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26.5.0

Highlights

  • More reliable data exports. The Export Data page now exports one experiment at a time and starts exports as async tasks, so the UI can wait for large exports instead of tying up a web request. Exports now write directly into the zip file, clean up stale partial artifacts, and stop early if disk space, memory, or SQLite WAL growth gets too close to unsafe limits.

  • Automation schedules now live with the automation. Automations can choose the right trigger for their behavior: fixed timers, biomass updates, phase boundaries, or manual execution. For example, turbidostat now reacts to fresh biomass readings instead of polling every few seconds, while light_dark_cycle schedules exact light/dark phase boundaries.

  • New repair workflow. Added pio repair, richer pio status --json checks, and a UI Repair system action under Inventory for fixing common local ownership, permission, and runtime-storage issues without rebooting or stopping running jobs.

    pio status --json
pio repair

Breaking changes

  • Removed the old dosing_automation/media_throughput and dosing_automation/alt_media_throughput MQTT variables. Use the retained bioreactor cumulative dosing variables instead:

    pioreactor/<unit>/<experiment>/bioreactor/cumulative_media_added_ml
pioreactor/<unit>/<experiment>/bioreactor/cumulative_alt_media_added_ml
pioreactor/<unit>/<experiment>/bioreactor/cumulative_waste_removed_ml

  • Removed the shared --duration and --skip-first-run CLI flags from pio run dosing_automation and pio run led_automation. Timer-based automations now expose their own fields instead. For example:

    pio run dosing_automation --automation-name chemostat --duration 20 --skip-first-run 1
pio run led_automation --automation-name light_dark_cycle --light-duration-minutes 12.5 --dark-duration-minutes 12.5

  • Removed the old pio update ... and pios update ... aliases. Use the explicit subcommand:

    pio update app --version <version>
pios update app --version <version>

  • Moved passive Pioreactor card setting descriptors out of ui/jobs/ and into the new ui/settings/ descriptor directory. Plugin and custom UI descriptors for fields such as LED intensity, PWM intensity, and bioreactor state should now live under ~/.pioreactor/plugins/ui/settings/. The old /api/bioreactor/descriptors endpoint has been replaced by /api/settings/descriptors and /api/workers/<unit>/settings/descriptors.

Enhancements

  • Added retained bioreactor variables for cumulative dosing totals: cumulative_media_added_ml, cumulative_alt_media_added_ml, and cumulative_waste_removed_ml. These are updated from dosing events and can be used for media-use, alt-media-use, and waste-removal alerts.
  • Added YAML-backed UI settings descriptors, allowing built-in, plugin, and custom fields to control whether passive Pioreactor card fields are shown and how they appear in Manage / Settings.
  • Improved automation start forms so each automation can define its own fields, including boolean options like skip_first_run, and required fields now block Start until valid.
  • Improved the Light/Dark Cycle LED automation to support fractional-minute light and dark phases and reschedule immediately when phase durations change.
  • Added per-Pioreactor Stop all actions on Pioreactor cards, so a single unit can be stopped without broadcasting to every assigned unit.
  • Added YAML download buttons for individual calibrations and estimators, alongside the existing source preview.
  • Improved frontend load performance by lazily loading route-level UI pages.

Bug fixes

  • Fixed large exports that could exhaust memory or leave incomplete CSV/tmp files behind after interruption.
  • Fixed experiment profile save and delete requests so the API waits for the underlying file operation and reports failures instead of returning success too early.
  • Fixed experiment profile start errors so the UI keeps the dialog open and shows the backend error.
  • Fixed Advanced Config dialogs to refresh config from the selected worker when opened, avoiding stale values after jobs persist updated settings.
  • Fixed cluster fan-out reads so offline or slow workers resolve to per-unit failures instead of turning the whole request into a ResultTimeout.
  • Fixed plugin pages for worker-specific views so offline workers show a clear Could not reach this Pioreactor. error, and Install across cluster is shown only when there is more than one unit.
  • Fixed model-hardware checks to apply to HAT v1.x hardware generally, not just model version 1.5.
  • Fixed dosing automations to check required pump calibrations and PWM assignments before starting, so missing media or waste pump setup is reported immediately.

26.4.4

Enhancements

  • New multi-pioreactor flow in the UI to run simultaneous protocols for stirring calibrations.

Breaking changes

  • Changed async task polling responses from /unit_api/task_results/<task_id> and related leader callback helpers. Pending tasks now return 202 with status: pending or status: running, while terminal task results now return 200 with either status: succeeded plus result, or status: failed plus error details. Failed task polls no longer use HTTP 500 just because the underlying task failed.
  • Fixed cluster-wide app updates so the leader is updated only once during broadcast updates, including both internet-based updates and release-archive updates.

Bug fixes

  • Fixed dosing_automation to stop active pumps when the automation disconnects and fail custom multi-pump dosing requests before partially dosing if a required pump handler is missing.
  • Fixed crashes in the Experiment Profile editor
  • Fixed an error when using add_media or add_alt_media in an experiment profile

26.4.3

Bug fixes

  • Performance improvements in the UI frontend
  • Improved software update reliability by avoiding temp-file name collisions between web-uploaded release archives and pio update app downloads.
  • Fixed duplicate pio run od_reading starts to fail before reinitializing ADC hardware, avoiding disruptions to an already-running OD reader and spurious noisy-reference warnings.

26.4.2

Enhancements

  • Updated pio cache purge to parse Python literals for cache keys, so tuple-shaped entries can be removed directly. For example:

    pio cache purge leader_multicast_get_cache "('multicast_get', 'calibrations', '/unit_api/calibrations', 'unit1')"

Bug fixes

  • Fix new worker images not having the correct data in ~/.pioreactor/ui
  • Fix bioreactor diagram not responding to waste pump actions.
  • Improved experiment profile validation to catch more semantic errors before execution or save, including conflicting action time fields and invalid profile expressions.
  • Updated the Create/Edit Experiment Profile UI to show backend validation messages when a profile save fails, making profile errors easier to diagnose.
  • Fix for blinking self-tests on the Pioreactors page
  • Fix for Pioreactor page crashing.

26.4.1

  • hot fix release to fix PWM bug.

26.4.0

Breaking changes

  • Unit-specific configuration is now owned by each worker’s local unit_config.ini. The filename-based config editor APIs (/api/config/files*) have been removed; use /api/config/shared, /api/config/units/<unit>/specific, and /api/config/units/<unit> instead.
  • pios sync-configs --specific now refreshes leader-side snapshots from each worker’s unit_config.ini instead of pushing leader-local config_<unit>.ini files to workers.
  • Renamed the shared bioreactor volume setting max_working_volume_ml to efflux_tube_volume_ml, including the UI label (Efflux tube level), MQTT/API state, and device config/cache migration during update.
  • Job and Automation controls now use worker-provided descriptors for individual Pioreactors, so worker-only plugin jobs automations appear in per-unit UI even if the leader doesn’t have that plugin installed. Bulk “Control All Pioreactors” automation flows remain leader-driven. A update script will attempt to add the necessary UI files to workers.
  • growth_rate_calculating now assumes the new grpredict hidden-state filter and warmup-based initialization. It no longer supports --ignore-cache, cached growth-rate/filtered-OD startup state, or od_blank correction in this job. The parameters in [growth_rate_kalman] are no longer used.
  • od_blank correction is now applied upstream in od_reading on a per-experiment basis before readings reach growth_rate_calculating. If a blank exists for the experiment, od_reading now refuses to start with OD calibrations or fused estimators enabled, instead raising a ValueError.
  • new version of grpredict that has significant changes to the responsiveness of the growth-rate model.

Enhancements

  • Updated the config editor and worker-add flow for worker-owned unit configuration. The UI now edits shared cluster config separately from per-unit unit_config.ini, and existing leaders update their add-worker helper so new workers receive shared config without overwriting their unit-specific config.
  • Added pio config get <section> <parameter> and pio config set <section> <parameter> <value> for single-entry config access from the CLI. get defaults to the effective merged value and also supports --shared / --specific for file-specific reads. set uses --shared / --specific to target config.ini or unit_config.ini.
  • Added short-lived leader-side caching for several fan-out metadata APIs, reducing repeated worker fetches and improving UI load times for calibrations, protocols, estimators, automations, jobs, and installed plugins.
  • New growth-rate algorithm: designed the growth-rate EKF around a log-OD state model. You should see much faster convergence and better behaviour.
  • Added pio run stirring --measure-rpm-only to hold a fixed duty cycle while still measuring and publishing measured_rpm, making it easier to inspect fan RPM at settings like --duty-cycle 100.

Bug fixes

  • Fixed dosing_automation subdosing to emit only the top-level DosingStarted and DosingStopped events, avoiding duplicate nested dosing events during recursive IO actions.
  • Fixed repeated in-process actions such as dosing/pump runs to clean up MQTT listeners, signal handlers, and short-lived MQTT clients more reliably, preventing runaway socket/file-descriptor growth in long-lived jobs.
  • Fixed fed_batch dosing to skip additions that would push the vial past the configured hard-stop safety volume, pausing the automation instead of risking overflow.
  • Fixed non-interactive SSH and nohup command execution for pio and pios by installing /usr/local/bin wrappers that source /etc/pioreactor.env before execing the Pioreactor virtualenv binaries.
  • Fixed pump calibration dosing_events from changing retained bioreactor state such as vial volume and alt-media fraction.
  • Fixed overview chart legends so relabelled aliases are truncated consistently and still hide/show the correct series when clicked.
  • Fixed pio update app default release installs to download and apply the single release_<version>.zip archive, reusing the same archive update path as uploaded release bundles instead of fetching individual release assets.

26.3.3

Breaking changes

  • Changed the leader API route for updating per-unit bioreactor values. PATCH /api/workers/<unit>/experiments/<experiment>/bioreactor has been removed; use PATCH /api/workers/<unit>/bioreactor/update/experiments/<experiment> instead.

Bug fixes

  • Fixed reassignment history tracking in the leader web app's SQLite connection by enabling recursive triggers, preventing stale open rows from accumulating in experiment_worker_assignments_history.
  • Fixed worker reassignment so moving a Pioreactor from one experiment to another now stops jobs still running under the previous experiment.
  • Fixed missed pump dosing_events observations by publishing them with MQTT QoS 2 (EXACTLY_ONCE), and updated pio mqtt to subscribe at the same QoS when tailing topics.
  • Fixed recent log tables in the UI so live MQTT log events stay sorted by timestamp even if they arrive slightly out of order, instead of appearing under older events until refresh.
  • Fixed experiment profile previews so inline YAML comments like # 1/h, # mL, and timing notes now appear in the human-readable display in the create, edit, and profile preview UIs.

26.3.2

Bug fixes

  • Adjusted the UI's "Assign Pioreactors" dialog so Select all available no longer includes workers already assigned to another experiment, reducing accidental bulk reassignments while preserving individual reassignment.
  • fixed new images now having the experiment_tags table
  • fixed some UI bugs

26.3.1

Bug fixes

  • Fix temperature automation not recognizing Pioreactor 20ml v1.0 correctly
  • Fix bug that was causing /api/bioreactor/descriptors to fail on leader-only units.

26.3.0

Going forward, we are changing our versioning scheme from YY.M.D to YY.M.N, where N is a release counter within the month starting at 0.

We expect YY.M.0 releases to carry the larger changes, including system-level updates when needed. Subsequent releases in the same month, such as YY.M.1, YY.M.2, and so on, will typically be smaller bug-fix or incremental releases.

Enhancements

  • Redesigned the Experiments UI page into a management-focused table with search, status/tag filters, tag editing, and quick actions for exporting, ending, or deleting experiments.

  • Added experiment tags to the UI and API: tags can now be created when starting a new experiment, edited later from the Experiments and Overview page, and used to organize/filter experiments.

  • Calibration protocol sessions now persist a tab-scoped resume handle in the UI, so reloading the Protocols page in the same browser tab restores the existing Resume protocol action instead of losing the in-progress session.

  • Added persisted bioreactor state for each experiment, including current_volume_ml, max_working_volume_ml, and alt_media_fraction. These values are now exposed over MQTT plus new API endpoints:

    • GET /api/bioreactor/descriptors
    • GET|PATCH /api/workers/<unit>/experiments/<experiment>/bioreactor
    • GET /unit_api/bioreactor/experiments/<experiment>

  • Added live bioreactor controls to the Pioreactor UI so users can inspect and edit per-unit bioreactor values, with updated vessel diagrams for supported 20 mL and 40 mL models.

  • Added plugin hooks for custom self-tests. Plugins can now register additional checks that run with pio run self_test, for example:

    from pioreactor.actions.self_test import register_self_tests


def test_air_bubble_is_running(managed_state, logger, unit, experiment):
    assert ...


register_self_tests(test_air_bubble_is_running)

Breaking changes

  • Updated the leader UI's dosing-related chart and job descriptors to read live bioreactor state from bioreactor/current_volume_ml and bioreactor/alt_media_fraction, and to stop exposing the hidden duplicate dosing-automation volume settings. The app update also refreshes the deployed YAML descriptors automatically on leaders.

  • Removed the legacy dosing-automation MQTT settings/topic surface for bioreactor values. current_volume_ml, max_working_volume_ml, and alt_media_fraction are no longer published as dosing_automation settings or exposed as dosing-automation capability flags. Use the retained bioreactor topics and APIs instead:

    pioreactor/<unit>/<experiment>/bioreactor/current_volume_ml
pioreactor/<unit>/<experiment>/bioreactor/max_working_volume_ml
pioreactor/<unit>/<experiment>/bioreactor/alt_media_fraction

Bug fixes

  • Fixed a UI crash when MQTT button_down events triggered tactile-button notifications.
  • Fix plugins not being loaded correctly in the background task worker. This affected mostly plugin-sourced calibrations.
  • Added a <System> experiment option in Export Data and mapped it to "$experiment" so users can export system logs from the UI.
  • Fixed calibration session resume so reopening a saved protocol session returns to the current step instead of accidentally starting the protocol from the beginning again.
  • Fix leaking of self-test logs into the experiment.

26.2.26

Bug fixes

  • pio update app now always schedules systemctl restart pioreactor-web.target after a successful default release-asset update, matching other update paths.
  • Actually ship the HAT_PRESENT change from last time
  • OD reading now correctly uses the smoothing penalizer.
  • pio status now handles unassigned experiments and other local check failures gracefully, leaving unassigned experiments blank and avoiding early aborts.
  • fix self-test "Reference photodiode is correct magnitude" for v1.5s
  • Updated the REF-position self-test logic:
    • Previously, it compared normalized variances over a time series.
    • Now, it directly compares stirring ON/OFF deltas from controlled snapshots, aligned with the core idea: stirring should not materially change REF, while SIGNAL channels should respond.

