Pioreactor Versions Save

[!IMPORTANT] We strongly recommend you be on 24.4.11 (the previous release) before updating. If not, update to 24.4.11 first!

24.5.1

Highlights

• initial support for Pioreactor 20ml v1.1! This is our latest iteration of Pioreactor. Even though it's a minor 0.x release, there's lots of positives about it. We encourage you to check out the upgrade kit here.
• some further support for tracking the model and version of the Pioreactor you are using. Users can change the version in the config file. For example:

[pioreactor]
model=pioreactor_20ml
version=1.1

If you have a mixed cluster (some 1.0, some 1.1), then you should put this configuration in the unit specific config files.

• For v1.1: New temperature inference algorithm makes reaching the thermostat setpoint quicker, and the Pioreactor can reach higher temperatures (our internal testing could easily reach up to 45C in a cool room). This algorithm uses the magic of ✨statistics✨. We may update the themostat PID values in the future, but the default ones work okay for now. A Pioreactor v1.0 update for this algorithm should come out soon, too.

Enhancements

• When using turbidostat, there is now a small moving average filter on the raw OD readings. This will prevent the turbidostat from firing when an OD outlier occurs.
• MQTT data is no long persisted between leader power-cycles. This was the cause of a lot of bad UI state issues where users couldn't interact with the Pioreactor via the UI after a power-cycle (intentional or not). We originally persisted the data since we previously used MQTT as more like a database, but our engineering style has moved away from that idea, and we now only use MQTT for "ephemeral" data. Taking out the persistent MQTT data forces this style change. Users shouldn't notice anything different.
• The leader is now the source-of-truth for the cluster's clocks. For example, when a worker boots up, it will ask the leader what the time is, and will periodically continue asking. If the leader has access to the internet, it will pull the correct time (and periodically continue asking). If the leader doesn't have access to the internet, it will use the default time on the Pi. This solves the problem of workers' clocks getting out of sync when powered down, especially in a local-access-point network. ![https://i.imgur.com/vt5gxyy.png]
• Lots of small UI improvements, including accessibility, empty-state, and loading improvements.
• Previously, we would "kick" stirring by forcing the DC% to 100% for a moment, and then increasing the running DC% slightly. Going forward, we'll actually try the following when the sensor fails to read a signal: DC% to 0%, then DC% to 100%, and then a slight increase in the DC%. Why?
  • If the mixing fan has stalled, setting the DC% to 0% does nothing, since the fan is already stopped.
  • If the mixing fan is running, but the stir bar isn't in sync, this step will align the stir bar and fan again.
  • If the mixing fan is running too fast, but the sensor isn't reading it, this allows for a small pause.
• The recommend way to upgrade Pioreactors and clusters is now using release archives. We have more control over the upgrade process this way. However, users are still welcome use the command line, pio update, which is what we use in house.
• A chart legend's in the UI now displays the entire name of the worker, if there is enough room.

Breaking changes

• Temporary Pioreactor labels, set in the UI, are now unique across an experiment.
• config max_volume_to_warn was removed, it's now hardcoded as 90% of max_volume_to_stop

Bug fixes

• Fix pio ... commands that displayed the CLI options not working on workers.
• Potential fix for heater continuing to be on after requested to be turned off.

Upcoming

Highlights

• initial support for Pioreactor 20ml v1.1! This is our latest iteration of Pioreactor. Even though it's a minor 0.x release, there's lots of positives about it. We encourage you to check out the upgrade kit here.
• some further support for tracking the model and version of the Pioreactor you are using. Users can change the version in the config file. For example:

[pioreactor]
model=pioreactor_20ml
version=1.1

If you have a mixed cluster (some 1.0, some 1.1), then you should put this configuration in the unit specific config files.

• For v1.1: New temperature inference algorithm makes reaching the thermostat setpoint quicker, and the Pioreactor can reach higher temperatures (our internal testing could easily reach up to 45C in a cool room). This algorithm uses the magic of ✨statistics✨. We may update the themostat PID values in the future, but the default ones work okay for now. A Pioreactor v1.0 update for this algorithm should come out soon, too.

