This release intentionally breaks the high-temp plugin, and temperature-expansion plugin. Don't update until you're prepared to update those (and the plugins have been updated, follow along on our forums

Enhancements

• improvements to the UI's experiment profile preview.
• hours_elapsed() is a function in profile expressions, which returns the hours since the profile started.
• unit() can be used in mqtt fetch expressions. Example: unit():stirring:target_rpm is identical to ::stirring:target_rpm. The latter can be seen as a shortened version of the former.
• experiment profiles can have a description in the job field (i.e. at the same level as actions).
• Updated Raspberry Pi OS image to 2024-07-04.
• Vendoring the TMP1075 library, which also fixes the RPi5 error.
• In places where the ipv4 is displayed (Inventory page, System tab, pio workers status, etc), all ipv4 addresses are displayed.

Breaking changes

• remove the temperature_control, dosing_control, and led_control abstractions. These were introduced early in the Pioreactor software as a way to quickly change automations, but they have been more of a wort than a win. While working on the internals of experiment profiles recently, it became more and more clear how poor this abstraction was. The removal of them has some consequences and some backward incompatibilities:

• updating experiment profiles: experiment profiles that have a *_control job will need to be updated to use *_automation, eventually. For now, we are allowing *_control in profiles: in the backend, we are renaming *_control to *_automations, but a warning will be produced. Later, we'll remove this renaming and profiles will need to be completely updated. Example:

  experiment_profile_name: start_temp_control
  
  metadata:
    author: Cam DP
  
  common:
    jobs:
      temperature_control:
        actions:
          - type: start
            hours_elapsed: 0
            options:
              automation_name: thermostat
              target_temperature: 30
          - type: stop
            hours_elapsed: 12
      temperature_automation:
        actions:
          - type: update
            hours_elapsed: 6
            options:
              target_temperature: 35

  becomes:

  experiment_profile_name: start_temp_control
  
  metadata:
    author: Cam DP
  
  common:
    jobs:
      temperature_automation:
        actions:
          - type: start
            hours_elapsed: 0
            options:
              automation_name: thermostat
              target_temperature: 30
          - type: stop
            hours_elapsed: 12
          - type: update
            hours_elapsed: 6
            options:
              target_temperature: 35

  • update plugins. For users using, specifically, the high-temp plugin, or temperature-expansion-kit plugin, new plugins will be released. Look on the forums, or documentation, for update instructions.

The benefits of removing this abstraction is much less code, less overhead, easier developer experience, and overall simplification. Later, we may create a new abstraction, but now we are moving abstractions back to level 0.

• log in experiment profiles now uses expressions instead of Python string formatting. For example: The unit {unit} is running {job} in experiment {experiment} should be replaced by expressions in the string: The unit ${{unit()}} is running ${{job_name()}} in the experiment ${{experiment}}. Note: {job} is now ${{job_name()}}.
• cycle_media and cycle_alt_media now publish dosing events, and will be recorded by dosing automations, and the db.

Bug fixes

• When pausing temperature automations, the heater now turns off and stays off until unpaused. This is the intended behaviour.

24.7.18rc0

Upcoming

Enhancements

• improvements to the UI's experiment profile preview.
• hours_elapsed() is a function in profile expressions, which returns the hours since the profile started.
• unit() can be used in mqtt fetch expressions. Example: unit():stirring:target_rpm is identical to ::stirring:target_rpm. The latter can be seen as a shortened version of the former.
• experiment profiles can have a description in the job field (i.e. at the same level as actions).
• Updated Raspberry Pi OS image to 2024-07-04.
• Vendoring the TMP1075 library, which also fixes the RPi5 error.
• In places where the ipv4 is displayed (Inventory page, System tab, pio workers status, etc), all ipv4 addresses are displayed.

Breaking changes

• remove the temperature_control, dosing_control, and led_control abstractions. These were introduced early in the Pioreactor software as a way to quickly change automations, but they have been more of a wort than a win. While working on the internals of experiment profiles recently, it became more and more clear how poor this abstraction was. The removal of them has some consequences and some backward incompatibilities:

