CHANGELOG.md

Changelog

This page lists the main changes made to Myokit in each release.

Unreleased

• Added
• Changed
  • #1102 Replaced the HEKA method c_fast_tau with a method c_fast_detailed.
• Deprecated
• Removed
  • #1111 No longer testing on Python 3.7.
• Fixed
  • #1100 Added missing PatchMaster classes to the API and docs.
  • #1109 Fixed issue with meta data in Patchmaster class for files with alternative amplifier state storage.

[1.37.1] - 2024-11-05

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

[1.37.0] - 2024-06-17

• Added
  • #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 Improved the meta data loaded from HEKA files when creating a myokit.DataLog.
  • #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 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 Removed the PrefixCondition base class previously used in the expression system, as only Not inherited from it.
• Fixed
  • #1071 When DataLog.split_periodic does not make a split, a length 1 list is returned instead of a DataLog.
  • #1075 Added missing Expression base classes to public API.
  • #1077 Fixed bug where data log viewer crashed when reading an empty WCP file.
  • #1078 Added support for Numpy 2.

[1.36.1] - 2024-05-10

• Added
  • #1063 Added support for Sundials 7.0.0.
• Removed
  • #1061 Currently unable to test OpenCL features on Mac OS.
• Fixed
  • #1060 Fixed an issue with overflows in tau for HH analytical simulations leading to unnecessary NaNs in state and current simulation outputs.

[1.36.0] - 2024-03-22

This release fixes a potential issue in simulation output, please see #1055 for details.

• Added
  • #1051 Added a method Simulation.crash_inputs that returns the inputs (binding values) if the last run raised a SimulationError.
  • #1055 Added an abstract class CBasedExpressionWriter to use as base class for expression writers for C-like languages.
• Changed
  • #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 Expression.pyfunc now sorts its arguments in alphabetical order.
• Deprecated
  • #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 Simulation.last_state is deprecated in favour of crash_state.
• Fixed
  • #1045 Fixed an issue where the cache used in MarkovModel was not invalidated if set_constant() changed simulation parameters.
  • #1050 Fixed warnings about unknown escape sequences.
  • #1051 Numerical simulation errors in Simulation now re-evaluate the state using the last inputs, as well as the last state.
  • #1051 The Simulation class now provides error states and inputs for both cvode-detected crashes and too many zero-length step crashes.
  • #1055 ExpressionWriter classes now always output a PrefixPlus, including brackets where necessary.
  • #1055 The AnsiCExpressionWriter and related expression writers now wrap all conditions in brackets.
  • #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 Fixed bracket adding for PrefixPlus, PrefixMinus, and Not in LatexExpressionWriter.
  • #1055 Fixed bracket adding for PrefixPlus and PrefixMinus in Presentation MathML.

[1.35.4] - 2023-10-12

• Added
  • #1010 Added more information methods to formats.heka.Segment
  • #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 The PatchMaster file reading can now extract information for multiple amplifiers (if used), and more information methods were added.
• Fixed
  • #1020 Fixed an issue where the explorer time fields had a white background in dark mode.
  • #1021 Fixed a buggy deprecation warning in lib.plots.cumulative_current.

[1.35.3] - 2023-07-26

• Added
  • #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 Simulations now automatically add some meta data (units) to the data log.
  • #1006 The DataLog class can now save meta data to disk using the CSV-on-the-web format.
  • #1006 Added a class ColumnMetaData to represent per-column meta data of a table or DataLog.
  • #1006 ABF, WCP, and PatchMaster file classes now add meta data when creating a DataLog.
• Changed
  • #1006 Made core classes ObjectWithMetaData, MetaDataContainer, VarOwner, and VarProvider part of the public API. Similarly the method check_name.
  • #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 DataLog.clone() no longer replaces array.array objects with lists.

[1.35.2] - 2023-07-19

• Fixed
  • #1005 DataBlock viewer now shows user-set values when exporting a colormap.

[1.35.1] - 2023-07-19

• Added
  • #955 Added provisional HEKA PatchMaster file reading.
  • #985, #998 The AbfFile and WcpFile now implement a shared SweepSource interface.
  • #985 Added a method AtfFile.path that returns the full path.
  • #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 The DataBlock viewer now has fields to enter a lower and upper range for the colormap conversion.
  • #1003 Added new color maps for myokit.DataBlock viewing.
• Changed
  • #985, #998 The interface to the AbfFile class has changed significantly, and in a backwards incompatible ways. Please see the documentation for further details.
  • #991 Myokit no longer uses the logging module but makes calls to warnings.warn instead.
  • #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 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 The method WcpFile.myokit_log is deprecated in favor of WcpFile.log.
  • #985 The methods WcpFile.channels and WcpFile.records are deprecated in favor of WcpFile.channel_count and WcpFile.record_count.
  • #985 The method WcpFile.plot is deprecated in favor of WcpFile.matplotlib_figure.
  • #985 The method WcpFile.records is deprecated in favor of WcpFile.record_count or WcpFile.sweep_count.
  • #985 The method AtfFile.myokit_log is deprecated in favor of AtfFile.log.
  • #998 The method WcpFile.info is deprecated in favor of WcpFile.meta_str.
  • #998 The method AtfFile.info is deprecated in favor of AtfFile.meta_str.
• Fixed
  • #985 AbfFile.filename now returns the filename, not the full path.
  • #985 AtfFile.filename now returns the filename, not the full path.
  • #992 Simulation now sets any variable bound to a pacing label to 0 if no protocol for that label is set.
  • #998 Fixed a bug where channels in ABF v1 files were sometimes scaled using the wrong meta data.
  • #1003 Fixed a bug in the DataBlockViewer introduced when adding Qt6 support.

[1.35.0] - 2023-06-21

• Added
  • #979 Added support for PyQt6 and PySide6.
• Changed
  • #980 Python 2 is no longer supported. The minimum supported Python version is now 3.7.
• Removed
  • #979 Removed support for PyQt4 and PySide, which were deprecated since 2019.

[1.34.0] - 2023-06-07

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

[1.33.9] - 2022-11-08

• Fixed
  • #908 Added new homebrew location used on M1 apple devices, potentially solving #861.
  • #912 Reporting of numerical errors in Simulation now catches more exception types arising from evaluate_derivatives.
  • #951 Made syntax highlighting in IDE recognise units containing - and *.

[1.33.8] - 2022-10-21

• Added
  • #895 Added method Expression.depends_on_state().
  • #901 Added options compatibility.no_capture and compatibility.no_fd_capture to myokit.ini to allow users to tweak compiler output capturing.
  • #903 Fixed a bug in SimulationOpenCL that caused a CL_INVALID_ARG_SIZE error on strict systems.
• Changed
  • #893 Variable.convert_unit now returns True if a conversion was carried out or False if not.
• Fixed
  • #888 #892 Improved documentation for Unit.conversion_factor with help from @martinjrobins.
  • #895 Fixed the value returned by Name.diff() and Expression.diff() for the situation where the associated RHS depends on a bound variable.
  • #895 Fixed performance issue in Expression.depends_on.
  • #896 Small improvements to Model, Component, and Variable documentation.

[1.33.7] - 2022-07-27

• Fixed
  • #883 Fixed memory leak in myokit.Simulation when using the log_times argument.

[1.33.6] - 2022-07-04

• Added
  • #872 The myokit.Simulation class can now be initialised using a precompiled backend (see the documentation for the path argument).
• Changed
  • #872 Model.solvable_order now returns consistently ordered equations, regardless of the order components and variables were created/parsed in.
  • #872 myokit.tools.rmtree now takes an optional argument silent that can be set to True to ignore any exceptions.
  • #876 Model.import_component can now take a list of possibly interdependent components.

[1.33.5] - 2022-05-02

• Fixed
  • #873 Small bugfixes and improvements in numerical error reporting in FiberTissueSimulation.
  • #873 Fixed argument list in docstring of FiberTissueSimulation.

