Updated documentation; removed macos test skips

jrenaud90 · Dec 2, 2024 · 814c3c9 · 814c3c9
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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_CySolver_DenseOn.pdf b/Benchmarks/CyRK_CySolver_DenseOn.pdf
diff --git a/Benchmarks/CyRK_PySolver (njit).pdf b/Benchmarks/CyRK_PySolver (njit).pdf
diff --git a/Benchmarks/CyRK_PySolver.pdf b/Benchmarks/CyRK_PySolver.pdf
diff --git a/Benchmarks/CyRK_SciPy_Compare_predprey_v0-12-0.png b/Benchmarks/CyRK_SciPy_Compare_predprey_v0-12-0.png
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/...s/CyRK_SciPy_Compare_predprey_v0-11-4.png → ...e/CyRK_SciPy_Compare_predprey_v0-11-4.png b/...s/CyRK_SciPy_Compare_predprey_v0-11-4.png → ...e/CyRK_SciPy_Compare_predprey_v0-11-4.png
diff --git a/CHANGES.md b/CHANGES.md
@@ -18,6 +18,7 @@ Fixes:
 Tests:
 * Fixed tests where additional args were not being used.
 * Fixed issue with diffeq test 5.
+  * This fixes GitHub Issue [#67](https://github.com/jrenaud90/CyRK/issues/67)
 
 Documentation:
 * Updated the "Advanced CySolver.md" documentation that was out of date.

diff --git a/CyRK/cy/cysolve.cpp b/CyRK/cy/cysolve.cpp
@@ -1,7 +1,6 @@
 #include "cysolve.hpp"
 #include <exception>
 
-#include <cstdio>
 
 void baseline_cysolve_ivp_noreturn(
         std::shared_ptr<CySolverResult> solution_sptr,
@@ -35,7 +34,6 @@ void baseline_cysolve_ivp_noreturn(
     const double t_end         = t_span_ptr[1];
     const bool direction_flag  = t_start <= t_end ? true : false;
     const bool forward = direction_flag == true;
-    printf("t_start = %e; t_end = %e; direction_flag = %d; forward = %d\n", t_start, t_end, direction_flag, forward);
     const bool t_eval_provided = t_eval ? true : false;
 
     // Get new expected size

diff --git a/CyRK/cy/cysolver.cpp b/CyRK/cy/cysolver.cpp
@@ -1,4 +1,3 @@
-#include <cstdio>
 #include "cysolver.hpp"
 #include "dense.hpp"
 #include "cysolution.hpp"
@@ -67,29 +66,11 @@ CySolverBase::CySolverBase(
     {
         // Allocate memory for the size of args.
         // Store void pointer to it.
-        printf("Pre resize; size = %d\n", this->size_of_args);
-        printf("Pre resize; VECTOR size = %d\n", this->args_char_vec.size());
         this->args_char_vec.resize(this->size_of_args);
 
-        for (size_t i = 0; i < this->size_of_args; i++)
-        {
-            printf("\t %x\n", args_ptr[i] & 0xff);
-        }
-
-
         // Copy over contents of arg
-        printf("Pre Copy Over: arg_in_char = %p; sizeof = %d; args_in_char+size = %p\n", args_ptr, this->size_of_args, args_ptr + this->size_of_args);
-        // this->args_char_vec.insert(this->args_char_vec.begin(), args_ptr, args_ptr + this->size_of_args);
         this->args_ptr = this->args_char_vec.data();
         std::memcpy(this->args_ptr, args_ptr, this->size_of_args);
-
-        printf("Vector array size = %d\n", this->args_char_vec.size());
-        for (size_t i = 0; i < this->args_char_vec.size(); i++)
-        {
-            printf("\t %x\n", this->args_char_vec[i] & 0xff);
-        }
-
-        printf("Post\n");
     }
     else
     {
@@ -183,7 +164,6 @@ CySolverBase::CySolverBase(
 // Destructors
 CySolverBase::~CySolverBase()
 {
-    printf("CySolver Deconstructor called.\n");
     if (this->deconstruct_python)
     {
         // Decrease reference count on the cython extension class instance

diff --git a/CyRK/cy/cysolver_api.pyx b/CyRK/cy/cysolver_api.pyx
@@ -6,8 +6,6 @@ import numpy as np
 cimport numpy as cnp
 cnp.import_array()
 
