Chaste-codegen

- The singularities fixing code from release 0.6.3 has moved to the latest cellmlmanip release (0.3.0). You may see small differences in generated code, due to singularities now being fixed prior to any unit conversion taking place. These should not cause any differences in results when run with chaste.
- Improved capacitance unit checking.

- Fixed issue with backward euler opt models where unused state variables appeard in ComputeResidual
- Fixed memory leek on generated models within lookup table interpolation on nan/inf values in singularities.
- Removed chaste warnings from backward euler template for cases where inf/nan would end up in the table. Intead an error is thrown when multiple (more than 2) such warnings happen.

- Added an automatic fix for removable singularities in GHK equations (which can be switched off with --skip-ingularity-fixes).
The process looks for equations of any of the following forms, where U is a function of V:
- `U / (exp(U) - 1.0)`
- `U / (1.0 - exp(U))`
- `(exp(U) - 1.0) / U`
- `(1.0 - exp(U)) / U`
It replaces these with a piecewise 1e-7 either side of U==0 drawing a stright line in the region.
For example `(V + 5)/(exp(V + 5) - 1)` becomes `((fabs(-V - 5.0000000000000000) < fabs(-4.9999999000000000 / 2 - -5.0000001000000000 / 2)) ? ((-5.0000001000000000 + 5.0) / (-1.0 + exp(-5.0000001000000000 + 5.0)) + (--5.0000001000000000 + V) * ((-4.9999999000000000 + 5.0) / (-1.0 + exp(-4.9999999000000000 + 5.0)) - (-5.0000001000000000 + 5.0) / (-1.0 + exp(-5.0000001000000000 + 5.0))) / (--5.0000001000000000 - 4.9999999000000000)) : ((5.0 + V) / (-1.0 + exp(5.0 + V))))`

See for more details appendix B in: Johnstone, R. H. (2018). Uncertainty characterisation in action potential modelling for cardiac drug safety [PhD thesis]. University of Oxford. https://ora.ox.ac.uk/objects/uuid:0a28829c-828d-4641-bfb0-11193ef47195
- For lookup tables prevented expressions of the form 1 / A from being added, instead adding A. 1 / A type expressions were causing issues, when A is 0. While many cases have a piecewise to prevent hissing this case, lookup table interpolation might cause issues.
- Updated the way BackwardEuler models are calculated, to allow the jacobian to be taken into consideration for lookup tables.
- Fixed a bug with BackwardEuler models where jacobian common term equations (e.g. var_x0) ended up in lookup tables.

- Fixed sympy deprecation warning when using sympy 1.7 and bumped cellmlmanip recuirement up to ensure sympy 1.7 compatibility
- Improved support for secondary trigonometric functions such as sec and acoth.
- When used with Cellmlmanip version 0.2.2+ an improved printing of devisions is used. For example `1 / (1/cos(x))` now gets rendered as `cos(x)` whereas previously it would be `1 / 1 / cos(x)` giving the incorrect result. An side effcet of the change is that powers of formulas get extra brackets e.g. `pow((1 / x), 2)`.
- chaste_codegen uses placeholder functions for some common maths functions like exp, in order to delay evaluation till the point where the code is written. For programmers using chaste_codegen as a library, there now is a function called `subs_math_func_placeholders` which can be used on any sympy expression to substitute these placeholders.
E.g.

>> expr
2.0 * exp_(V)
>> subs_math_func_placeholders(expr)
2.0 * exp(V)

- Added an additional error messages if cellml files can't be loaded and a warning if a lookup table is specified for a tag not present in the model.

- Error messages have been improved, especially for errors caused by invalid or missing metadata.

- Corrected usage mentioned in the readme