[1.33.4] - 2022-04-22

• Added
  • #869 Added methods myokit.FiberTissueSimulation.fiber_shape and .tissue_shape (but see [#764] for an important open issue).
  • #869 Added a method myokit.FiberTissueSimulation.step_size().
• Changed
  • #865 Added more platform information to myokit system.
  • #866 Slightly tweaked the plotting in myokit.lib.plots.cumulative_current, and added two arguments line_args and fill_args that can be used to customize the plotting style.
  • #869 The class myokit.FiberTissueSimulation now raises ValueError for various method-argument errors, instead of the more generic Exception.
  • #869 The class myokit.FiberTissueSimulation now raises IndexError for various index-related errors, instead of the less appropriate KeyError.
• Deprecated
  • #869 The class myokit.FiberTissueSimulation is no longer considered deprecated.
• Fixed
  • #867 @DavAug Fixed a memory leak in myokit.Simulation.
  • #869 Added a missing y argument to FiberTissueSimulation.fiber_state() and FiberTissueSimulation.tissue_state().
  • #869 Fixed out-of-range checking in FiberTissueSimulation state and set_state methods.

[1.33.3] - 2022-03-17

• Changed
  • #860 Made myokit.tests into a module. Made tests runnable via setup.py. Added more meta data to setup.py.

[1.33.2] - 2022-03-17

• Changed
  • #843 Myokit is no longer tested on Python 3.5.
  • #844 Tweaked the CellML export's initial_value attribute to strip e+00 if present.
  • #845 Improved syntax highlighting and automatic detection of "dark mode" themes.
  • #849 Trying to pickle a myokit.Expression now raises a more helpful error message.
  • #849 The method myokit.parse_expression() now accepts a Model as a context.
  • #849 Model comparison with == now only returns True if both operands are the same object. Comparison based on code can be performed with Model.is_similar().
  • #852 Myokit is no longer tested on Python 3.6 for Windows (please use 3.7 and up).
• Fixed
  • #841 The MathMLExpressionWriter now uses type="e-notation" where necessary, instead of writing e.g. 1e-6.
  • #849 If Model.get() and Component.get() now raise a ValueError if a component or variable from a different model is passed in.
  • #849 Equation objects are now immutable, and their hash is consistent during the object's lifetime.
  • #849 The hash of a Quantity object is now consistent during its lifetime, regardless of unit representations.
  • #857 Fixed a memory leak in Simulation.run().
  • #858 OpenCL.info no longer raises CL_PLATFORM_NOT_FOUND_KHR if drivers but no devices are found.

[1.33.1] - 2022-01-24

• Added
  • #799 Added pL, MOhm, and GOhm as standard units.
  • #811 DatalogViewer now accepts .zip for binary data logs.
  • #817 Added support for Python 3.10.
  • #821 Sundials-based simulations now auto-detect the version number. The version indicated in myokit.ini is no longer used.
  • #823 Sundials 6.0.0 is now supported.
  • #826 Added a method myokit.tools.Benchmarker.print that prints elapsed time alongside a profiling message.
• Changed
  • Examples will be located in a separate repository, at https://github.com/myokit/myokit-examples
  • #815 Myokit will now warn when run on Python 2.7, as testing for 2.7 is being phased out.
  • #816 The method myokit.tools.Benchmarker.format can now be called without any arguments.
  • #817 The internal templating engine now uses ast instead of the deprecated (and removed in 3.10) parser module.
  • #825 The context manager myokit.tools.capture now takes an extra argument enabled which can be used to disabled output capturing.
  • #825, #826 The debugging arguments to myokit run have been split into five parts, see myokit run --help for details.
  • #834 The find/replace dialog in the IDE has been replaced with a toolbar.
  • #836 Colours in the IDE have been adapted to be clearer in "dark mode".
• Removed
  • #796 The Graph Data Extractor tool is now a separate project, hosted at https://github.com/myokit/gde.
  • #804 The command line utility system no longer reports on the cma module.
  • #821 Removed the method myokit.Sundials.version_int.
• Fixed
  • #805 Added missing command line utilities to the documentation, and re-organised the command-line tool docs.
  • #831 @DavAug Fixed bug in SBML parser that caused it to ignore terms in differential equations for products of reactions.

[1.33.0] - 2021-08-04

• Added
  • #581 Myokit's expression system now includes a PartialDerivative and an InitialValue class. Both are for use in sensitivity calculations and may not appear in models.
  • #581 Expressions now have a method diff(lhs) that returns the (partial) derivative of an expression with respect to the given LhsExpression.
  • #581 Expressions now have methods is_derivative, is_name, and is_number.
  • #581 Added a method Number.value().
  • #581 The method Expression.depends_on now has an argument deep that can be set to True to perform a recursive dependency check.
  • #595 A class myokit.CModel was added that can generate multi-purpose C code for use in simulations. This is mainly for internal use.
  • #682 OpenCL code now recognises error code -1001.
  • #683 Now testing OpenCL code in CI.
  • #704 Added first example notebook to the github repository.
  • #728 Added a context manager myokit.tools.capture that can redirect and capture output from Python stdout and stderr via a Python-only method or file-descriptor redirection and should be thread-safe.
  • #735 The new module myokit.float contains several functions related to floating point numbers that were previously in the main myokit namespace or not part of the public API.
  • #735 The new module myokit.tools contains several stand-alone tools that are used by Myokit and were previously in the main myokit namespace or not part of the public API.
  • #735 The method pid_hash, which is used by compiled code to generate (hopefully) unique ids is now part of the public API.
  • #744 Added a method myokit.OpenCL.available to check if OpenCL is supported and at least one OpenCL device is detected.
  • #754 Added a method myokit.OpenCL.current_info(x) that returns information about the currently selected platform and device; support of OpenCL extensions can then be checked with OpenCLPlatformInfo.has_extension.
  • #754 Improved error message when an OpenCLSimulation with double precision is run on a device that does not support it.
  • #763 Added a method OpenCLSimulation.set_conductance_field to apply heterogeneous conductance on a rectangular grid.
  • #769 @Rebecca-Rumney Added a method myokit.Model.import_component to import a component from one model to another.
  • #769 @Rebecca-Rumney Added an exception type VariableMappingError to be raised when there is an error in a variable mapping.
  • #776 Added a method OpenCLSimulation.monodomain_conductance to replace the deprecated method calculate_conductance.
  • #780 Alt-up and alt-down can now be used in the text editor to move selected lines up or down.
  • #782 The IDE can now import CellML files on opening, e.g. by typing myokit ide example.cellml.
  • #786 Added a method myokit.Variable.clamp() to fix any variable to a constant value.
  • #786 Added a method myokit.Variable.remove_child_variables() to remove all child (nested) variables from a given variable.
  • #788 The IDE will now suggest filenames for model exports.
  • #792 @DavAug SBML import now handles equations that explicitly use time.
• Changed
  • #581 Powers are now rendered without spaces in mmt code, e.g. x^2 instead of x ^ 2.
  • #595 The Simulation class now uses CVODES instead of CVODE as backend, which may require changes to your installation.
  • #595 The Simulation can now calculate sensitivities of variables with respect to parameters and/or initial conditions (see docs for details).
  • #595 The Simulation class no longer has apd_var as a constructor argument. Instead, you can pass an argument apd_variable to its run() method.
  • #595 The Simulation class no longer suppresses CVODES warnings but passes them on to the warnings module.
  • #595 Fix to Simulation for Sundials 4.1.0.
  • #687 Variable.set_rhs(None) now removes an RHS, instead of setting it to Number(0).
  • #687 Calling SimulationOpenCL.set_conductance will now override any conductances previously set with set_connections.
  • #687 SimulationOpenCL.set_connections no longer accepts None as a valid argument.
  • #687 The SimulationOpenCL methods set_conductance, conductance, set_connections, neighbours, set_paced_cells, set_paced_cell_list, and is_paced, will now raise a RuntimeError if diffusion was disabled at construction.
  • #687 The method SimulationOpenCL.remove_field now raises a KeyError if no field is set for the given variable.
  • #689 In Python 2, an ImportError is now raised if myokit.ini contains the sequence " ;" in any of its value (as this cannot be processed by Python 2's ConfigParser).
  • #728 The LegacySimulation class no longer suppresses CVODE warnings but passes them on to the warnings module (backported from new Simulation class).
  • #789 The method myokit.DataLog.save_csv() now stores the keys using natural sort order (time is still the first field, if present).
• Deprecated
  • #595 The classes myokit.PSimulation and myokit.ICSimulation have been deprecated in favor of the new Simulation class.
  • #735 The class myokit.Benchmarker is deprecated in favor of myokit.tools.Benchmarker.
  • #735 The method myokit.format_float_dict is deprecated and will be removed in future versions.
  • #735 The method myokit.format_path is deprecated in favor of myokit.tools.format_path.
  • #735 The method myokit.strfloat is deprecated in favor of myokit.float.str.
  • #758 The class myokit.FiberTissueSimulation is deprecated and will be removed in future versions.
  • #776 The method OpenCLSimulation.calculate_conductance is deprecated in favor of the new method calculate_conductance, which takes slightly different parameters.
  • #787 The method myokit.Model.eval_state_derivatives is deprecated in favor of myokit.Model.evaluate_derivatives.
• Removed
  • #683 No longer testing on Python 2.7.6 on linux (still testing latest 2.7). No longer testing any Python 2.7 on Windows.
  • #728 The classes myokit.PyCapture and myokit.SubCapture have been replaced by a single context manager myokit.tools.capture.
  • #730 Removed the method myokit.pack_snapshot.
  • #737 The method Model.merge_interdependent_components was removed. This method was deprecated since 2018-05-30.
  • #737 The method Model.show_line was removed. This method was deprecated since 2018-05-30.
  • #737 The method Protocol.guess_duration was removed. This method was deprecated since 2016-02-06.
• Fixed
  • #684 @DavAug Fixed OpenCL loading issue on MacOS (with special thanks to Martin Aguilar).
  • #686 Fixed a (windows only) bug in myokit.tools.format_path().
  • #687 Simulation1d now logs pacing as a global variable, and can log diffusion currents.
  • #689 Path lists read from myokit.ini are now filtered for empty entries and closing semicolons.
  • #744 Fixed a bug in OpenCLSimulation.find_nan(), that occurred for very small simulations (e.g. 2 cells).
  • #744 Fixed a bug in OpenCLSimulation that made it impossible to use set_connections() with double precision.
  • #744 Fixed a bug in OpenCLSimulation that made it impossible to use set_connections() on Python 2.
  • #754 Improved error message when an OpenCLSimulation with double precision is run on a device that does not support it.
  • #766 Improved error message when an empty MathML <cn> element is encountered.