Breaking changes

  • ADCReader.tune_adc was renamed to ADCReader.tune_adc_with_ir_on to make the LED-on precondition explicit.

26.2.23

Enhancements

  • Added pios jobs list and pios jobs list running to inspect worker job history and running jobs from the leader CLI.
  • Added --config-override <section> <param> <value> to pios run to temporarily override config values when launching worker jobs.
  • Added GET /unit_api/jobs for per-unit job history (ordered by newest first), complementing the existing GET /unit_api/jobs/running endpoint.
  • Updated pio cache view to accept an optional key filter: pio cache view <cache> <key> now returns only that key when provided.
  • Added pio update --sha <commit> (and pio update app --sha <commit>) to install from a specific git commit.
  • Added a new calibration coverage matrix page in the UI (linked from Calibrations) to show cluster-wide per-unit/per-device coverage and quick actions: open active calibration details, view available calibrations for a device, or create missing calibrations via /protocols/<unit>/<device>.
  • Added card-level quick controls to both /pioreactors and /pioreactor/<unit>: clicking an activity state now runs contextual actions (start, stop, pause, resume), and shows an in-place spinner until MQTT reports the expected state transition.
  • Added inline quick-edit popovers for card settings values.
  • Improved the UI's "Assign Pioreactors" dialog: units already assigned to another experiment can now be selected for reassignment, and "Select all" now applies consistently to all listed units.
  • Automation advanced config now discovers and displays both [<x>_automation.config] and per-automation sections like [<x>_automation.<automation_name>], enabling section-specific overrides from the UI.

Breaking changes

  • Changed Turbidostat biomass signal behavior:
    • Default behavior is now biomass_signal=auto, with selection order:
      1. active od_fused estimator
      2. active OD calibration for the configured angle (od)
      3. normalized OD
    • You can still explicitly override biomass_signal in config (including via profiles).
    • Moved config from [turbidostat.config] to [dosing_automation.turbidostat].
    • Update scripts migrate existing values from the legacy section/key when present.
  • Renamed pio cache clear to pio cache purge.
  • Renamed /api/is_local_access_point_active to /api/local_access_point (now returns {active: <bool>}).
  • Consolidated experiment profile routes:
    • Kept /api/experiment_profiles and /api/experiments/<experiment>/experiment_profiles/*.
    • Removed /api/contrib/experiment_profiles and /api/experiment_profiles/running/experiments/<experiment>.
    • PATCH now targets /api/experiment_profiles/<filename>.
  • Consolidated config API routes under /api/config/*:
    • /api/units/<pioreactor_unit>/configuration is now /api/config/units/<pioreactor_unit>.
    • /api/configs + /api/configs/<filename> + /api/configs/<filename>/history are now /api/config/files + /api/config/files/<filename> + /api/config/files/<filename>/history.
  • Removed /api/contrib/* endpoints in favor of resource-scoped routes: /api/automations/descriptors/<automation_type>, /api/jobs/descriptors, /api/charts/descriptors, and /api/datasets/exportable*.
  • Renamed pio jobs remove to pio jobs purge.
  • Replaced pio jobs running with pio jobs list running (list running is now a running-only filter of pio jobs list output).

Bug fixes

  • Fixed usage of the duration_between_led_off_and_od_reading config.
  • OD reading now uses a trimmed-mean + prior smoother on ADS1114-based units (v1.5s), while keeping sinusoidal regression on non-ADS1114 units where AC hum is present. This also skips unnecessary AC frequency detection on ADS1114 channels.
  • Simplified ADS1114 reads in pioreactor.utils.adcs to use continuous conversion mode, replacing per-sample config-write + ready-poll cycles with paced conversion-register reads. This reduces I2C traffic and lowers cross-process bus contention risk on ADS1114-based units.
  • Fixed /api/config/units/$broadcast to correctly merge each unit's own config_<unit>.ini instead of using a shared (and wrong) config_$broadcast.ini path.
  • Bumped rpi_hardware_pwm to avoid a race condition setting up PWMs.
  • Fixed calibration detail pages so Set active / Set inactive waits for backend task completion before refetching, preventing stale "Set active" and missing "Active" status until manual refresh.
  • Made IR reference-noise gating in OD reading scale with the configured reading interval (baseline std <= 0.01 at 5.0s), including when the interval is changed at runtime.
  • Fixed Inventory model updates and active/inactive toggles to show success only after confirmed backend 2xx responses, with explicit error feedback on failure.
  • Fixed an issue where changing RPM while stirring was paused would restart stirring.
  • self_test now cleans up better when interrupted.
  • CLI change gives plugin-registered commands precedence, enabling intentional overrides to existing pio run commands.
  • Fixed UI bugs on the Configuration page
  • Fixed HAT_PRESENT not being respected in the UI flow.
  • PWMs clean up better, and display a warning if something looks wrong.

26.2.3

Enhancements

  • removed System tab from the Pioreactor's "Control" dialog. You can see (most) of this data on the Inventory page
  • added a Self-test tab back to the Pioreactor's "Control" dialog, and to the "Control all Pioreactors"
  • added pio status for a quick local health summary (identity, versions, MQTT, web API, Huey, jobs, storage)
  • improved pio db, pio cache, and pio log help output with clearer descriptions and examples
  • improved pio workers status to use unit API health checks for reachability and provide brief reasons when state/version are unknown
  • improved pios help output with clearer descriptions and examples for cluster actions
  • removed the redundant --job flag from pios kill (use --job-name)

Bug fixes

  • reused cached IR LED reference normalization per experiment when ref_normalization=unity, instead of always taking the first reading
  • improved unit API retry safety by returning in-progress responses when Huey task locks are held
  • improved API error messages with structured causes and remediation hints for agents and UI clients
  • fixed pio run command resolution to load plugins before looking up job commands

26.1.30

Highlights

  • Run calibrations from the UI.
  • New Protocols page with guided calibration sessions, step-by-step instructions, and live charts.

Enhancements

  • Support for Pioreactor XR.
  • Faster Stop commands in the UI, plugin listing, and data exports.
  • Added dosing start/stop events to dosing_automation_events, including exports.
  • Added unit-relative IR LED reference normalization for OD readings via ref_normalization=unity. This should align different Pioreactors to similar starting values, especially v1.5 models. However, this changes OD levels, so existing OD calibrations are not adjusted automatically.
  • New query pattern for faster Experiment Overview chart loading; large datasets may show randomized sampling in time series. Let us know if this is too distracting. Max point targets per series increased to 1400.
  • OD calibrations now support multiple photodiode angles; pio calibrations run --device od can emit per-angle calibrations for 45/90/135.
    • Added an update helper to migrate legacy OD calibrations into per-angle devices.
  • Calibration protocols are now exposed via API.
  • When a Pioreactor model is changed, a (non-blocking) hardware check is performed.
  • You can now restart the web server (lighttpd) and the background task queue, Huey, from the UI. Go to Leader -> "Long-running jobs", and see the "web server and queue" line.
  • Added spline and akima curve support for calibrations, including OD standards sessions and calibration charts.
  • pio calibrations analyze now supports --fit poly|spline|akima. You can use this to refit a dataset to a spline or akima curve.
  • Added estimator artifacts alongside calibrations, including OD fusion estimators stored under storage/estimators and managed via the calibration session flow. Estimators are a generalized calibration for more complex algorithms. Calibrations will be restricted to 1D models.
  • New unit APIs for estimators:
    • /unit_api/estimators/<device>
    • /unit_api/estimators/<device>/<estimator_name>
  • Faster startup and shutdown of Pioreactor jobs.
  • Charts on Experiment Overview now scale with window size.
  • New Estimators page in the UI.

Breaking changes

  • Moved Self-test to the Inventory page. Pioreactors no longer need to be assigned to an experiment to run self-test.
  • Removed /api/workers/<pioreactor_unit>/configuration; use /api/units/<pioreactor_unit>/configuration.
  • Self-test logs are now part of $experiment.
  • Calibration flow modules were merged into protocol modules; old import paths like pioreactor.calibrations.pump_calibration and pioreactor.calibrations.od_calibration_* are removed.
  • Removed experimental pump-detection failure handling from chemostat and turbidostat.
  • OD calibration devices are now per-angle (od45, od90, od135) instead of just od. Physically, this changes the calibration directory in ~/.pioreactor/storage/calibrations/od to ~/.pioreactor/storage/calibrations/{od45,od90,od135}. Existing od calibration files and active calibrations are migrated during the update.
  • Self-test no longer creates a stirring calibration.
  • OD reading charts in the UI previously had a sensor label next to the unit, ex: worker01-2. Now it is the corresponding angle from config.ini. Note: only the global config.ini is used, not specific unit_config.ini files.
  • New OD and stirring calibrations are now fit with a akima, and not a polynomial.
  • Calibration curve data is now serialized as tagged structs (poly/spline/akima) instead of raw lists. curve_type is removed and existing calibration files are migrated during the update.
  • Reorganized calibration protocol modules into core/pioreactor/calibrations/protocols/ and extracted a registry.py for protocol registration.
  • Removed OD calibration using a single vial.

Bug fixes

  • Fix self-test logging closing prematurely.
  • Fix floating point error at the boundary of OD calibrations.
  • Fix runtime forward-reference errors in type annotations after dropping __future__ imports.
  • Fix timeouts being too short on some UI export operations.
  • Re-save calibration files on pio calibrations analyze confirmation even when the curve is unchanged.
  • UI now logs all warnings and errors, including from the web backend.
  • Fix Mosquitto's pw.txt file.

25.12.10

Enhancements

  • Added a pio jobs command group with running, list, info, and remove subcommands to inspect and tidy job records, including published settings.

Breaking changes

  • pio job-status has been replaced by pio jobs info.
  • changed /unit_api/jobs/stop from using query params to json body.

Bug fixes

  • fix OD blank not being able to be run.
  • OD calibration now clamps out-of-range voltages to the OD values paired with the calibration’s voltage extrema, preventing inverted mappings on non-monotonic curves.
  • Images ship with DAC43608 library (missed the previous OS jump!)
  • Improvements to "Updating your model" on first boot.
  • Fix /pioreactor page crashing if a worker is inactive in the experiment.
  • Fixed clock syncing on the cluster

25.11.19

Enhancements

  • Added pio job-status for a quick view of running jobs.

  • Easier time syntax for experiment profiles!

    1. Use the t field to specify times using suffixes, like 15s, 1m, 2.5h
    2. In repeat blocks, every replaces repeat_every_hours, and max_time replaces max_hours. Both the same time syntax above.
    3. In when blocks, wait_until replaces condition.
    experiment_profile_name: demo_stirring_repeat

metadata:
  author: Cam Davidson-Pilon
  description: A simple profile that starts stirring, increases it every 5min, and stops when the RPM exceeds 2000.

common:
  jobs:
    stirring:
      actions:
        - type: start
          t: 0
        - type: repeat
          t: 5m
          every: 5m
          actions:
            - type: update
              t: 0.0s
              options:
                target_rpm: ${{::stirring:target_rpm + 100}}
        - type: when
          t: 0s
          wait_until: ${{::stirring:target_rpm > 2000}}
          actions:
             - type: stop
               t: 0s

    This is now the preferred way (though the old syntax isn't going away), and docs will be updated to reflect this.

Bug fixes

  • Cluster CLI commands now use click.Abort() (instead of bare sys.exit) so failed prompts, copy/install operations, and OD blanking exit cleanly with Click’s messaging.
  • Background jobs now only clear MQTT/db cache entries for attributes that were actually set, preventing accidental removal of unset metadata.
  • Dodging jobs keep their OD-reading interval topic published even if a second OD reader attempts to start and fails, so dodging continues uninterrupted.
  • Fix pios update ... breaking the web server from starting. (pio update is fine)

25.11.12

Highlights

  • Added support for Pioreactor v1.5.
  • Upgrade to Trixie Debian 13!
  • New Pioreactor architecture:
    • New environment variable file /etc/pioreactor.env
    • The old pioreactorui Python package is now part of the pioreactor Python package, under pioreactor.web
    • Moved temporary files from /tmp to /run/pioreactor/
    • New pioreactor-web.service to handle both huey.service and lighttpd.service

Enhancements

  • pioreactor.hardware: reworked GPIO, PWM, and I2C configuration to load from layered YAML mods so new HAT+model combinations can be described without code changes. See new ~/.pioreactor/hardware directories.
  • pioreactor.hardware: constants are now resolved lazily through accessor functions (e.g., determine_gpiochip(), get_pwm_to_pin_map()); direct module constants remain but are deprecated shims that emit warnings.
  • Export images (PNGs and SVGs) of the Overview's and Calibrations' charts.
  • MCP server: added tools for creating experiments and managing worker assignments.
  • Show and hide calibration curves in Calibrations page by clicking the dot beside the calibration (similar to the Overview page).
  • Adding pio workers update-model <unit> -m <name> -v <version> to leader's CLI.
  • Added time-window and time-format options to the individual Pioreactors pages.
  • New workflow to set your Pioreactor leader-worker model on first load of the UI.
  • Add new APIs and MCP tools via plugins. Example: drop the following in your ~/.pioreactor/plugins folder: 
    

    • 



-- coding: utf-8 --


from future import annotations
from pioreactor.plugin_management import get_plugins
from pioreactor.web.plugin_registry import register_mcp_tool


plugin_name = "mcp-plugins"
plugin_version = "0.1.0"
plugin_summary = "Adds convenience MCP utilities for Pioreactor plugin introspection."
plugin_author = "Cam DP"


@register_mcp_tool()
def list_installed_plugins():
"""
Return metadata for installed Pioreactor plugins registered with the system.
"""
plugins = get_plugins()
details = [
{
"name": name,
"version": plugin.version,
"summary": plugin.description,
"author": plugin.author,
} for name, plugin in plugins.items()
]
return {"plugins": details}


- New import of system files (the `~/.pioreactor` directory) into Pioreactors. This means that it's easy to "back up" a pioreactor (leader or worker), and then reupload this to a (new) pioreactor in your cluster via the import system. This is available on the Inventory page.
- support for up to four PDs.

#### Breaking changes

- Changed `start_od_reading` API. It now accepts a dict instead of args for each PD position.