Enhancements

• When using turbidostat, there is now a small moving average filter on the raw OD readings. This will prevent the turbidostat from firing when an OD outlier occurs.
• MQTT data is no long persisted between leader power-cycles. This was the cause of a lot of bad UI state issues where users couldn't interact with the Pioreactor via the UI after a power-cycle (intentional or not). We originally persisted the data since we previously used MQTT as more like a database, but our engineering style has moved away from that idea, and we now only use MQTT for "ephemeral" data. Taking out the persistent MQTT data forces this style change. Users shouldn't notice anything different.
• The leader is now the source-of-truth for the cluster's clocks. For example, when a worker boots up, it will ask the leader what the time is, and will periodically continue asking. If the leader has access to the internet, it will pull the correct time (and periodically continue asking). If the leader doesn't have access to the internet, it will use the default time on the Pi. This solves the problem of workers' clocks getting out of sync when powered down, especially in a local-access-point network. ![https://i.imgur.com/vt5gxyy.png]
• Lots of small UI improvements, including accessibility, empty-state, and loading improvements.
• Previously, we would "kick" stirring by forcing the DC% to 100% for a moment, and then increasing the running DC% slightly. Going forward, we'll actually try the following when the sensor fails to read a signal: DC% to 0%, then DC% to 100%, and then a slight increase in the DC%. Why?
  • If the mixing fan has stalled, setting the DC% to 0% does nothing, since the fan is already stopped.
  • If the mixing fan is running, but the stir bar isn't in sync, this step will align the stir bar and fan again.
  • If the mixing fan is running too fast, but the sensor isn't reading it, this allows for a small pause.
• The recommend way to upgrade Pioreactors and clusters is now using release archives. We have more control over the upgrade process this way. However, users are still welcome use the command line, pio update, which is what we use in house.
• A chart legend's in the UI now displays the entire name of the worker, if there is enough room.

Breaking changes

• Temporary Pioreactor labels, set in the UI, are now unique across an experiment.
• config max_volume_to_warn was removed, it's now hardcoded as 90% of max_volume_to_stop

Bug fixes

• Fix pio ... commands that displayed the CLI options not working on workers.
• Potential fix for heater continuing to be on after requested to be turned off.

Upcoming

Highlights

• initial support for Pioreactor 20ml v1.1! This is our latest iteration of Pioreactor. Even though it's a minor 0.x release, there's lots of positives about it. We encourage you to check out the upgrade kit here.
• some further support for tracking the model and version of the Pioreactor you are using. Users can change the version in the config file. For example:

[pioreactor]
model=pioreactor_20ml
version=1.1

If you have a mixed cluster (some 1.0, some 1.1), then you should put this configuration in the unit specific config files.

• For v1.1: New temperature inference algorithm makes reaching the thermostat setpoint quicker, and the Pioreactor can reach higher temperatures (our internal testing could easily reach up to 45C in a cool room). This algorithm uses the magic of ✨statistics✨. We may update the themostat PID values in the future, but the default ones work okay for now. A Pioreactor v1.0 update for this algorithm should come out soon, too.

Enhancements

• When using turbidostat, there is now a small moving average filter on the raw OD readings. This will prevent the turbidostat from firing when an OD outlier occurs.
• MQTT data is no long persisted between leader power-cycles. This was the cause of a lot of bad UI state issues where users couldn't interact with the Pioreactor via the UI after a power-cycle (intentional or not). We originally persisted the data since we previously used MQTT as more like a database, but our engineering style has moved away from that idea, and we now only use MQTT for "ephemeral" data. Taking out the persistent MQTT data forces this style change. Users shouldn't notice anything different.
• The leader is now the source-of-truth for the cluster's clocks. For example, when a worker boots up, it will ask the leader what the time is, and will periodically continue asking. If the leader has access to the internet, it will pull the correct time (and periodically continue asking). If the leader doesn't have access to the internet, it will use the default time on the Pi. This solves the problem of workers' clocks getting out of sync when powered down, especially in a local-access-point network. ![https://i.imgur.com/vt5gxyy.png]
• Lots of small UI improvements, including accessibility, empty-state, and loading improvements.
• Previously, we would "kick" stirring by forcing the DC% to 100% for a moment, and then increasing the running DC% slightly. Going forward, we'll actually try the following when the sensor fails to read a signal: DC% to 0%, then DC% to 100%, and then a slight increase in the DC%. Why?
  • If the mixing fan has stalled, setting the DC% to 0% does nothing, since the fan is already stopped.
  • If the mixing fan is running, but the stir bar isn't in sync, this step will align the stir bar and fan again.
  • If the mixing fan is running too fast, but the sensor isn't reading it, this allows for a small pause.
• The recommend way to upgrade Pioreactors and clusters is now using release archives. We have more control over the upgrade process this way. However, users are still welcome use the command line, pio update, which is what we use in house.
• A chart legend's in the UI now displays the entire name of the worker, if there is enough room.

