Fix exception propagation logic for numpy 2.4

.github/workflows/ci.yml

@@ -11,7 +11,6 @@ on:
       - ".github/ISSUE_TEMPLATE/**"
 
   pull_request:
-    branches: [main]
     paths-ignore:
       - "*.md"
       - "docs/**"
@@ -33,7 +32,7 @@ jobs:
 
     defaults:
       run: 
-        shell: bash -l {0}
+        shell: bash -el {0}
 
     steps:
       - name: Checkout repository
@@ -65,7 +64,7 @@ jobs:
 
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -el {0}
 
     steps:
       - name: Checkout repository

CHANGELOG.md

@@ -1,5 +1,10 @@
 # scikit-SUNDAE Changelog
 
+## [v1.1.1](https://github.com/NREL/scikit-sundae/tree/v1.1.1)
+
+### Bug Fixes
+- Ensures exception propagations work correctly with numpy 2.4 releases ([#43](https://github.com/NREL/scikit-sundae/pull/43))
+
 ## [v1.1.0](https://github.com/NREL/scikit-sundae/tree/v1.1.0)
 
 ### New Features

pyproject.toml

@@ -11,7 +11,7 @@ dynamic = ["version"]
 requires-python = ">=3.10,<3.15"
 license = "BSD-3-Clause"
 license-files = ["LICENSE*"]
-description = "Python bindings to SUNDIALS differential aglebraic equation solvers."
+description = "Python bindings to SUNDIALS differential algebraic equation solvers."
 keywords = ["sundials", "dae", "ode", "integrator", "ivp", "cvode", "ida"]
 authors = [
     { name = "Corey R. Randall" },

src/sksundae/__init__.py

@@ -62,4 +62,4 @@
 
 __all__ = ['ida', 'utils', 'cvode', 'jacband', 'SUNDIALS_VERSION']
 
-__version__ = '1.1.0'
+__version__ = '1.1.1'

src/sksundae/_cy_common.pyx

@@ -39,7 +39,7 @@ elif SUNDIALS_INT_TYPE == "long int":
 
 cdef svec2np(N_Vector nvec, np.ndarray[DTYPE_t, ndim=1] np_array):
     """Fill a numpy array with values from an N_Vector."""
-    cdef sunrealtype* nvec_ptr
+    cdef sunrealtype* nv_ptr
 
     nv_ptr = N_VGetArrayPointer(nvec)
     ptr2np(nv_ptr, np_array)

src/sksundae/_cy_cvode.pyx

@@ -17,7 +17,13 @@ cimport numpy as np
 
 from scipy import sparse as sp
 from scipy.optimize._numdiff import group_columns
-from cpython.exc cimport PyErr_CheckSignals, PyErr_Occurred
+from cpython.exc cimport (
+    PyErr_Fetch, PyErr_NormalizeException,
+    PyObject, PyErr_CheckSignals, PyErr_Occurred,  # PyErr_GetRaisedException,
+)
+
+# PyErr_Fetch and PyErr_NormalizeException are deprecated at 3.12. When support
+# for <3.12 is dropped, replace with PyErr_GetRaisedException.
 
 # Extern cdef headers
 from .c_cvode cimport *
@@ -235,8 +241,18 @@ cdef void _err_handler(int line, const char* func, const char* file,
                        const char* msg, int err_code, void* err_user_data,
                        SUNContext ctx) except *:
     """Custom error handler for shorter messages (no line or file)."""
-
-    if not PyErr_Occurred():
+    cdef PyObject *errtype, *errvalue, *errtraceback
+
+    if PyErr_Occurred():
+        aux = <AuxData> err_user_data
+        # aux.pyerr = <object> PyErr_GetRaisedException()
+
+        PyErr_Fetch(&errtype, &errvalue, &errtraceback)
+        PyErr_NormalizeException(&errtype, &errvalue, &errtraceback)
+
+        aux.pyerr = <object> errvalue
+
+    else:
         decoded_func = func.decode("utf-8")
         decoded_msg = msg.decode("utf-8").replace(", ,", ",").strip()
         print(f"\n[{decoded_func}, Error: {err_code}] {decoded_msg}\n")
@@ -262,6 +278,7 @@ cdef class AuxData:
     cdef bint with_userdata
     cdef bint is_constrained
 
+    cdef object pyerr           # Exception
     cdef object rhsfn           # Callable
     cdef object userdata        # Any
     cdef object eventsfn        # Callable
@@ -272,6 +289,7 @@ cdef class AuxData:
     cdef object jactimes        # CVODEJacTimes
 
     def __cinit__(self, sunindextype NEQ, object options):
+        self.pyerr = None
         self.np_yy = np.empty(NEQ, DTYPE)
         self.np_yp = np.empty(NEQ, DTYPE)
 
@@ -740,7 +758,7 @@ cdef class CVODE:
 
