CyRK v0.8.0

Changes

New Features

• Added new interp functions that work with c pointers. These can only be cimported.
• Added new "CyRK.cy.common.pyx" file for functions that are used by both cyrk_ode and CySolver.
  • Moved interpolation functionality into CyRK.cy.common. Restructured cyrk_ode and CySolver to use this new function for interpolations.

Changes:

• Refactored many CySolver internal attributes to reflect to change from memoryviews to pointers. The most important ones for the user are:
  • CySolver.y_new_view -> CySolver.y_ptr
  • CySolver.dy_new_view -> CySolver.dy_ptr
  • CySolver.t_new -> CySolver.t_now
  • CySolver.arg_array_view -> CySolver.args_ptr
• Changed RK constants back to c arrays initialized with PyMem_Malloc. The memory for these arrays are setup in the cython-based solvers. Afterwards, there are helper functions in CyRK.rk to populate the arrays with correct values.
• Moved to a more generalized scheme for compiling cython files. See "cython_extensions.json", "_build_cyrk.py", and "setup.py" for details.

Performance

• Transitioned many arrays from numpy to c arrays allocated with PyMem_Malloc, etc. These changes led to a significant performance boost for cython-based solvers.
• Copied some performance lessons that were learned from the cython-based solvers to the numba-based nbrk_ode.

GitHub Tracked Changes

• 0.8.0 by @jrenaud90 in #36

Full Changelog: v0.7.1...v0.8.0

CyRK v0.7.1

Changes

Other Changes

• Changed cyrk_ode to match the format used by CySolver for its rk_step.

Performance

• Minor calculation taken out of tight inner loops in cython-based solvers.

Bug Fixes

• Added back noexcepts to dabs functions used by cyrk_ode that were mistakenly removed in final dev commit of v0.7.0.
• Fixed issue where cython-based solvers could overshoot t_span[1].
• Fixed issue where interp functions would give wrong result when requested x was between x_array[0] and x_array[1].
• Fixed issue where interp functions would give wrong results if requested x was negative and x_array was positive (or vice versa).
• The use of carrays for RK constants led to floating point rounding differences that could impact results when step sizes are small.
  • Converted RK constants to numpy arrays which seem to handle the floats much better.
  • Also changed the interaction with these variables to be done solely through constant memoryviews. This may provide a bit of a performance boost.

GitHub Tracked Changes

• 0.7.1 by @jrenaud90 in #35

Full Changelog: v0.7.0...v0.7.1

CyRK v0.7.0

Changes

Major Changes

• Added support for Cython 3.0.0
  • Added noexcept to pure cython functions to avoid a potential python error check.

New Features

• Added the ability to pass arrayed versions of rtol and atol to both the numba and cython-based solvers (cyrk_ode and CySolver).
  • For both solvers, you can pass the optional argument "rtols" and/or "atols". These must be C-contiguous numpy arrays with float64 dtypes. They must have the same size as y0.
  • Added tests to check functionality for all solvers.
  • This resolves Issue #1.
• Added new optional argument to all solvers max_num_steps which allows the user to control how many steps the solver is allowed to take.
  • If exceeded the integration with fail (softly).
  • Defaults to 95% of sys.maxsize (depends on system architecture).
• New CySolver.update_constants method allows for significant speed boosts for certain differential equations.
  • See test diffeqs, which have been updated to use this feature, for examples.

Other Changes

• Improved documentation for most functions and classes.
• To make more logical sense with the wording, CySolver.size_growths now gives one less than the solver's growths attribute.
• Cleaned up status codes and created new status code description document under "Documentation/Status and Error Codes.md"
• Fixed compile warning related to NPY_NO_DEPRECATED_API.
• Converted RK variable lengths to Py_ssize_t types.
• Changed default tolerances to match scipy: rtol=1.0e-3, atol=1.0e-6.

Performance

• Various minor performance gains for cython-based solvers.
• Moved key loops in CySolver into self-contained method so that gil can be released.
• New CySolver.update_constants method allows for significant speed boosts for certain differential equations.

Bug Fixes:

• Fixed potential seg fault when accessing CySolver's arg_array_view.
• Fixed potential issue where CySolver's first step size may not be reset when variables that affect it are.
• Fixed missed declaration in cyrk_ode.
• Fixed bug where the state reset flag was not being passed from CySolver.solve wrapper method.

GitHub Tracked Changes

• v0.7.0 by @jrenaud90 in #34

Full Changelog: v0.6.2...v0.7.0

CyRK v0.6.2

Changes

New Features

• Added auto_solve key word to CySolver class. This flag defaults to True. If True, then the solver will automatically call self.solve() after initialization.
• Added new parameter change functions to CySolver so that certain parameters can be changed after the class is initialized for a performance boost.
  • Look for the "self.change_*" methods in cysolver.pyx/pxd. There is a main change method, CySolver.change_parameters which allows you to change multiple parameters at once.

Bug Fixes:

• Fixed issue where CySolver could give incorrect results if the solve() method was called multiple times on the same instance.
• Removed extraneous code from CySolver.__init__.
• Changed several cython integer variables to all use Py_ssize_t types. Corrected type conversions.

GitHub Tracked Changes

• V0.6.2 by @jrenaud90 in #33

Full Changelog: v0.6.1...v0.6.2

CyRK v0.6.1

Changes

New Features

• Added top level parameters (like MAX_STEP) used in CySolver to cysolver.pxd so they can be cimported.
• Added new argument to array.interp and array.interp_complex: provided_j the user can provide a j index,
  allowing the functions to skip the binary search.
• Added new function interpj to array module that outputs the interpolation result as well as the j index that was found.

Bug Fixes

• Fixed issue with array tests not actually checking values.

Other Changes

• Reordered tests since numba tests take the longest.
• Added initializedcheck=False to the array module compile arguments.

GitHub Tracked Changes

• 0.6.1 by @jrenaud90 in #32

Full Changelog: v0.6.0...v0.6.1

CyRK v0.6.0

Changes

New Features

• CyRK now works with python 3.11.
• Created the CySolver class which is more efficient than the cyrk_ode function.
  • Solves issue 28
• New functions in CyRK.cy.cysolvertest to help test and check performance of CySolver.

Performance

• Removed python lists from cyrk_ode leading to an increase in performance of 15--20%.
  • Solves issue 27

Bug Fixes:

• Fixed compile error with cyrk_ode "complex types are unordered".
  • This was not a problem before so likely something has changed in newer cython versions.
• Fixed missing declarations for variables in cyrk_ode.
• Fixed potential problems during installation where paths may be incorrect depending on OS.

GitHub Tracked Changes

• V0.6.0 by @jrenaud90 in #29

Full Changelog: v0.5.3...v0.6.0

CyRK v0.5.3

Changes

Performance

• Removed dynamic optional arguments from cyrk_ode. Now it checks if those arguments are set to None.

Other Changes

• Changed cyrk_ode arguments to const to avoid memoryview buffer problems. (Change made by David Meyer)

GitHub Tracked Changes

• Allow read-only buffers for initial conditions of cython solver by @dihm in #26

Full Changelog: v0.5.2...v0.5.3

CyRK v0.5.2

Changes

• Fixed issue with MacOS wheel on pypi

Full Changelog: v0.5.1...v0.5.2

CyRK v0.5.1

Changes

• Fixed issue with MacOS Wheel build

Github Change Log

Full Changelog: v0.5.0...v0.5.1

CyRK v0.5.0

Changes

New Features

• cyrk_ode now supports both float and complex-typed y and dydt functions.
  • Resolves issue 3. (Fix made by David Meyer)

Performance

• Converted various ints to shorts, chars, or Py_ssize_t. Py_ssize_t is recommended by Cython for loop integers to better support 64-bit architecture.
• Added custom interpolation functions which, depending on the size of the array, can be up to 10x faster than numpys.
• Removed unnecessarily variables from cyrk_ode.
• Had to turn off fastmath for nbrk_ode. See issue 24. This negatively impacted the numba integrator's performance by around 5%.

Other Changes:

• Refactored, cleaned up, and added comments and docstrings to cyrk_ode.
• Changed both nbrk_ode and cyrk_ode tests to use pytest parameterization.
• Changed the accuracy test for both nbrk_ode and cyrk_ode to check against a known function.
• Added openmp dependence during compile time to allow for the use of prange.
• Moved cyrk_ode's Runge-Kutta constants to a separate module CyRK.rk.

Bug Fixes:

• Fixed issue (for nbrk_ode and cyrk_ode) where incorrect step size could be used due to bad minimum step check (see issue 20).

GitHub Generated Change Log

• 0.5.0 by @jrenaud90 and @dihm in #25

Full Changelog: v0.4.0...v0.5.0