Breaking changes

• Temporary Pioreactor labels, set in the UI, are now unique across an experiment.
• config max_volume_to_warn was removed, it's now hardcoded as 90% of max_volume_to_stop

Bug fixes

• Fix pio ... commands that displayed the CLI options not working on workers.
• Potential fix for heater continuing to be on after requested to be turned off.

24.4.11

[!IMPORTANT] We strongly recommend you be on 24.4.3 (the previous release) before updating. If not, update to 24.4.3 first!

Enhancements

• Faster app start-up performance, which should translate to faster response times.
• Log when workers change experiment assignments.
• Log when workers change active status.
• Adding [pioreactor] section to config.inis
• improvements to calibration charts

Breaking changes

• pio install-plugin is now pio plugins install. Likewise for uninstall.
• pio list-plugins is now pio plugins list.
• pios install-plugin is now pios plugins install. Likewise for uninstall.

Bug fixes

• fixed Log table in the UI not showing all entries.
• fixed HAT button response in the UI.

Upcoming

Enhancements

• Faster app start-up performance, which should translate to faster response times.
• Log when workers change experiment assignments.
• Log when workers change active status.
• Adding [pioreactor] section to config.inis

Breaking changes

• pio install-plugin is now pio plugins install. Likewise for uninstall.
• pio list-plugins is now pio plugins list.
• pios install-plugin is now pios plugins install. Likewise for uninstall.

Bug fixes

• fixed Log table in the UI not showing all entries.
• fixed HAT button response in the UI.

24.4.3

Highlights

• The Pioreactor leader can now support multiple experiments! If you have more than one Pioreactor, this change allows you to run multiple experiments simultaneously, assign Pioreactors to different experiments, and manage all experiments concurrently. No more multi-leader set ups - all you need is a single leader and multiple workers! See video here.
• Ability to delete experiments from the UI.
• Better control over your cluster, using the Inventory page in the UI.
• Ship with network configuration of local-link connections: plug in an ethernet from your Pioreactor to your computer, and after invoking sudo nmcli c PioreactorLocalLink up, you should be able to visit http://pioreactor.local in your browser.

Enhancements

• replace the ip file that is written to on startup with a new network_info.txt file that contains the hostname, IPv4 address, and MAC addresses.
• Adding the ethernet (wired) mac address to the system tab.
• new Python module for controlling workers: pioreactor.cluster_management
• by default, for new installs, the local-access-point SSID is now pioreactor_<hostname>.
• UI performance improvements
• New database tables to handle workers (workers) and experiments assignments (experiment_assignments).
• New pio workers CLI to mange your inventory. Try pio workers --help to see all the commands available.
• Better error messages when a self-test fails.
• pio kill has new options to kill specific actions. Ex: pio kill --experiment this-exp, pio kill --job-source experiment_profile

Breaking changes

• When a experiment profile stops early (i.e. via "stop early" in the UI), it now will halt any jobs that it started. This is a change from how they worked previously, but this new behaviour is less of a surprise to users.
• pio add-pioreactor <name> is now pio workers add <name>
• pio cluster-status is now pio workers status
• utils.publish_ready_to_disconnected_state changed names to utils.managed_lifecycle
• config.inventory in the config.ini is no longer used. All that data is now handled in the database on the leader, and managed in the UI or CLI.
• pio kill <job_name> is removed, use pio kill --name <job_name>.

Bug fixes

• fix for not being able to access http://pioreactor.local reliably.
• fix for multiple exporting datasets when selecting "All experiments"

Known bugs

• removing a Pioreactor leader from an experiment will stop any experiment profiles running that are associated to that experiment.

Upcoming

Highlights

• The Pioreactor leader can now support multiple experiments! If you have more than one Pioreactor, this change allows you to run multiple experiments simultaneously, assign Pioreactors to different experiments, and manage all experiments concurrently. No more multi-leader set ups - all you need is a single leader and multiple workers!
• Ability to delete experiments from the UI.
• Better control over your cluster, using the Inventory page in the UI.
• Ship with network configuration of local-link connections: plug in an ethernet from your Pioreactor to your computer, and after invoking sudo nmcli c PioreactorLocalLink up, you should be able to visit http://pioreactor.local in your browser.