• updating experiment profiles: experiment profiles that have a *_control job will need to be updated to use *_automation, eventually. For now, we are allowing *_control in profiles: in the backend, we are renaming *_control to *_automations, but a warning will be produced. Later, we'll remove this renaming and profiles will need to be completely updated. Example:

  experiment_profile_name: start_temp_control
  
  metadata:
    author: Cam DP
  
  common:
    jobs:
      temperature_control:
        actions:
          - type: start
            hours_elapsed: 0
            options:
              automation_name: thermostat
              target_temperature: 30
          - type: stop
            hours_elapsed: 12
      temperature_automation:
        actions:
          - type: update
            hours_elapsed: 6
            options:
              target_temperature: 35

  becomes:

  experiment_profile_name: start_temp_control
  
  metadata:
    author: Cam DP
  
  common:
    jobs:
      temperature_automation:
        actions:
          - type: start
            hours_elapsed: 0
            options:
              automation_name: thermostat
              target_temperature: 30
          - type: stop
            hours_elapsed: 12
          - type: update
            hours_elapsed: 6
            options:
              target_temperature: 35

  • update plugins. For users using, specifically, the high-temp plugin, or temperature-expansion-kit plugin, new plugins will be released. Look on the forums, or documentation, for update instructions.

The benefits of removing this abstraction is much less code, less overhead, easier developer experience, and overall simplification. Later, we may create a new abstraction, but now we are moving abstractions back to level 0.

• log in experiment profiles now uses expressions instead of Python string formatting. For example: The unit {unit} is running {job} in experiment {experiment} should be replaced by expressions in the string: The unit ${{unit()}} is running ${{job_name()}} in the experiment ${{experiment}}. Note: {job} is now ${{job_name()}}.
• cycle_media and cycle_alt_media now publish dosing events, and will be recorded by dosing automations, and the db.

Bug fixes

• When pausing temperature automations, the heater now turns off and stays off until unpaused. This is the intended behaviour.

24.7.7

24.7.5 & 24.7.6 & 24.7.7

Hotfix release for 24.7.3. This pins blinka to a specific version which does not install numpy.

24.7.5rc0

24.7.5rc0

Testing hotfix for numpy 2.0 incompatibility.

24.7.3

24.7.3

Enhancements

• A new live preview in the UI's experiment profile editor. This preview tool is useful for getting immediate feedback when writing a profile. We'll keep on adding to this to improve the edit-profile workflow - please send us feedback!
• new when action type in experiment profiles that will execute an action (or list of actions) when some expression is true. For example, start a chemostat when a threshold OD is first achieved, log a message when event is triggered, or monitor a bioreactor parameter and execute an action if it goes out of bounds.
• New config turbidostat.config that can be used to modify some internal turbidostat settings:

  [turbidostat.config]
  signal_channel=2
  od_smoothing_ema=0.5
  

• Better user interaction on the Pioreactors page when the assigned experiment and "viewing" experiment are different.
• Select / Deselect all Pioreactors to assign to an experiment faster.
• Added unit() function to experiment profiles expressions that returns the unit name the expression is evaluated for. Ex: if: ${{ unit() == worker01 }}.
• Added job_name() function to experiment profiles expressions that returns the job_name the expression is evaluated for. Ex: if: ${{ job_name() == stirring }}.
• Added experiment() function to experiment profiles expressions that returns the experiment the expression is evaluated for. Ex: if: ${{ experiment() == exp001 }}.

Breaking changes

• significant web backend API changes! See list of rules in docs.

Bug fixes

• Fix UI code editor from being unresponsive when all the text was removed.
• Experiment profiles won't be overwritten if providing the same filename as an existing profile.

24.7.3rc0

Upcoming

Highlights

• A new live preview in the UI's experiment profile editor. This preview tool is useful for getting immediate feedback when writing a profile. We'll keep on adding to this to improve the edit-profile workflow - please send us feedback!
• new when action type in experiment profiles that will execute an action (or list of actions) when some expression is true. For example, start a chemostat when a threshold OD is first achieved, log a message when event is triggered, or monitor a bioreactor parameter and execute an action if it goes out of bounds.

Enhancements

• New config turbidostat.config that can be used to modify some internal turbidostat settings:

  [turbidostat.config]
  signal_channel=2
  od_smoothing_ema=0.5
  

• Better user interaction on the Pioreactors page when the assigned experiment and "viewing" experiment are different.

• Select / Deselect all Pioreactors to assign to an experiment faster.

• Added unit() function to experiment profiles expressions that returns the unit name the expression is evaluated for. Ex: if: ${{ unit() == worker01 }}.

• Added job_name() function to experiment profiles expressions that returns the job_name the expression is evaluated for. Ex: if: ${{ job_name() == stirring }}.

• Added experiment() function to experiment profiles expressions that returns the experiment the expression is evaluated for. Ex: if: ${{ experiment() == exp001 }}.

Breaking changes

• significant web backend API changes! See list of rules in docs.

Bug fixes

• Fix UI code editor from being unresponsive when all the text was removed.
• Experiment profiles won't be overwritten if providing the same filename as an existing profile.