-from libc.stdio cimport printf
-
 # =====================================================================================================================
 # Import CySolverResult (container for integration results)
 # =====================================================================================================================

diff --git a/CyRK/cy/cysolver_test.pyx b/CyRK/cy/cysolver_test.pyx
@@ -2,12 +2,9 @@
 # cython: boundscheck=False, wraparound=False, nonecheck=False, cdivision=True, initializedcheck=False
 
 from libcpp cimport bool as cpp_bool
-from libcpp.memory cimport make_shared, shared_ptr
-from libcpp.vector cimport vector
 from libcpp.limits cimport numeric_limits
-from libc.math cimport sin, cos, fabs, fmin, fmax
+from libc.math cimport sin, cos
 from libc.stdlib cimport malloc, free, realloc
-from libc.stdio cimport printf
 
 cdef double d_NAN = numeric_limits[double].quiet_NaN()
 
@@ -156,7 +153,6 @@ cdef void arbitrary_arg_test(double* dy_ptr, double t, double* y_ptr, char* args
     cdef double g = arb_args_ptr.g
     cdef cpp_bool cause_fail = arb_args_ptr.cause_fail
     cdef cpp_bool checker    = arb_args_ptr.checker
-    printf("arbitrary_arg_test:: l = %e, m = %e, g = %e; cause_fail = %d\n", l, m, g, cause_fail)
 
     cdef double coeff_1 = (-3. * g / (2. * l))
     cdef double coeff_2 = (3. / (m * l**2))
@@ -224,31 +220,22 @@ cdef void pendulum_preeval_diffeq(double* dy_ptr, double t, double* y_ptr, char*
 
 def cy_extra_output_tester():
 
-    printf("cy_extra_output_tester Pt1\n")
-
     cdef double[2] t_span = [0., 10.]
     cdef double* t_span_ptr = &t_span[0]
 
-    printf("cy_extra_output_tester Pt2\n")
     cdef double[3] y0 = [1., 0., 0]
     cdef double* y0_ptr = &y0[0]
 
-    printf("cy_extra_output_tester Pt3\n")
     cdef size_t num_y     = 3
     cdef size_t num_extra = 3
     cdef int int_method   = 1
 
-    printf("cy_extra_output_tester Pt4\n")
-    cdef size_t arg_size = sizeof(double)*3
-    printf("cy_extra_output_tester Pt5\n")
+    cdef size_t arg_size = sizeof(double) * 3
     cdef double* args_ptr = <double*>malloc(arg_size)
-    printf("cy_extra_output_tester Pt6\n")
     args_ptr[0] = 10.0
     args_ptr[1] = 28.0
     args_ptr[2] = 8.0 / 3.0
-    printf("cy_extra_output_tester Pt7\n")
-
-    printf("cy_extra_output_tester Pt8\n")
+
     cdef CySolveOutput result = cysolve_ivp(
         lorenz_extraoutput_diffeq,
         t_span_ptr,
@@ -261,18 +248,14 @@ def cy_extra_output_tester():
         arg_size,
         num_extra
         )
-    printf("cy_extra_output_tester Pt9\n")
 
