Merge pull request #34 from jrenaud90/v0.7.0

v0.7.0

.coveragerc

@@ -1,4 +1,5 @@
 [run]
+plugins = Cython.Coverage
+source = CyRK
 omit =
     Tests/*
-    CyRK/cy/_cyrk.pyx

.github/workflows/push_tests_ubun.yml

@@ -42,7 +42,7 @@ jobs:
       - name: Install Dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install pytest pytest-cov
+          python -m pip install pytest pytest-cov cython
       - name: Install package
         run: |
           python -m pip install . -v

CHANGES.md

@@ -2,6 +2,42 @@
 
 ## 2023
 
+### v0.7.0
+
+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 [https://github.com/jrenaud90/CyRK/issues/31][Issue 31].
+- 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.
+co
+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.
+
 #### v0.6.2
 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.

CyRK/_test.py

@@ -54,12 +54,12 @@ def test_cysolver():
     from CyRK.cy.cysolvertest import CySolverTester
 
     # TODO: Currently CySolver only works with floats not complex
-    CySolverTesterInst = CySolverTester(time_span, np.asarray(np.real(initial_conds), dtype=np.float64))
+    CySolverTesterInst = CySolverTester(time_span, np.asarray(np.real(initial_conds), dtype=np.float64, order='C'))
     CySolverTesterInst.solve()
 
     assert CySolverTesterInst.success
-    assert type(CySolverTesterInst.solution_t) == np.ndarray
-    assert type(CySolverTesterInst.solution_y) == np.ndarray
-    assert CySolverTesterInst.solution_y.shape[0] == 2
+    assert type(CySolverTesterInst.t) == np.ndarray
+    assert type(CySolverTesterInst.y) == np.ndarray
+    assert CySolverTesterInst.y.shape[0] == 2
 
     print("CyRK's CySolver was tested successfully.")

CyRK/array/interp.pxd

@@ -1,21 +1,21 @@
 # distutils: language = c++
 
-cdef Py_ssize_t binary_search_with_guess(double key, double[:] array, Py_ssize_t length, Py_ssize_t guess) nogil
+cdef Py_ssize_t binary_search_with_guess(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 = *) nogil
+                                    Py_ssize_t provided_j = *) noexcept nogil
 
 cpdef (double complex, Py_ssize_t) interp_complexj(double desired_x, double[:] x_domain,
-                                                    double complex[:] dependent_values, Py_ssize_t provided_j = *) nogil
+                                                    double complex[:] dependent_values, Py_ssize_t provided_j = *) noexcept nogil
 
 cpdef double interp(double desired_x, double[:] x_domain, double[:] dependent_values,
-                    Py_ssize_t provided_j = *) nogil
+                    Py_ssize_t provided_j = *) noexcept nogil
 
 cpdef double complex interp_complex(double desired_x, double[:] x_domain, double complex[:] dependent_values,
-                                    Py_ssize_t provided_j = *) nogil
+                                    Py_ssize_t provided_j = *) noexcept nogil
 
 cpdef void interp_array(double[:] desired_x_array, double[:] x_domain, double[:] dependent_values,
-                        double[:] desired_dependent_array) nogil
+                        double[:] desired_dependent_array) noexcept nogil
 
 cpdef void interp_complex_array(double[:] desired_x_array, double[:] x_domain, double complex[:] dependent_values,
-                                double complex[:] desired_dependent_array) nogil
+                                double complex[:] desired_dependent_array) noexcept nogil

CyRK/array/interp.pyx

@@ -20,7 +20,7 @@ EPS = np.finfo(dtype=np.float64).eps
 cdef Py_ssize_t LIKELY_IN_CACHE_SIZE = 8
 
 
-cdef Py_ssize_t binary_search_with_guess(double key, double[:] array, Py_ssize_t length, Py_ssize_t guess) nogil:
+cdef Py_ssize_t binary_search_with_guess(double key, double[:] array, Py_ssize_t length, Py_ssize_t guess) noexcept nogil:
     """ Binary search with guess.
 
     Based on `numpy`'s `binary_search_with_guess` function.
@@ -94,7 +94,7 @@ cdef Py_ssize_t binary_search_with_guess(double key, double[:] array, Py_ssize_t
 
 
 cpdef (double, Py_ssize_t) interpj(double desired_x, double[:] x_domain, double[:] dependent_values,
-                                    Py_ssize_t provided_j = -1) nogil:
+                                    Py_ssize_t provided_j = -1) noexcept nogil:
     """ Interpolation function for floats. This function will return the index that it found during interpolation.
 
     Provided a domain, `x_domain` and a dependent array `dependent_values` search domain for value closest to 
@@ -186,7 +186,7 @@ cpdef (double, Py_ssize_t) interpj(double desired_x, double[:] x_domain, double[
 
 
 cpdef (double complex, Py_ssize_t) interp_complexj(double desired_x, double[:] x_domain,
-                                                    double complex[:] dependent_values, Py_ssize_t provided_j = -1) nogil:
+                                                    double complex[:] dependent_values, Py_ssize_t provided_j = -1) noexcept nogil:
     """ Interpolation function for complex numbers.
 
     Provided a domain, `desired_x` and a dependent array `dependent_values` search domain for value closest to 
@@ -305,7 +305,7 @@ cpdef (double complex, Py_ssize_t) interp_complexj(double desired_x, double[:] x
     return result, j_out
 
 
-cpdef double interp(double desired_x, double[:] x_domain, double[:] dependent_values, Py_ssize_t provided_j = -1) nogil:
+cpdef double interp(double desired_x, double[:] x_domain, double[:] dependent_values, Py_ssize_t provided_j = -1) noexcept nogil:
     """ Interpolation function for floats.
 
     Provided a domain, `x_domain` and a dependent array `dependent_values` search domain for value closest to 
@@ -391,7 +391,7 @@ cpdef double interp(double desired_x, double[:] x_domain, double[:] dependent_va
 
 
 cpdef double complex interp_complex(double desired_x, double[:] x_domain,
-                                    double complex[:] dependent_values, Py_ssize_t provided_j = -1) nogil:
+                                    double complex[:] dependent_values, Py_ssize_t provided_j = -1) noexcept nogil:
     """ Interpolation function for complex numbers.
 
     Provided a domain, `desired_x` and a dependent array `dependent_values` search domain for value closest to 
@@ -505,7 +505,7 @@ cpdef double complex interp_complex(double desired_x, double[:] x_domain,
 
 
 cpdef void interp_array(double[:] desired_x_array, double[:] x_domain, double[:] dependent_values,
-                        double[:] desired_dependent_array) nogil:
+                        double[:] desired_dependent_array) noexcept nogil:
 
     # Array variables
     cdef Py_ssize_t index 
@@ -575,7 +575,7 @@ cpdef void interp_array(double[:] desired_x_array, double[:] x_domain, double[:]
 
 
 cpdef void interp_complex_array(double[:] desired_x_array, double[:] x_domain, double complex[:] dependent_values,
-                                double complex[:] desired_dependent_array) nogil:
+                                double complex[:] desired_dependent_array) noexcept nogil:
 
     # Array variables
     cdef Py_ssize_t index