Myokit

This release fixes a potential issue in simulation output, please see [1055](https://github.com/myokit/myokit/pull/1055) for details.

- Added
- [1051](https://github.com/myokit/myokit/pull/1051) Added a method `Simulation.crash_inputs` that returns the inputs (binding values) if the last run raised a `SimulationError`.
- [1055](https://github.com/myokit/myokit/pull/1055) Added an abstract class `CBasedExpressionWriter` to use as base class for expression writers for C-like languages.
- Changed
- [1051](https://github.com/myokit/myokit/pull/1051) `Model.evaluate_derivatives` will now use `numpy.errstate(all='raise')` when `ignore_errors` is set to `False`, causing more numerical issues to be reported.
- [1055](https://github.com/myokit/myokit/pull/1055) `Expression.pyfunc` now sorts its arguments in alphabetical order.
- Deprecated
- [1051](https://github.com/myokit/myokit/pull/1051) `Simulation.eval_derivatives` is deprecated in favour of an `evaluate_derivatives` method that uses `default_state` instead of `state` when no state is given, and has better support and clearer rules for handling bindings.
- [1051](https://github.com/myokit/myokit/pull/1051) `Simulation.last_state` is deprecated in favour of `crash_state`.
- Fixed
- [1045](https://github.com/myokit/myokit/pull/1045) Fixed an issue where the cache used in MarkovModel was not invalidated if `set_constant()` changed simulation parameters.
- [1050](https://github.com/myokit/myokit/pull/1050) Fixed warnings about unknown escape sequences.
- [1051](https://github.com/myokit/myokit/pull/1051) Numerical simulation errors in `Simulation` now re-evaluate the state using the last inputs, as well as the last state.
- [1051](https://github.com/myokit/myokit/pull/1051) The `Simulation` class now provides error states and inputs for both cvode-detected crashes and too many zero-length step crashes.
- [1055](https://github.com/myokit/myokit/pull/1055) `ExpressionWriter` classes now always output a `PrefixPlus`, including brackets where necessary.
- [1055](https://github.com/myokit/myokit/pull/1055) The `AnsiCExpressionWriter` and related expression writers now wrap all conditions in brackets.
- [1055](https://github.com/myokit/myokit/pull/1055) The `PythonExpressionWriter`, `NumPyExpressionWriter`, `StanExpressionWriter`, and `LatexExpressionWriter` now output brackets around double `Power` operations, so that the Myokit expression `a**b**c` is interpreted as `(a**b)**c`.
- [1055](https://github.com/myokit/myokit/pull/1055) Fixed bracket adding for `PrefixPlus`, `PrefixMinus`, and `Not` in `LatexExpressionWriter`.
- [1055](https://github.com/myokit/myokit/pull/1055) Fixed bracket adding for `PrefixPlus` and `PrefixMinus` in Presentation MathML.

- 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.