Merge pull request #36 from jrenaud90/0.8.0

0.8.0
jrenaud90 · Sep 6, 2023 · 148fba1 · 148fba1
2 parents f4feddf + 6bf5bc8
commit 148fba1
Show file tree

Hide file tree

Showing 33 changed files with 14,157 additions and 1,632 deletions.
diff --git a/Benchmarks/CyRK - SciPy Comparison.ipynb b/Benchmarks/CyRK - SciPy Comparison.ipynb
diff --git a/Benchmarks/CyRK_CySolver.pdf b/Benchmarks/CyRK_CySolver.pdf
diff --git a/Benchmarks/CyRK_SciPy_Compare_predprey_v0-8-0.png b/Benchmarks/CyRK_SciPy_Compare_predprey_v0-8-0.png
diff --git a/Benchmarks/CyRK_cyrk_ode.pdf b/Benchmarks/CyRK_cyrk_ode.pdf
diff --git a/Benchmarks/CyRK_numba.pdf b/Benchmarks/CyRK_numba.pdf
diff --git a/Benchmarks/SciPy.pdf b/Benchmarks/SciPy.pdf
diff --git a/...ks/CyRK_SciPy_Compare_predprey_v0-7-1.png → ...ve/CyRK_SciPy_Compare_predprey_v0-7-1.png b/...ks/CyRK_SciPy_Compare_predprey_v0-7-1.png → ...ve/CyRK_SciPy_Compare_predprey_v0-7-1.png
diff --git a/CHANGES.md b/CHANGES.md
@@ -2,6 +2,26 @@
 
 ## 2023
 
+### v0.8.0
+
+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.
+
 #### v0.7.1
 
 Changes

diff --git a/CyRK/array/interp.pxd b/CyRK/array/interp.pxd
@@ -2,6 +2,8 @@
 
 cdef Py_ssize_t binary_search_with_guess(double key, double[:] array, Py_ssize_t length, Py_ssize_t guess) noexcept nogil
 
+cdef Py_ssize_t binary_search_with_guess_ptr(double key, double* array, Py_ssize_t length, Py_ssize_t guess) noexcept nogil
+
 cpdef (double, Py_ssize_t) interpj(double desired_x, double[:] x_domain, double[:] dependent_values,
                                     Py_ssize_t provided_j = *) noexcept nogil
 
@@ -17,5 +19,11 @@ cpdef double complex interp_complex(double desired_x, double[:] x_domain, double
 cpdef void interp_array(double[:] desired_x_array, double[:] x_domain, double[:] dependent_values,
                         double[:] desired_dependent_array) noexcept nogil
 
+cdef void interp_array_ptr(double* desired_x_array, double* x_domain, double* dependent_values,
+                            double* desired_dependent_array, Py_ssize_t len_x, Py_ssize_t desired_len) noexcept nogil
+
 cpdef void interp_complex_array(double[:] desired_x_array, double[:] x_domain, double complex[:] dependent_values,
-                                double complex[:] desired_dependent_array) noexcept nogil
+                                double complex[:] desired_dependent_array) noexcept nogil
+
+cdef void interp_complex_array_ptr(double* desired_x_array, double* x_domain, double complex* dependent_values,
+                                   double complex* desired_dependent_array, Py_ssize_t len_x, Py_ssize_t desired_len) noexcept nogil