     cdef double dy1, dy2, dy3, e1, e2, e3
     cdef double check_t = 4.335
 
     # Call the result to get the baseline values for extra output
-    printf("cy_extra_output_tester Pt10\n")
     cdef double[6] y_interp
     cdef double* y_interp_ptr = &y_interp[0]
-    printf("cy_extra_output_tester Pt11\n")
     result.get().call(check_t, y_interp_ptr)
-    printf("cy_extra_output_tester Pt12\n")
     dy1 = y_interp_ptr[0]
     dy2 = y_interp_ptr[1]
     dy3 = y_interp_ptr[2]
@@ -284,25 +267,23 @@ def cy_extra_output_tester():
     args_ptr[0] = -99.0
     args_ptr[1] = -99.0
     args_ptr[2] = -99.0
-    printf("cy_extra_output_tester Pt13\n")
-    args_ptr = <double*>realloc(args_ptr, sizeof(double)*50)
+    args_ptr = <double*>realloc(args_ptr, sizeof(double) * 50)
     cdef size_t i 
     for i in range(50):
         args_ptr[i] = -99.0
 
 
     # Recall the solution to see if it still produces the expected values
-    printf("cy_extra_output_tester Pt14\n")
     result.get().call(check_t, y_interp_ptr)
-    printf("cy_extra_output_tester Pt15\n")
 
     np.testing.assert_allclose(dy1, y_interp_ptr[0])
     np.testing.assert_allclose(dy2, y_interp_ptr[1])
     np.testing.assert_allclose(dy3, y_interp_ptr[2])
     np.testing.assert_allclose(e1, y_interp_ptr[3])
     np.testing.assert_allclose(e2, y_interp_ptr[4])
     np.testing.assert_allclose(e3, y_interp_ptr[5])
-    printf("cy_extra_output_tester Pt16\n")
+
+    free(args_ptr)
 
     return True
 
@@ -324,7 +305,6 @@ def cytester(
         double max_step = MAX_STEP,
         double first_step = 0.0
         ):
-    printf("Cytester pt0\n")
     cdef size_t i
     cdef double* t_eval_ptr = NULL
     cdef size_t len_t_eval = 0
@@ -342,7 +322,6 @@ def cytester(
     cdef size_t num_extra = 0
     cdef DiffeqFuncType diffeq = NULL
     cdef PreEvalFunc pre_eval_func = NULL
-    printf("Cytester pt1\n")
     if diffeq_number == 0:
         diffeq = baseline_diffeq
     elif diffeq_number == 1:
@@ -366,7 +345,6 @@ def cytester(
         pre_eval_func = pendulum_preeval_func
     else:
         raise NotImplementedError
-    printf("Cytester pt2\n")
 
     # Set up additional argument information
     cdef char* args_ptr = NULL
@@ -380,7 +358,6 @@ def cytester(
     cdef ArbitraryArgStruct arb_arg_struct = ArbitraryArgStruct(1.0, False, True, 1.0, 9.81)
 
     # Check if generic testing was requested.
-    printf("Cytester pt3\n")
     if y0 is None:
         # Generic Testing Requested
 
@@ -482,7 +459,6 @@ def cytester(
         else:
             raise NotImplementedError
     else:
-        printf("Cytester pt4bn")
         # Regular testing requested.
         num_y = len(y0)
         for i in range(num_y):
@@ -501,7 +477,6 @@ def cytester(
         size_of_args = sizeof(args_arr)
 
     # Parse rtol
-    printf("Cytester pt5\n")
     cdef double* rtols_ptr = NULL
     if rtol_array is not None:
         rtols_ptr = &rtol_array[0]
@@ -511,10 +486,6 @@ def cytester(
     if atol_array is not None:
         atols_ptr = &atol_array[0]
 
-
-    printf("EXTRA ARGS SIZE = %d; Ptr = %p\n", size_of_args, args_ptr)
-
-    printf("PRE CySolve\n")
     cdef CySolveOutput result = cysolve_ivp(
         diffeq,
         t_span_ptr,
@@ -538,8 +509,6 @@ def cytester(
         first_step = first_step,
         expected_size = expected_size
         )
-    printf("POST CySolve\n")
-
     cdef WrapCySolverResult pysafe_result = WrapCySolverResult()
     pysafe_result.set_cyresult_pointer(result)
 

diff --git a/Demos/1 - Getting Started.ipynb b/Demos/1 - Getting Started.ipynb