[1.32.0] - 2021-01-19

• Added
  • #672 Added more detailed error output to several CVODE errors related to RHS-related numerical issues.
  • #672 Now tested on Sundials 5 (locally).
  • #672 Now testing on Python 3.9 (Linux).
  • #672 Simulation.run documentation is now more clear on what happens for very short simulation durations (or zero).
  • #674 Added a method Model.has_parse_info that checks if the model contains information from parsing (i.e. line numbers).
  • #674 Added a parameter raw to Model.show_line_of that returns the line number as an integer
  • #674 Added a method to the IDE that lets you jump to the definition of a selected variable.
  • #680 Now testing on Python 3.9 and Miniconda 3.8 (Windows).
• Removed
  • #681 Removed the deprecated library myokit.lib.fit. For fitting see e.g. PINTS and this tutorial on fitting ion channel data with Myokit & PINTS.
• Fixed
  • #672 Fixed bug in Variable.convert_unit() that caused unexpected (and quite arbitrary) results.
  • #672 Fixed bug where calling Simulation.run() with a very short runtime caused a zero state to be returned.
  • #676 Fixed a bug in CellML (1 and 2) export when inferring units for a state variable.
  • #679 Fixed "DLL load failed while importing myokit" issue on Windows 10 with Python 3.8 (via miniconda).

[1.31.1] - 2020-12-01

• Added
  • #623 The changes made with each release are now stored in CHANGELOG.md.
  • #622 SimulationOpenCL now includes a method is_paced and neighbours that provide information about the simulated cells.
  • #622 SimulationOpenCL.find_nan now has an option to return a DataLog with the final logged variables before the error occurred.
  • #632 Added methods DataBlock1d.to_log and DataBlock2d.to_log.
  • #633 DataBlockViewer now shows mouse coordinates in status bar for video and graph view.
  • #652 Added methods to remove 1d and 2d traces from DataBlock1d and DataBlock2d.
• Changed
  • #610 If numerical errors occur when evaluating an expression, the IDE now shows these in the console instead of in a pop-up.
  • #622 myokit.strfloat now takes a precision argument.
  • #622 Model.format_state and Model.format_state_derivatives now take a precision argument.
  • #622 If errors occur, the SimulationOpenCL now displays improved (and hopefully more informative) output.
  • #623 Updated licensing info.
  • #653 Model.pyfunc() now validates the model before running (and fails if the model does not validate).
  • #661 When importing MathML, the inverse hyperbolic trig functions are now rendered using slightly simpler equations.
  • #664 EasyML export now adds meta data, a group of CVODE-solved variables, a group of variables to trace, and a group of parameters (based on code contributed by Ed Vigmond).
  • #664 EasyML export now converts voltage, current, and time variables to the preferred units.
  • #664 EasyML export now has consistently ordered output when re-run.
  • #664 EasyML expression writer now uses expm1 where possible.
• Deprecated
  • #622 SimulationOpenCL.is2d() was deprecated in favor of SimulationOpenCL.is_2d().
  • #632 DataBlock1d.from_DataLog and DataBlock2d.from_DataLog have both been deprecated, in favor of new from_log methods.
• Fixed
  • #650 Fix to myokit.lib.plots.cumulative_current for normalisation in areas with zero current.
  • #603 Improved handling of types (ints resulting from logical operators) in OpenCLSimulation.
  • #613 Model.map_component_io now respects the omit_constants argument for Rush-Larsen variables.
  • #622 If Model.format_state_derivatives needs to evaluate the derivatives, it will now use the given state instead of the model state.
  • #628 The DataBlockViewer now shows a working colour bar for 1d simulations.
  • #638 The DataBlockViewer now handles blocks with t[0] > 0 correctly.
  • #655 Fixed bug where wrong initial state was shown by myokit.step().
  • #663 Fixed deprecation warning in save_state_bin().

[1.31.0] - 2020-08-26

• Added
  • #548 Models, protocols, and CVODE simulations can now be pickled, and tests have been added that check that simulations can be run in parallel (even on Windows).
  • #548 Model and protocol now support comparison with ==.
  • #553 The cumulative-current plot now has a maximum-number-of-currents option (all further currents will be bundled into one).
  • #567 Added support for Simulation building on Python 3.8 on Windows.
  • #574, #599, #547, #528 @DavAug A completely rewritten SBML API and parser that's capable of handling models that define species and reactions.
• Changed
  • #536 Ohm is now a quantifiable unit in the mmt syntax, i.e. 1 [MOhm]. This replaces the non-standard R unit which has been removed.
  • #556 CellML imports now import models that contain unsupported units (but with warnings).
  • #557 Imports and exports now raise warnings instead of using the Myokit textlogger for this.
  • #559, #541 Unit tests are now included in the PyPI package.
  • #560 Sympy is no longer a required dependency (but still an optional one).
  • #565 Some slight changes to simulation building: Now uses --inplace instead of --old-and-unmanageable and should delete any temporary files created in the process.
  • #566 Simulations now include a time and process number dependent hash in their generated-module names.
  • #569 The CellML export now ensures there are no spaces in initial value or unit multiplier attributes.
  • #576 Non-integer exponents are now allowed in the unit system, which compares units with a close() method that expects a certain numerical tolerance, instead of using exact comparison.
  • #576 CellML imports now import models with non-integer unit exponents.
  • #597 The output of the step() method has been improved, and the method now only warns about relative differences bigger than 1 epsilon.
  • commit The method show_evalution_of now has consistently ordered output.
  • CellML imports treat new base units as dimensionless.
  • The IDE now checks the protocol even if the model is invalid or unchanged.
• Removed
  • #563, #564 The myokit.mxml module has been removed.
• Fixed
  • #539 Bugfix for simulations that ended at a time numerically indistinguishable from an event time.
  • #570 Bugfixes and fewer warnings for various matplotlib versions.
  • #572 Bugfix to lib.common.StrenghtDuration.
  • #585 A recently introduced bug in the HHSimulation's steady_state() method was fixed.

