Myokit

- Added
- [1010](https://github.com/myokit/myokit/pull/1010) Added more information methods to `formats.heka.Segment`
- [1012](https://github.com/myokit/myokit/pull/1012) The method `Model.add_variable` now has keyword arguments `unit`, `rhs`, `label`, `binding`, and `initial_value` to allow one-line variable creation and initialisation.
- [1018](https://github.com/myokit/myokit/pull/1018) The PatchMaster file reading can now extract information for multiple amplifiers (if used), and more information methods were added.
- Fixed
- [1020](https://github.com/myokit/myokit/pull/1020) Fixed an issue where the explorer time fields had a white background in dark mode.
- [1021](https://github.com/myokit/myokit/pull/1021) Fixed a buggy deprecation warning in `lib.plots.cumulative_current`.

- Added
- [1006](https://github.com/myokit/myokit/pull/1006) The `DataLog` class can now store global meta data in `.meta` and per-column meta data in `.cmeta`. Both must be string-string key-value pairs.
- [1006](https://github.com/myokit/myokit/pull/1006) Simulations now automatically add some meta data (units) to the data log.
- [1006](https://github.com/myokit/myokit/pull/1006) The `DataLog` class can now save meta data to disk using the [CSV-on-the-web](https://w3c.github.io/csvw/) format.
- [1006](https://github.com/myokit/myokit/pull/1006) Added a class `ColumnMetaData` to represent per-column meta data of a table or DataLog.
- [1006](https://github.com/myokit/myokit/pull/1006) ABF, WCP, and PatchMaster file classes now add meta data when creating a `DataLog`.
- Changed
- [1006](https://github.com/myokit/myokit/pull/1006) Made core classes `ObjectWithMetaData`, `MetaDataContainer`, `VarOwner`, and `VarProvider` part of the public API. Similarly the method `check_name`.
- [1008](https://github.com/myokit/myokit/pull/1008) The `PatchMasterFile` reader no longer performs "zero offset subtraction" (in which a recorded current trace is shifted until a user-specified segment has zero current) by default.
- Fixed
- [1006](https://github.com/myokit/myokit/pull/1006) `DataLog.clone()` no longer replaces `array.array` objects with lists.

- Fixed
- [1005](https://github.com/myokit/myokit/pull/1005) DataBlock viewer now shows user-set values when exporting a colormap.

- Added
- [955](https://github.com/myokit/myokit/pull/955) Added provisional HEKA PatchMaster file reading.
- [985](https://github.com/myokit/myokit/pull/985), [#998](https://github.com/myokit/myokit/pull/998) The `AbfFile` and `WcpFile` now implement a shared `SweepSource` interface.
- [985](https://github.com/myokit/myokit/pull/985) Added a method `AtfFile.path` that returns the full path.
- [985](https://github.com/myokit/myokit/pull/985) Added a method `WcpFile.info` that returns a string version of the file's meta data, and a method `WcpFile.sample_count` that returns the number of samples per channel.
- [1003](https://github.com/myokit/myokit/pull/1003) The DataBlock viewer now has fields to enter a lower and upper range for the colormap conversion.
- [1003](https://github.com/myokit/myokit/pull/1003) Added new color maps for `myokit.DataBlock` viewing.
- Changed
- [985](https://github.com/myokit/myokit/pull/985), [#998](https://github.com/myokit/myokit/pull/998) The interface to the `AbfFile` class has changed significantly, and in a backwards incompatible ways. Please see the documentation for further details.
- [991](https://github.com/myokit/myokit/pull/991) Myokit no longer uses the `logging` module but makes calls to `warnings.warn` instead.
- [992](https://github.com/myokit/myokit/pull/992) If a `Simulation` is created with `protocol={}`, then `pace` will not be set as a binding label. To stay backwards compatible it _will_ be set if `protocol=None`.
- [994](https://github.com/myokit/myokit/pull/994) Simulations can now start at arbitrary times, including negative ones. Note that protocol events have a default offset of 0, so no events are usually expected at negative times.
- Deprecated
- [985](https://github.com/myokit/myokit/pull/985) The method `WcpFile.myokit_log` is deprecated in favor of `WcpFile.log`.
- [985](https://github.com/myokit/myokit/pull/985) The methods `WcpFile.channels` and `WcpFile.records` are deprecated in favor of `WcpFile.channel_count` and `WcpFile.record_count`.
- [985](https://github.com/myokit/myokit/pull/985) The method `WcpFile.plot` is deprecated in favor of `WcpFile.matplotlib_figure`.
- [985](https://github.com/myokit/myokit/pull/985) The method `WcpFile.records` is deprecated in favor of `WcpFile.record_count` or `WcpFile.sweep_count`.
- [985](https://github.com/myokit/myokit/pull/985) The method `AtfFile.myokit_log` is deprecated in favor of `AtfFile.log`.
- [998](https://github.com/myokit/myokit/pull/998) The method `WcpFile.info` is deprecated in favor of `WcpFile.meta_str`.
- [998](https://github.com/myokit/myokit/pull/998) The method `AtfFile.info` is deprecated in favor of `AtfFile.meta_str`.
- Fixed
- [985](https://github.com/myokit/myokit/pull/985) `AbfFile.filename` now returns the filename, not the full path.
- [985](https://github.com/myokit/myokit/pull/985) `AtfFile.filename` now returns the filename, not the full path.
- [992](https://github.com/myokit/myokit/pull/992) `Simulation` now sets any variable bound to a pacing label to 0 if no protocol for that label is set.
- [998](https://github.com/myokit/myokit/pull/998) Fixed a bug where channels in ABF v1 files were sometimes scaled using the wrong meta data.
- [1003](https://github.com/myokit/myokit/pull/1003) Fixed a bug in the DataBlockViewer introduced when adding Qt6 support.

- Added
- [979](https://github.com/myokit/myokit/pull/979) Added support for PyQt6 and PySide6.
- Changed
- [980](https://github.com/myokit/myokit/pull/980) Python 2 is no longer supported. The minimum supported Python version is now 3.7.
- Removed
- [979](https://github.com/myokit/myokit/pull/979) Removed support for PyQt4 and PySide, which were deprecated since 2019.

