Myokit

- Added
- [1073](https://github.com/myokit/myokit/pull/1073) Added export to [DiffSL](https://github.com/martinjrobins/diffeq-js/).
- [1088](https://github.com/myokit/myokit/pull/1088) The DataLogViewer now displays meta data for myokit DataLogs.
- [1088](https://github.com/myokit/myokit/pull/1088) The HEKA file format now supports more meta data, including filters.
- [1092](https://github.com/myokit/myokit/pull/1092) The method `DataLog.load_csv` can now read CSV files with duplicate column names.
- [1095](https://github.com/myokit/myokit/pull/1095) Myokit is now tested on Python 3.12 and 3.13.
- Fixed
- [1083](https://github.com/myokit/myokit/pull/1083) Fixed bug when passing initial state `Expression` objects to `myokit.step`.
- [1088](https://github.com/myokit/myokit/pull/1088) The HEKA file format meta data now shows the correct value for fast capacitance correction.
- [1088](https://github.com/myokit/myokit/pull/1088) The ABF reader no longer crashes if degrees Celsius are encountered.
- [1093](https://github.com/myokit/myokit/pull/1093) `DataLog.load_csv` will now ignore an initial byte order marker.

- Added
- [1075](https://github.com/myokit/myokit/pull/1075) Add a `myokit.TypeError` exception, which inherits from `myokit.IntegrityError` but is used specifically if one type of expression was expected but another was found.
- Changed
- [1067](https://github.com/myokit/myokit/pull/1067) Improved the meta data loaded from HEKA files when creating a `myokit.DataLog`.
- [1074](https://github.com/myokit/myokit/pull/1074) Expressions will now raise a `myokit.IntegrityError` in the constructor if their operands are not expression objects: previously, this check was only performed by `Expression.validate()`.
- [1075](https://github.com/myokit/myokit/pull/1075) Expressions will now raise a `myokit.TypeError` in the constructor if their operands are unexpected expression types, e.g. if numbers and booleans are mixed.
- Removed
- [1075](https://github.com/myokit/myokit/pull/1075) Removed the `PrefixCondition` base class previously used in the expression system, as only `Not` inherited from it.
- Fixed
- [1071](https://github.com/myokit/myokit/pull/1071) When DataLog.split_periodic does not make a split, a length 1 list is returned instead of a `DataLog`.
- [1075](https://github.com/myokit/myokit/pull/1075) Added missing `Expression` base classes to public API.
- [1077](https://github.com/myokit/myokit/pull/1077) Fixed bug where data log viewer crashed when reading an empty WCP file.
- [1078](https://github.com/myokit/myokit/pull/1078) Added support for Numpy 2.

- Added
- [1063](https://github.com/myokit/myokit/pull/1063) Added support for Sundials 7.0.0.
- Removed
- [1061](https://github.com/myokit/myokit/issues/1061) Currently unable to test OpenCL features on Mac OS.
- Fixed
- [1060](https://github.com/myokit/myokit/pull/1060) Fixed an issue with overflows in tau for HH analytical simulations leading to unnecessary NaNs in state and current simulation outputs.

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.