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CHANGELOG.md

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Changelog

Version 0.14.0

  • Improve cli commands, in particular, list-stored and get-eds.
  • Add more parsing and typing to Machine.list_runs_in_storage and Machine.list_files (breaking change if relying on atime/mtime/ctime being floats instead of datetime objects).
  • Use setuptools_scm to write version number.

Version 0.13.0

  • Add PlateSetup.from_picklist method to generate a PlateSetup from a Kithairon PickList, if Kithairon is installed.
  • Improve ssl support for monitor.
  • Have monitor complain to matrix if it exits unexpectedly.
  • Fix compile_eds when there is no folder to compile (if, eg, something else has already compiled the EDS).

Version 0.12.0

  • Machine.block command to directly control block temperatures.
  • Certificate support for SSL, and new connection recommendations.
  • Stage lines and event spans now are now not plotted if they are outside of the selected time range / stages.
  • Step now supports repeats.
  • Stage.stepped_ramp can now take multiple data points per temperature.
  • Fix hanging connection bug.

Version 0.11.0

  • Initial support for 384-well blocks, at least in data/file reading.
  • Initial support for v2.0 EDS specification machines (eg, QS6Pro), at least in data/file reading.
  • Parsing of multicomponent data for v1 and v2 machines, and partial analysis data for v1 machines.
  • Available data is shown in experiment information.
  • Change license to EUPL-1.2.
  • Fixes for new matplotlib versions.
  • Support for Python 3.12.

Version 0.10.1

  • SSL/non-SSL autoconnection speed improvements
  • Drawer/cover annotation improvements

Version 0.10.0

  • Add annotations to plots for drawer and cover open and close events.
  • Add support for SSL / firmware 1.3.4.

Version 0.9.4

  • Fix multi-temperature plotting bug.

Version 0.9.3

  • Update dependencies, convert to pyproject.toml.
  • Fix cycle selection and direct pandas selection for normalization processes.

Version 0.9.2

  • Fix a communications bug where a packet that can cause commands to hang in certain rare situations.

Version 0.9.1

  • Minor bug fixes and dependency updates (to fix pandas errors).
  • Fixes to support Pandas 2.0.
  • Ensure that some invalid characters are not used in machine names.
  • Check for files with and without spaces on machine when loading a new experiment (in case run was started outside of qslib).
  • Parse IOError messages from the machine.

Version 0.9.0

  • Fix Stage.stepped_ramp when all temperature increments are the same, but temperatures are not.
  • Add a start_increment option to Stage.stepped_ramp for cases where the user does not want the ramp to actually start at the starting temperature, but at the first increment away from it (eg, when continuing a previous ramp).
  • Ensure that units are delta units when appropriate in protocols, regardless of whether the user entered them as delta units (eg, so "2°C" will work as a temperature step).

Version 0.8.2

  • Add check for existing, completed EDS files with same name, and option to Experiment.run to overwrite completed or working files.
  • Fix XML protocol parsing bug for increment units with non-qslib EDS files.
  • Fix stage lines in plots.
  • Improve error messages.

Version 0.8.1

  • Fix bug with BytesIO not being recognized by Experiment.save_file.

Version 0.8.0

  • Ensure that protocols don't have incorrect stage index and label information when being sent to machine.
  • MachineStatus now includes temperature information, as does the qslib machine-status CLI command.
  • Experiment.sync_from_machine can exclude tiffs, and has better logging.
  • Custom steps are now approximated in xml files, keeping them somewhat compatible with the machine's android interface.
  • Several testing and documentation improvements.
  • Python 3.11 fixes.

Version 0.7.1

  • QSLib-initiated experiments should now be partially compatible with the machine's android interface. Status, time, and the (possibly approximate) protocol should be displayed. Data and samples will likely not. Pause/resume/stop/open/close buttons on the interface should function properly.
  • Processor and plotting improvements.

