Merge branch 'v0.8.6' into testing-python-versions

.gitignore

@@ -5,6 +5,7 @@
 
 # Include non-generated c files
 !CyRK/array/interp_common.c
+!CyRK/cy/rk_step.c
 
 # Ignore coverage files
 .coverage
@@ -17,6 +18,7 @@ __pycache__/
 # Objext files
 *.so
 *.o
+*.exe
 
 # Distribution / packaging
 .Python

.vscode/settings.json

@@ -0,0 +1,58 @@
+{
+    "files.associations": {
+        "iterator": "c",
+        "xmemory": "c",
+        "xutility": "c",
+        "atomic": "c",
+        "bit": "c",
+        "cctype": "c",
+        "charconv": "c",
+        "clocale": "c",
+        "cmath": "c",
+        "compare": "c",
+        "complex": "c",
+        "concepts": "c",
+        "cstddef": "c",
+        "cstdint": "c",
+        "cstdio": "c",
+        "cstdlib": "c",
+        "cstring": "c",
+        "ctime": "c",
+        "cwchar": "c",
+        "exception": "c",
+        "format": "c",
+        "initializer_list": "c",
+        "ios": "c",
+        "iosfwd": "c",
+        "istream": "c",
+        "limits": "c",
+        "locale": "c",
+        "memory": "c",
+        "mutex": "c",
+        "new": "c",
+        "ostream": "c",
+        "ratio": "c",
+        "sstream": "c",
+        "stdexcept": "c",
+        "stop_token": "c",
+        "streambuf": "c",
+        "string": "c",
+        "system_error": "c",
+        "thread": "c",
+        "tuple": "c",
+        "type_traits": "c",
+        "typeinfo": "c",
+        "utility": "c",
+        "xfacet": "c",
+        "xiosbase": "c",
+        "xlocale": "c",
+        "xlocbuf": "c",
+        "xlocinfo": "c",
+        "xlocmes": "c",
+        "xlocmon": "c",
+        "xlocnum": "c",
+        "xloctime": "c",
+        "xstring": "c",
+        "xtr1common": "c"
+    }
+}

.vscode/tasks.json

@@ -0,0 +1,28 @@
+{
+    "tasks": [
+        {
+            "type": "cppbuild",
+            "label": "C/C++: gcc.exe build active file",
+            "command": "C:\\Software\\mingw64\\bin\\gcc.exe",
+            "args": [
+                "-fdiagnostics-color=always",
+                "-g",
+                "${file}",
+                "-o",
+                "${fileDirname}\\${fileBasenameNoExtension}.exe"
+            ],
+            "options": {
+                "cwd": "${fileDirname}"
+            },
+            "problemMatcher": [
+                "$gcc"
+            ],
+            "group": {
+                "kind": "build",
+                "isDefault": true
+            },
+            "detail": "Task generated by Debugger."
+        }
+    ],
+    "version": "2.0.0"
+}

CHANGES.md

@@ -6,10 +6,15 @@
 
 Major Changes:
 - Added support for Python 3.12.
+- Converted `CySolver`'s `rk_step` method into a pure-c implementation to allow for further optimizations.
+- Changed all files to compile with c rather than c++.
+  - Had to change cpp_bools to bints to make this change.
 
 Bug Fixes:
 - Fixed issue where CyRK was not installing on MacOS due to issue with LLVM and OpenMP. 
   - Have opted to go to gcc for macOS install due to issues with OpenMP and clang.
+- Fixed incorrect type for rk method in CySolver (should eliminate some compile warnings).
+- Fixed issue in benchmark where incorrect results were being displayed for CySolver.
 
 #### v0.8.5 (2023-10-27)
 

CyRK/array/interp.pyx

@@ -1,4 +1,4 @@
-# distutils: language = c++
+# distutils: language = c
 # cython: boundscheck=False, wraparound=False, nonecheck=False, cdivision=True, initializedcheck=False
 from cython.parallel import prange
 

CyRK/cy/common.pxd

@@ -1,10 +1,8 @@
-# distutils: language = c++
+
 ctypedef fused double_numeric:
     double
     double complex
 
-from libcpp cimport bool as bool_cpp_t
-
 cdef double SAFETY
 cdef double MIN_FACTOR
 cdef double MAX_FACTOR
@@ -33,16 +31,16 @@ cdef void interpolate(
         size_t t_len_full,
         size_t t_len_reduced,
         size_t target_len,
-        bool_cpp_t is_complex
+        bint is_complex
         ) noexcept
 
 cdef size_t find_expected_size(
         size_t y_size,
         size_t num_extra,
         double t_delta_abs,
         double rtol_min,
-        bool_cpp_t capture_extra,
-        bool_cpp_t is_complex
+        bint capture_extra,
+        bint is_complex
         ) noexcept nogil
 
 
@@ -51,7 +49,7 @@ cdef void find_max_num_steps(
         size_t num_extra,
         size_t max_num_steps,
         size_t max_ram_MB,
-        bool_cpp_t capture_extra,
-        bool_cpp_t is_complex,
-        bool_cpp_t* user_provided_max_num_steps,
+        bint capture_extra,
+        bint is_complex,
+        bint* user_provided_max_num_steps,
         size_t* max_num_steps_touse) noexcept nogil

CyRK/cy/common.pyx

@@ -1,4 +1,4 @@
-# distutils: language = c++
+# distutils: language = c
 # cython: boundscheck=False, wraparound=False, nonecheck=False, cdivision=True, initializedcheck=False
 import cython
 