[1.30.6] - 2020-04-29

• Fixed
  • #531 Fixed bug where GUI CellML export didn't export stimulus current.

[1.30.5] - 2020-04-20

• Added
  • #525 Added support for CellML 2.0.
• Changed
  • #516 Rewrote SBML import to use etree instead of DOM.
• Removed
  • #522 Removed myokit.formats.mathml.parse_mathml_dom function.
  • #522 Removed mxml myokit.mxml.dom_child and myokit.mxml.dom_next methods.
• Fixed
  • #515 Now setting OpenCL framework as linker flag on MacOS.

[1.30.4] - 2020-03-27

• Added
  • #503 Added clone() and __repr__() methods to myokit.Equation.
  • #507 Fixed a bug with running simulations in Spyder on Windows.
• Fixed
  • #496 Some fixes and tweaks to CellML 1.0/1.1 API.

[1.30.3] - 2020-03-02

• Small fixes to CellML validation.
• Fixed typo in units becquerel.
• Added notanumber and infinity to MathML parser.

[1.30.2] - 2020-02-01

• Removed myo script.
• Fixed EasyML issue for inf/tau variables used by more than one state.

[1.30.1] - 2020-01-03

• Added more import/export options to the IDE menu.
• Updated component.code() to always outout aliases in the same order.
• Added method to find Markov models in a Myokit model.
• Added method to convert Markov models to compact form.
• Added method to convert Markov models to full ODE form.
• LinearModel now converts to full ODE form.
• Added method lib.guess.membrane_capacitance.
• Added method lib.guess.membrane_currents.
• Added (experimental) EasyML export.
• Small bugfixes and documentation updates.
• Improved exception handling when evaluating a unit containing an invalid power.
• Made default script and protocol robust against incompatible units.
• Made CellML API from_myokit_model more robust against invalid units.

[1.30.0] - 2019-12-30

• Rewrote CellML import and export, with improved error handling and validation.
• CellML import now converts hardcoded stimulus equation to Myokit protocol.
• CellML export now converts Myokit protocol to hardcoded stimulus equation.
• CellML import now generates more approprate default scripts.
• CellML import now supports unit conversion between components.
• CellML export now infers units from RHS if no unit set.
• CellML import and export can now both handle Web Lab oxmeta annotations.
• Various changes and improvements to MathML parsing.
• Added missing __iter__ to Model and VarOwner.
• The myokit.Name expression can now wrap objects other than myokit.Variable, allowing Myokit's expression system to be re-used for non-myokit expressions.
• Removed myokit.UnsupportedFunction.

[1.29.1] - 2019-11-24

• Added guessing module, with method to guess which variables (if any) represent the membrane potential and stimulus current.
• Fix for sundials development versions.
• Fixes for PySide2 support.

[1.29.0] - 2019-10-11

• Myokit is now released under a BSD 3-clause license
• Bugfix to myokit step command line tool.

[1.28.9] - 2019-09-11

• Added PySide2 support.
• Deprecated PyQt4 and PySide.
• Added a method Model.remove_derivative_references().
• Bugfix to Model.repr() for models with no name.
• Added Model.timex(), labelx() and bindingx(), which work like time(), label() and binding() but raise an exception if no appropriate variable is found.
• Deprecated lib.multi.time(), label(), and binding().

[1.28.8] - 2019-09-03

• Added method Variable.convert_unit() that changes a variable's units and updates the model equations accordingly.
• Unit.conversion_factor now returns a Quantity instead of a float, and accepts helper Quantity objects for incompatible conversions.
• Added Unit.clarify() method that gives clear representation.
• Added Unit.multiplier_log_10() method.
• Added rtruediv and pow operators to Quantity class.
• Small bugfixes to myokit.lib.hh.
• Stopped requiring HH alphas/betas and taus/infs to depend on V (allows drug-binding work).
• Bugfix: Time variable in CellML export no longer has equation or initial value.
• CellML export: components now ordered alphabetically.
• Variables with an oxmeta: time meta annotation are now exported to CellML with an oxmeta RDF annotation.
• CellML import now allows deca prefix.
• Added CellML identifier checks to cellml import.
• Renamed DataLog.find() to find_after().
• Added DataLog.interpolate_at(name, time) method.
• Improved colormap used in plots.cumulative_current().
• Bugfix to 'myokit step' for models without a name meta property.
• Updated sign error handling in myokit.step().
• Added IDE shortcuts for unit checking.
• IDE now jumps to unit errors, if found.
• Improved exception display in IDE.
• Var_info now includes unit.
• Fixed bug in Unit.__repr__ for small multipliers.
• Improved notation of units when complaining about them.

[1.28.7] - 2019-08-03

• Added option to register external formats.
• Added option to avoid certain prefixes when generating unique variable names.
• Model.expressions_for() now accepts more than 1 argument, and handles dependencies on derivatives correctly.
• Removed deprecated method Model.solvable_subset().

[1.28.6] - 2019-07-26

• Added debug option to myokit compiler command.

[1.28.5] - 2019-07-16

• Bugfix: Removing variables now also removes their bindings and labels.
• Added unit tests.
• Improved performance in lib.markov analytical simulations.
• Updated the myo script to use the python3 executable.
• Fixed a bug in the default script used when creating or importing a model.
• Made GNOME/KDE icons install using sys.executable instead of a hardcoded python command.
• Fixed handling of string encoding in cellml import.

[1.28.4] - 2019-05-28

• Myokit is now tested on Python 3.7, but no longer on 3.4.
• Updated default OpenCL paths for windows.
• GUI fixes for matplotlib 3.1.0+.
• Added set_constant() method to markov simulations.
• Added log_times option to lib.markov.AnalyticalSimulation, and started pre-allocating arrays.
• Added option to cumulative current plot to normalise currents.

[1.28.3] - 2019-05-02

• Fixed some floating point issues with protocols and pacing.
• Updated OpenCL code to work with VS 9.
• Some small changes to the Protocol API.
• Added format protocol option to IDE.

[1.28.2] - 2018-12-19

• Improved support for native OpenCL on MacOS.
• Native maths in OpenCL simulations is now configurable and disabled by default.

[1.28.1] - 2018-12-19

• Added support for Sundials 4.0.0
• Made SymPy a dependency.
• Made current loggable in discrete markov simulations.
• Added log_times argument to analytical HH simulation.
• Improved performance of analytical HH simulation.
• Added AbfFile.extract_channel method that joins sweeps.
• Added ATF capability to datalog viewer.
• Added limited .pro support to DataLogViewer.
• Added ProgressReporter that cancels the operation after a time out.
• Added cut/copy/paste options to menu in IDE.
• Bugfix: myokit.system didn't check for SymPy version.
• Deprecated myo script.
• Changed myokit.VERSION to myokit.__version__.
• Various minor tweaks and fixes.