Enhancements

• replace the ip file that is written to on startup with a new network_info.txt file that contains the hostname, IPv4 address, and MAC addresses.
• Adding the ethernet (wired) mac address to the system tab.
• new Python module for controlling workers: pioreactor.cluster_management
• by default, for new installs, the local-access-point SSID is now pioreactor_<hostname>.
• UI performance improvements
• New database tables to handle workers (workers) and experiments assignments (experiment_assignments).
• New pio workers CLI to mange your inventory. Try pio workers --help to see all the commands available.
• Better error messages when a self-test fails.
• pio kill has new options to kill specific actions. Ex: pio kill --experiment this-exp, pio kill --job_source experiment_profile

Breaking changes

• When a experiment profile ends early, it now will halt any jobs that it started. This is a change from how they worked previously, but this new behaviour is less of a surprise to users.
• pio add-pioreactor <name> is now pio workers add <name>
• pio cluster-status is now pio workers status
• publish_ready_to_disconnected_state changed names to managed_lifecycle
• config.inventory in the config.ini is no longer used. All that data is now handled in the database on the leader, and managed in the UI or CLI.
• pio kill <job_name> is removed, use pio kill --name <job_name>.

Bug fixes

• fix for not being able to access http://pioreactor.local reliably.
• fix for multiple exporting datasets when selecting "All experiments"

Known bugs

• removing a Pioreactor leader from an experiment will stop any experiment profiles running that are associated to that experiment.

Upcoming

Highlights

• The Pioreactor leader can now support multiple experiments! If you have more than one Pioreactor, this change allow you to run multiple experiments simultaneously, assign Pioreactors to different experiments, and control all experiments concurrently. No more multi-leader set ups - all you need is a single leader and multiple workers!
• Ability to delete experiments from the UI.
• Better control over your cluster, using the Inventory page in the UI.
• Ship with network configuration of local-link connections: plug in an ethernet from your Pioreactor to your computer, and after invoking sudo nmcli c PioreactorLocalLink up, you should be able to visit http://pioreactor.local in your browser.

Enhancements

• replace the ip file that is written to on startup with a new network_info file that contains the hostname, IPv4 address, and MAC addresses.
• Adding the ethernet (wired) mac address to the system tab.
• new Python module for controlling workers: pioreactor.cluster_management
• by default, for new installs, the local-access-point SSID is now pioreactor_<hostname>.
• UI performance improvements
• New database tables to handle workers (workers) and experiments assignments (experiment_assignments).
• New pio workers CLI to mange your inventory. Try pio workers --help to see all the commands available.
• Better error messages when a self-test fails.
• pio kill has new options to kill specific actions. Ex: pio kill --experiment this-exp, pio kill --job_source experiment_profile

Breaking changes

• When a experiment profile ends early, it now will halt any jobs that it started. This is a change from how they worked previously, but this new behaviour is less of a surprise to users.
• pio add-pioreactor <name> is now pio workers add <name>
• pio cluster-status is now pio workers status
• publish_ready_to_disconnected_state changed names to managed_lifecycle
• config.inventory in the config.ini is no longer used. All that data is now handled in the database on the leader, and managed in the UI or CLI.
• pio kill <job_name> is removed, use pio kill --name <job_name>.

Bug fixes

• fix for not being able to access http://pioreactor.local reliably.
• fix for multiple exporting datasets when selecting "All experiments"

24.3.10

Enhancements

• For better consistency between Pioreactors, we've introduced a new configuration option that will automatically adjust the IR LED intensity to match a target value in the reference photodiode, at the start of OD reading. This means that if your IR LEDs are slightly different between Pioreactors, the IR LED output will be adjusted to match a hardcoded value. To enable this feature, change the [od_config] config parameter ir_led_intensity value to auto. For new installs, this is the default configuration. This shouldn't change your actual OD readings very much (since we normalize raw PD by REF, and increase or decrease in REF is balanced by increase or decrease in PD), but it will make analysis easier.
• Significant UI performance improvements: we are use less MQTT clients, which should mean faster loading, less network overhead, and overall lower resource-usage.

Bug fixes

• Fixes updating automations in experiment profiles

Upcoming

Enhancements

• For better consistency between Pioreactors, we've introduced a new configuration option that will automatically adjust the IR LED intensity to match a target value in the reference photodiode, at the start of OD reading. This means that if your IR LEDs are slightly different between Pioreactors, the IR LED output will be adjusted to match a hardcoded value. To enable this feature, change the [od_config] config parameter ir_led_intensity value to auto. For new installs, this is the default configuration. This shouldn't change your actual OD readings very much (since we normalize raw PD by REF, and increase or decrease in REF is balanced by increase or decrease in PD), but it will make analysis easier.
• Significant UI performance improvements: we are use less MQTT clients, which should mean faster loading, less network overhead, and overall lower resource-usage.

Bug fixes

• Fixes updating automations in experiment profiles