### 25.9.18

- Experiment profile editor: added a searchable capabilities browser. You can now search across available jobs, automations, actions, and options directly in the editor. This should make building and editing profiles faster and reduce syntax errors.
- Experiment Overview charts: no longer hide older data on long experiments. Instead, each series is downsampled on the client to a maximum of 720 points while preserving trends, regardless of experiment length. For very large clusters this may increase initial load time — narrowing the time range or hiding unused series can help if you notice slowness.
- Eye-spy optics: initial support is included. If detected, the OD reading job can use it via the existing interfaces. Nothing changes if you don’t have this hardware connected; more documentation will follow.
- Inventory export: from the Inventory page, you can export a worker’s `~/.pioreactor` directory as a zip. The Leader page also includes an export for the leader’s `~/.pioreactor`. This is useful for backups, support, or migration. Review the archive before sharing — it may contain configuration and credentials.
- Pump scripting: `pio run pumps ...` now accepts a `sleep` step to pause between actions. Example: `pio run pumps --media 2 --sleep 1 --waste 1.5` runs media for 2 mL, waits 1 s, then runs waste for 1.5 mL. In experiment profiles, you can repeat actions by suffixing keys with `_`, for example:
```yaml
jobs:
  pumps:
    actions:
      - type: start
        options:
          media: 2
          sleep: 1
          waste: 1.5
          sleep_: 2   # repeat keys by adding underscores
          waste_: 0.5



    

  • Advanced config for automations: the UI’s “Advanced” menu (temporary config overrides at start) is now available when launching automations, not just individual jobs. The options shown come from the [<job_name>.config] section.
    • 

  • CLI: added leader-only experiment management commands — pio experiments create <NAME>, pio experiments list, and pio experiments delete <NAME>.
    • 



Bug fixes


    

  • Restored live updates in real‑time charts in the UI (regression fixed).
    • 

  • Corrected timestamps on exported dataset folders in the archive.
    • 

  • Removed cases of duplicate log lines shown in the UI.
    • 

  • MCP now correctly respects configured notification methods.
    • 

  • Fixed model selection in the “Add a new Pioreactor worker” dialog in Inventory.
    • 

  • For leader-only Pioreactors, fixed leaders not showing up in "Cluster clocks" (and likely other places)
    • 



Breaking changes


    

  • Turbidostat now enforces duration = 0.25s for its frequent checks. The UI already used this value; CLI runs will now match it for more consistent behavior.
    • 



25.8.14


Highlights


    

  • 

    Custom Bioreactor Models
Our community has been incredibly creative in adapting Pioreactor hardware and software for different vessel types. Now, you can officially add your own custom bioreactor models to the Pioreactor software!
Place your model definitions as yaml files in the new .pioreactor/models/ directory. For example:
    

    model_name: custom_100ml
model_version: "1.0"
display_name: "Custom 100 mL, v1.0"
reactor_capacity_ml: 100.0
reactor_max_fill_volume_ml: 95.0
reactor_diameter_mm: 50.0
max_temp_to_reduce_heating: 80.0
max_temp_to_disable_heating: 85.0
max_temp_to_shutdown: 90.0
    

    Example file name: custom_100ml.yaml
    

    This information is used throughout the software (including the UI) to support different shapes, sizes, and safety limits. Tell us what else you’d like supported!
    

    • 

  • 

    New MCP Server (Experimental)
You can now run an MCP server alongside your leader’s web server. It adds a new SSE-based endpoint at:
    

    http://<leader-address>/mcp/

    

    This exposes some Pioreactor tools in real time. It’s still experimental — your feedback and suggestions for additional tools/resources are welcome!
    

    • 



Enhancements


    

  • 

    Added Time Range filter to the Export Data UI page.
    

    • 

  • 

    The “Add a new Pioreactor worker” dialog now automatically scans for and lists local workers available to join your cluster.
    

    • 

  • 

    New config.ini option:
    

    [od_reading.config]
duration_between_led_off_and_od_reading = <seconds>

    

    This adjusts the pause between turning off LEDs and taking an OD snapshot.
    

    • 

  • 

    pios X --experiments <experiment> now lets you target workers by experiment from the leader CLI.
    

    • 

  • 

    More CLI options are available for jobs with settable: True published_settings.
    

    • 

  • 

    New API endpoints:
    

      

    • /unit_api/capabilities
      • 

    • /api/units/<pioreactor_name>/capabilities
These provide detailed information about what each Pioreactor can run.
      • 

    

    • 



Breaking changes


    

  • 

    API changes:
    

      

    • 

      api/units/<unit>/configuration response format updated.
      

      • 

    • 

      Settings endpoint now scoped to experiments:
      

      /api/workers/unit1/jobs/settings/job_name/stirring/experiments/<exp>

      

      • 

    • 

      Removed: /api/workers/jobs/stop/experiments/<exp>
Use: /api/workers/$broadcast/jobs/stop/experiments/<exp>
      

      • 

    • 

      Removed: /api/experiments/<experiment>/jobs/settings/job_name/<job_name>
Use: /workers/$broadcast/jobs/settings/job_name/<job_name>/experiments/<experiment>
      

      • 

    

    • 

  • 

    pio logs no longer follows by default — use -f to follow.
    

    • 

  • 

    Developers: We’ve merged our three main repositories (pioreactor, pioreactorui, pioreactorui_frontend) into a single monorepo: pioreactor. The old repos will be archived, and update code in pio.py will now point to the new repo. If you have branches on the old repos, rebase onto pioreactor. Discussion: GitHub issue #576.
    

    • 



Bug fixes


    

  • Fixed default sorting when exporting CSV.
    • 

  • Fixed crash in UI profile editor.
    • 

  • Fixed pumps not shutting down correctly if active when dosing_automation stopped.
    • 

  • Fixed cleanup issue in growth rate calculation.
    • 

  • Fixed plugins page crashing when a plugin doesn't have a homepage associated to it.
    • 



25.7.2


🔥 hot fix release


Bug fixes


    

  • Fix error when target_rpm_during_od_reading is 0 and dodging is active.
    • 

  • Fix exporting pioreactor unit labels dataset.
    • 

  • Fix LED not working when booting a fresh worker.
    • 

  • Fix for plugins that use the "dodging" behaviour. Your air-bubbler plugin probably broke - this fixes it.
    • 



25.6.25


Enhancements


    

  • We previously introduced the ability for stirring to "dodge" OD reading by turning itself off during an OD snapshot. This proved useful, but users wanted the generalized ability to modify the RPM to any value during a snapshot. For example, slow down the RPM during a snapshot, instead of stopping stirring. Another use case is to set the RPM during a snapshot to be equal to the RPM when an OD calibration was performed. We've introduced two new stirring configuration parameters, only used when dodging is active:

      

    1. target_rpm_during_od_reading: the RPM when an OD snapshot is performed.
      2. 

    2. target_rpm_outside_od_reading: the RPM outside a snapshot.
We highly recommend having a stirring calibration active while using these.
      3. 

    

    • 

  • There's a new "Advanced" start option in the UI to modify configuration temporarily when starting a job. The options shown are from the section [<job_name>.config]. This is useful for changing different configurations without changing the config files.
    • 

  • The above uses a new convention in pio run CLI command. You can provide configuration overrides with the --config-override option. Example:

    pio run --config-override od_reading.config interval 0.1 od_reading

    
or

    pio run --config-override stirring.config initial_duty_cycle 25 --config-override mqtt username pp stirring

    

    • 

  • You can even use config overrides in experiment profiles (must be applied to the start action.)

    common:
  jobs:
    od_reading:
      actions:
         - type: start
           hours_elapsed: 0.5
           config_overrides:
             samples_per_second: 0.1
             ir_led_intensity: 70
         ...
    

    • 

  • We moved our Extended Kalman Filter code out of this repo into it's own Python library: grpredict.
    • 

  • Chemostat modal in the UI now shows the computed dilution rate
    • 

  • New "Duplicate" profiles button.
    • 

  • Experimental: Adding an experimental new feature that will detect a pump malfunction by comparing the OD before and after dosing. If the post-OD falls outside some expected bound (default is 20%), the dosing is paused until a user comes to unpause it. To enable this feature, set dosing_automation.config parameter experimental_detect_pump_malfunction to True.

      

    • This only applies to the current implementations of turbidostat and chemostat in our software.
      • 

    • This feature relies on 1) Accurate initial volume (inputted when you start the automation), 2) accurate pump calibrations, 3) clear media
      • 

    

    • 

  • Calibration charts have new crosshairs
    • 

  • The config [mqtt]  broker_address can now be a list of addresses, separated by ;. Example:

    [mqtt]
broker_address=pio01.local;100.119.150.2;localhost

    

    • 

  • Performance improvements
    • 

  • Backing up database now checks if the worker and local machine have enough disk space, and skips if not.
    • 



Breaking changes


    

  • In configuration, [stirring.config] parameter target_rpm is renamed to initial_target_rpm. This is better for letting users know that the RPM can be changed during a run.
    • 

  • floats are rounded to 12 decimals points in data exports.
    • 

  • localtime in data exports have subsecond precision.
    • 

  • Changed dosing automation variables names:
    • 

  • max_volume to max_working_volume_ml (also changed in config.ini)
    • 

  • liquid_volume to current_volume_ml
    • 

  • Chemostat and Turbidostat automations stopped using volume kwarg and now use exchange_volume_ml.
    • 

  • the chart liquid_volumes is renamed current_volume_ml. This should be updated in your config.ini under [ui.overview.charts] if you are using that chary.
    • 



Bug fixes


    

  • included new export dataset yaml for raw OD readings. This was missed in a previous release.
    • 

  • experiment profiles now check the syntax of nested actions before starting the execution.
    • 



25.6.3


(hotfix patch)


Bug fixes


    

  • update Adafruit-Blinka to fix USB issue.
    • 

  • Fix for HardwarePWM on RPi5 on linux kernel 6.6
    • 



25.5.22


Enhancements


    

  • new System logs under Inventory to track logs happening outside of experiments in your cluster.
    • 

  • Better organization of logs in the UI. System logs, like calibrations, worker additions, etc. won't show up on the Overview page.
    • 

  • Exported data zips have folders for each dataset requested.
    • 

  • Improvements to the Kalman filter. For users using the growth-rate model with media dosing, you should see improvements to your growth-rate time series. We recommend the following configuration:
    • 



[growth_rate_kalman]
# obs_std ↑ smooths growth rate, rate_std ↑ more responsive growth rate
obs_std=1.5
od_std=0.0025
rate_std=0.25



Note: the acceleration term is removed


    

  • Added the column hours_since_experiment_created to dataset exports that details hours since experiment was created.
    • 

  • A running pump now fires off an incremental dosing event every N seconds (N=0.5 currently) to tell the software its progress. Previously, we would fire off a single event that represented the total amount moved. This is most noticeable when watching the vial volume change over time (looks more accurate over a short period).
    • 

  • When a pump runs, it first fires off a dosing_event, which stores information about how much liquid is moved. However, if the pump is stopped early, there was no correction issued to the amount of liquid actually moved. Now, when a pump is stopped early, a negative volume is sent s.t. the delta between the initial amount and new amount is equal to the dosed amount (so when you sum up the volume changes, you get the actual change, as expected).
    • 

  • Performance optimizations
    • 

  • New image installs only:

      

    • updated base OS to the latest 25-05-06 Raspberry Pi OS. The big change is using Linux kernel 6.12.
      • 

    

    • 



Bug fixes


    

  • fixed stir bar not spinning on Pioreactor page (UI) in some cases
    • 

  • alert user if their OD reading is constant before starting the growth-rate calculator, which would break things.
    • 

  • alert user if their software is installed in a non-standard location. If so, try pip uninstall pioreactor -y.
    • 

  • Added a warning if the OD calibration is invalid (ex: a constant line)
    • 

  • Fix for Raspberry Pi 5 using upstream Adafruit libraries.
    • 



25.5.1


Enhancements


    

  • new Upload Calibration dialog in the UI
    • 



Breaking changes


    

  • new OD calibrations are of type od600 (instead of od). Nothing needs to change for the user.
    • 



Bug fixes


    

  • stirring calibration was using too many points from the lower bound, this is fixed.
    • 

  • fix for stirring calibration in the self-test creating an empty file
    • 

  • Fix custom charts that were not fetching from the database correctly due to the backend table being a sqlite3 view (VIEWs don't have ROWID, which was breaking a filter).
    • 



25.4.11


Bug fixes


    

  • Fix for heater PCB not shutting down correctly.
    • 



25.4.9


Bug fixes


    

  • Fix OD Reading not displaying correctly on Pioreactor pages
    • 

  • Fix duplicates in Raw OD Reading chart's legend
    • 

  • Improvements to pump calibration flow that will ask user what volumes they wish to calibrate for.
    • 

  • Fix self-test "REF is correct magnitude"
    • 

  • self-tests don't use calibrated OD readings anymore.
    • 



25.4.3


Enhancements


    

  • Support for Pioreactor 40mL

      

    • UI and backend now accommodates the new Pioreactor 40mL. Change the Pioreactor model on the Inventory page.
      • 

    

    • 

  • Device models and versions now tracked in the database

      

    • Models and versions for each Pioreactor are now stored in the workers database table. We're deprecating the [pioreactor] section in config.ini. You can manage models and versions on the Inventory page.
      • 

    

    • 

  • Improvements to dosing automation settings:

      

    • When starting a dosing automation, you can set the initial and max culture volumes.
      • 

    

    • 

  • Raw vs. calibrated OD readings now separated

      

    • When a calibration is applied in the ODReading job:

        

      • New MQTT topics are published:

          

        • od_reading/raw_od1 and od_reading/raw_od2 for raw (un-calibrated) values
          • 

        • od_reading/calibrated_od1 and od_reading/calibrated_od2 for calibrated values
          • 

        

        • 

      

      • 

    • The raw readings will be stored in new database tables, raw_od_readings. The calibrated values still occupy the table od_readings.
      • 

    • Existing topics like od_reading/od1, od_reading/od2, and od_reading/ods remain unchanged, but note they may contain either calibrated or raw data depending on calibration status.
      • 

    • To display a chart of the raw OD readings when a calibration is being used, switch the config entry raw_optical_density from 0 to 1 in the section [ui.overview.charts]
      • 

    

    • 



Breaking changes


    

  • Changes to pio workers add

      

    • This command has been updated to better reflect the new model/version management.
      • 

    

    • 

  • Removed config parameter max_volume_to_stop.

      

    • This is now hardcoded into the software. For 20ml, it's 18ml, and for 40ml, it's 38ml.
      • 

    

    • 



Bug Fixes


    

  • Fixed occasional crash on the Overview page in the UI.
    • 

  • Stirring dodging now correctly respects the first OD reading.
    • 

  • Stirring (and other software PWM-based jobs) now clean up properly more often on disconnect.
    • 

  • Fixed issue where dodging background jobs would run a final, incorrect action_to_do_before_reading after OD reading stops.
    • 

  • The OD calibration flow now correctly ignores existing calibrations when creating a new one.
    • 

  • UI page /pioreactors/<some_unit> now uses that unit's specific configuration from config_<some_unit>.ini.
    • 

  • Fix error "cannot schedule new futures after shutdown" when stopping a dosing automation during a pump execution.
    • 

  • Reverted a change to job's exit protocol introduced in 25.3.5 that would cause on_disconnected to run twice sometimes.
    • 

  • Fixed "manual adjustments" pump actions not firing an MQTT event.
    • 

  • Fixed OD calibrations using the wrong min, max thresholds.
    • 

  • pio calibrations analyze --device od will use regression weights for OD calibrations (like they do during the OD calibration)
    • 



25.3.5


Enhancements


    

  • New faster ADC firmware with less noise

      

    • Upgraded ADC firmware improves signal processing speed and reduces measurement noise, leading to more reliable readings for all sensors.
      • 

    

    • 

  • led_intensity is now registered in our database

      

    • This means that running pio kill --all-jobs (and related pio kill commands) will now also turn off all LEDs, ensuring a complete shutdown of active processes.
      • 

    

    • 

  • New option in pio workers add to specify an IPv4 address

      

    • When adding a new worker, you can now explicitly provide an IPv4 address instead of relying on the default hostname.local. This is useful in networks where mDNS resolution is unreliable or unavailable. Ex: pio workers add <name> -a 192.168.0.3
      • 

    

    • 

  • New time option on the Overview page: "Now" for only real-time data

      

    • The UI now has a “Now” option that filters out historical data, displaying only real-time sensor readings and status updates.
      • 

    

    • 

  • Logs for experiment profiles now include an action step number

      

    • Each log entry related to an experiment profile now contains a step number, making it easier to track progress and diagnose issues in multi-step workflows.
      • 

    

    • 

  • Improved outlier detection in nOD and growth rates

      

    • Our outlier detection algorithms for normal optical density (nOD) and growth rates have been refined, reducing false positives and improving tracking accuracy during experiments.
      • 

    

    • 

  • Changing OD readings interval programmatically

      

    • OD Reading job now exposes interval as a editable published_setting. For example, you can PATCH to http://pioreactor.local/api/workers/<pioreactor_unit>/jobs/update/job_name/od_reading/experiments/<experiment> with body:

      {
  "settings": {
    "interval": 10
  },
}

      
to change OD readings interval to 10s.
      • 

    

    • 



Breaking Changes


    

  • id → job_id in pio_metadata_settings table

      

    • Database schema update: The primary identifier column in pio_metadata_settings has been renamed to job_id.
      • 

    

    • 

  • Changed the scaling of smoothing_penalizer

      

    • The smoothing_penalizer parameter now operates on a scale that is ~100x lower than before.
      • 

    

    • 

  • Deprecation of /unit_api/jobs/stop/... endpoint

      

    • The /unit_api/jobs/stop/... API endpoint is being deprecated in favor of using query parameters:

        

      • Instead of /unit_api/jobs/stop/job_name, use /unit_api/jobs/stop/?job_name=....
        • 

      • The special case /unit_api/jobs/stop/all remains valid and unchanged.
        • 

      

      • 

    

    • 

  • Timestamp precision change: From xxxxx milliseconds → xxx milliseconds

      

    • All timestamps will now be stored with three-digit millisecond precision instead of five. This change optimizes storage efficiency and speeds up queries while maintaining sufficient accuracy for most use cases.
      • 

    

    • 



Bug Fixes


    

  • Fix for "More" button in the Logs UI page

      

    • Previously, clicking "More" in the Logs UI would default to "Standard" log level instead of retaining the selected filter. Now, it correctly uses the log level chosen by the user.
      • 

    

    • 

  • Multiple experiment profiles no longer overwrite each other in MQTT

      

    • Previously, running multiple experiment profiles could cause MQTT messages to overwrite each other. This is now fixed, but note that the new MQTT topic format introduces job_id, deviating from our usual topic structure.
      • 

    

    • 

  • Fix for API returning incorrect responses for Huey-related tasks

      

    • API responses related to background tasks (e.g., adding a new Pioreactor, syncing configs, updating firmware) were sometimes incorrect or missing details. This has been fixed.
      • 

    

    • 

  • Correction to od_reading.config's smoothing_penalizer scaling error

      

    • A miscalculated scaling factor in od_reading.config caused the smoothing factor to be larger than intended. This has been corrected, and your config.ini file has been automatically updated to reflect the new values.
      • 

    

    • 

  • Fix for missing log events in Event Logs after worker unassignment

      

    • Some log events (such as clean-up and assignment events) were missing when they occurred after a worker was unassigned. These now appear correctly. Additionally, some unrelated log entries that were mistakenly displayed have been removed.
      • 

    

    • 

  • Scaling bug fix in the extended Kalman filter affecting nOD detection

      

    • A bug in the extended Kalman filter was causing outlier detections too frequently. In extreme cases, these detections could compound, driving nOD values negative and corrupting the filter’s internal state. This issue has been fixed with a new, more stable filtering algorithm that significantly improves robustness.
      • 

    

    • 



25.2.20


Important, any OD calibrations made on software versions 25.1.21 and 25.2.10 have incorrect metadata, and it needs to be updated. Use this hot fix release to fix them. You'll still need to rerun:


pio calibrations analyze --device od --name <cal name>



to recreate the calibration curves.


    

  • Hot fix for OD Calibrations bug.
    • 



25.2.11


Enhancements


    

  • 

    New OD Calibration: Introduced a new OD calibration using standards (requires multiple vials). Run:
    

    pio calibrations run --device od

    

    Inspired by the plugin by @odcambc.
    

    • 

  • 

    UI Improvements:
    

      

    • Improved chart colors.
      • 

    • Added the ability to choose the level of detail on the new Event Logs page.
      • 

    

    • 

  • 

    New OD Reading Option: The OD reading CLI now includes a --snapshot option to start the job, take a single reading, and exit. This is useful for scripting.
    

    • 

  • 

    New Pump Control CLI: Introduced a new CLI for pumps:
    

    pio run pumps --media 1 --waste 2

    

    This command will add 1ml of media and remove 2ml of waste. The order matters, and pumps can be specified multiple times:
    

    pio run pumps --waste 2 --media 1 --waste 2

    

    This new CLI is really useful for experiment profiles. For example, a chemostat can be "programmed" as (but don't actually do this, using a dosing automation):
    

    common:
  jobs:
    pumps:
      actions:
        - type: repeat
          hours_elapsed: 0 # start immediately
          repeat_every_hours: 0.5 # every 30m, run the following actions
          actions:
            - type: start
              hours_elapsed: 0
              options:
                media: 1
                waste: 2

    

    • 

  • 

    Experiment & System Enhancements:
    

      

    • Initial support for 40ml model.
      • 

    • Ability to run multiple experiment profiles per experiment.
      • 

    • Users can now specify which Pioreactor to update on the Updates page (available only with release archives).
      • 

    • Stirring calibration is now included as part of the self-test.
      • 

    • Improved stirring job handling when OD readings have long pauses.
      • 

    

    • 

  • 

    Previously, if a worker’s web server was down, an update would be blocked. Now, the leader will first attempt the web server, and if a 5xx error is observed, it will attempt SSH communication instead.
    

    • 





Web API Changes


    

  • Introduced:

      

    • GET /unit_api/jobs/running/<job>
      • 

    • GET /api/experiment_profiles/running/experiments/<experiment>
      • 

    

    • 





Breaking Changes


    

  • 

    Calibration Structs:
    

      

    • predict → x_to_y
      • 

    • ipredict → y_to_x
      • 

    • This change makes naming clearer.
      • 

    

    • 

  • 

    Plugin Migration (Upcoming):
    

      

    • Plugins should migrate from click_some_name to auto-discovered plugins by importing run.
      • 

    • Example migration:

      import click
from pioreactor.cli.run import run

@run.command("my_name")
@click.option("--my_option")
def my_name(my_option):
    ...
      

      • 

    

    • 

  • 

    Select workers by experiment (Upcoming):
    

      

    • Add --experiments option to pios commands to select all active workers assigned to the specified experiment(s).
      • 

    

    • 



Bug Fixes


    

  • Fixed UI not displaying third-party calibrations.
    • 

  • Experiment profiles now directly use unit_api/, potentially mitigating Huey worker stampedes when starting multiple jobs.
    • 

  • Fixed pio calibrations run ... -y not saving as active.
    • 

  • Fixed manual dosing issues in the UI.
    • 

  • Fixed manual log recording in the UI.
    • 

  • There was a race condition between monitor and a db creation job that was preventing the monitor job from starting. Awkwardly, this only seemed to happen on power cycles, and only sometimes. This escaped our testing. We've fixed it by improving how we initialize the dbs, and how we connect to them.
    • 



25.1.21


Highlights


    

  • 

    New UI updates:
    

      

    • An Event Logs page for seeing the logs generated by your Pioreactors
      • 

    • A detailed overview of your cluster's leader-specific duties on the new Leader's page.

        

      • See the Leader's filesystem, logs, update cluster clocks, and view important running jobs.
        • 

      

      • 

    • View different Pioreactors' plugins on the Plugins page, and install to specific Pioreactor vs entire cluster.
      • 

    • Manage your calibrations from the UI's new Calibrations page.

        

      • View existing calibrations, set active calibrations, and download calibration files.
        • 

      

      • 

    

    • 

  • 

    New calibrations API. A calibration now creates a YAML file as an artifact, stored in ~/.pioreactor/calibrations. This makes editing, creating, sharing, and transferring calibrations much easier.
    

    • 

  • 

    There's also a new CLI for calibrations:
    

    Usage: pio calibrations [OPTIONS] COMMAND [ARGS]...

  interface for all calibration types.

Options:
  --help  Show this message and exit.

Commands:
  delete      Delete a calibration file from local storage.
  display     Display the contents of a calibration YAML file.
  list        List existing calibrations for the given device.
  run         Run an interactive calibration assistant for a specific device.
  set-active  Mark a specific calibration as 'active' for that device
  analyze     Analyze the data from a calibration.

    

    For example, to run a pump calibration, use pio calibrations run --device media_pump. View all your media pump calibrations with:  pio calibrations list --device media_pump.
    

    • 

  • 

    For now, the actual calibrations are the same protocol as before, but in the near future, we'll be updating them with new features. Adding this unified CLI and YAML format was the first step.
    

    • 



Web API changes


    

  • New API to retrieve and set clocks on Pioreactors

      

    • GET /api/units/<pioreactor_unit>/system/utc_clock
      • 

    • GET /unit_api/system/utc_clock
      • 

    • POST /api/system/utc_clock
      • 

    • POST /unit_api/system/utc_clock
      • 

    

    • 

  • New log APIs

      

    • GET /api/experiments/<experiment>/recent_logs
      • 

    • GET /api/experiments/<experiment>/logs
      • 

    • GET /api/logs
      • 

    • GET /api/workers/<pioreactor_unit>/experiments/<experiment>/recent_logs
      • 

    • GET /api/workers/<pioreactor_unit>/experiments/<experiment>/logs
      • 

    • GET /api/units/<pioreactor_unit>/logs
      • 

    • POST /workers/<pioreactor_unit>/experiments/<experiment>/logs
      • 

    

    • 

  • New calibrations APIs

      

    • GET /api/workers/<pioreactor_unit>/calibrations
      • 

    • GET /unit_api/calibrations
      • 

    • GET /unit_api/active_calibrations
      • 

    • GET /api/workers/<pioreactor_unit>/calibrations/<device>
      • 

    • GET /unit_api/calibrations/<device>
      • 

    • PATCH /api/workers/<pioreactor_unit>/active_calibrations/<device>/<cal_name>
      • 

    • PATCH /unit_api/active_calibrations/<device>/<cal_name>
      • 

    • DELETE /api/workers/<pioreactor_unit>/active_calibrations/<device>/<cal_name>
      • 

    • DELETE /api/workers/<pioreactor_unit>/calibrations/<device>/<cal_name>
      • 

    • DELETE /unit_api/active_calibrations/<device>/<cal_name>
      • 

    • DELETE /unit_api/calibrations/<device>/<cal_name>
      • 

    • POST /unit_api/calibrations/<device>
      • 

    

    • 

  • New API for plugins

      

    • GET /api/units/<pioreactor_unit>/plugins/installed
      • 

    • PATCH /api/units/<pioreactor_unit>/plugins/install
      • 

    • PATCH /api/units/<pioreactor_unit>/plugins/uninstall
      • 

    

    • 

  • Changed the settings API (see docs).
    • 

  • New /api/units that returns a list of units (this is workers & leader). If leader is also a worker, then it's identical to /api/workers
    • 

  • New /api/experiments/<experiment>/historical_worker_assignments that stores historical assignments to experiments
    • 

  • New Path API for getting the dir structure of ~/.pioreactor:

      

    • /unit_api/system/path/<path>
      • 

    

    • 



Enhancements


    

  • new SQL table for historical_experiment_assignments that stores historical assignments to experiments.
    • 

  • UI performance improvements
    • 

  • Better terminal plots
    • 

  • Customs charts in the UI are now downsampled like the other charts.
    • 

  • More logging in experiment profiles
    • 



Breaking changes


    

  • 

    use_calibration under od_reading.config is deprecated. Use the calibrations "active" state instead.
    

    • 

  • 

    Note: by default, all calibrations are not active, even if they were "current" before. You must set them to be active.
    

    • 

  • 

    removed Python library diskcache.
    

    • 

  • 

    any stirring calibrations needs to be redone. On the command line, run pio calibrations run --device stirring to start the calibration assistant.
    

    • 

  • 

    fixed typo utils.local_persistant_storage to utils.local_persistent_storage.
    

    • 

  • 

    Kalman Filter database table is no longer populated. There is a way to re-add it, lmk.
    

    • 

  • 

    moved intermittent cache location to /tmp/pioreactor_cache/local_intermittent_pioreactor_metadata.sqlite. This also determined by your configuration, see [storage].
    

    • 

  • 

    removed pioreactor.utils.gpio_helpers
    

    • 

  • 

    removed calibrations export dataset. Use the export option on the /Calibrations page instead.
    

    • 

  • 

    persistent storage is now on single sqlite3 database in /home/pioreactor/.pioreactor/storage/local_persistent_pioreactor_metadata.sqlite. This is configurable in your configuration.
    

    • 

  • 

    When checking for calibrations in custom Dosing automations, users may have added:
    

       with local_persistant_storage("current_pump_calibration") as cache:
       if "media" not in cache:
       ...
    

    This should be updated to (Note the spelling in local_persistant_storage changed, too!):
    

        with local_persistent_storage("active_calibrations") as cache:
        if "media_pump" not in cache:
        ...
    

    • 



Bug fixes


    

  • Fix PWM3 not cleaning up correctly
    • 

  • Fixed Stirring not updating to best DC % when using a calibration after changing target RPM
    • 

  • Fixed a bug that could cause OD calibrations to map a small voltage value to a max OD.
    • 

  • Fixed bug where dataset exports were not sorted correctly.
    • 

  • em-dashes are now replaced in config.ini on save.
    • 

  • Fixed a bug where errors on the Experiment Profiles page weren't properly displayed.
    • 



24.12.10


    

  • Hotfix for UI settings bug
    • 



24.12.5


Highlights


    

  • New export datasets improvements!

      

    • new export dataset API. The datasets on the Export Data UI page are now provided via YAML files on the leader's disk. This makes it easy to add new datasets to that UI to be exported. These YAML files can be added to ~/.pioreactor/exportable_datasets.
      • 

    • new Export Data page in the UI. Preview datasets before you export them, and new partition options for the exported CSVs.
      • 

    • Plugins can now add datasets to the Export Data page. The plugin's datasets are automatically added to the Export Data page when installed.
      • 

    

    • 

  • Stirring can now pause itself during an OD reading. This is accomplished by "dodging OD readings". You can activate this feature by setting the enable_dodging_od to True in config.ini, under [stirring.config]. The replaces an older, less reliable plugin that was on our forums. Users have wanted this feature to have a very fast RPM between OD measurements (to get more aeration), and avoid noisy OD measurements. There's no reason to believe this will decrease the noise if using a "moderate" RPM though.
    • 



Enhancements


    

  • improvements to Dodging background job code, including the ability to initialize the class based on dodging or not.
    • 

  • better error handling for failed OD blank action.
    • 

  • better button state management in the UI.
    • 

  • a job YAMLs' published_settings can have a new field, editable (bool), which controls whether it shows up on the Settings dialog or not. (False means it won't show up since it's not editable!). Default is true. This should align with the published_setting in Python's job classes.
    • 

  • you can add IPv4 addresses to the (new) [cluster.addresses] section to specify IPs for pioreactors. Example:

    [cluster.addresses]
pio01=10.42.0.2
pio02=10.42.0.3


    
Note that the leader's address is automatically added in our software.
    • 

  • new installs only: updated RPiOS to version 2024-11-19
    • 

  • improvements to correlation self-tests
    • 



Bug fixes


    

  • Fixed "circulate X" actions in the Manage All dialog in the UI.
    • 



Breaking changes


    

  • moved all the temporary caches, which previously where their own sqlite3 dbs in /tmp/ to /tmp/local_intermittent_pioreactor_metadata.sqlite. This shouldn't break anything unless you update during an experiment - don't do that!
    • 



24.10.29


Enhancements


    

  • dosing_automation.vial_volume replaced with dosing_automation.liquid_volume. You can see the values by watching pio mqtt -t "pioreactor/+/+/dosing_automation/liquid_volume"  after starting a dosing automation.
    • 

  • Adding a SQL table for tracking liquid_volume.
    • 

  • Because we are now storing liquid_volume in the database, you can add charts in the UI that track the volume over time:

      

    1. Add the following yaml contents to ~/.pioreactor/plugins/ui/contrib/charts/liquid_volume.yaml: https://gist.github.com/CamDavidsonPilon/95eef30189101da69f706d02ef28d972
      2. 

    2. In your config.ini, under ui.overview.charts, add the line liquid_volume=1.
      3. 

    

    • 

  • New dataset exports from the Export data page in the UI: calibrations and liquid-volumes.
    • 

  • Added a "partition by unit" option to the Export data page that will create a csv per Pioreactor in the export, instead of grouping them all together.
    • 

  • od calibrations can use the --json-file to edit calibration polynomial coefficients. In the json file, specify curve_data_ fields with values of the curve's polynomial coefficients (leading term first), and set curve_type as "poly". The routine will begin with that calibration curve displayed.
    • 

  • faster UI response times when starting jobs.
    • 

  • faster syncing configs.
    • 

  • faster copying files across cluster via pio cp.
    • 

  • faster clean up of jobs using PWMs.
    • 

  • new installs only: updated base RPiOS to 2024-10-22.
    • 

  • new database table in /tmp/local_intermittent_pioreactor_metadata.sqlite called pio_job_published_settings that stores the published settings for each job. This powers the next API endpoints:
    • 

  • New API endpoints for getting the current settings of a running job:

      

    • Per pioreactor:

        

      • GET: /unit_api/jobs/settings/job_name/<job_name>
        • 

      • GET: /unit_api/jobs/settings/job_name/<job_name>/setting/<setting>
        • 

      

      • 

    • Across the cluster:

        

      • GET: /api/jobs/settings/job_name/<job_name>/setting/<setting>
        • 

      • GET: /api/jobs/settings/job_name/<job_name>/experiments/<experiment>
        • 

      • GET: /api/jobs/settings/job_name/<job_name>/experiments/<experiment>/setting/<setting>
        • 

      • GET: /api/jobs/settings/workers/<pioreactor_unit>/job_name/<job_name>
        • 

      • GET: /api/jobs/settings/workers/<pioreactor_unit>/job_name/<job_name>/setting/<setting>
Ex: query the temperature of a Pioreactor: curl http://pio01.local/unit_api/jobs/settings/job_name/temperature_automation/setting/temperature
        • 

      

      • 

    

    • 



Breaking changes


    

  • pio kill --name x is now pio kill --job-name x
    • 

  • removed publishing published_settings metadata to mqtt. Ex $properties, $settable, $unit, $datatype are no longer being sent mqtt. This was never used, and just a bandwidth suck.
    • 



Bug fixes


    

  • fix for OD calibration graph showing "two lines" in the terminal display
    • 

  • fix for updating over the internet when a Pioreactor is on a A.devX or B.rcY release
    • 

  • pio kill --all-jobs will no longer kill long-running jobs from plugins (specifically, logs2x jobs.)
    • 

  • updating the UI software won't prematurely stop any currently running activities
    • 

  • correct ethernet mac address on RPi5s
    • 

  • We weren't passing all the OS environment variables when jobs were started from the UI. This is fixed now.
    • 

  • Fixed circulate media / alt. media in the UI.
    • 

  • Fixed manual dosing updates in the UI.
    • 



24.10.1


Enhancements


    

  • amount of data shown on charts is now a function of the OD sampling rate
    • 

  • allow for showing more than 16 workers in a chart.
    • 



Bug fixes


    

  • Bug fix for "Manage all" that would start activities in all Pioreactors, whether they were in the experiment or not.
    • 

  • Fix for bug when clicking a legend element it not hiding
    • 

  • led_intensity (i.e. changes to LEDs) now respect whether a worker is active or not.
    • 

  • Fix bug for UI crashing with "colors" error.
    • 

  • If a worker is referenced in a profile, but is not part of the current experiment, the actions will not be schedualed for it.
    • 



24.9.26


Enhancements


    

  • UI improvements to the experiment select box.
    • 

  • Better clean up of configs when a worker is removed from the cluster.
    • 

  • Improved UI loading time
    • 



Bug fixes


    

  • only show ipv4 in UI and in avahi aliases.
    • 

  • fixed experiment profile plugin checks.
    • 

  • fixed experiment profile display crashing the UI when editing plugins section.
    • 



Breaking changes


    

  • pio clear-cache renamed to pio cache clear
    • 

  • pio view-cache renamed to pio cache view
    • 

  • some more web API changes to endpoints that manage updates
    • 

  • We no longer use monitor to start jobs. This has a slowdown when changing LEDs or starting pumps, unfortunately, but generally better performance elsewhere.
    • 

  • watchdog job has been merged with monitor. watchdog no longer exists.
    • 



24.9.19


Highlights


    

  • Workers now have a webserver on them. This is one of the largest architectural changes to Pioreactor, and lays the foundation for better plugin, version, and calibration cluster management, plus future features.

      

    • As an example, in your browser, you can enter the url: http://some-worker.local/unit_api/jobs/running to see a list of jobs running on a worker.
      • 

    • Note: there is no interactive user interface for workers, just a web API
      • 

    • Previous actions that would involve SSHing from leader to a worker are replaced by web requests.
      • 

    

    • 



Bug fixes


    

  • fixed an issue where a calibrated OD reading would be mapped to max OD signal if it was too low.
    • 

  • fixed an issue where the Pioreactor UI would lock up if trying to create a new experiment with an existing name.
    • 

  • fixed Hours Elapsed not updating in Overview
    • 



Breaking changes


    

  • Lots and lots of web API changes. You'll want to review them on our docs: https://docs.pioreactor.com/developer-guide/web-ui-api
    • 

  • We no longer recommend the Raspberry Pi Zero (the original Zero, not the Zero 2.) since supporting a web server + pioreactor functions is too much for a single core.
    • 

  • watchdog is neutered. It used to try to "wake-up" a job, but this was flaky and causing more problems than it solved.
    • 

  • removed python library dependency sh
    • 

  • APIs that initiate a background task either return with the result, or return a task id that be be looked up at /unit_api/task_status/.
    • 

  • pios update now updates the UI too.
    • 



Enhancements


    

  • Better MQTT re-connection logic.
    • 

  • New Manage Inventory menu on the Inventory page that can be used for bulk actions.
    • 

  • pio update is a new command to update both the UI and app.
    • 

  • adding more network logs to network_info.txt
    • 

  • pios commands now return quicker since they post to the workers servers and don't wait around. You can view the status of the worker's by using the output from including --json.
    • 



24.8.22


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.
    • 



24.7.18


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.
    • 



24.7.5 & 24.7.6 & 24.7.7


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


24.7.3


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.
    • 



24.6.10


Enhancements


    

  • we changed the "auto" algorithm for picking a good ir_led_intensity. We now try to maximize the intensity, up to some constraints around saturating ADCs, LED longevity, and signal. In general, we expect a higher IR intensity, but this will help with noise and detecting lower signals.
    • 

  • More improvements on the Pioreactor-specific page: added charts and a logs table.
    • 

  • Added a "retry failed tests" to the UI's self-test dialog.
    • 

  • pio run self_test has a new flag --retry-failed to only retry tests that failed in the previous run (if any).
    • 

  • better clean up when a worker is removed from a cluster.
    • 

  • reduce the mosquitto logs to reduce writes to disk and speed up connections.
    • 

  • Use lexicographical ordering for all displays of workers in the UI
    • 

  • This only applies to new installed images, and not updates. Updated to the latest RPI image, 2024-03-15, -> linux kernel update to 6.6. Recent versions of linux have improved support for usb wifi devices.
    • 

  • This only applies to new installed images, and not updates. leader-only images will install worker Python libraries.
    • 

  • This only applies to new installed images, and not updates. all experiment data will be deleted when the experiment is deleted.
    • 

  • performance improvements
    • 



Breaking changes


    

  • Changed the web backend API endpoints for time-series, logs, shutdown, reboot, and plugins to be more RESTful. See docs for updated rules in the docs.
    • 



Bug fixes


    

  • fix performing an "undo" when editing the config.ini and experiment profiles.
    • 

  • fix Pioreactor v1.1 bug when change target temperature mid cycle causing the inferred temperature to change significantly.
    • 

  • if a worker disconnected from the network, messages are queued in memory until the network reconnects. This has two problems. The first is that there is a finite amount of memory, and we don't want to OOM. The second is that when the worker(s) reconnect, there is a flurry of messages. For some jobs that use messages as events, this can cause multiple triggers in quick succession. We've added some logic that helps avoid these situations:

      

    1. we max the queue of unsent messages to 100 (arbitrary)
      2. 

    2. in important jobs, like temperature automations, it will only respond to "recent" messages and not old messages.
      3. 

    

    • 



24.5.31


Highlights


    

  • New /pioreactor/worker-name page in the UI for a detailed view of an individual Pioreactor, including a realtime visualization of the Pioreactor!
    • 



Enhancements


    

  • UI backend now supports external MQTT broker. This configuration lives in the same place as the existing MQTT settings: in the config.ini, under [mqtt].
    • 

  • Added groupings on the Experiment drop down to organize "Active" and "Inactive" experiments. An active experiment has >= 1 Pioreactor assigned to it.
    • 



Breaking changes


    

  • New log topic that partitions by the level. This should make subscribers to the log topic slimmer (like the UI, who previously would have to accept all messages and filter to what they needed). Should result in a performance increase.
    • 



Bug fixes


    

  • Fix for Pioreactors page when no workers are added to the cluster.
    • 

  • Fix for UI labels when trying to remove labels from Pioreactors.
    • 

  • Improvements to REF self-tests.
    • 



24.5.22


Enhancements


    

  • Significant performance increase by using force_turbo=1 in the Raspberry Pi. Expect a noticeable improvement in interacting with the Pioreactor. This pushes the Pi to always run "hot" (but we aren't overclocking). This does slightly increase the Pi's internal temperature, so be wary about putting the Pioreactor in very hot environment. This settings requires a reboot to take affect.
    • 

  • adding support for changing the port and protocol of the Pioreactor UI webserver in the software. Add the following to your config.ini:

    [ui]
port=80
proto=http

    
This doesn't set the port and proto, that involves changing settings in the lighttpd configuration.
    • 



Bug fixes


    

  • more sane defaults for OD reading for v1.1 when using auto.
    • 

  • fix pios plugins uninstall
    • 

  • fix leader not correctly being identified in pio workers status
    • 

  • For RPi Zero W (first gen), sometimes the load_rp2040 script was failing. A new script will retry a few times. This only applies to new images.
    • 

  • fix pio workers update-active using the wrong HTTP verb.
    • 

  • Fix using ethernet cable to connect Pioreactor to a router: a new simple ethernet nmconnection has been added, and has higher connection priority than the PioreactorLocalLink nmconnection.
    • 

  • Fix race conditions occurring between stirring and growth-rate when they were started too quickly.
    • 



Known issues


    

  • When the local access point would start on a fresh boot, the SSID would start as pioreactor, and then change to pioreactor-<leader-name> after the next reboot.
    • 



24.5.13


Enhancements


    

  • UI chart legend's will support more than 8 Pioreactors.
    • 

  • UI chart colors are consistent across charts in the Overview.
    • 

  • reduce the severity of some messages, so there will be less pop-ups in the UI.
    • 

  • UI performance improvements.

      

    • Upgraded to React 18.3.1
      • 

    • Removed unused dependencies
      • 

    

    • 

  • UI's code sections use syntax-highlighting and other nicer features for editing yaml and ini files.
    • 

  • App performance improvements

      

    • Upgrade paho-mqtt to 2.1
      • 

    • faster pio kill
      • 

    • faster job start from UI
      • 

    

    • 

  • more humane error messages.
    • 

  • updated temperature inference model.
    • 

  • added exponentiation ** to profile expressions. Ex: ${{ pio1:growth_rate_calculating:growth_rate.growth_rate ** 0.5 }}
    • 

  • added random() to profile expressions. This returns a number between 0 and 1. Ex: ${{ 25 + 25 * random() }}
    • 



Bug fixes


    

  • fix pio plugins not working on workers.
    • 

  • fix enable_dodging_od=0 for background jobs that can dodge OD.
    • 

  • fix PWM jobs not cleaning up correctly if too many jobs try to end at the same time.
    • 

  • fix pio kill not returning the correct count of jobs being killed.
    • 

  • fix older Pioreactor HATs, with the ADS1115 chip, not have the method from_voltage_to_raw_precise.
    • 

  • fix "Manage all" not sending the correct dosing command to workers.
    • 



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.
    

    

    • 

  • 

    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


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.
    • 



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.
    • 



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
    • 



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
    • 



24.2.26


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!
    • 



24.2.11


    

  • boot-up performance improvements
    • 

  • job start performance improvements
    • 

  • improved RPM calculation for lower RPMs.
    • 

  • Added buttons to the Overview UI to change common settings.
    • 



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


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. 

  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, support@pioreactor.com!
    

    3. 



    

  • 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.


24.1.12


Enhancements


    

  • optimized performance and memory consumption of experiment profiles.
    • 



Bug fixes


    

  • fix initial state of boolean switches in UI.
    • 

  • fix Raspberry Pi 5 not addressing PWMs correctly.
    • 



24.1.9


Enhancements


    

  • Initial support for RPi5! To use an RPi5, we recommend not upgrading the software, but using a fresh image install. Under the hood:

      

    • we are using a new route to load the firmware on the HATs RP2040 (using linuxgpio)
      • 

    • the hardware PWMs on the RPi5 use a different chip location. This required a new rpi_hardware_pwm release.
      • 

    

    • 

  • new ENV variable, HAT_PRESENT=1, can be set to skip is_HAT_present checks.
    • 

  • added the RPis unique MAC addresses to the Manage -> System tab on the Pioreactors page.
    • 

  • added table ir_led_intensities to be able to be exported on the Exports page.
    • 

  • added a new smoothing_penalizer config option to [od_config]. This parameter, which has default value 700, controls how much smoothing to apply to optical density measurements. This smoothing has always been applied, but now it's a config option.
    • 

  • Cleaned up some UI interactions
    • 



Breaking changes


    

  • PWM class is no longer initialized with a duty_cycle, instead:
    • 

  • PWM class must be started with start(initial_duty_cyle)
    • 

  • moved get_rpi_machine to pioreactor.version
    • 



Bug fixes



23.12.11


Enhancements


    

  • Improvements to OD calibration and pump calibrations. Both now have a -f option to provide a json file with calibration data, to skip rerunning data-gathering routines. For example: pio run pump_calibration -f pump_data.json.
    • 

  • Ability to update via our release_archives (available on the Github release page) via the UI. To turn this feature off (which is a recommended practice when you expose your UI publicly), add an empty file called DISALLOW_UI_UPLOADS to the ~/.pioreactor directory.
    • 

  • A new config option to change the max volume to dose when a larger dose volume is split. For example, if your chemostat asks to dose 1.6 ml, our internal algorithm will dose 0.75, 0.75 and 0.1 (this is to avoid overflow). The 0.75 was previously hardcoded, but is now a config max_subdose under section [dosing_automation.config] (default is still 0.75 ml).
    • 



Breaking changes


    

  • Changes to types.DosingProgram, now it requires an MQTT client. Usually this is automation.pub_client. This is to avoid a memory leak!
    • 



Bug fixes


    

  • Fixed an problem where an automation would not successfully end due to it being "blocked" by a while loop in the execute.
    • 

  • Fixed a memory leak in dosing control when the automation would pump many many times.
    • 



23.11.29


    

  • fix for exporting data from the UI
    • 



23.11.28


Breaking changes



Enhancements


    

  • Both "Target OD" and "Target nOD" displayed and editable in the UI.
    • 

  • Previously, if the LED channel was locked (most common when OD reading was running), then any changes to the LED intensity (via the UI) would be silently rejected. This is changed: we have added retry logic that will attempt to keep changing it a few more times (hopefully to avoid the lock)
    • 

  • Added some light form validation in the automations dialog in the UI.
    • 

  • New environment variable to skip loading plugins, SKIP_PLUGINS. Useful for debugging. Ex:

    SKIP_PLUGINS=1 pio run stirring

    

    • 

  • elements in the field array in automation yamls now can include a type option (numeric or string for now). Default is numeric if not specified.
    • 



Bug Fixes


    

  • Fix experiment profile validation error
    • 

  • The "Stop" button is always available now in the "Dosing" tab for "Manage all Pioreactors".
    • 

  • Fix for Ngrok remote access.
    • 

  • Fixed a race condition between starting an automation and not getting OD data in time.
    • 

  • The automation form in the UI for pid_morbidostat was missing volume, that's been added now.
    • 



23.11.18


    

  • No more waiting around for growth-rate-calculating to get to "Ready" state
    • 

  • The "Label" step in the New Experiment flow is skipped if there is only 1 active Pioreactor in the cluster.
    • 

  • Silenced the "LED is locked" warning - now it's a DEBUG level message.
    • 

  • Fixed bug that wasn't passing lists correctly  in TopicToParserToTable
    • 

  • Faster boot times.
    • 

  • Faster UI load times by gzip-ing assets.
    • 

  • Fixed a bug where a plugin would not be loaded if it's name collided with a module in the stdlib. For example, putting test.py in .pioreactor/plugins would not be loaded, since when we tried to import test, it would load the stdlib's test, not the local plugin. This has been fixed.
    • 

  • Simplify some UI elements.
    • 

  • Security improvements.
    • 

  • Reduce the default LED intensity in light_dark_cycle from 50% to 5%. This is more appropriate for sparse cultures.
    • 

  • Fixed a race condition when starting a hotspot with boot config.ini.
    • 

  • changed how is_HAT_present determine is the HAT is on the Pi. Previously, it used the i2c bus to check if the RP2040's firmware was active. This would fail if the HAT was present, but the firmware or i2c wasn't working. Now we check the EEPROM, which is a much more robust test.
    • 



23.11.08


    

  • 

    fix bug in timeout in Stirrer.block_until_rpm_is_close_to_target that wasn't using time correctly.
    

    • 

  • 

    Workers can now also be the local-access-point (aka the "router" in a network). Previously only leaders could.
    

    • 

  • 

    Experiment profiles now support a log directive with some dynamic templating:
    

       - type: log
     hours_elapsed: 0.025
     options:
       message: "{job} increasing to 800 RPM" # alerts the message: "stirring increasing to 800 RPM"

    

    See full example here.
    

    • 

  • 

    Experiment profiles now supports changing LEDs like any other job (i.e. they can use start, update and stop directives). See example here.
    

    • 

  • 

    Experiment profile clean up. I think there are less bugs!
    

    • 

  • 

    pio clear_cache now has an as_int option to look for ints - useful when clearing caches with ints as keys.
    

    • 

  • 

    fix issue where if an extra config.ini was provided in the /boot dir before a worker startup, adding the worker to a cluster would fail due to a permission issue.
    

    • 

  • 

    potential fix for RPi 3B and RPi Zeros not connecting to hotspots: change the proto to wpa in your config.ini on the Pioreactor with the local-access-point, and restart that Pioreactor. You config.ini should look like:
    

    [local_access_point]
ssid=pioreactor
passphrase=raspberry
proto=wpa

    

    Changing to WPA does weaken the security however! It's easier for unwanted users to get onto this wifi.
    

    A more robust solution is in the works for RPi 3B and Zeros.
    

    • 

  • 

    Slight change to the API initialization of ADCReader. Take a look if you were using that class.
    

    • 



23.10.23


Bookworm release!


The Raspberry Pi Foundation provides new operating system every few years (built off of Debian's work). Earlier this month, they released RPi OS Bookworm. There are lots of nice changes, but the important details for us:


    

  • New Python version
    • 

  • New GPIO libraries
    • 

  • New local-access-point improvements
    • 



We strongly recommend you upgrade to this release. However, upgrading to this new operating system requires a full SD rewrite. See steps below on how to preserve and transfer your data.


Optimizations


With some other optimizations, we have significantly improved the performance and responsiveness of the Pioreactor software. You should notice things will feel snappier! For example, the command-line responsiveness is about 33% faster, which means actions from the the UI will start faster. Because of this new performance, we can even squeeze some more data into our algorithms and get improved accuracy.


Along with Python being faster, our database is also faster now => faster inserts, UI graphs, and data exports.


Export and import your existing data into a new image


Note: you don't need to do this. This is only if you want to move existing data to the new Pioreactor.


See instructions here.


Full Changelog


    

  • Replaced RPi.GPIO with lgpio
    • 

  • Python 3.9 is replaced by 3.11
    • 

  • Ability to choose the x-axis scale in the UI Overview: clock time, or elapsed time. Use (or add) time_display_mode under section [ui.overview.settings], with values clock_time or hours respectively.
    • 

  • Fixed bug that was not clearing OD blanks from the UI
    • 

  • dropped RaspAP for a native solution. The native solution is much simpler, and should show up faster than our RaspAP solution.
    • 

  • If your leader Raspberry Pi has an ethernet port, you can connect this into an internet-accessible router and give your cluster access to the internet!
    • 

  • Updated lots of our Python dependencies
    • 

  • Improved start up time by hiding dependencies
    • 

  • Added database table to track experiment profile starts.
    • 



23.10.12


Bug fixes


    

  • Web server was crashing on start! Solution was to upgrade flask.
    • 



23.10.10


Bug fixes


    

  • Fix bug that wasn't allowing for manual dosing / LED updates.
    • 

  • Fix bug that was disconnecting workers with using "stop all activity" in the UI when pumps were running.
    • 



Enhancements


    

  • pios update now has a --source parameter.
    • 



23.10.5


Bug fixes


    

  • Fix an OD calibration bug that would produce an extremely high value when the signal was below the minimum signal (the blank) during OD calibration.
    • 

  • IPv4 is really IPv4 now.
    • 



Enhancements


    

  • Adding ability to install plugins by name via the UI.
    • 

  • New tools to update Pioreactors on a local access point. More docs coming soon!
    • 

  • New turbidostat_targeting_od dosing automation. This is just like the existing turbidostat, but
targets the raw OD instead of normalized OD. This is most useful post-OD calibration.
    • 

  • In the UI, the dosing automation "Turbidostat" has been renamed "Turbidostat Targeting nOD"
    • 



23.9.20


The previous change:




    

  • Base automations now subclass from pioreactor.automations.BaseAutomationJob. You may need to change custom automation imports from, for example, from pioreactor.automations import DosingAutomationJobContrib to from pioreactor.automations.dosing.base import DosingAutomationJobContrib
    • 





had an import error that we didn't see in testing. We changed this to:


    

  • Base automations now subclass from pioreactor.automations.base.AutomationJob.
    • 

  • Fix bug on /updates page.
    • 



23.9.19


    

  • When installing plugins, any leader-only commands would not be run. This is fixed.
    • 

  • Base automations now subclass from pioreactor.automations.BaseAutomationJob. You may need to change custom automation imports from, for example, from pioreactor.automations import DosingAutomationJobContrib to from pioreactor.automations.dosing.base import DosingAutomationJobContrib
    • 

  • Fixed bug that ignored .yml files in the UI.
    • 

  • Improvements to experiment profiles, both in the UI and in the backend. Executing now verifies common mistakes in experiment profiles before it runs.
    • 

  • Fixed a bug that could cause controllers to have a disconnected automation. #422
    • 

  • SPI is on by default on all new image installs
    • 

  • Plugin author information is presented on the /plugins page in the UI.
    • 



23.8.29


    

  • Pioreactor's IPv4 and hostname is now displayed under System in the UI.
    • 

  • In configuration, renamed section dosing_automation to dosing_automation.config (only applies to new installs). It's recommended for existing users to make this change, too.
    • 

  • new safety check that will stop automated dosing if vial liquid volume is above 18ml during dosing. This can be changed with max_volume_to_stop under [dosing_automation.config]
    • 

  • New configuration option waste_removal_multiplier to run the waste pump for a different multiplier (default 2), under [dosing_automation.config]
    • 

  • A warning will appear if the reference PD is measuring too much noise.
    • 

  • added another self-test test to confirm that an aturbid liquid in vial will produce a near 0 signal.
    • 

  • general improvements to self-test
    • 

  • New CLI command: pio clear-cache <cache> <key> to remove a key from a cache.
    • 

  • New CLI subcommand delete of pio run od_blank to remove the current experiment's blank values. This is also exposed in the UI.
    • 



23.7.31


    

  • Using builtin PID controller logic, instead of a 3rd party library. This shouldn't require any updates to PID code or parameters.
    • 

  • Better error handling when the PioreactorUI API can't be reached.
    • 

  • Some initial support for Basic Auth in the PioreactorUI
    • 

  • improved sensitivity of self-test test_REF_is_in_correct_position.
    • 

  • executing experiment profiles now checks for required plugins.
    • 

  • pio rm now asks for confirmation before executing.
    • 

  • Some minor noise reduction in OD reading job.
    • 

  • Plugins can be built with a flag file LEADER_ONLY to only be installed on the leader Pioreactor.
    • 

  • Stirring now pauses and restart during OD calibration. Thanks @odcambc!
    • 

  • Breaking: Light/Dark cycle LED automation uses minutes instead of hours now! Thanks @c-bun!
    • 



23.6.27


Highlights


    

  • The UI now offers a way to upgrade to the bleeding-edge Pioreactor app and UI software, called "development". This software is unstable (and fun!).
    • 



Better thermostat


    

  • Improved temperature inference accuracy.
    • 

  • After some testing, we've found that the following set of PID parameters for temperature_automation.thermostat works better¹ than the previous set of parameters:
    • 



Kp=3.0
Ki=0.0
Kd=4.5



This set now ships with all new installations of Pioreactor software. Existing users can update their parameters in the config.ini


¹ Better == less thermal runaways, less sensitive to shocks, similar overshoot and settling time.


Everything else


    

  • On startup, the Raspberry Pi will write its IP address to a text file /boot/ip. This means that if you (carefully) remove the SD card, you should be able see the IP address (hopefully it hasn't changed).
    • 

  • Fixed source in BackgroundJobContrib - thanks @odcambc!
    • 

  • pio add-pioreactor will now accept an option that is the password of the RPi being added (default: raspberry). Ex: pio add-pioreactor worker1 -p mypass
