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Change Log

Version 2.0.0

Major overhaul and package rebuilt from the ground. First released 27 Jun 2025.

Added

  • added tests/ written with pytest
  • added test execution with tox
  • added documentation building with Mkdocs
  • added documentation hosting with ReadTheDocs
  • added proper logging facility with Python logging module
  • [core] new core modules and features added
  • [control] added TwoTierQueue for queuing both priority and normal jobs; new Controller to relay data over a communication gap (either application-wise or network-wise) to enable remote calls; new Proxy to mimic object behavior that is on the other end of a Controller-Controller bridge
  • [datalogger] functions to trigger data streaming and recording, conversion of data sequence to Pandas dataframe, and live plotting of data
  • [device] base classes for tools of different connection modes (e.g. serial, socket)
  • [file_handler] added function to zip files, and add repository to sys.path
  • [interpreter] added interpreters to serialize data for transfer over network (i.e. JSONInterpreter)
  • [log_filters] added logging filters to selectively toggle the verbosity of individual objects
  • [notification] added notifiers to send large data/files (i.e. EmailNotifier)
  • [position] added Position class, consisting of a numpy.ndarray for 3D coordinates and a scipy.spatial.transform.Rotation for 3D rotation for better description of positioning in 3D space; added Slot that defines the available space on Deck for Labware to be placed on; BoundingVolume and BoundingBox to describe an envelope of space to avoid or stay within
  • [Make.Heat] added new HeaterMixin to augment objects with temperature control related methods
  • [Make.Mixture] added new class for magnetic stirrer TwoMag
  • [Measure.Electrical.BioLogic] added BioLogic via easy-biologic library
  • [Move] added a generic GCode that can use different variants of G-code (i.e. GRBL, Marlin)
  • [Transfer.Liquid.Pipette.Sartorius] added separate API module/class for direct implementation from manual
  • [View] added placeholder image as bytestring in .py file
  • [View] added Camera.processImage() method to allow user to define custom image processing callbacks, including detection algorithms
  • [external] added sub-package to contain required libraries written by external parties that are not installable through PyPI; credits documented in docs/ATTRIBUTIONS.md
  • [examples.control] added example implementations for Controller communication layers using FastAPI and sockets
  • [examples.gui] GUI example implementation in tkinter with only implementations for translation, liquid transfer, and vision
  • [example.sila] added XML generator for SiLA2 configuration files; refer to SiLA2 documentation for full usage of SiLA; Control-lab-ly simplifies the implementation definition step in using SiLA

Changed

  • consolidated packaging to single pyproject.toml file
  • move all requirements_*.txt files to dev/
  • change minimum Python version to 3.10 from 3.8
  • changed to core from misc sub-package to better reflect how these modules in core underpin the functionalities of Control-lab-ly
  • [core] clearer separation of scope in core modules
  • [compound] new complex tool definitions described below, containing Compound, Combined, Ensemble, and Multichannel
  • [connection] functions relating to getting the IP, port, and machine addresses
  • [factory] functions to procedurally parse config files, retrieve object classes, initialize objects, and returning tool setups in preferred form (e.g. dict, namedtuple, NameSpace, dataclass)
  • [file_handler] functions relating to file and folder creation, path resolution, and reading files
  • [logging] makes use of Python native logging module to log messages from package
  • [position] classes that define location (e.g. Well, Labware, Deck)
  • [safety] unchanged
  • [core.compound] updated paradigm of how complex tools are defined, with Compound for multiple connections, dissimilar parts; Ensemble for multiple connections, similar parts; Combined for single connection, dissimilar parts (or use mixins); Multichannel for single connection, similar parts
  • example implementation (usingCompound and mixins) can be found in Compound sub-package, and (using Ensemble and Multichannel) in Transfer.Liquid.Pump.TriContinent.tricontinent
  • [core.device] all equipment API that does read/write actions inherits from these device classes that provide methods for parsing, connecting, read/write actions, streaming; takes in user-defined templates for read/write parsing
  • [Make.Light] uses threading.Timer for timing actions (via core.device.TimedDeviceMixin), instead of running a separate thread to count time
  • [Measure.Electrical.Keithley] updated code to leverage PyMeasure library
  • [Move] support for GRBL and Marlin separated into their respective APIs, and brought up to top level of Move, as G-code can also be used for jointed robots
  • [Move.Jointed.Dobot] moved dobot API into external sub-module (see above in the 'Added' section)
  • [Transfer.Liquid] reorganized tools based on type (i.e. Pump, Pipette), then brands
  • [Transfer.Substrate] generalized GripperMixin that can be used with any translation robot, instead of just Dobot attachments

