Merge pull request #81 from jrenaud90/fix-bad-array-returns

Fix bad array returns

.github/workflows/push_tests_ubun.yml

@@ -38,33 +38,33 @@ jobs:
       - name: Run pytest
         run: pytest -n auto -v Tests/
 
-  test-39-with-coverage:
-    name: Test Python 3.9 and Upload Coverage Report
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.9
-      - name: Install Dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install pytest pytest-cov cython pytest-xdist
-      - name: Install package
-        run: |
-          python -m pip install . -v
+  # test-39-with-coverage:
+  #   name: Test Python 3.9 and Upload Coverage Report
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - name: Set up Python 3.9
+  #       uses: actions/setup-python@v5
+  #       with:
+  #         python-version: 3.9
+  #     - name: Install Dependencies
+  #       run: |
+  #         python -m pip install --upgrade pip
+  #         python -m pip install pytest pytest-cov cython pytest-xdist
+  #     - name: Install package
+  #       run: |
+  #         python -m pip install . -v
 
-      - name: Run pytest
-        run: pytest -n auto --capture=sys -v --cov=CyRK Tests/
-        env:
-          # Disable numba so that njited functions can have their coverage checked.
-          NUMBA_DISABLE_JIT: 1
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
-        with:
-          env_vars: OS,PYTHON
-          fail_ci_if_error: false
-          flags: unittests
-          verbose: true
-          name: coverage
+  #     - name: Run pytest
+  #       run: pytest -n auto --capture=sys -v --cov=CyRK Tests/
+  #       env:
+  #         # Disable numba so that njited functions can have their coverage checked.
+  #         NUMBA_DISABLE_JIT: 1
+  #     - name: Upload coverage to Codecov
+  #       uses: codecov/codecov-action@v3
+  #       with:
+  #         env_vars: OS,PYTHON
+  #         fail_ci_if_error: false
+  #         flags: unittests
+  #         verbose: true
+  #         name: coverage

CHANGES.md

@@ -2,6 +2,14 @@
 
 ## 2024
 
+#### v0.12.1 (2024-12-02)
+
+Fixes:
+* Added fix so that arrays returned by `WrapCySolverResult` class are not destroyed when class is. Instead they are managed by python's garbage collector once they are held by a python variable. This addresses Github issues [#80](https://github.com/jrenaud90/CyRK/issues/80) and [#78](https://github.com/jrenaud90/CyRK/issues/78)
+
+Tests:
+* Added test to check that arrays stay alive after underlying `WrapCySolverResult` class is destroyed.
+
 #### v0.12.0 (2024-12-02)
 
 New & Changes:

CyRK/cy/cysolver.cpp

@@ -43,17 +43,17 @@ CySolverBase::CySolverBase(
         const double* t_eval,
         const size_t len_t_eval,
         PreEvalFunc pre_eval_func) :
-            t_start(t_start),
-            t_end(t_end),
             diffeq_ptr(diffeq_ptr),
             size_of_args(size_of_args),
             len_t_eval(len_t_eval),
-            num_extra(num_extra),
             use_dense_output(use_dense_output),
             pre_eval_func(pre_eval_func),
             status(0),
             num_y(num_y),
-            storage_sptr(storage_sptr)
+            num_extra(num_extra),
+            storage_sptr(storage_sptr),
+            t_start(t_start),
+            t_end(t_end)
 {
     // Parse inputs
     this->capture_extra = num_extra > 0;

CyRK/cy/cysolver.hpp

@@ -103,6 +103,9 @@ class CySolverBase {
 
 
 public:
+    // Differential equation information
+    DiffeqFuncType diffeq_ptr = nullptr;
+
     // Integration step information
     size_t max_num_steps = 0;
 
@@ -111,9 +114,6 @@ class CySolverBase {
     std::vector<char> args_char_vec = std::vector<char>();
     char* args_ptr = nullptr;
 
-    // Differential equation information
-    DiffeqFuncType diffeq_ptr = nullptr;
-
     // t_eval information
     std::vector<double> t_eval_vec = std::vector<double>();
     double* t_eval_ptr       = t_eval_vec.data();
@@ -122,9 +122,6 @@ class CySolverBase {
     bool skip_t_eval         = false;
     bool use_t_eval          = false;
 
-    // Function to send to diffeq which is called before dy is calculated
-    PreEvalFunc pre_eval_func = nullptr;
-
     // Keep bools together to reduce size
     bool direction_flag = false;
     bool reset_called   = false;
@@ -134,6 +131,9 @@ class CySolverBase {
 
     // Dense (Interpolation) Attributes
     bool use_dense_output = false;
+
+    // Function to send to diffeq which is called before dy is calculated
+    PreEvalFunc pre_eval_func = nullptr;
 