[1.28.0] - 2018-11-22

• Added myokit.lib.hh module for recognising Hodgkin-Huxley style ion current models and using them in fast analytical simulations.
• Added Rush-Larsen (RL) option to OpenCLSimulation.
• Added CUDA kernel export with RL updates.
• Added OpenCLRLExporter for OpenCL kernel with Rush-Larsen.
• Improved logging of intermediary variables in OpenCL simulations.
• Improved logging in Simulation1d.
• Fix to ABF reader for (unsupported) userlists (abf v2).
• Fixes to Sundials configuration on Windows.
• Small bugfixes, documentation updates, etc.

[1.27.7] - 2018-11-01

• Various fixes to make Myokit work with Python 2.7.6 (and later).

[1.27.6] - 2018-09-27

• Now running sundials auto-detection with every import myokit if not set in config file.

[1.27.5] - 2018-09-20

• Bugfix to OpenCL.load_selection.
• Added system info command.
• Added command option to show C Compiler support.
• Added command option to show Sundials support.
• Bugfix to Unit.rdiv.
• Small fixes to lib.fit.
• Documentation config update for sphinx >=1.8.
• Parsing now has full test cover.
• Removed special line feed code from parser, as in unicode they are treated as newlines (and stripped out by splitlines()).
• Removed obsolete TEXT_OPS code from parser.
• Removed redundant check from parser.
• Removed another redundant check from parser.
• Various small bugfixes and tweaks.

[1.27.4] - 2018-08-12

• Added sundials version detection on first run.
• Moved myokit config files from ~/.myokit to ~/.config/myokit.
• Renamed NumpyExpressionwriter to NumPyExpressionWriter.
• Fixed test issues on MacOS.

[1.27.3] - 2018-08-06

• Updated the way sundials library locations are stored on windows systems.

[1.27.2] - 2018-08-04

• Added script that creates icons for windows.
• Updated script that creates icons for linux.

[1.27.1] - 2018-08-03

• Placeholder release to fix Pypi issue.

[1.27.0] - 2018-08-03

• Added support for Python 3.4, 3.5, and 3.6.
• Added support for Sundials 3 (by @teosbpl).
• Added support for various Visual C++ compilers.
• Made Myokit pip-installable, stopped providing windows installer.
• Replaced windows sundials binaries with Visual-Studio compiled ones.
• Added a system-wide myokit command (after pip install on unix systems).
• Moved development from private repo to GitHub.
• Set up automated testing with Travis (linux) and Appveyor (windows).
• Greatly increased unit-test coverage (and set up checking with codecov.io).
• Added contribution guidelines.
• Added style checking with flake8.
• Removed OrderedPiecewise, Polynomial, Spline, and lib.approx.
• Deprecated lib.fit. Please have a look at PINTS instead.
• Removed quadfit() methods from lib.fit.
• Deprecated lib.common
• Removed HTML page generating classes from mxml.
• Simplified some of the error classes.
• Simplified Benchmarker.
• DataLog.apd() now has same output as Simulation threshold crossing finder.
• On-the-fly compilation switched from distutils to setuptools.
• Tidied up.
• Lots of bugfixes.
• Made IDE show Python version in about screen.

[1.26.3] - 2018-02-09

• Fixed critical bug introduced in version 1.26.2 that stopped Windows simulations from running.

[1.26.2] - 2018-01-11

• Fixed a small bug in Simulation's logging when using the new log_times argument.
• Added Matlab and text file tab to DataLog viewer.
• Removed ancient restriction on components not being called external.
• Refactored code to pass flake8 tests.
• Added len() method to Protocol.
• Now setting runtime_libraries parameter for all compiled classes (simulations), removing the need to set LD_LIBRARY_PATH on some systems.

[1.26.1] - 2017-11-24

• Updated licensing info.

[1.26.0] - 2017-11-24

• Myokit can now be installed as library using python setup.py develop.
• Fixed a bug in the gnome scripts that install icons.
• The DataLog trim, itrim and extend methods now return copies, instead of modifying the data 'in place'. This makes the DataLog's methods more consistent, and prevents accidental data loss. However, this change makes Myokit 1.26.0 slightly backwards incompatible.
• Added a DataLog.keys_like method to iterate over 1d or 2d logs.

[1.25.3] - 2017-10-06

• Small tweaks to IDE
• Fix to DataLog.fold() to discard remainder if period doesn't exactly divide the log length.
• Various bugfixes.
• Improved cvode error catching.
• More control over lib.fit verbosity
• Added random starting point option to lib.fit methods.
• Added the option to explicitly specify log points in the single-cell Simulation class.
• CVODE sim now raises SimulationError if maximum number of repeated zero-steps is made, instead of plain Exception.
• Fix fit.cmaes to work with cma version 2.x

[1.25.2] - 2017-08-03

• Small tweaks to IDE.
• Fixed bug with saving the time variable in DataLog.save_csv().

[1.25.1] - 2017-07-18

• Added xNES and SNES optimisation methods.
• Added interface to CMA-ES optimisation method.
• Replaced the 'tolerance' arguments in myokit.lib.fit with more accurate counterparts.
• Removed ga() optimisation method.

[1.25.0] - 2017-07-10

• Added model export to Stan.
• Added data-clamp to CVODE simulation (works, but generally a bad idea).
• Added Protocol.add_step convenience method for building sequential step protocols.
• Added log() method to ExportError.
• Fixed bug in ABF reading (ABF channel index can be greater than number of channels in file).
• Small fixes to DataLogViewer.
• Fixed issue with PySide file open/save dialogs.
• Several small fixes to docs.

[1.24.4] - 2017-05-04

• Bugfix in PyQt4 support.

[1.24.3] - 2017-05-03

• Fixed PyQt4/5 and PySide compatibility issue that was causing errors in the DataBlock viewer's open function.

[1.24.2] - 2017-03-28

• Added missing #pragma directive to enable double-precision simulations OpenCL.

[1.24.1] - 2016-10-24

• Added support for PyQt5.

[1.24.0] - 2016-10-14

• The IDE now has a model navigator, that displays the model components alphabetically and lets you navigate large models more easily.
• Fixed a bug in the implementation of DataBlock1d.grid(), and updated its documentation: this method returns coordinates for squares where each square represents a data point. See the Stewart 2009 OpenCL example for an example of its use.
• Added a second method DataBlock1d.image_grid() that returns coordinates for points where each point in space represents a data point.
• Fixed bug with Ctrl+Shift+Home in IDE.
• Various small bugfixes in IDE.
• Updated installation instructions on website.

[1.23.4] - 2016-09-04

• Fixed bug (with new numpy) in DataLog.split_periodic.
• Fixed warnings in GDE.
• Fixed issue with pyside/pyqt difference.

[1.23.3] - 2016-07-21

• Updated documentation and examples.
• Added extra callback option to pso for detailed feedback.
• Updated default search paths for Sundials headers and libraries.

[1.23.2] - 2016-06-16

• Small bugfix to IDE.
• Added pre() method to Markov simulations (AnalyticalSimulation and DiscreteSimulation).
• Fixed a bug in lib.markov.AnalyticalSimulation.run when log_interval >= duration.
• IDE now shows exact location of recent files in status bar.
• Fixed bug in SymPyExpressionWriter.eq() and renamed classes to use SymPy with capital P.

[1.23.1] - 2016-06-05

• Updated documentation.
• Fixed opencl issue.

[1.23.0] - 2016-05-30

• Added methods for easier symbolic addition of names/components for situations where exact names aren't important.
• Bugfix to datalog viewer.
• Bugfix to vargrapher.

[1.22.7] - 2016-05-25

• Update to ide: Can now add/remove comments.
• Bugfixes to protocol reading in AbfFile.
• Bugfix in AbfFile string reading.
• DataLog viewer now opens multiple files if specified on the command line.
• Fix to OpenCL sim reserved names list.
• Various tweaks and fixes.

[1.22.6] - 2016-03-11

• Fixed bug in IDE.
• Fix to windows start menu icons.

[1.22.5] - 2016-02-25

• Updated online examples.
• Bugfix in deprecated method Protocol.guess_duration().

[1.22.4] - 2016-02-24

• Fixed bug with auto-indenting and smart up/down arrows in IDE.
• Fixed bug in parsing of indented multi-line meta-data properties.
• Fixed bug with [[script]] sections being added to files when saved.
• Slight update to DataLog.apd().
• Updated the docs of both apd methods to make clear that they use fixed thresholds.

[1.22.3] - 2016-02-19

• Added hybrid PSO option to myokit.lib.fit.
• Added option to return multiple particles' results to PSO.
• Bugfixes and updates to documentation.
• Added BFGS method (interface to scipy) to myokit.lib.fit.

[1.22.2] - 2016-02-08

• Small bugfix in markov simulation class.

[1.22.1] - 2016-02-08

• Updates to source highlighting in the IDE.
• Various small bugfixes.
• Protocols and events now define a 'characteristic time'.
• The protocol class is now slightly stricter than before, removed its validate() method.
• Both markov model simulation classes can now run simulations based on myokit.Protocol objects.

[1.22.0] - 2016-01-28

• Rewrote the Markov model module.
• Added a method to perform stochastic simulations with Markov models.
• Various small bugfixes.

[1.21.12] - 2016-01-20

• The CellML export now includes a simple periodic pacing protocol.
• Various small bugfixes.

[1.21.11] - 2016-01-05

• Tidied up code.

[1.21.10] - 2016-01-04

• Various small bugfixes.

[1.21.9] - 2015-12-28

• Various small bugfixes.

[1.21.8] - 2015-11-05

• Removed option to run mmt files in threads (was not used and caused issues with GUI).
• Giving up on multiprocessing on windows. Adding switches to disable it in the examples.
• Various bugfixes and improvements.

[1.21.7] - 2015-10-27

• Improved logging in simulations, made it more consistent throughout Myokit.

[1.21.6] - 2015-10-23

• Various small bugfixes, improvements and website updates.

[1.21.5] - 2015-10-14

• Changed the way states are stored in the model (list instead of OrderedDict). Was causing funny bug. Now has less redundant info.
• Fixed bug in remove_component().

[1.21.4] - 2015-10-06

• Added debug options to openclsim.
• OpenCL sim can now pace based on rules again, which is far more efficient for large numbers of cells.

[1.21.3] - 2015-10-06

• Various bugfixes.

[1.21.2] - 2015-10-05

• Added OpenCL device selection.
• Updated cumulative current plot method.

[1.21.1] - 2015-09-12

• Various small bugfixes and improvements.

[1.21.0] - 2015-09-04

• Add Powell's method to fit library.
• Added model statistics screen to IDE.
• Presence of <import> tag in CellML now causes exception instead of warning.
• Improved CellML import error messages.
• There is no longer a restriction on the type of expression used as a first argument to piecewise and if.
• Fixes to MathML parser and CellML import.
• Added option to extract colormap to DataBlock viewer.
• Added section about uninstalling on windows and slight hints about filesizes to website.
• Introduced "evaluator" class used for parallelized optimization algorithms. Rewrote PSO to use it.
• Added a genetic algorithm optimization method (does not outperform PSO).
• Added reset script to myo that removes all user settings i.e. the entire DIR_MYOKIT.
• Added version check to avoid Python3.
• Myokit for WinPython now has an uninstaller that shows up in "Add/Remove programs".
• Various small bugfixes and improvements.

[1.20.5] - 2015-06-01

• Added Python version check.
• Fitting library: Adding quadratic polynomial fit used to test local optima.
• Various small bugfixes.

[1.20.4] - 2015-05-11

• Improved export of units to CellML.
• DataLogViewer can now open CSV.
• Fixed windows newline issue when writing \r\n.
• Small fix to OpenCL memory management.
• OpenCL sim now also cleans when cancelled with keyboard interrupt.
• Added a finally: sim_clean() to all simulations.
• Various small bugfixes and improvements.

[1.20.1] - 2015-04-21

• Various bugs fixed in the IDE.

[1.20.0] - 2015-04-08

• Added 'next' keyword to protocol syntax.

[1.19.0] - 2015-04-07

• Explorer now shows output in IDE console.
• PSimulation now tracks arbitrary variables dz/dp, no longer only states dy/dp.
• Various small bugfixes.

[1.18.6] - 2015-03-29

• Various small bugfixes in the GUI.

[1.18.5] - 2015-03-24

• Even more improvements to the GUI.

[1.18.4] - 2015-03-23

• Several improvements to the new GUI.

[1.18.3] - 2015-03-18

• Added new icons for datablock viewer and gde.
• Update to settings.py for CUDA.
• Added string highlighting in script editor.
• JacobianCalculator bugfix due to Enno.
• Various small bugfixes and improvements.

[1.18.2] - 2015-03-16

• Removed last traces of previous GUI.
• Fixes to output capturing so that it works on Windows.
• Various small bugfixes.

[1.18.1] - 2015-03-15

• New IDE seems stable.
• Added monkey patch for os.popen issue on windows.

[1.18.0] - 2015-03-14

• Completely new GUI in QT instead of WX, should solve mac problems, improve performance throughout.
• Integrated GDE with Myokit classes.
• Updated docs for command line tools.
• Dropping idea of supporting msvc9 compiler on windows. Too many issues.
• Various small bugfixes.

[1.17.4] - 2015-03-09

• Bugfix in settings.py

[1.17.3] - 2015-03-09

• GDE is now a part of Myokit.
• Added "monkey patch" for old windows compilers.
• Some changes for C89 compatibility.

[1.17.1] - 2015-03-05

• SI units named after people are now also accepted when capitalized. Never used for output in this fashion.

[1.17.0] - 2015-03-05

• Now allowing (but not guaranteeing correctness of) arbitrary connections in OpenCL sim.
• Various improvements and bugfixes.

[1.16.3] - 2015-02-25

• Added Quantity class for number-with-unit arithmetic.
• Fix to CellML export of dimensionless variables with a multiplier.
• Various small bugfixes and improvements.

[1.16.2] - 2015-02-22

• Added current calculating method to Markov model class.
• Added on multi-model experiment convenience classes.

[1.16.1] - 2015-02-19

• Binds and labels now share a namespace.

[1.16.0] - 2015-02-19

• Added unit conversion method to unit class.
• Various small bugfixes and improvements.

[1.15.0] - 2015-02-05

• Various small bugfixes and improvements.

[1.14.2] - 2015-02-02

• Added NaN check to PSimulation.
• Added on model comparison method.
• Nicer output of numbers in expressions and unit quantifiers.
• Tiny fixes in Number representation and GUI.
• Imrpoved video generation script.
• Various small bugfixes and improvements.

[1.14.1] - 2015-01-25

• Added partial validation to Markov model class.
• Moved OpenCLInfo into separate object.
• GUI now shows remaining time during experiment.
• Various small bugfixes and improvements.

[1.14.0] - 2015-01-16

• Added Alt-1,2,3 tab switching to GUI.
• Updates to DataLog.
• Fixed opencl issue: constant memory is limited, using __constant for parameter fields can give a strange error (invalid_kernel_args instead of out of memory errors). Fixed this by chaning __constant to __global.
• Various small bugfixes and improvements.

[1.13.2] - 2014-12-05

• Various improvements and bugfixes.

[1.13.1] - 2014-12-03

• Fixed a bug with fixed interval logging in CVODE sim.

[1.13.0] - 2014-11-30

• Checked all load/save methods for expanduser() after issues during demo in Ghent.
• Changed model.var_by_label() to model.label().
• Added option to show variables dependent on selected var.
• Added support for reading WinWCP files.
• Various improvements and bugfixes.

[1.12.2] - 2014-11-19

• Added parse_model() etc methods to parser.
• Made sure protocol is cloned in all simulations. Protocols are not immutable and changes made after setting the protocol should not affect the simulation (or vice versa).
• Added a simulation that calculates the derivative of a state w.r.t. a parameter.
• Working on MarkovModel class.
• Added method to convert monodomain parameters to conductances to opencl simulation.
• Various small bugfixes.

[1.12.1] - 2014-11-08

• Various small bugfixes.

[1.12.0] - 2014-11-07

• Added ATF support.
• Added a Python-based PacingSystem to evaluate protocols over time in Python.
• Added Protocol to SimulationLog conversion.
• Improvements to GUI classes.
• Added protocol preview to GUI.
• Various small bugfixes.

[1.11.13] - 2014-11-04

• Fixed memory use and halting issue in lib.fit.
• Fixed bug in aux.run(). APDs are now returned in SimulationLogs instead of plain dicts. This allows saving as csv and is more consistent with what users would expect the simulation to return.

[1.11.12] - 2014-11-03

• Bugfix in PSO code: Initial positions weren't set properly, could end up out of bounds.

[1.11.11] - 2014-10-30

• Made threaded run() an option in settings.py.

[1.11.10] - 2014-10-30

• Added quick figure method to abf.
• Various small bugfixes.

[1.11.9] - 2014-10-18

• Added PySilence context manager, made CSilence extend it.
• myokit.run() now runs the script inside a separate thread. This allows sys.exit() to be used in a script.
• myokit.run() now handles exceptions correctly.
• Various improvements and bugfixes.

[1.11.8] - 2014-10-17

• Added rectangular grid mapping of parameter spaces.
• Removed custom open dialog from GUI.
• Various improvements and bugfixes.

[1.11.7] - 2014-10-14

• Added jacobian examples.
• Various improvements and bugfixes.

[1.11.6] - 2014-10-10

• Added parallelized particle search optimization method (PSO).
• Made linear system solving much faster.
• Looked at using matrix exponentials in markov model code, over 1000 times slower than eigenvalue method!
• Added method to draw colored Voronoi diagram.
• Further annotated the example files.
• Various small bugfixes.

[1.11.5] - 2014-09-24

• Added note about csv import to SimulationLog.save_csv.
• Added publications to website. Uploaded hand-outs for workshop.
• Updated GDE version to 1.3.0.

[1.11.4] - 2014-09-22

• Added hyperbolic functions to CellML import.
• Updated cellml import: Unused variables without an rhs are now removed, used variables without an rhs are given an automatic rhs of 0. Both cases generate a warning.
• Update to cellml import: If a variable is mentioned but never declared (i.e. if it is an external input) a dummy variable is now created and a warning is given.
• Added method to myo to get version number.
• Fixed string encoding issue in CellML import.
• Tweaks to the gui based on workshop feedback.
• Fixed windows issue: IE likes to download .cellml files as .xml, making them invisible to the gui. Added a glob rule for .xml to the cellml import in the gui.

[1.11.3] - 2014-09-19

• Moving to next version.
• Small bugfixes and a variable.value() method.

[1.11.2] - 2014-09-18

• Various small bugfixes.

[1.11.1] - 2014-09-18

• Added a formatting option to the Benchmarker.
• Fixed OS/X GUI issues with progress bar.

[1.11.0] - 2014-09-15

• Adding Sympy to formats list.
• Added sympy exporter and importer.
• Added LinearModel class for working with markov models.

[1.10.3] - 2014-09-11

• Now raising exception when user cancels simulation instead of silent exit.
• Added zero-step detection to cvode sim that now raises a SimulationError after too many consecutive zero steps.

[1.10.2] - 2014-09-10

• Improvement debugging in the GUI: Now shows line numbers of error in script.

[1.10.1] - 2014-09-08

• Fixed bug in error handling.

[1.10.0] - 2014-08-30

• Added Windows installer.

[1.9.11] - 2014-08-29

• Updates to Windows install script.

[1.9.10] - 2014-08-27

• Added (valid) CellML export.
• Various small bugfixes.

[1.9.9] - 2014-08-26

• Added update script.

[1.9.8] - 2014-08-25

• Various improvements and bugfixes.

[1.9.7] - 2014-08-21

• Fixed bug with dialogs on OS/X.
• Bundled all scripts into a single script myo.
• Updated installation script for Windows.

[1.9.6] - 2014-08-19

• Fixed bug with dialogs on OS/X

[1.9.5] - 2014-08-14

• Added device info to OpenCL debug output.
• Improved memory handling in OpenCL simulations.
• Various small bugfixes.

[1.9.4] - 2014-08-13

• Added a script that installs a desktop icon for the gui under Windows.
• Added a global readme.txt.
• Various small bugfixes.

[1.9.3] - 2014-08-08

• Various small bugfixes.

[1.9.2] - 2014-08-01

• Improved ABF support.
• Various small bugfixes.

[1.9.1] - 2014-07-31

• Bugfix in GUI for Windows.

[1.9.0] - 2014-07-31

• Added stable point finding method.
• Added icons for windows version.
• Rebranding as 'Myokit' (with capital M, no more mention of the "Maastricht Myocyte Toolkit").
• Changed license to GPL.

[1.8.1] - 2014-07-16

• Various improvements and bugfixes.

[1.8.0] - 2014-07-16

• Updates to website
• Various small bugfixes.

[1.7.5] - 2014-07-10

• Added method to fold log periodically (based on split_periodic).
• Various small bugfixes.

[1.7.4] - 2014-07-08

• Various small bugfixes.

[1.7.3] - 2014-07-07

• Reinstated logging of derivatives in CVODE simulation.
• Various small bugfixes.

[1.7.2] - 2014-07-07

• Various small bugfixes.

[1.7.1] - 2014-07-07

• Added load/save methods to DataBlock1d.
• Made ICSimulation work with DataBlock2d to calculate eigenvalues.
• Various small bugfixes.

[1.7.0] - 2014-07-04

• Added a JacobianGenerator class.
• Added a simulation that integrates partial derivatives to find the derivatives of the state w.r.t. the initial conditions.
• Added latex export.
• Various small bugfixes.

[1.6.2] - 2014-06-18

• Various small bugfixes.

[1.6.1] - 2014-06-13

• Added IV curve experiment.
• Improved error detection in CVODE simulation.

[1.6.0] - 2014-06-06

• Added a diffusion on/off switch to the OpenCL simulation.
• The OpenCL sim can now replace constants by scalar fields. This allows it to be used to test parameter influence or to simulate heterogeneity.

[1.5.2] - 2014-06-04

• Better handling of unknown units.
• Added eval_state_derivs option to GUI.
• Added trim trailing whitespace method to gui.
• Gui and step script now show numerical errors if they occur.
• Added trim() and itrim() methods to simulation log.
• Added a 2-variable parameter range exploration class.
• DataBlock viewer now can export frames and graphs.
• Various improvements and bugfixes.

[1.5.1] - 2014-05-08

• Added method Model.set_name().
• Updated installer script for GNOME/KDE.
• Various small bugfixes.

[1.5.0] - 2014-04-24

• Added on Strength-Duration experiment.
• Added method to create cumulative current/charge plots.

[1.4.8] - 2014-04-22

• Changed SimulationLog.integrate() to use left-point rule instead of midpoint rule. This makes much more sense for the stimulus current when using CVODE.
• Various improvements and bugfixes.

[1.4.7] - 2014-04-17

• Various small bugfixes.

[1.4.6] - 2014-04-10

• Added RestitutionExperiment to lib.common.
• Various small bugfixes.

[1.4.5] - 2014-04-07

• Re-organised code.
• Various small bugfixes.

[1.4.4] - 2014-03-27

• Various improvements and bugfixes.

[1.4.3] - 2014-03-17

• Various small bugfixes.

[1.4.2] - 2014-03-11

• Added unit methods to IDE.
• Updated the installation guide.
• Added method to 'walk' over the operands in an expression, depth-first.
• Added a few default unit representations
• Various small bugfixes.

