Merge pull request #68 from jrenaud90/dev0.11.0

ver0.11.0
jrenaud90 · Nov 8, 2024 · 37dc62f · 37dc62f
2 parents a2fc0ae + 1fdc2f5
commit 37dc62f
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diff --git a/Benchmarks/Accuracy.ipynb b/Benchmarks/Accuracy.ipynb
@@ -53,17 +53,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from CyRK import pysolve_ivp, cyrk_ode\n",
+    "from CyRK import pysolve_ivp\n",
     "from scipy.integrate import solve_ivp"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 5,
    "id": "a1305367",
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -128,7 +126,6 @@
     "rtols = [1.0e-5, 1.0e-7, 1.0e-9, 1.0e-11]\n",
     "\n",
     "integration_method = 'RK45'\n",
-    "rk_method = 1\n",
     "t_span = (0., 10.)\n",
     "t_eval = np.linspace(0.0, 10.0, 100)\n",
     "\n",
@@ -142,21 +139,16 @@
     "    scipy_sol   = solve_ivp(diffeq_accuracy_3, t_span, y0, rtol=rtol, atol=atol, method=integration_method)\n",
     "    scipy_teval = solve_ivp(diffeq_accuracy_3, t_span, y0, rtol=rtol, atol=atol, method=integration_method, t_eval=t_eval)\n",
     "    \n",
-    "    cyrk_sol   = cyrk_ode(diffeq_accuracy_2, t_span, y0, rtol=rtol, atol=atol, rk_method=rk_method, raise_warnings=False)\n",
-    "    cyrk_teval = cyrk_ode(diffeq_accuracy_2, t_span, y0, rtol=rtol, atol=atol, rk_method=rk_method, t_eval=t_eval, raise_warnings=False)\n",
-    "    \n",
     "    pysolve_sol   = pysolve_ivp(diffeq_accuracy, t_span, y0, rtol=rtol, atol=atol, method=integration_method, dense_output=True, pass_dy_as_arg=True)\n",
     "    pysolve_teval = pysolve_ivp(diffeq_accuracy, t_span, y0, rtol=rtol, atol=atol, method=integration_method, t_eval=t_eval, pass_dy_as_arg=True)\n",
     "    print(pysolve_sol.t.shape)\n",
     "    chi_sci_sol = np.nansum((scipy_sol.y - correct_answer(scipy_sol.t, c1, c2))**2 / correct_answer(scipy_sol.t, c1, c2))\n",
-    "    chi_crykode_sol = np.nansum((cyrk_sol[1] - correct_answer(cyrk_sol[0], c1, c2))**2 / correct_answer(cyrk_sol[0], c1, c2))\n",
     "    chi_pysolve_sol = np.nansum((pysolve_sol.y - correct_answer(pysolve_sol.t, c1, c2))**2 / correct_answer(pysolve_sol.t, c1, c2))\n",
     "    \n",
-    "    print(f\"SciPy (sol)\\t|\\tPySolve (sol)\\t|\\tcyrk_ode (sol)\")\n",
-    "    print(f\"{chi_sci_sol:0.5e}\\t|\\t{chi_pysolve_sol:0.5e}\\t|\\t{chi_crykode_sol:0.5e}\")\n",
+    "    print(f\"SciPy (sol)\\t|\\tPySolve (sol)\")\n",
+    "    print(f\"{chi_sci_sol:0.5e}\\t|\\t{chi_pysolve_sol:0.5e}\")\n",
     "    \n",
     "    chi_sci_teval = np.nansum((scipy_teval.y - correct_answer(scipy_teval.t, c1, c2))**2 / correct_answer(scipy_teval.t, c1, c2))\n",
-    "    chi_crykode_teval = np.nansum((cyrk_teval[1] - correct_answer(cyrk_teval[0], c1, c2))**2 / correct_answer(cyrk_teval[0], c1, c2))\n",
     "    chi_pysolve_teval = np.nansum((pysolve_teval.y - correct_answer(pysolve_teval.t, c1, c2))**2 / correct_answer(pysolve_teval.t, c1, c2))\n",
     "    dense_sol = pysolve_sol(t_eval)\n",
     "    chi_pysolve_dense = np.nansum((dense_sol - correct_answer(t_eval, c1, c2))**2 / correct_answer(t_eval, c1, c2))\n",
@@ -202,24 +194,15 @@
     "#     ax5.scatter(pysolve_sol.t, np.zeros_like(scipy_sol.t), c='purple', s=5)\n",
     "#     ax5.set(title=\"SciPy (sol) - pysolve\")\n",
     "    \n",
-    "#     fig5, ax5 = plt.subplots()\n",
-    "#     ax5.plot(cyrk_sol[0], (cyrk_sol[1][0] - pysolve_sol.y[0]) / cyrk_sol[1][0], c='b')\n",
-    "#     ax5.plot(cyrk_sol[0], (cyrk_sol[1][1] - pysolve_sol.y[1]) / cyrk_sol[1][1], c='r')\n",
-    "#     ax5.scatter(scipy_sol.t, np.zeros_like(scipy_sol.t), c='g', s=1)\n",
-    "#     ax5.scatter(pysolve_sol.t, np.zeros_like(scipy_sol.t), c='purple', s=5)\n",
-    "#     ax5.set(title=\"cyrk_ode - pysolve_sol\")\n",
-    "    \n",
     "#     sci_step_size = np.diff(scipy_sol.t)\n",
     "#     solpy_step_size = np.diff(pysolve_sol.t)\n",
-    "#     cyrk_step_size = np.diff(cyrk_sol[0])\n",
     "    \n",
     "#     fig5, ax5 = plt.subplots()\n",
     "# #     ax5.plot(scipy_sol.t, (scipy_sol.y[0] - pysolve_sol.y[0]) / scipy_sol.y[0], c='b', ls=':')\n",
     "# #     ax5.plot(scipy_sol.t, (scipy_sol.y[1] - pysolve_sol.y[1]) / scipy_sol.y[1], c='r', ls=':')\n",
     "#     ax5b = ax5.twinx()\n",
     "#     ax5b.plot(scipy_sol.t[1:], sci_step_size, c='b', marker='.')\n",
     "#     ax5b.plot(pysolve_sol.t[1:], solpy_step_size, c='r', marker='.')\n",
-    "# #     ax5b.plot(cyrk_sol[0][1:], cyrk_step_size, c='orange', marker='.')\n",
     "#     ax5b.set(ylim=(0.3, 0.4))\n",
     "#     plt.show()\n",
     "    \n",
@@ -444,7 +427,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