         # 16) Set optional inputs
         SUNContext_ClearErrHandlers(self.ctx)
-        SUNContext_PushErrHandler(self.ctx, _err_handler, NULL)
+        SUNContext_PushErrHandler(self.ctx, _err_handler, <void*> self.aux)
 
         cdef sunrealtype first_step = <sunrealtype> self._options["first_step"] 
         flag = CVodeSetInitStep(self.mem, first_step)
@@ -921,10 +939,12 @@ cdef class CVODE:
 
                 ind += 1
 
-            if stop:
-                break
+            if self.aux.pyerr is not None:
+                raise self.aux.pyerr
             elif PyErr_CheckSignals() == -1:
                 return
+            elif stop:
+                break
 
         if self.aux.eventsfn:
             i_ev, t_ev, y_ev = _collect_events(self.aux)
@@ -1004,10 +1024,12 @@ cdef class CVODE:
 
                 ind += 1
 
-            if stop:
-                break
+            if self.aux.pyerr is not None:
+                raise self.aux.pyerr
             elif PyErr_CheckSignals() == -1:
                 return
+            elif stop:
+                break
 
         if self.aux.eventsfn:
             i_ev, t_ev, y_ev = _collect_events(self.aux)

src/sksundae/_cy_ida.pyx

@@ -17,7 +17,13 @@ cimport numpy as np
 
 from scipy import sparse as sp
 from scipy.optimize._numdiff import group_columns
-from cpython.exc cimport PyErr_CheckSignals, PyErr_Occurred
+from cpython.exc cimport (
+    PyErr_Fetch, PyErr_NormalizeException,
+    PyObject, PyErr_CheckSignals, PyErr_Occurred,  # PyErr_GetRaisedException,
+)
+
+# PyErr_Fetch and PyErr_NormalizeException are deprecated at 3.12. When support
+# for <3.12 is dropped, replace with PyErr_GetRaisedException.
 
 # Extern cdef headers
 from .c_ida cimport *
@@ -239,8 +245,18 @@ cdef void _err_handler(int line, const char* func, const char* file,
                        const char* msg, int err_code, void* err_user_data,
                        SUNContext ctx) except *:
     """Custom error handler for shorter messages (no line or file)."""
-
-    if not PyErr_Occurred():
+    cdef PyObject *errtype, *errvalue, *errtraceback
+
+    if PyErr_Occurred():
+        aux = <AuxData> err_user_data
+        # aux.pyerr = <object> PyErr_GetRaisedException()
+
+        PyErr_Fetch(&errtype, &errvalue, &errtraceback)
+        PyErr_NormalizeException(&errtype, &errvalue, &errtraceback)
+
+        aux.pyerr = <object> errvalue
+
+    else:
         decoded_func = func.decode("utf-8")
         decoded_msg = msg.decode("utf-8").replace(", ,", ",").strip()
         print(f"\n[{decoded_func}, Error: {err_code}] {decoded_msg}\n")
@@ -267,6 +283,7 @@ cdef class AuxData:
     cdef bint with_userdata
     cdef bint is_constrained
 
+    cdef object pyerr           # Exception
     cdef object resfn           # Callable
     cdef object userdata        # Any
     cdef object eventsfn        # Callable
@@ -277,6 +294,7 @@ cdef class AuxData:
     cdef object jactimes        # IDAJacTimes
 
     def __cinit__(self, sunindextype NEQ, object options):
+        self.pyerr = None
         self.np_yy = np.empty(NEQ, DTYPE)
         self.np_yp = np.empty(NEQ, DTYPE)
         self.np_rr = np.empty(NEQ, DTYPE)
@@ -764,7 +782,9 @@ cdef class IDA:
 
         # 15) Set optional inputs
         SUNContext_ClearErrHandlers(self.ctx)
-        SUNContext_PushErrHandler(self.ctx, _err_handler, NULL)
+        SUNContext_PushErrHandler(self.ctx, _err_handler, <void*> self.aux)
+
+        # Set algebraic variable indices
 
         np_algidx = np.ones(self.NEQ, DTYPE)
         if self._options["algebraic_idx"] is not None:
@@ -992,10 +1012,12 @@ cdef class IDA:
 
                 ind += 1
 
-            if stop:
-                break
+            if self.aux.pyerr is not None:
+                raise self.aux.pyerr
             elif PyErr_CheckSignals() == -1:
                 return
+            elif stop:
+                break
 
         if self.aux.eventsfn:
             i_ev, t_ev, y_ev, yp_ev = _collect_events(self.aux)
@@ -1083,10 +1105,12 @@ cdef class IDA:
 
                 ind += 1
 
-            if stop:
-                break
+            if self.aux.pyerr is not None:
+                raise self.aux.pyerr
             elif PyErr_CheckSignals() == -1:
                 return
+            elif stop:
+                break
 
         if self.aux.eventsfn:
             i_ev, t_ev, y_ev, yp_ev = _collect_events(self.aux)