    • 

  • Improved some warning and error messages.
    • 

  • Improved watchdog detecting and fixing "lost" Pioreactors.
    • 

  • Starting to test software against Python 3.11, in anticipation of a Python 3.11 coming to Raspberry Pi OS.
    • 

  • Improvements to bash scripts to make them more robust.
    • 

  • Adding pios rm <filepath> to remove a file across the cluster.
    • 

  • Adding -r option to pio update. Example: pio update <x> -r <repo> to install from a repo (default is Pioreactor's repos).
    • 

  • structs.ODCalibration has a new schema, inferred_od600s is now od600s. See pioreactor.structs.
    • 



23.6.7


Highlights


    

  • Support for viewing, starting and stopping experiment profiles in the UI!
    • 

  • Adding manual dosing adjustment form under Dosing tab in the UI!
    • 



Everything else


    

  • New API for experiment profiles: pio run experiment_profile, with subcommands execute and verify. So what use to be pio run execute_experiment_profile <filename> is now: pio run experiment_profile execute <filename>. The verify subcommand is for checking the yaml file for errors.
    • 

  • new leader CLI command: pios cp <filepath> will move a file on your leader to the entire cluster. This is useful for distributing plugins and Python wheels across your workers.
    • 

  • plugins can now add post_install.sh and pre_uninstall.sh bash scripts.
    • 

  • added [stirring] option duration_between_updates_seconds to config, default is 23.0.
    • 

  • PIDMorbidostat has a configuration parameter [dosing_automation.pid_morbidostat].minimum_dosing_volume_ml (default 0.1). If a calculated volume to be dosed is less than this parameter, then it's set to 0.0 instead.
    • 

  • adding --manually flag to pump actions, ex: pio run add_media --ml 1 --manually. This doesn't run the pump, but still fires a dosing event, which downstream jobs listen to (ex: saves to database, will update metrics). See next change:
    • 



23.5.16


    

  • UX improvements to pio run pump_calibration
    • 

  • monitor is more robust, so as to give users better access to information instead of hard-failing.
    • 

  • monitor now checks for access to web service
    • 

  • monitor now checks the voltage on the PWM rail and will alert if falls to much. If not using the an AUX power supply, this is directly tied to the RPi's power supply.
    • 

  • monitor also publishes the read voltage as a published setting. This is available in the /pioreactor card under System in the UI.
    • 

  • sqlite3worker is now vendored in the core app. This means we can publish on PyPI.
    • 

  • improved systemctl start up.
    • 

  • added [dosing_automation] section to config.ini (existing users will have to add this manually), with an option pause_between_subdoses_seconds to control how long to wait between sub doses (these are the smaller doses that make up a larger dose, i.e. 0.5ml + 0.5ml = 1.0ml). Default is 5 seconds
    • 



Beta feature: Pioreactor experiment profiles


Also shipping this version is early support for experiment profiles. What are they? They are "scripts" that will start, stop, pause, resume, update jobs and actions without user interaction. They are defined with a yaml file, according to the following spec (subject to change):


For examples of yaml files, see the repo: https://github.com/Pioreactor/experiment_profile_examples


To use a profile, save the yaml file to your leader Pioreactor. Run it with pio run execute_experiment_profile <path_to_yaml>. Note that killing the execute_experiment_profile will only stop execution of upcoming actions, and won't stop any jobs that have already started from the profile.


23.4.28


    

  • improved detection of under-voltage, and power supply problems.
    • 

  • pumps will halt if a MQTT disconnect occurs. This is to prevent the edge case when pumps are running on a worker, but not controllable from the UI due to an MQTT disconnect.
    • 

  • improvements to backing up the SQLite3 database.
    • 

  • improvements to self-test "Reference photodiode is correct magnitude"
    • 



Bug fixes


    

  • fix bug in pio run od_calibration list
    • 



23.4.14


    

  • pio update app will default to installing the succeeding release of Pioreactor app, which may or may not be the latest. This is to ensure that no update script is skipped.
    • 

  • Added new "Past Experiments" page
    • 

  • Fix for "Reference photodiode is correct magnitude" self-test.
    • 



23.4.4


    

  • Job growth_rate_calculating will dynamically choose initial values for its internal statistics.
    • 

  • New entry in stirring section in config.ini: use_rpm (a boolean) can be used to engage or disengage the closed loop RPM system.
    • 

  • Calibration structs change timestamp -> created_at.
    • 

  • Backend work to complete calibrations utilities:

      

    • Edits to the calibrations table in the database require a full drop and recreation.
      • 

    • New API endpoints on the webserver to store calibrations, get calibrations, set as current, etc.
      • 

    • New CLI: pio run <x>_calibration publish will publish a calibration to the webserver
      • 

    

    • 



23.3.21


    

  • Python files in plugins/ folder on leader are viewable on the /plugins page in the UI.
    • 

  • Python files in plugins/ folder on leader are uninstallable (aka deleted) on the /plugins page in the UI.
    • 

  • pio uninstall-plugin will delete Python plugins in the .pioreactor/plugins/ dir if provided the python file name, sans .py.
    • 

  • pios reboot should now work for the leader.
    • 

  • Using the Pioreactor with an ethernet connection will provide the correct ip address.
    • 



23.3.16


    

  • files in ~/.pioreactor/plugins are now loaded lexographically. Previously it was up the the filesystem.
    • 

  • Performance improvements for PioreactorUI
    • 

  • Added new indexes to the SQLite database to improve read performance. This change will only impact new installs of Pioreactor.
    • 

  • Improvements in error handling when plugins can't load.
    • 



Bug fixes


    

  • fixed bug in adding new pioreactor not passing an avahi check.
    • 



23.3.9


    

  • Removed the scaling difference between hardware versions in OD Reading.
    • 

  • Moving some Python dependencies into this repo.
    • 

  • More error handling around hardware versions
    • 

  • fix self_test.test_ambient_light_interference test failing for HAT 1.1.
    • 



23.3.2


    

  • fix bug in ending experiments not cleaning up automations properly.
    • 



23.3.1


    

  • Performance improvements
    • 

  • Python dependencies for Pioreactor UI are now handled by this project.
    • 

  • Better initialization of jobs from UI
    • 

  • Version information now presented in UI
    • 

  • More support for HAT version 1.1
    • 

  • more Linux permission updates.
    • 

  • Refactor internal pumping code. There's more flexibility that allows for solving parts of #384. Including:
    • 

  • creating cleaning scripts
    • 

  • creating cycling scripts, that also respect the rates of specific pumps vs waste (so that you don't overflow if addition rate > removal rate)
    • 

  • Namely, new functions circulate_media and circulate_alt_media are introduced that will cycle both a pump and the waste pump simultaneously. The waste pump starts first and ends second.
    • 

  • removed the dosing automation continuous cycling. It was redundant, and a leftover from an old feature.
    • 



Bug fixes


    

  • Fixed pio kill <job> to actually kill a job
    • 

  • Fix for running PID morbidostat
    • 



23.2.17


Bug fixes


    

  • Fix "End experiment" killing all jobs.
    • 

  • Fix pio view-cache not working outside the home directory.
    • 

  • Fixes for hardware HAT version 1.1.
    • 

  • led_intensity cleans itself up better.
    • 



23.2.8


Bug fixes


    

  • Fix error in growth rate calculating job that prevented it from starting.
    • 



23.2.6


New features


    

  • Watchdog job now listens for new workers that join the network and are not part of the cluster. A NOTICE message is logged and sent to the UI.
    • 

  • Initial API support for adding more pumps to the Pioreactor. See docs here.
    • 

  • Time series charts are now able to be added the the UI via contrib folders. Put a yaml file under ~/.pioreactor/plugins/ui/contrib/charts. See examples here.
    • 

  • New roll-up table available to be exported from the UI: Pioreactor unit activity data roll-up. This is a rolled-up of Pioreactor unit activity data rolled up to every minute, so it should be about one order of magnitude less data versus the original table.
    • 



API changes


    

  • Pioreactor UI has a more RESTful API, so some internal urls have changed. See full new API here. UI version >= 23.2.0 required.
    • 

  • SummableList is replaced with SummableDict
    • 

  • execute_io_action returns a dictionary now (instead of a list).
    • 

  • Config: Removed daily_growth_rate from [ui.overview.settings]
    • 

  • Config: Added implied_daily_growth_rate under [ui.overview.charts]
    • 

  • Dropped pio run-always. Jobs just use pio run now.
    • 



23.1.3


    

  • Fix dosing_events table not be populated caused by an incorrect SQLite3 trigger.
    • 

  • Running a pump continuously will produce MQTT events with new timestamps (previously it was the same timestamp.)
    • 

  • Faster loading for some pages in Pioreactor UI
    • 

  • Fix for RaspAP not turning on when requested using local_access_point file
    • 

  • Caching in Pioreactor UI is improved.
    • 

  • systemd services should boot in an even better order
    • 

  • Bug fixes
    • 

  • New 64bit images are available on the CustoPiZer release page. Default is still 32bit until more testing can be done.
    • 



23.1.2


    

  • fix pio update bugs
    • 

  • new config for [logging] section, console_log_level which control which level of logging to show on the command line (does not effect logs in the database, or disk)
    • 

  • systemd services should boot in a better order
    • 

  • the latest experiment from the database is always the most recently inserted experiment, ignoring the created_at column (i.e. we use ROWID). This is to avoid cases where users change times (or use a local access point).
    • 

  • Fixes for fraction_of_volume_that_is_alternative_media chart in the UI
    • 



23.1.1


    

  • fix pio update bugs
    • 



23.1.0


    

  • early support for HATs with Pico hardware
    • 

  • new modules pioreactor.util.adcs and pioreactor.utils.dacs to abstract DACs and ADCs.
    • 

  • pio update has a new api: pio update app <options>, pio update ui <options>.
    • 

  • added version of UI & firmware to pio version -v
    • 

  • PioreactorUI has a different way to update, rather than using git. We now version the PioreactorUI, so it's easier to know if which version is being used.
    • 

  • pio update app now has a --version option to specify a version of the Pioreactor software.
    • 

  • pio update ui now has a --version option to specify a version of the Pioreactor UI.
    • 

  • power-saving improvements
    • 

  • image size optimizations
    • 

  • simplify logging, and avoid an eventual recursion error.
    • 

  • source in logging events is now correct.
    • 

  • experiment data is no longer published to MQTT. The source of truth is the db, via the web API.
    • 

  • correctly publish alt_media_fraction to MQTT in dosing jobs
    • 

  • dosing automations now keep track of vial volume, as attribute vial_volume. This is also published to MQTT.
    • 

  • corrections to how alt_media_fraction is calculated. It no longer assumes constant vial size, which was
producing slightly incorrect results.
    • 

  • execute_io_action has been changed to add the same ratio of media and alt_media before removing liquid. This satisfies:

      

    1. If users asks to dose X, X will be dosed.
      2. 

    2. Ratio between media and alt_media is constant between remove_waste actions.
      3. 

    3. Not more than Y volume is added before liquid is removed.
The catch is that if there is a lot of volume of one being added, and only a little of another, it's possible
that accuracy of the latter one will be affected.
      4. 

    

    • 

  • users can now provide the initial ratio of media to alt_media (not yet from the UI or config.ini).
    • 

  • users can specify, in their config.ini under section bioreactor, values max_volume_ml and initial_volume_ml. The former is used to provide the stable limit of volume (i.e. the position of the outflow tube determines this). The latter is how much volume is in the bioreactor initially. This is useful for users who wish to add medias manually.
    • 



22.12.3


    

  • fix for chemostat
    • 



22.12.2


    

  • Remove some errant debugging statements
    • 

  • Reduce MQTT's load on the leader by tuning the keepalive interval to something larger (for less sensitive connections).
    • 

  • pio reboot will now work on leader, but will happen last.
    • 

  • More strict msgspec Structs
    • 

  • fix od_blank error
    • 

  • Added a last will to actions that will fire if the action disconnects ungracefully.
    • 

  • Better handling of LED flashing from error codes.
    • 



22.12.1


    

  • Support latest HAT version 1.0
    • 

  • Serial number is available under pioreactor.version.serial_number
    • 

  • Serial number is also printed with pio version -v
    • 



22.12.0


    

  • Fixed config.ini not being update in the UI.
    • 

  • Fixed bug in adding worker to cluster
    • 

  • pio add-pioreactor now returns an error signal if the addition failed.
    • 

  • remove testing data from being added to database
    • 



22.11.7


    

  • Improvements to UI
    • 

  • Fix bug in leader's firstboot.sh
    • 

  • Fix bug when temperature is changed too quickly in thermostat
    • 



22.11.6


    

  • PWM DC% changes are logged to MQTT under pioreactor/<unit>/<exp>/pwms/dc as a JSON value (similar to LED intensities).
    • 

  • The pioreactor cards in the UI display the PWM DC %.
    • 

  • user defined callbacks in ODReader have changed to be bound methods on the class (hence, you
can use self in the callback.)
    • 

  • New SQL table pwm_dcs.
    • 

  • Performance improvements to the UI
    • 

  • Adding authentication on mosquitto, the MQTT broker running on leader.
    • 



22.11.5


    

  • Replace dbm with disk-cache in core. Benefits: makes storing types easier, comparable performance to dbm, promises of process-safety and thread-safety, align all datastores to sqlite3.
    • 

  • Some caching in the UI now for common API calls.
    • 

  • Improvements to UI
    • 



22.11.4


    

  • Fixes for UI
    • 

  • Smoother transitions in UI
    • 

  • new ENV variable LOCAL_ACCESS_POINT that represents if local access point is online
    • 



22.11.3


    

  • Fix bug in UI that wasn't letting users update software
    • 

  • during pio update --app, we now check for additional files in the github release that are to be executed. This provides a path of upgrading non-Python things.
    • 

  • Improvements to PioreactorUI
    • 



22.11.2


    

  • Removing parent from BackgroundSubJob
    • 

  • Make thermostat heuristic slightly better
    • 

  • fix bug in OD Calibration
    • 

  • If the ADC has an offset (due to hardware, or ambient light), it will now be removed from all inputs before being processed in OD Readings.
    • 



22.11.1


    

  • Fix bug where users are not able to start a job.
    • 

  • Revisit pump and od calibrations. Some changes to the CLI.
    • 

  • Some improvements to stirring calibration.
    • 

  • Fix stirring calibration not responding in the UI
    • 

  • Fix uninstall plugin bug
    • 

  • Fix booleans not showing correctly in the PioreactorUI
    • 



22.10.4


    

  • removed the dbm storage pio_jobs_running. Instead, each job will write metadata about its currently running state to the (tmp) file job_metadata_<job_name>. This fixes issue #350.
    • 

  • Fixed UI issue where specific configs weren't being saved.
    • 



22.10.3


    

  • no-op release
    • 



22.10.2


    

  • no-op release
    • 



22.10.1


    

  • BackgroundJobWithDodging now looks for the config.ini section [<job_name>.config].
    • 



22.10.0


    

  • New API for adding SQL tables via plugins, and for registering MQTT -> DB parsers.