Removed

  • removed GUI as a top-level sub-package; downgraded to an example implementation using tkinter (see above in 'Added' section)
  • removed reference guide GUI window in favor of a proper documentation site (i.e. GitHub Pages, ReadTheDocs)
  • [core.factory] removed registration of imported modules to keep track of modules
  • [Measure] simplify inheritance structure by removing Programmable class
  • [Measure.Electrical] removed Keithley programs that were based on old implementation (before PyMeasure)
  • [Measure.Mechanical] removed PiezoRobotics from tool list due to inactive development and use
  • [Transfer.Liquid] removed implementations for "syringe" and peristaltic pump due lack of use
  • [Transfer.Powder] removed due to lack of use
  • [Transfer.Substrate.Dobot] removed Dobot specific implementations; prefer mixins instead (see above in 'Changed' section)
  • [View] removed detection methods in Camera due to out of scope
  • [View.Classifiers] removed due to out of scope

Version 1.3.2

Feature enhancements, bug fixes and patches. First released 24 Apr 2024.

Added

  • add new delay parameter in Keithley.programs.IV_Scan

Changed

  • fix critical bug in setting sense/source limits for KeithleyDevice
  • fix bugs in KeithleyDevice, Peltier, ForceSensor

Version 1.3.1

Feature enhancements, bug fixes and patches. First released 11 Apr 2024.

Added

  • implementation of TriContinent.pullback()
  • new Well properties and option in return list of wells by rows instead of columns

Changed

  • fix bugs in Peltier (setTemperature() and getTemperature())
  • fix bugs in Ender (setTemperature() and getTemperature())
  • fix bug in Keithley.setFunction()
  • generalise IV_Scan to take either currents or voltages

Version 1.3.0

Feature enhancements, bug fixes and patches. First released 19 Feb 2024.

Added

  • added check for poor physical connection with PiezoRoboticsDevice
  • Keithley
  • added new subclasses of KeithleyDevice: DAQ6510 and SMU2450
  • added way to read and save model name of KeithleyDevice
  • added new Keithley program for DAQ to scan multiple channels
  • new methods clearErrors(), setDisplay(), setFunction()

Changed

  • changed the way travel times are calculated for Mover tools, so that they reflect the actual physical travel times more accurately
  • changed ability to delay initialisation of TriContinent pumps until it is in a more convenient location
  • fixed few bugs with SentronProbe tool

Removed

  • removed old archived files

Version 1.2.0

Feature enhancements, bug fixes and patches. First released 22 Aug 2023.

Added

  • ForceClampSetup class
  • LoadCell class
  • Balance class (subclass of LoadCell)

Changed

  • update LEDArray to delay timing loop by 0.1s
  • fix bug with initialising PiezoRoboticsDevice
  • update getTemperature() across multiple classes to standardise output
  • Mover class
  • speed-related attributes and properties
  • add method to calculate travel time based on target speed, acceleration and deceleration
  • modify how speeds and max speeds interact with move() and safeMoveTo()
  • Cartesian class
  • setSpeed() and setSpeedFraction()
  • get max speed settings from device upon connecting
  • change calculation of movement wait times using device speed and acceleration
  • Primitiv class
  • change the class name to Grbl and Primitiv as a subclass name to retain compatibility
  • overload moveTo() and _query() methods to use jogging mode
  • modify the sequence of commands to halt movement
  • implement getAcceleration(), getCoordinates(), getMaxSpeed()
  • clear errors and setting feed rate upon establishing connection
  • Ender class
  • change the class name to Marlin and Ender as a subclass name to retain compatibility
  • added method to immediately stop movement
  • implement getAcceleration(), getCoordinates(), getMaxSpeed()
  • separate methods for setSpeed() (absolute speed in mm/s) and setSpeedFraction() (proportional speed to max speed)
  • Dobot class
  • added stop() method
  • Flir AX8 class
  • added invertPalette() method
  • added data parsing methods _decode_from_modbus() and _encode_to_modbus()
  • KeithleyDevice() class
  • added ip_address property
  • added options for _read() method
  • added readline() method
  • implement disconnect() method
  • fix bug with Keithley programs using device.run() instead of device.start()