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_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_v0-11-0.png b/Benchmarks/CyRK_SciPy_Compare_predprey_v0-11-0.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_v0-10-0.png → ...e/CyRK_SciPy_Compare_predprey_v0-10-0.png b/...s/CyRK_SciPy_Compare_predprey_v0-10-0.png → ...e/CyRK_SciPy_Compare_predprey_v0-10-0.png
diff --git a/...s/CyRK_SciPy_Compare_predprey_v0-10-1.png → ...e/CyRK_SciPy_Compare_predprey_v0-10-1.png b/...s/CyRK_SciPy_Compare_predprey_v0-10-1.png → ...e/CyRK_SciPy_Compare_predprey_v0-10-1.png
diff --git a/CHANGES.md b/CHANGES.md
@@ -2,6 +2,37 @@
 
 ## 2024
 
+#### v0.11.0 (2024-NNN)
+
+New:
+* `WrapCySolverResult` result class now provides user access to attribute `num_y`.
+
+Removed:
+* Removed previous `cyrk_ode` and older version of the `CySolver` class-based solver.
+  * The functionality of `cyrk_ode` is now handled by the new (as of v0.10.0) `pysolve_ivp` function.
+  * The functionality of `CySolver` is partly handled by the new (as of v0.10.0) `cysolve_ivp` function.
+    * Note that the new cysolve_ivp is a functional approach. A class based approach like the older CySolver class supported is no longer available but could be easy to implement. If there is interest please create a Github issue for it.
+
+Refactors:
+* Refactored the new cysolver and pysolver files to remove "New". This will break imports based on previous versions.
+* Broke up cysolver and pysolver into different files to isolate each other's code.
+
+Other:
+* Changed the default ordering for diffeq function inputs to follow the scheme dydt(dy, t, y); previously it was dydt(t, y, dy). This affects the `cy2nb` and `nb2cy` helper functions.
+* Updated performance module to use new methods over old.
+
+Demos:
+* Fixed typo in the type of the mixed-type args container.
+* Updated to work with new refactoring.
+
+Tests:
+* Updated tests to use pysolver where cyrk_ode was used.
+* Changed tolerances and other inputs to try to make some tests faster.
+
+Dependencies:
+* Tested that CyRK works with numpy v2.X; but a lot of other packages don't right now. So setting it as upper limit.
+* Tested that CyRK can not work with Python 3.13 yet due to numba dependence. See issue 
+
 #### v0.10.2 (2024-11-05)
 
 New:

diff --git a/CyRK/__init__.pxd b/CyRK/__init__.pxd
@@ -1,2 +1,2 @@
-from CyRK.cy.cysolverNew cimport cysolve_ivp, cysolve_ivp_gil, DiffeqFuncType, PreEvalFunc, CySolverResult, WrapCySolverResult, CySolverBase, CySolveOutput, RK23_METHOD_INT, RK45_METHOD_INT, DOP853_METHOD_INT
+from CyRK.cy.cysolver_api cimport cysolve_ivp, cysolve_ivp_gil, DiffeqFuncType, PreEvalFunc, CySolverResult, WrapCySolverResult, CySolverBase, CySolveOutput, RK23_METHOD_INT, RK45_METHOD_INT, DOP853_METHOD_INT
 from CyRK.cy.helpers cimport interpolate_from_solution_list
diff --git a/CyRK/__init__.py b/CyRK/__init__.py
@@ -6,14 +6,12 @@
 # Import numba solver
 from .nb.nbrk import nbsolve_ivp
 
-# Import cython solver
-from CyRK.cy.cyrk import cyrk_ode
-
 # Import helper functions
 from .helper import nb2cy, cy2nb
 
 # Import test functions
 from ._test import test_nbrk, test_cysolver, test_pysolver
 
 # Import python solver
-from CyRK.cy.cysolverNew import pysolve_ivp
+from CyRK.cy.cysolver_api import WrapCySolverResult
+from CyRK.cy.pysolver import pysolve_ivp
diff --git a/CyRK/_test.py b/CyRK/_test.py
@@ -54,7 +54,7 @@ def test_pysolver():
 
 def test_cysolver():
 
-    from CyRK.cy.cysolverNew_test import cytester
+    from CyRK.cy.cysolver_test import cytester
 
     result = cytester(0,
                       time_span,

diff --git a/CyRK/cy/common.pxd b/CyRK/cy/common.pxd