    • 

  • New topic for experiment name in MQTT: pioreactor/latest_experiment/experiment.
    • 

  • New topic for experiment timestamp in MQTT: pioreactor/latest_experiment/created_at.
    • 

  • stable renamed to thermostat
    • 

  • new callback API for pushing the HAT button down, see Monitor class.
    • 



22.9.6


    

  • improve reliability of self-test test_REF_is_in_correct_position
    • 

  • improve the early OD reading signal behaviour.
    • 

  • new API on jobs for job_name (class level now)
    • 



22.9.5


    

  • The SQL triggers were not added to the images, so pioreactor_unit_activity_data was never populated. This is fixed.
    • 

  • New web server backend. Went from js/Node to python (Flask)/lighttp.
    • 

  • Export datasets now cleans up its csvs.
    • 



22.9.4


    

  • Bug fixes
    • 



22.9.3


    

  • temperature automation silent is now only_record_temperature.
    • 

  • using new official RPi image from 2022-09-06 as a source image.
    • 

  • Bug fixes
    • 



22.9.2


    

  • added subcommands display_current, change_current, list to pump calibration
    • 

  • Pump calibration follows the same format as LED calibrations. Current calibrations can be replaced with previous.
    • 

  • Adding calibration curves to calibrations' display_current
    • 

  • pio run export_experiment_data now has an flag argument to partition csvs by unit.
    • 

  • pump calibrations are now keyed by media, waste, alt_media in storage current_pump_calibrations
    • 

  • Dosing automation have access to latest_od now.
    • 

  • Bump plotext.
    • 



22.9.1


    

  • local_ac_hz is now optional
    • 

  • maybe fix bugs for local AP
    • 

  • add retries for button detection
    • 



22.9.0


    

  • Stirring now has the ability to restart itself if it detects it has stalled.
    • 

  • od_normalization has been removed. Instead, there is a small routine od_statistics that is called by both od_blank and growth_rate_calculating. The latter also now stores the required od statistics to storage (previous it was the od_normalization job).
    • 

  • The LEDs in the pioreactor have been moved up 0.5mm.
    • 

  • Error-handling and user improvements to pump_calibration.
    • 

  • pid_turbidostat was removed, replaced with the simpler turbidostat.
    • 

  • Adding new table pioreactor_unit_activity_data that makes analysis much easier.
    • 

  • Adding new table calibrations.
    • 

  • New action od_calibration that easily allows you to add an OD600 calibration to your pioreactor. See docs: https://docs.pioreactor.com/user-guide/calibrate-od600
    • 

  • paramiko library is no longer a dependency
    • 

  • in growth_rate_calculating job, kalman_filter_outputs is now included in published_settings
    • 

  • Fix bug that wasn't saving automation events to the database.
    • 

  • new function voltage_in_aux that measures what voltage is in the AUX.
    • 

  • od_readings_raw db table renamed to od_readings
    • 

  • od_readings_raw.od_reading_v renamed to od_readings
    • 

  • Changes to structs.ODReadings and structs.ODReading
    • 

  • Changes to where job od_reading publishes data in MQTT: now .../od_reading/ods/ and .../od_reading/od/<channel>
    • 

  • Rename latest_od property in all automations to latest_normalized_od. Later we will introduce latest_od which refers to data directly from od_reading job.
    • 

  • turbidostat automation now accepts target_normalized_od instead of target_od. Likewise for pid_morbidostat.
    • 

  • new config option under od_config: use_calibration is a boolean to ask the od_reading job to use the current calibration or not.
    • 

  • PIDTurbidostat automation has been nuked completely.
    • 

  • New base background job, BackgroundJobWithDodging, that makes it easy to change an action during od reading
    • 



22.7.0


    

  • Subtle changes to how jobs disconnect and clean up. job.set_state("disconnected") won't clean up connections to loggers, MQTT, etc, but will signal to the app that it's no longer available to use.
    • 

  • In config.ini, ir_intensity -> ir_led_intensity
    • 

  • caches that keep state (like led_locks) now use absence and presence to determine state, instead of specific value in the cache.
    • 

  • network.inventory -> cluster.inventory
    • 

  • network.topology -> cluster.topology
    • 

  • sql table experiments.timestamp ->  experiments.created_at
    • 

  • sql table pioreactor_unit_labels has new column created_at
    • 

  • Added TMPDIR the env variables, which points to /tmp/
    • 

  • Aided development on Windows machines
    • 

  • Added new LED automation: light_dark_cycle. This allows for LEDs to follow a day/night cycle, at a specific LED intensity.
    • 

  • Leader now accesses other machines always using the .local TLD.
    • 

  • New config option local_ac_hz
    • 

  • New self-test routine that checks if the REF is in the correct PD channel.
    • 

  • IR REF now uses a moving average of the first few values, instead of only the initial value. This produces much more accurate normalization values.
    • 



22.6.0


    

  • You can now edit the config.ini without having to boot a Pioreactor. By adding a file called config.ini to the boot folder when the SD card is interested in a computer, the /boot/config.ini will be merged with the Pioreactor's config.ini. This is useful for changing settings before ever starting up your Pioreactor for the first time. See below.
    • 

  • config.ini is now the place where the local-access-point's SSID and passphrase are stored.
    • 

  • new pio command on leader: pio discover-workers returns a list of workers on the network (may be a superset of inventory in the config.ini)
    • 

  • new pios command on leader: pios reboot. Reboots all active workers in the cluster.
    • 

  • self-test tests run in parallel
    • 

  • Adding NOTICE log level, which will appear in the UI.
    • 

  • New schemas for kalman_filter_outputs and od_blanks tables in the db.
    • 



22.4.3


    

  • table led_events is renamed to led_change_events
    • 

  • automation events returned from execute are published to MQTT under the published setting latest_event
    • 

  • new tables led_automation_events, dosing_automation_events, temperature_automation_events
    • 

  • pioreactor.automation.events.Event renamed to pioreactor.automation.events.AutomationEvent. The have a second kwarg that accepts a dict of data (must be json-serializable).
    • 

  • new leader command pios reboot: reboot RPis on the network, optionally specific ones with --unit flag.
    • 

  • new CLI tool: pio log -m <message> which will post a message to the pioreactors logs (everywhere). Example: this is used internally after systemd finish to log to our system.
    • 



22.4.2


    

  • Added ability to add callbacks to ODReader. See add_pre_read_callback and add_post_read_callback.
    • 

  • Fix bug associated with user changes.
    • 

  • pio logs no longer uses MQTT. Also, it now prints their entire log file.
    • 

  • BETA: testing shipping with access-point capabilities. See docs.
    • 



22.4.1


    

  • Fix bug associated with user changes.
    • 



22.4.0


    

  • store more experiment metadata, like strain and media, in the database.
    • 

  • adding temporary labels of Pioreactors into the database in pioreactor_unit_labels table
    • 

  • renaming some tables, alt_media_fraction -> alt_media_fractions, ir_led_intensity -> ir_led_intensities
    • 

  • pumps now throw a CalibrationError exception if their calibration is not defined.
    • 

  • default user is no longer pi. It is now pioreactor. Any coded paths like /home/pi/ should be updated to home/pioreactor/.
    • 

  • new image metadata file added to home/pioreactor/.pioreactor/.image_metadata
    • 



22.3.0


    

  • fixed memory leak in MQTT connections
    • 

  • better clean up after a job disconnects
    • 

  • If the temperature of the heating PCB gets too high, the automation switches to Silent (previously it did not switch at all.)
    • 

  • "datatype" field in published_settings is now used to cast before being given to set_* methods.
    • 

  • Internally, the repo uses the msgspec library for complex MQTT message validation. This also introduces the pioreactor.structs module which details the structure of the messages.
    • 

  • Name change: DosingAutomation -> DosingAutomationJob, TemperatureAutomation -> TemperatureAutomationJob, LEDAutomation -> LEDAutomationJob.
    • 

  • New json-encoded datatype for changing automations over MQTT: see pioreactor.struct.Automation
    • 

  • pio run led_intensity has new API: use the flags, ex: --A 10.0, to set the intensities on different channels.
    • 

  • pioreactor.actions.led_intensity has a new API that accepts the desired state as a dict.
    • 

  • pump actions are now under pioreactor.actions.pump instead of their own files.
    • 



22.2.0


    

  • Added more error codes for the ADC, network issues, and high temperature
    • 

  • Reduce chance of running multiple growth_rate_calculating jobs
    • 

  • Custom exceptions thrown in the Python software.
    • 

  • New checks for HAT being present, and Heating PCB being present, before a job is run (if required in the job).
    • 

  • QOL improvements to stirring calibration
    • 

  • Calibrations now store the data locally, alongside the calibration results, in the local storage.
    • 

  • New API in DosingController to add custom pumps
    • 

  • Some job_names are disallowed to avoid MQTT conflicts
    • 

  • ADCReader now will estimate the local AC hertz to get a better OD reading signal.
    • 

  • Custom Python exceptions were introduced.
    • 

  • pioreactor.hardware_mappings is renamed to pioreactor.hardware
    • 

  • New is_HAT_present and is_heating_pcb_present functions
    • 

  • ErrorCodes is gone - use global variables in error_codes
    • 

  • Adding logic for 180° sensor to growth_rate_calculating
    • 

  • Pumps now have a state broadcast to MQTT, and thus can be "disconnected" over MQTT.
    • 

  • Improved the response time of stopping pumps from the web UI.
    • 



22.1.0


    

  • improved temperature-recording frequency (10m to 4m)
    • 

  • removed the PWM's DC maximum on the heating output.
    • 

  • New pioreactor.version.hardware_verion which reads from the HAT's EEPROM which version
of board is being used.
    • 

  • removed PD channels 3 & 4.
    • 

  • angle column in od_readings_raw table in database is now an integer.
    • 



21.12.0


    

  • pid_stable automation renamed to stable
    • 

  • jobs can now publish to pioreactor/<unit>/+/monitor/flicker_led_with_error_code/<error code>
to have the LED flash a specific error code.
    • 

  • fixed errors raised when not able to connect to leader's MQTT
    • 

  • improvements to error handling in monitor job.
    • 

  • replaced turn_off_leds_temporarily with the more useful and more general change_leds_intensities_temporarily
    • 

  • UX improvements to the pump_calibration action
    • 

  • improving *-Controller jobs:

      

    • automation is now a dict attribute (json in MQTT)
      • 

    • automation_name is a new published_setting, with string. This is what is read from the UI.
      • 

    • CLI has a slightly changed API to pick the automation
      • 

    

    • 

  • pio_jobs_running renamed to pio_processes_running
    • 



21.11.1


    

  • a version cut to test building images
    • 



21.11.0


    

  • too much to list
    • 



21.5.1


    

  • New plugin architecture
    • 

  • New database tables: od_reading_statistics, stirring_rates
    • 

  • New pio commands: install-plugin, uninstall-plugins
    • 

  • improvements to continous_cycle dosing automation.
    • 

  • hardware based PWM available on pins 1 & 3.
    • 



21.5.0


    

  • IR LED now turns off between OD readings. This allows other LEDs to trigger and take readings.
    • 

  • Removed leader jobs time_series_aggregating and log_aggregating
    • 

  • logs table in database has more metadata
    • 

  • New Kalman filter algorithm that includes an acceleration term
    • 

  • New database table, kalman_filter_outputs, stores the output of the internal Kalman Filter.
    • 

  • workers report back to leader additional system information including available memory and CPU usage.
    • 

  • Added new temperature control and temperature automations for this app and to the UI.
    • 

  • Added undervoltage alerts to logging
    • 

  • Added initial version of a plugin system
    • 

  • pio run-always for jobs not tied to an experiment (monitor, watchdog, etc.)
    • 

  • faster database backup sync between Pioreactors
    • 

  • Ability to measure your blank vials is available using the pio run od_blank, and in the UI under "Calibrate"
    • 

  • Smarter algorithm for displaying time series in the UI
    • 

  • Log table only shows the past 24 hours of events.
    • 



21.3.18


    

  • new dosing automation: continous_cycle. Designed for using the Pioreactor as an inline sensor.
    • 

  • stirring can now be dynamically adjusted between OD readings, for improved mixing (and hence more oxygen transfer). See settings in UI.
    • 

  • custom timezone support is added in config.ini
    • 

  • download_experiment_data is now called export_experiment_data - this has been updated on the UI as well.
    • 

  • unpausing stirring will return the rate to the previous value, not necessarily the default value.
    • 



21.3.3


    

  • fix GPIO mappings
    • 

  • fix keyboard interrupts in pump actions
    • 

  • fix race conditions in MQTT disconnects
    • 

  • fixed a bug where a job's state would change to lost when another job (of the same type) would try to start.
    • 

  • in ADCReader, changed from windowed moving average to exp. moving average to be more sensitive to recent changes in signal.
    • 

  • Growth rate calculating is a bit more robust to i) users pausing the job to inspect the vial, and ii) to changing the stirring speed.
    • 

  • mDNS alias is now configurable via the config.ini, so users could have multiple clusters without domain aliases colliding in the DNS.
    • 

  • fixed GPIO mappings for PWM Amplifiers
    • 

  • inventory in config.ini is now called cluster.inventory
    • 

  • ui.overview.rename in config.ini is now called ui.rename
    • 



21.2.4


    

  • fixed reconnect issues when leader went offline and then online
    • 

  • pausing dosing_control now pauses sub jobs dosing_automation
    • 

  • renamed _algorithm to _automation everywhere.
    • 

  • ADC measurements are now run at exact time intervals (previously there was some drift). The adc job now publishes metadata about it's recording times.
    • 

  • Improved error handling in od_reading
    • 



21.2.3


    

  • The logs table in the database now contains, by default, all the DEBUG and up logs
from all Pioreactors. It also has a new column to denote the software source of the log. A separate topic is now set up for the logging in the UI.
    • 

  • pioreactor.local is now the default URL of the PioreactorUI.
    • 

  • on Pioreactor install, a seed experiment is created so users aren't dropped into a "blank" UI.
    • 

  • pubsub.subscribe_and_callback can now filter retained messages.
    • 

  • "algorithms" is now called "automations" throughout
    • 

  • reduced the number of threads per job
    • 

  • new topic for raw ADC measurements: pioreactor/<unit>/<experiment>/adc/<channel>
    • 

  • improved MQTT QOS for important jobs
    • 



21.2.2


    

  • pios sync is now pios upgrade.
    • 

  • pio upgrade requires flags: --app and / or --ui to upgrade the PioreactorApp and PioreactorUI respectively.
    • 



21.2.1


    

  • new SQL tables: led_events, led_algorithm_settings
    • 

  • dosing_algorithm_settings has a new schema: a json blob to represent any editable settings.
    • 

  • new pio command: pio run led_intensity, ex: pio run led_intensity --channel B intensity 50
    • 

  • new pio command: pio update will update the software to the latest code on Github (later will be latest released version), and if possible, update the UI code as well.
    • 

  • new library dependency DAC43608 that supports our LED driver.
    • 

  • config.ini now has abstracted any RaspberryPi pins: we only refer to the PCB labels now in config.ini
    • 

  • pio kill can accept multiple jobs, ex: pio kill stirring od_reading
    •