Myokit

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

- Fixed
- [873](https://github.com/myokit/myokit/pull/873) Small bugfixes and improvements in numerical error reporting in `FiberTissueSimulation`.
- [873](https://github.com/myokit/myokit/pull/873) Fixed argument list in docstring of `FiberTissueSimulation`.

- Added
- [869](https://github.com/myokit/myokit/pull/869) Added methods `myokit.FiberTissueSimulation.fiber_shape` and `.tissue_shape` (but see [https://github.com/myokit/myokit/issues/764] for an important open issue).
- [869](https://github.com/myokit/myokit/pull/869) Added a method `myokit.FiberTissueSimulation.step_size()`.
- Changed
- [865](https://github.com/myokit/myokit/pull/865) Added more platform information to `myokit system`.
- [866](https://github.com/myokit/myokit/pull/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](https://github.com/myokit/myokit/pull/869) The class `myokit.FiberTissueSimulation` now raises `ValueError` for various method-argument errors, instead of the more generic `Exception`.
- [869](https://github.com/myokit/myokit/pull/869) The class `myokit.FiberTissueSimulation` now raises `IndexError` for various index-related errors, instead of the less appropriate `KeyError`.
- Deprecated
- [869](https://github.com/myokit/myokit/pull/869) The class `myokit.FiberTissueSimulation` is no longer considered deprecated.
- Fixed
- [867](https://github.com/myokit/myokit/pull/867) DavAug Fixed a memory leak in `myokit.Simulation`.
- [869](https://github.com/myokit/myokit/pull/869) Added a missing ``y`` argument to `FiberTissueSimulation.fiber_state()` and `FiberTissueSimulation.tissue_state()`.
- [869](https://github.com/myokit/myokit/pull/869) Fixed out-of-range checking in `FiberTissueSimulation` `state` and `set_state` methods.

- Changed
- [860](https://github.com/myokit/myokit/pull/860) Made `myokit.tests` into a module. Made tests runnable via `setup.py`. Added more meta data to `setup.py`.

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

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