[1.4.0] - 2014-02-18

• Added unit checking methods.
• Improved CellML unit reading from constants.
• Added pack_snapshot() method that creates a copy of the current Myokit version.
• Created DataBlock classes for alternative view of rectangular simulation data.
• Added GUI for viewing 1D and 2D simulation data.
• Various small bugfixes.

[1.2.0] - 2014-01-27

• Changed [[plot]] to [[script]].
• Various improvements and bugfixes.

[1.1.0] - 2014-01-24

• Updated interface of opencl simulations.
• Added OpenCL-based parameter RangeTester class.
• Various small bugfixes.

[1.0.2] - 2014-01-09

• Updates to documentation.

[1.0.0] - 2013-12-24

• Improved documentation.
• Added a 'running simulations' guide.
• Added SymPy export.
• Added unit tests.
• Added binary format for simulation logs.
• Aliases are now retained in model export.
• Various small bugfixes.

[0.17.2] - 2013-12-19

• Improved documentation.
• Various small bugfixes.

[0.17.1] - 2013-12-19

• New model syntax, model stars with: [[model]].
• Various small bugfixes.

[0.17.0] - 2013-12-11

• Added binary version of save_state and load_state.
• Added ProgressPrinter to show progress during long simulations.
• Added precision switch to prepare_log and load_csv.
• Added method to find solvable equations dependent on one or more variables.
• Improved support for ABF protocol and data reading.
• Various small bugfixes.

[0.16.3] - 2013-11-06

• Improved OpenCL simulation error output.
• Various improvements and bugfixes.

[0.16.2] - 2013-11-01

• Improvements to GUI.
• Improved find_nan method in OpenCL sim.
• Added method to expression's eval() to evaluate with numpy.Float32 objects. This helps finding the source of OpenCL single-precision NaN errors.
• Various small bugfixes.

[0.16.1] - 2013-10-31

• Refactored code, reduced size of giant modules.
• Various small bugfixes.

[0.16.0] - 2013-10-31

• Added recovery-from-inactivation experiment.
• Updated ActivationExperiment, added boltzmann fit.
• Added boltzmann fit to InactivationExperiment.
• Added time constant of activation method to ActivationExperiment.
• Rewrote unit system.
• Various improvements and bugfixes.

[0.15.9] - 2013-10-22

• Various small bugfixes.

[0.15.8] - 2013-10-16

• Slight optimizations in OpenCL code.
• Various small bugfixes.

[0.15.7] - 2013-10-15

• Various small bugfixes.

[0.15.6] - 2013-10-15

• Updated step method to accept models as reference.
• Reinstated Model.load_state() method.
• Imrpoved find dialog.
• Various small bugfixes.

[0.15.5] - 2013-10-14

• Added quick var info to gui.
• Renamed current_diff to diffusion_current.

[0.15.4] - 2013-10-12

• Added on ChanneML import.
• FiberTissueSimulation now works with 2D fibers.

[0.15.2] - 2013-10-10

• Added data extraction features to abf format.
• Added on Fiber-Tissue simulation class.
• Various improvements and bugfixes.

[0.15.0] - 2013-09-18

• Number of cells to pace can now be set in OpenCLCableSimulation.
• Added function to find origin of NaN errors in an OpenCLCableSimulation.
• Updated SimulationLog to return mesh grid for pyplot.
• Added 1D CV calculation to SimulationLog.
• Renamed cable simulation classes.
• Made 1D OpenCL Simulation suitable for 2D use.
• Added method to list component cycles.
• Added a method that checks which variables cause mutually dependent components.
• Various small bugfixes.

[0.14.1] - 2013-08-23

• Fixed direction convention for diffusion current.
• Simulation log now has local and global variables (for multi-cell simulations).
• Added OpenCL export.
• Added a C header file with pacing functions, shared by several simulations.
• Added a settings file settings.py.
• Added OpenCL simulation object.
• Various small bugfixes.

[0.14.0] - 2013-07-19

• Various performance boosts.
• Rewrite of expression classes.
• Improved parser.
• Added options to move variables, delete variables.
• Improved Model.clone() method.
• Added strand simulations via Python interface.
• Various improvements and bugfixes.

[0.13.9] - 2013-06-06

• Working CUDA kernel export.

[0.13.8] - 2013-06-06

• Various small bugfixes.

[0.13.7] - 2013-06-06

• Added simple Ansi-C forward euler export.
• Various small bugfixes.

[0.13.6] - 2013-05-31

• Added progress bars to explorer in gui (F6).
• Worked on dependency graphs.
• Added meta data to components.
• Added option to SimulationLog to split into periodic pieces.
• Various improvements and bugfixes.

[0.13.5] - 2013-05-23

• Various improvements and bugfixes.

[0.13.4] - 2013-05-23

• Made engine.realtime contain the elapsed system time, not the absolute system time.
• Made SimulationLog suitable for multi-dimensional data.
• Added StrandSimulation object.
• Added Graph Data Extractor.
• Added RhsBenchmarker.
• Began work on CUDA export.
• Added Coffman-Graham algorithm for directed acyclic graph layer assignment.
• Added get_last_number_of_evaluations() method to Simulation.
• Various updates to the documentation.
• Various small bugfixes.

[0.13.0] - 2013-03-28

• Added export to strand/fiber simulation in Ansi-C.
• Added syntax for binding to external values.
• Various small bugfixes.

[0.12.7] - 2013-02-27

• Added plotting methods.
• Added benchmarking to simulation.
• Various improvements and bugfixes.

[0.12.6] - 2013-02-26

• Refactored myokit.lib.
• Added APD calculating function.
• Added APD measurement to simulation using CVode's root finding.
• Added padding function to save_csv.
• Created SimulationLog class.
• Various small bugfixes.

[0.12.4] - 2013-02-20

• Refactored import/export modules.
• Updated documentation.
• Added method to interpolate logged results.
• Improved performance in CVODE simulations.
• Added periodic logging option to simulation.
• Improved Explorer GUI.
• Added method to run euler/rk4 simulations.
• Added OrderedPiecewise class.
• Added progress bar to gui.
• Various small bugfixes.

[0.10.8] - 2013-01-15

• Bugfix in metadata export.

[0.10.7] - 2013-01-15

• Various improvements and bugfixes.

[0.10.6] - 2013-01-15

• Rewrote cellml import.
• Worked on methods to fit simplify functions.
• Updates to mmt syntax
• Added multi-line comments to mmt syntax.
• Various small bugfixes.

[0.10.5] - 2012-11-12

• Added tests.
• Added piecewise() expressions.
• Various improvements and bugfixes.

[0.10.3] - 2012-10-30

• Improved import and export interfaces.
• Added save_state() method.
• Improved documentation
• Conversion of Myokit expressions to Python functions.
• Added benchmarking methods.
• Implemented unit parsing.
• Added SBML import.
• Added methods for function simplification (via approximations).
• Introduced website.
• Various small bugfixes.

[0.9.17] - 2012-07-27

• Added local aliases to syntax.
• Simplified syntax.
• Simulation and gui now allow unlogged pacing.
• Added search function to GUI.
• Templating based exports, available from GUI.
• Import of CellML metadata.
• Added protocol wizard to GUI.
• Added simple component dependency graph to GUI.
• Added model debug options.
• Added matlab export.
• Introduced three-section mmt file.
• ABF protocol import.
• Added Sphinx-based documentation.
• Added routine that shows sizes of integrator steps.
• Various small bugfixes.

[0.9.0] - 2012-03-12

• First mmt syntax, parser and model classes.
• Initial CellML import.
• C++ export.
• Ansi-C export, python export.
• Beat script that uses generated Ansi-C and CVODE, compiled on the fly.
• First working GUI.

[0.0.0] - 2011-12-19

• Working on simple model syntax, parser and export to C++.