- Added
- [898](https://github.com/myokit/myokit/pull/899) martinjrobins Initial conditions for state variables can now be (constant-valued) expressions. Previously, only literals were allowed.
- [918](https://github.com/myokit/myokit/pull/918) Added `Model.initial_values`, which returns the model's initial values as a list of expressions, floats, or equations.
- [918](https://github.com/myokit/myokit/pull/918) Added `Model.set_initial_values`, which sets the model's initial values using a list of expressions or anything accepted by `map_to_state`.
- [918](https://github.com/myokit/myokit/pull/918) Added `Variable.initial_value`, which returns a state variable's initial value as an expression or float.
- [918](https://github.com/myokit/myokit/pull/918) Added `Variable.set_initial_value`, which sets a state variable's initial value using an expression, string expression, or float.
- [918](https://github.com/myokit/myokit/pull/918) Added `IllegalReferenceInInitialValueError` for illegal references made in initial value expressions.
- [947](https://github.com/myokit/myokit/pull/947) martinjrobins The `Simulation` class can now handle multiple protocols during a single simulation.
- [947](https://github.com/myokit/myokit/pull/947) Fixed-form protocols are now implemented in a `TimeSeriesProtocol`.
- Changed
- [898](https://github.com/myokit/myokit/pull/899) `Variable.promote` can now take an expression, a number, or a string (which will be parsed as an expression) for the argument `initial_value`.
- [909](https://github.com/myokit/myokit/pull/909) Myokit is now tested on Python 3.11.
- [909](https://github.com/myokit/myokit/pull/909) Myokit is no longer tested on Python 3.6.
- [918](https://github.com/myokit/myokit/pull/918) The only argument to `Variable.promote` has been renamed from `state_value` to `initial_value`.
- [918](https://github.com/myokit/myokit/pull/918) `Model.import_component` now preserves the ordering of the imported states.
- [953](https://github.com/myokit/myokit/pull/953) The DataLogViewer now overlaps traces with numbering (e.g. 0.membrane.V and 1.membrane.V), and toggles between files and variables with Page up and down Or Ctrl+Page up and down.
- [962](https://github.com/myokit/myokit/pull/962) Scipy is no longer a required dependency.
- [962](https://github.com/myokit/myokit/pull/962) The DataLogViewer only supports Matlab file loading if SciPy is installed.
- [975](https://github.com/myokit/myokit/pull/975) Global parameters in imported SBML documents are now placed in a component named `global` instead of `myokit`.
- [978](https://github.com/myokit/myokit/pull/978) The IDE now validates _either_ the model _or_ the protocol, depending on the current tab (previously both were validated).
- Deprecated
- [918](https://github.com/myokit/myokit/pull/918) `Model.state` is deprecated in favor of `Model.initial_values`.
- [918](https://github.com/myokit/myokit/pull/918) `Model.set_state` is deprecated in favor of `Model.set_initial_values`.
- [918](https://github.com/myokit/myokit/pull/918) `Model.inits` is deprecated.
- [918](https://github.com/myokit/myokit/pull/918) `Variable.state_value` is deprecated in favor of `Variable.initial_value`.
- [918](https://github.com/myokit/myokit/pull/918) `Variable.set_state_value` is deprecated in favor of `Variable.set_initial_value`.
- [918](https://github.com/myokit/myokit/pull/918) `Model.save_state` and `Model.load_state` are deprecated.
- [918](https://github.com/myokit/myokit/pull/918) The `Variable.promote` keyword argument `state_value` is deprecated in favor of `initial_value`.
- [947](https://github.com/myokit/myokit/pull/947) `Simulation.set_fixed_form_protocol` is deprecated in favor of using `Simulation.set_protocol` with a `TimeSeriesProtocol`
- [962](https://github.com/myokit/myokit/pull/962) The method `DataLog.regularize` is deprecated.
- [974](https://github.com/myokit/myokit/pull/974) `Variable.indice` is deprecated in favor of `Variable.index`.
- [976](https://github.com/myokit/myokit/pull/976) `SimulationOpenCL.neighbours` is deprecated in favor of `SimulationOpenCL.neighbors`.
- Removed
- [898](https://github.com/myokit/myokit/pull/899) `NonLiteralValueError` is now no longer raised by Myokit and so has been removed.
- [921](https://github.com/myokit/myokit/pull/921) Removed deprecated `LegacySimulation` class.
- [921](https://github.com/myokit/myokit/pull/921) Removed deprecated `PSimulation` class.
- [921](https://github.com/myokit/myokit/pull/921) Removed deprecated `ICSimulation` class.
- [957](https://github.com/myokit/myokit/pull/957) Removed the method `Model.prepare_bindings`.
- [961](https://github.com/myokit/myokit/pull/961) Removed the module `myokit.lib.common`, which had been deprecated since April 2018.
- Fixed
- [918](https://github.com/myokit/myokit/pull/918) Fixed error when `var()` was called on a `PartialDerivative` with a `Derivative` as first argument.
- [933](https://github.com/myokit/myokit/pull/933) Made `myokit.step` base its error classification (large/small/none) on numerics, not representation.
- [947](https://github.com/myokit/myokit/pull/947) Fixed minor memory leak (reference counting issue) when using fixed form protocols.
- [967](https://github.com/myokit/myokit/pull/967) Myokit no longer calls `logging.basicConfig()` when used as a library.
- [977](https://github.com/myokit/myokit/pull/977) `myokit.save()` now raises a `ValueError` if `model`, `protocol`, and `script` are all None.
- [978](https://github.com/myokit/myokit/pull/978) Clarified message shown in IDE after re-validation of valid model or protocol.