Changelog

Unreleased

  • Added commands for querying and setting the status led.

  • Moved documentation hosting from Read the Docs to Codeberg Pages, built via Forgejo Actions and served at https://cge.codeberg.page/qslib/. The Read the Docs site now redirects there.

Version 0.15.2

(Generated with LLM assistance.)

Protocol fixes

  • Correct collection-filter attributes in tcprotocol.xml for hacform filter strings.

Communication fixes

  • Treat zero-byte reads as disconnects.

  • Resynchronize malformed messages at newline boundaries.

  • Bound response waits and make Python waits interruptible.

  • End log subscriptions when the connection closes.

  • Prevent response-channel backpressure from blocking the receive loop or dropping terminal responses.

  • Report response parse failures when their identifier is recoverable.

Stage identity fixes

  • Add raw stage names to RunStatus and distinguish PRERUN from POSTRUN positions.

  • Use Polars APIs for Altair stage selection.

  • Warn when collected-data stage values are nonnumeric.

Version 0.15.1

(LLM-generated descriptions below.)

Data fixes

  • Fix welldata / filter_data time columns on v1-spec EDS files. In 0.15.0 the v1 codepath was rewritten to go through filter_data_polars (which emits Datetime[ms, UTC]) and reformat back to the legacy pandas multi-index; the timestamp conversion assumed astype("int64") returned nanoseconds, so it divided by 1e9 and produced timestamps 1e6× too small (and huge negative seconds/hours). Now uses a time-unit-agnostic subtraction from the Unix epoch.

  • Add temperatures_polars_wide for callers that need the 0.14-era wide schema (timestamp as Datetime[ms, UTC], one column per (kind, zone) — sample_1..N, heatsink, cover, block_1..N). temperatures_polars itself remains long-format (the intentional 0.15 default), now also with a time column derived from timestamp.

Version 0.15.0

Robustness improvements to communication, consolidation of parsing into Rust, and a new quant/calibration data pipeline:

Communication fixes

  • Fix READY message read to handle partial TCP reads (TCP does not guarantee message boundaries).

  • Fix double newline on command send when content already has a trailing newline.

  • Fix quoted string parser to handle backslash escape sequences (\", \\, \n, \t).

  • Fix ErrorResponse parser to handle errors without brackets.

  • Fix Rust parser tag character set to include underscore (e.g. <quote_reply>).

  • Fix DRAW? returning “false” instead of “Open” by not coercing open/closed to Bool in response parser.

  • Add single-quote string support to Rust parser.

  • Extend boolean parsing to cover all server-recognized forms (yes/no, on/off, open/close).

  • Extend command name character set to include +, -, ~, < (e.g. SUBS+, FLAG-).

  • Add WARNing response type to Rust parser.

  • Add tag stack timeout to message receiver, preventing unclosed tags from absorbing all subsequent messages.

  • Send QUIT command on disconnect for clean server-side cleanup.

  • Handle auth-required gracefully in Machine.connect() with a clear error message for remote connections.

  • Handle ExclusiveAccess and AccessGiven errors as specific exception subclasses.

Data and protocol fixes

  • Fix IncrementCycle/IncrementStep defaults to match server (default=2, not 1).

  • Fix SampleTemperatures separator mismatch in multicomponent data parsing.

  • Remove overly strict temperature zone and plate type assertions.

  • Parameterize plate type in Experiment._new_xml_files instead of hardcoding 96-well.

New features

  • Consolidate Python parsing to Rust: AccessLevel, FilterSet, SCPICommand, PlateSetup all now handled in Rust; pyparsing dependency removed.

  • Add Rust quant/calibration file parsers and filterdata reconstruction from quant + calibrations (matches filterdata.xml to <0.1 error).

  • Add ROI calibration parsing and TIFF-to-quant processing pipeline (exact match to instrument output).

  • Migrate FilterDataCollection loading and timestamp-setting to Rust.

  • Dynamic zone count querying via Machine.get_zone_count() instead of hardcoded 6.

  • Expose server random key auth mechanism via Machine.generate_random_key().

  • Validate READY message capabilities on connection.

  • Make subscribe_log() actually send SUBS+ command to the server.

  • Parse MESSage timestamp structurally in LogMessage.

  • Extend Subscribe command builder with timestamp and multi-topic support.

  • Add exclusive and stealth flags to AccessLevelSet command.

Testing

  • ~226 new tests across Rust and Python, covering communication, parsing, plate setup, processors, and machine logic.

Security

  • Update rustls-webpki 0.102 → 0.103 to fix four advisories: CRL distribution-point matching (RUSTSEC-2026-0049), URI name-constraint bypass (RUSTSEC-2026-0098), wildcard name-constraint bypass (RUSTSEC-2026-0099), and reachable panic in CRL parsing (RUSTSEC-2026-0104).

  • Bump bytes to 1.11.1 (integer overflow in BytesMut::reserve, RUSTSEC-2026-0007), quinn-proto to 0.11.14 (QUIC endpoint DoS, RUSTSEC-2026-0037), and time to 0.3.47 (stack-exhaustion DoS, RUSTSEC-2026-0009).

  • Port qs-monitor from matrix-sdk 0.9 to 0.16, fixing three advisories: encrypted-event sender spoofing (RUSTSEC-2025-0041), panic in RoomMember::normalized_power_level() (RUSTSEC-2025-0065), and DoS via custom m.room.join_rules events (RUSTSEC-2025-0135).

Build

  • Vendor matrix-sdk 0.16 with #![recursion_limit = "512"] added to work around rust-lang/rust#152942 (query-depth overflow on rustc 1.94+ due to matrix-sdk’s deeply nested #[tracing::instrument] async chain picking up an extra ManuallyDrop layer).

  • qs-monitor/src/main.rs gets the same attribute to raise the trait-solver limit for Send-ness of Client::sync() when passed to tokio::spawn.

CI

  • Bump GitHub Actions past the Node.js 20 deprecation: actions/checkout v4→v6, setup-python v5→v6, upload-artifact v4→v7, download-artifact v4→v8, extractions/setup-just v2→v4, astral-sh/setup-uv v7→v8.1.0, codecov/codecov-action v5→v6.

  • Fix wheel-test jobs on Linux: RUSTC_WRAPPER=sccache was leaking from maturin-action into subsequent uv sync invocations where sccache isn’t on PATH, failing silently on macOS (sccache pre-installed) but breaking Linux. Now overridden per-step.

  • Drop macOS x86_64 (Intel) from the wheel matrix (<8 Darwin downloads/month across all arches on PyPI).

Version 0.14.0

A significant reorganization:

  • Core communication and parsing code in Rust.

  • Polars dataframe support, in addition to pandas.

  • A new, rust-based qs-monitor with improved reliability and a matrix bot with commands.

  • Altair plotting support.

  • Numerous bug fixes and improvements.

  • Python 3.10 is now the minimum supported Python.

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

  • Fix pyparsing 3.0.7 whitespace parsing problem (pyparsing/pyparsing#359).

  • Use Hypothesis for some tests.

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.