Removed

  • Thermal class
  • removed dependency on imutils package

Versions 1.1.2 & 1.1.1

Bug fixes and patches. First released 12 Jul 2023.

Added

  • import Device classes in init files to view documentation
  • added library for GRBL status and error codes
  • add update_root_direcctory() function to Helper

Changed

  • fix bug with adding new rows into Dataframes
  • use reset_input_buffer() instead of flushInput() for pyserial.Serial objects
  • print the actual string sent to Serial devices
  • update methods in Deck, Labware, and Well to camelCase
  • update Deck.isExcluded() to apply strict inequalities when determining out-of-range coordinates
  • update LiquidMover to insert a portion of tip into rack before ejecting
  • update Spinner
  • fix bug with sending commands
  • added _query() method
  • pass verbosity to individual spinners
  • verbosity of Measure objects pass through to devices
  • update PiezoRoboticsDevice
  • initialize upon connection
  • raise errors when encountering them
  • update Mover
  • modifysetFlag() to print kwargs instead of raising error if assigned values are not boolean
  • use safe_height (if defined) instead of z-coordinate of home in safeMoveTo()
  • added getSettings() method
  • update Gantry class
  • read multiple flines in _query()
  • check that commands end with newline before sending to device
  • fix bug with changing speeds
  • update Ender
  • added getTemperature(), holdTemperature(), isAtTemperature() methods
  • modified setTemperature() to use Marlin code to wait for temperature
  • update Primitiv class
  • add getStatus() and stop() methods
  • add _get_settings() method
  • fix bug in M1Pro.setHandedness()
  • update Sartorius class
  • tip_inset_mm now an instance attribute with initialisation parameters
  • set tip_on flag to False when performing eject()

Version 1.1.0

Bug fixes and feature enhancements. First released 15 Jun 2023.

Added

  • ForceSensor - DIY force sensor (#55)
  • BioShake - orbital shaker from QInstruments (#56)
  • SentronProbe - pH meter probe from Sentron (#75)
  • Maker
  • added execute() abstract method and implemented in subclasses
  • GUI
  • Guide - documentation guide
  • MakerPanel - daptive GUI controls for Maker objects (#87)

Changed

  • M1Pro
  • fix issue with changing handedness (#86)
  • Peltier
  • rename getTemperatures() to getTemperature()
  • rename isReady() to isAtTemperature()
  • rename set_point to set_temperature
  • Ender
  • rename set_point to set_temperature
  • TriContinent
  • rename step_limit to limits
  • Refactor and reorganize GUI code
  • Refactor code in helper and factory
  • Updated documentation

Removed

  • Analyse sub-package removed
  • Control.Schedule sub-package removed
  • Unnecessary commented-out blocks of code

Version 1.0.1

Bug fixes and minor feature enhancements. First released 08 May 2023.

Added

  • LiquidMover
  • Added LiquidMover.touchTip() method to touch the pipette tip against the walls of the vessel to remove excess liquid on the outside of the tip (#62)
  • Added option to indicate the position of the first available pipette tip in LiquidMover (#61)
  • Added adaptive GUI controls for Liquid objects (#70)
  • Added option to indicate which digital IO channel to use with Dobot attachments (#53)

Changed

  • MassBalance
  • Updated to the use pd.concat() instead of pd.DataFrame.append(), which is going ot be deprecated (#63)
  • Fixed endless loop for when MassBalance tries to zero() while recording data (#60)
  • Changed the Image class and methods into functions within a module (#54)
  • Fixed the tool offset of pipette when pipette tip is attached, and accounts for the length of pipette that enters the pipette tip (#64)
  • Changed to using more precise time interval measurements by moving from time.time() to time.perf_counter() (#68)
  • Fixed discrepancy in aspirate and dispense speed for Sartorius (#73) and let speed return to a global default value (#72)
  • Updated documentation

Version 1.0.0

Major overhaul in package structure. Standardisation of methods and consolidation of common methods. First released 12 Apr 2023.