     // PySolver Attributes
     bool use_pysolver = false;

CyRK/cy/cysolver_api.pyx

@@ -124,11 +124,11 @@ cdef class WrapCySolverResult:
 
     @property
     def t(self):
-        return np.asarray(self.time_view, dtype=np.float64, order='C')
+        return np.copy(np.asarray(self.time_view, dtype=np.float64, order='C'))
 
     @property
     def y(self):
-        return np.asarray(self.y_view, dtype=np.float64, order='C').reshape((self.size, self.num_dy)).T
+        return np.copy(np.asarray(self.y_view, dtype=np.float64, order='C')).reshape((self.size, self.num_dy)).T
 
     @property
     def size(self):

README.md

@@ -2,7 +2,7 @@
 <div style="text-align: center;">
 <a href="https://doi.org/10.5281/zenodo.7093266"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.7093266.svg" alt="DOI"></a>
 <a href="https://www.python.org/downloads/"><img src="https://img.shields.io/badge/Python-3.8|3.9|3.10|3.11|3.12-blue" alt="Python Version 3.8-3.12" /></a>
-<a href="https://codecov.io/gh/jrenaud90/CyRK" ><img src="https://codecov.io/gh/jrenaud90/CyRK/branch/main/graph/badge.svg?token=MK2PqcNGET" alt="Code Coverage"/></a>
+<!-- <a href="https://codecov.io/gh/jrenaud90/CyRK" ><img src="https://codecov.io/gh/jrenaud90/CyRK/branch/main/graph/badge.svg?token=MK2PqcNGET" alt="Code Coverage"/></a> -->
 <br />
 <a href="https://github.com/jrenaud90/CyRK/actions/workflows/push_tests_win.yml"><img src="https://github.com/jrenaud90/CyRK/actions/workflows/push_tests_win.yml/badge.svg?branch=main" alt="Windows Tests" /></a>
 <a href="https://github.com/jrenaud90/CyRK/actions/workflows/push_tests_mac.yml"><img src="https://github.com/jrenaud90/CyRK/actions/workflows/push_tests_mac.yml/badge.svg?branch=main" alt="MacOS Tests" /></a>
@@ -11,7 +11,7 @@
 
 ---
 
-<a href="https://github.com/jrenaud90/CyRK/releases"><img src="https://img.shields.io/badge/CyRK-0.12.0 Alpha-orange" alt="CyRK Version 0.12.0 Alpha" /></a>
+<a href="https://github.com/jrenaud90/CyRK/releases"><img src="https://img.shields.io/badge/CyRK-0.12.1 Alpha-orange" alt="CyRK Version 0.12.1 Alpha" /></a>
 
 
 **Runge-Kutta ODE Integrator Implemented in Cython and Numba**

Tests/D_PySolver_Tests/test_d_pysolve_array_lifetime.py

@@ -0,0 +1,45 @@
+import numpy as np
+from CyRK import pysolve_ivp
+import gc
+
+
+def diffeq(dy, t, y):
+    dy[0] = (1. - 0.01 * y[1]) * y[0]
+    dy[1] = (0.02 * y[0] - 1.) * y[1]
+
+initial_conds = np.asarray((20., 20.), dtype=np.float64, order='C')
+time_span = (0., 10.)
+time_span_large = (0., 1000.)
+rtol = 1.0e-4
+atol = 1.0e-7
+
+def run_diffeq_array_return():
+    result = pysolve_ivp(diffeq, time_span, initial_conds, method="RK45", rtol=rtol, atol=atol, pass_dy_as_arg=True)
+
+    t = result.t
+    y = result.y
+    del result
+    gc.collect()
+    return t, y
+
+def run_diffeq_result_return():
+    result = pysolve_ivp(diffeq, time_span, initial_conds, method="RK45", rtol=rtol, atol=atol, pass_dy_as_arg=True)
+    return result
+
+def test_pysolve_array_lifetimes():
+    """ Tests that the underlying arrays returned by the WrapCySolverResult class can outlive the class instance. """
+
+    # Run in a loop because sometimes memory corruptions can take a while to appear
+    for i in range(50):
+        # Get result from the result instance class
+        result = run_diffeq_result_return()
+
+        # Get arrays from the array return
+        t, y = run_diffeq_array_return()
+
+        # Check that they contain the same data
+        assert result.y.size == y.size
+        assert result.t.size == t.size
+
+        assert np.allclose(result.y, y)
+        assert np.allclose(result.t, t)

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name='CyRK'
-version = '0.12.0'
+version = '0.12.1'
 description='Runge-Kutta ODE Integrator Implemented in Cython and Numba.'
 authors= [
     {name = 'Joe P. Renaud', email = 'joe.p.renaud@gmail.com'}