Version 0.7.0

  • Protocol now has Protocol.stage, and Stage now has Stage.step, to provide convenient, 1-indexed access, such that protocol.stage[5] of is stage 5 of protocol, not stage 6.
  • Protocol now supports setting PRERUN and POSTRUN stages, as a series of SCPI commands. This allows the setting of things like idling temperatures and exposure times. It is not easily usable yet, however.
  • Experiment.change_protocol_from_now allows convenient changes to a currently-running experiment.
  • Normalization has been renamed to Processor. Plotting functions can take sequences of processors to process data. These now include:
    • Normalization as before: NormByMeanPerWell, NormByMaxPerWell
    • SubtractMeanPerWell: subtracts the mean of a particular region, applied to each well.
    • SmoothEMWMean: smooths data using Pandas' ExponentialMovingWindow.mean.
    • SmoothWindowMean: smooths data using Pandas' Rolling.mean or Window.mean.
  • Some initial implementation changes to allow repeated steps (not stages).
  • Fixes bug that prevented loading of some aborted runs.
  • Fixes monitor's recording of temperatures.
  • Experiment.all_filters uses data if it exists; Experiment.filter_strings as a convenience function alternative.
  • SCPICommand parsing improvements.
  • Protocol printing improvements.

Version 0.6.3

  • Fixes drawer check bug.

Version 0.6.2

  • Add checks for cover and drawer position after changing positions.

Version 0.6.1

Version 0.6.0

  • Improved plots, including new Experiment.plot_temperatures.
  • Comments in SCPI commands, allowing save/load of default filters in protocols
  • Licensing switched to AGPL 3.0, CLA in docs.
  • Command comment parsing, also used to store whether steps are using default filters.
  • Example notebook
  • Working parsing of Exposure commands
  • Dependency version fixes

Version 0.5.1

  • CustomStep.collect (and subclasses, including Step) is now CustomStep.collects. The collect parameter for Step can now be None, which will collect data if the step has a filter setting (ie, if you want to collect the default Protocol filters, you need to use collect=True).
  • Stage.stepped_ramp and Stage.hold_for are now safer in requiring some keyword arguments, are documented, and are more flexible.

Version 0.5.0

  • Units throughout protocols, thanks to Pint: you can now use strings like '1 hr' or '52 °C' when defining protocols.
  • Automatic connections throughout Machine and Experiment, by default.
  • Change safe titles from spaces-as-"-" to spaces-as-"_", consistent with machine.
  • Deprecated paramiko tunnel.
  • Documentation rewrite
  • Implement EDS-file (in-progress and complete) synchronization for monitor.
  • Reorganization of modules: common is no longer needed

Version 0.4.1

  • Allow setting of Experiment.sample_wells.
  • Improve plotting code.

Version 0.4.0

  • Much faster Experiment.sync_from_machine, only transferring additional log entries rather than the entire log.
  • Common plotting routines for fluorescence data.
  • More reliable monitoring.
  • More reliable connections, and testing.
  • Stage.stepped_ramp convenience function.
  • Fixes to bugs inhibiting exposure setting, and some basic implementations for this.
  • Fixes to qs-monitor for cycle counts > 999 (and other large stage / step / cycle counts).

Version 0.3.1

  • CLI improvements.
  • Fix qs-monitor and various functions when run titles have spaces in them.
  • Improve tests and typing.

Version 0.3.0

  • Add qslib CLI, with some basic utility functions.
  • Include calculation using 1.6°c/s ramp (standard mode default) in temperature protocols, initiating from 25°c. This makes experiment temperature data match reasonably well with protocol calculations. It needs to be expanded to handle different ramp rates and run modes, however.
  • Added some tests.

Version 0.2.0

  • Add internal SSH tunnel support, so that this doesn't need to be set up separately, and can be configured with parameters to Machine.
  • Fix mid-run syncing bugs related to directory creation.
  • Handle some different inputs for Protocol creation.
  • Try to handle spaces in names better; this is still a problem, howver.

Version 0.1.1

Various small improvements and bug fixes.

Version 0.1.0

Initial implementation of full communication (OK/NEXT/ERRor), Experiment files, Machine connection interface. Adaptation of QSConnectionAsync to use new communication. Move of monitor system into qslib.

Version 0.0.0 / etc

Initial version of QSConnectionAsync and other low-level portions to support rawquant and qpcr_data_updater.