Added

  • Usage of Abstract Base Classes (ABCs) to define a base class with abstract methods that needs to be implemented through sub-classing (#31)
  • Usage of Protocols to provide an interface between different classes of objects (#30)
  • Usage of Dataclasses to store complex data
  • Usage of decorators to modify methods
  • Introduced different functions to parse the program docstring and find program parameters

Changed

  • Standardised methods and consolidated common methods
  • Added type hints (#28)
  • Moved Dobot attachments from Mover to Transfer.Substrate
  • Split GUI Panels into individual files
  • Split Dobot arms into individual files
  • Split functions/methods in misc.py into individual files.
  • Changed _flags to a public attribute flags
  • Update documentation (#27, #28, #29)

Removed

  • Unnecessary commented-out blocks of code

Version 0.0.x

(0.0.4.x) Introduced control for Peltier device and TriContinent Series C syringe pumps. First released 10 Mar 2023.\ (0.0.3.x) Minor changes to movement robot safety and pipette control. Introduced control for LED array. First released 08 Mar 2023.\ (0.0.2.x) Updates in setting up configuration files. First released 24 Feb 2023.\ (0.0.1.x) First release of Control.lab.ly distributed on 23 Feb 2023.\ (0.0.0.x) Pre-release packaging checks

Added

0.0.4

  • Added control for Peltier (#23)
  • set and get temperatures
  • hold temperatures for desired duration
  • checks if target temperature has been reached by checking power level lower than a threshold or time passed over a predefined duration, once the temperature is within tolerance
  • ability to record temperatures and timestamps
  • Added control for TriContinent and TriContinentEnsemble (#25)
  • single actions such as empty, fill, initialise, move actions, set speeds and valves, and wait
  • compound actions such as aspirate, dispense, and prime

0.0.3

  • Added safety measures for movement actions (#24)
  • In Deck, added exclusion zones when reading the layout.json file and new method is_excluded() to check if target coordinate is within the exclusion zone
  • In Mover, update isFeasible() method to check if target coordinates violates the deck's exclusion zone
  • New function set_safety() defines safety modes when starting a new session to pause for input (in "high" safety setting) and to wait for safety countdown (in "low" safety setting)
  • Make.Light.LEDArray for controlling LEDs in the photo-reactor, as well as timing the LED "on" durations (#35)

0.0.2.2

  • Added import of CompoundSetup class

0.0.2

  • Deck.at() method for directly referencing slots using either index numbers or names
  • New CompoundSetup class for common methods of Compound devices
  • New load_deck() function to load Deck after initialisation

0.0.1

  • Make
  • Multi-channel spin-coater [Arduino]
  • Measure
  • (Keithley) 2450 Source Measure Unit (SMU) Instrument
  • (PiezoRobotics) Dynamic Mechanical Analyser (DMA)
  • Precision mass balance [Arduino]
  • Move
  • (Creality) Ender-3
  • (Dobot) M1 Pro
  • (Dobot) MG400
  • Primitiv [Arduino]
  • Transfer
  • (Sartorius) rLINE® dispensing modules
  • Peristaltic pump and syringe system [Arduino]
  • View
  • (FLIR) AX8 thermal imaging camera - full functionality in development
  • Web cameras [General]
  • misc
  • Helper class for most common actions
  • create_configs: make new directory for configuration files
  • create_setup: make new directory for specific setup-related files
  • load_setup: initialise setup on import during runtime

Changed

0.0.4

  • Update documentation

0.0.3.1

  • Update documentation

0.0.3

  • Sartorius
  • made the blowout/home optional for the dispense method upon emptying the pipette
  • Update documentation

0.0.2.1

  • Changed template files for lab.create_setup()

0.0.2

  • Update documentation