@@ -46,7 +46,7 @@ cdef void interpolate(
         size_t t_len_full,
         size_t t_len_reduced,
         size_t target_len,
-        bool_cpp_t is_complex
+        bint is_complex
         ) noexcept:
     """ Interpolate the results of a successful integration over the user provided time domain, `time_domain_full`. """
 
@@ -107,8 +107,8 @@ cdef size_t find_expected_size(
         size_t num_extra,
         double t_delta_abs,
         double rtol_min,
-        bool_cpp_t capture_extra,
-        bool_cpp_t is_complex) noexcept nogil:
+        bint capture_extra,
+        bint is_complex) noexcept nogil:
 
     cdef double temp_expected_size
     # Pick starting value that works with most problems
@@ -145,9 +145,9 @@ cdef void find_max_num_steps(
         size_t num_extra,
         size_t max_num_steps,
         size_t max_ram_MB,
-        bool_cpp_t capture_extra,
-        bool_cpp_t is_complex,
-        bool_cpp_t* user_provided_max_num_steps,
+        bint capture_extra,
+        bint is_complex,
+        bint* user_provided_max_num_steps,
         size_t* max_num_steps_touse) noexcept nogil:
 
     # Determine max number of steps

CyRK/cy/cyrk.pyx

@@ -1,4 +1,4 @@
-# distutils: language = c++
+# distutils: language = c
 # cython: boundscheck=False, wraparound=False, nonecheck=False, cdivision=True, initializedcheck=False
 
 import cython
@@ -7,9 +7,7 @@ from cpython.mem cimport PyMem_Free
 
 import numpy as np
 cimport numpy as np
-np.import_array()
 
-from libcpp cimport bool as bool_cpp_t
 from libc.math cimport sqrt, fabs, nextafter, NAN, floor
 
 from CyRK.utils.utils cimport allocate_mem, reallocate_mem
@@ -80,9 +78,9 @@ def cyrk_ode(
         double first_step = 0.,
         unsigned char rk_method = 1,
         double[:] t_eval = None,
-        bool_cpp_t capture_extra = False,
+        bint capture_extra = False,
         size_t num_extra = 0,
-        bool_cpp_t interpolate_extra = False,
+        bint interpolate_extra = False,
         size_t expected_size = 0,
         size_t max_num_steps = 0,
         size_t max_ram_MB = 2000
@@ -148,7 +146,7 @@ def cyrk_ode(
             ```
     num_extra : int = 0
         The number of extra outputs the integrator should expect. With the previous example there is 1 extra output.
-    interpolate_extra : bool_cpp_t, default=False
+    interpolate_extra : bint, default=False
         Flag if interpolation should be run on extra parameters.
         If set to False when `run_interpolation=True`, then interpolation will be run on solution's y, t. These will
         then be used to recalculate extra parameters rather than an interpolation on the extra parameters captured
@@ -181,7 +179,7 @@ def cyrk_ode(
     # Determine information about the differential equation based on its initial conditions
     cdef size_t y_size
     cdef double y_size_dbl, y_size_sqrt
-    cdef bool_cpp_t y_is_complex
+    cdef bint y_is_complex
     y_size       = y0.size
     y_is_complex = False
     y_size_dbl   = <double>y_size
@@ -201,7 +199,7 @@ def cyrk_ode(
 
     # Build time domain
     cdef double t_start, t_end, t_delta, t_delta_check, t_delta_abs, direction_inf, t_old, t_now, time_
-    cdef bool_cpp_t direction_flag
+    cdef bint direction_flag
     t_start       = t_span[0]
     t_end         = t_span[1]
     t_delta       = t_end - t_start
@@ -218,7 +216,7 @@ def cyrk_ode(
         direction_inf = -INF
 
     # Pull out information on args
-    cdef bool_cpp_t use_args
+    cdef bint use_args
     if args is None:
         use_args = False
     else:
@@ -271,7 +269,7 @@ def cyrk_ode(
 
     # Determine max number of steps
     cdef size_t max_num_steps_touse
-    cdef bool_cpp_t user_provided_max_num_steps
+    cdef bint user_provided_max_num_steps
     find_max_num_steps(
         y_size,
         num_extra,
@@ -363,7 +361,7 @@ def cyrk_ode(
     cdef double_numeric[::1] diffeq_out_view = diffeq_out_array
 
     # Determine interpolation information
-    cdef bool_cpp_t run_interpolation
+    cdef bint run_interpolation
     cdef size_t len_t_eval
     if t_eval is None:
         run_interpolation = False
@@ -486,7 +484,7 @@ def cyrk_ode(
     cdef double step, step_size, min_step, step_factor
 
     # Integration flags and variables
-    cdef bool_cpp_t success, step_accepted, step_rejected, step_error
+    cdef bint success, step_accepted, step_rejected, step_error
     cdef size_t len_t
 
     # Integration completion variables
@@ -666,7 +664,7 @@ def cyrk_ode(
                                     # Initialize
                                     y_view[i] = y_old_ptr[i]
 
-                                y_view[i] += K_ptr[j * y_size + i] * A_at_sj
+                                y_view[i] = y_view[i] + K_ptr[j * y_size + i] * A_at_sj
 
                     if use_args:
                         diffeq(time_, y_array, diffeq_out_array, *args)
@@ -686,7 +684,7 @@ def cyrk_ode(
                             # Initialize
                             y_view[i] = y_old_ptr[i]
 
-                        y_view[i] += K_ptr[j * y_size + i] * B_at_j
+                        y_view[i] = y_view[i] + K_ptr[j * y_size + i] * B_at_j
 
                 # Find final dydt for this timestep
                 if use_args: