Merge pull request #187 from aragilar/support-sundials-v7

Support sundials v7

.github/workflows/test-namespace.yml

@@ -11,57 +11,57 @@ jobs:
       matrix:
         include:
           #- python-version: "3.7"
-          #  sundials-version: "6.5.0"
+          #  sundials-version: "7.1.1"
           #  tox-env: py37
           #  sundials-precision: double
           #  sundials-index-size: 64
           - python-version: "3.8"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py38
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.9"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py39
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.10"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py310
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.11"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py311
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.12"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py312
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.11"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: check-manifest
             sundials-precision: double
             sundials-index-size: 64
           #- python-version: "3.11"
-          #  sundials-version: "6.5.0"
+          #  sundials-version: "7.1.1"
           #  tox-env: checkreadme
           #  sundials-precision: double
           #  sundials-index-size: 64
           - python-version: "3.11"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py311
             sundials-precision: double
             sundials-index-size: 32
           #- python-version: "3.11"
-          #  sundials-version: "6.5.0"
+          #  sundials-version: "7.1.1"
           #  tox-env: py311
           #  sundials-precision: single
           #  sundials-index-size: 64
           - python-version: "3.11"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py311
             sundials-precision: extended
             sundials-index-size: 64

.github/workflows/test-overall.yml

@@ -11,62 +11,62 @@ jobs:
       matrix:
         include:
           #- python-version: "3.7"
-          #  sundials-version: "6.5.0"
+          #  sundials-version: "7.1.1"
           #  tox-env: py37-test
           #  sundials-precision: double
           #  sundials-index-size: 64
           - python-version: "3.8"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py38-test
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.9"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py39-test
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.10"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py310-test
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.11"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py311-test
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.12"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py312-test
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.11"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: apidocs
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.11"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: docs
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.11"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py311-test
             sundials-precision: double
             sundials-index-size: 32
           #- python-version: "3.11"
-          #  sundials-version: "6.5.0"
+          #  sundials-version: "7.1.1"
           #  tox-env: py311-test
           #  sundials-precision: single
           #  sundials-index-size: 64
           - python-version: "3.11"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py311-test
             sundials-precision: extended
             sundials-index-size: 64
           #- python-version: "3.12"
-          #  sundials-version: "6.5.0"
+          #  sundials-version: "7.1.1"
           #  tox-env: py312-notebooks
           #  sundials-precision: double
           #  sundials-index-size: 64

.github/workflows/test-sundials.yml

@@ -11,57 +11,57 @@ jobs:
       matrix:
         include:
           #- python-version: "3.7"
-          #  sundials-version: "6.5.0"
+          #  sundials-version: "7.1.1"
           #  tox-env: py37
           #  sundials-precision: double
           #  sundials-index-size: 64
           - python-version: "3.8"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py38
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.9"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py39
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.10"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py310
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.11"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py311
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.12"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py312
             sundials-precision: double
             sundials-index-size: 64
           - python-version: "3.11"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: check-manifest
             sundials-precision: double
             sundials-index-size: 64
           #- python-version: "3.11"
-          #  sundials-version: "6.5.0"
+          #  sundials-version: "7.1.1"
           #  tox-env: checkreadme
           #  sundials-precision: double
           #  sundials-index-size: 64
           - python-version: "3.11"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py311
             sundials-precision: double
             sundials-index-size: 32
           #- python-version: "3.11"
-          #  sundials-version: "6.5.0"
+          #  sundials-version: "7.1.1"
           #  tox-env: py311
           #  sundials-precision: single
           #  sundials-index-size: 64
           - python-version: "3.11"
-            sundials-version: "6.5.0"
+            sundials-version: "7.1.1"
             tox-env: py311
             sundials-precision: extended
             sundials-index-size: 64

packages/scikits-odes-sundials/setup_build.py

@@ -135,10 +135,21 @@ def get_sundials_config_pxi(include_dirs, dist):
     else:
         has_lapack = False
 
+    if check_macro_true(
+        config_cmd,
+        "SUNDIALS_MPI_ENABLED", headers=[SUNDIALS_CONFIG_H],
+        include_dirs=include_dirs,
+    ):
+        SUNDIALS_MPI_ENABLED = True
+    else:
+        SUNDIALS_MPI_ENABLED = False
+
+
     cfg = dict(
         float_type = SUNDIALS_FLOAT_TYPE,
         index_size = SUNDIALS_INDEX_SIZE,
         has_lapack = has_lapack,
+        with_mpi = SUNDIALS_MPI_ENABLED,
     )
 
     return write_pxi(join(BASE_PATH, "sundials_config.pxi"), dict(
@@ -207,15 +218,15 @@ def _get_cython_ext(self):
                         CVODE_LIBRARY_DIRS.append(str(d))
                     for d in cvode_pkgconf.get('include_dirs', []):
                         CVODE_INCLUDE_DIRS.append(str(d))
-                    for lib in cvode_pkgconf.get('include_dirs', []):
+                    for lib in cvode_pkgconf.get('libraries', []):
                         CVODE_LIBRARIES.append(str(lib))
 
                     ida_pkgconf = pkgconfig.parse(PKGCONFIG_IDA)
                     for d in ida_pkgconf.get('library_dirs', []):
                         IDA_LIBRARY_DIRS.append(str(d))
                     for d in ida_pkgconf.get('include_dirs', []):
                         IDA_INCLUDE_DIRS.append(str(d))
-                    for lib in ida_pkgconf.get('include_dirs', []):
+                    for lib in ida_pkgconf.get('libraries', []):
                         IDA_LIBRARIES.append(str(lib))
 
 
@@ -224,15 +235,15 @@ def _get_cython_ext(self):
                         CVODES_LIBRARY_DIRS.append(str(d))
                     for d in cvodes_pkgconf.get('include_dirs', []):
                         CVODES_INCLUDE_DIRS.append(str(d))
-                    for lib in cvodes_pkgconf.get('include_dirs', []):
+                    for lib in cvodes_pkgconf.get('libraries', []):
                         CVODES_LIBRARIES.append(str(lib))
 
                     idas_pkgconf = pkgconfig.parse(PKGCONFIG_IDAS)
                     for d in idas_pkgconf.get('library_dirs', []):
                         IDAS_LIBRARY_DIRS.append(str(d))
                     for d in idas_pkgconf.get('include_dirs', []):
                         IDAS_INCLUDE_DIRS.append(str(d))
-                    for lib in idas_pkgconf.get('include_dirs', []):
+                    for lib in idas_pkgconf.get('libraries', []):
                         IDAS_LIBRARIES.append(str(lib))
                 except (EnvironmentError, PackageNotFoundError) as e:
                     pass
@@ -242,9 +253,27 @@ def _get_cython_ext(self):
         sundials_pxi, cfg = get_sundials_config_pxi(SUNDIALS_INCLUDE_DIRS,
                 self.distribution)
 
-        has_lapack = cfg['has_lapack']
-
         if not SUNDIALS_LIBRARIES:
+            has_lapack = cfg['has_lapack']
+            with_mpi = cfg["with_mpi"]
+            if with_mpi:
+                # use pkgconfig to find mpi
+                try:
+                    import pkgconfig
+                    from pkgconfig.pkgconfig import PackageNotFoundError
+                    try:
+                        mpi_pkgconf = pkgconfig.parse("mpi")
+                        for d in mpi_pkgconf.get('library_dirs', []):
+                            SUNDIALS_LIBRARY_DIRS.append(str(d))
+                        for d in mpi_pkgconf.get('include_dirs', []):
+                            SUNDIALS_INCLUDE_DIRS.append(str(d))
+                        for lib in mpi_pkgconf.get('libraries', []):
+                            SUNDIALS_LIBRARIES.append(str(lib))
+                    except (EnvironmentError, PackageNotFoundError) as e:
+                        pass
+                except ImportError:
+                    info("pkgconfig module not found, using preset paths")
+
             # This is where to put N_vector codes (currently only serial is
             # supported)
             SUNDIALS_LIBRARIES.append('sundials_nvecserial')

packages/scikits-odes-sundials/src/scikits_odes_sundials/c_cvode.pxd

@@ -1,6 +1,7 @@
 from .c_sundials cimport *
 from libc.stdio cimport FILE
 
+
 cdef extern from "cvode/cvode.h":
     # lmm
     enum: CV_ADAMS # 1
@@ -123,6 +124,7 @@ cdef extern from "cvode/cvode.h":
     char *CVodeGetReturnFlagName(long int flag)
     void CVodeFree(void **cvode_mem)
 
+
 cdef extern from "cvode/cvode_ls.h":
     #CVDLS return values
     enum: CVLS_SUCCESS         #  0
@@ -186,15 +188,6 @@ cdef extern from "cvode/cvode_ls.h":
     int CVodeGetLastLinFlag(void *cvode_mem, long int *flag)
     char *CVodeGetLinReturnFlagName(long int flag)
 
-cdef extern from "cvode/cvode_direct.h":
-    ctypedef CVLsJacFn CVodeJacFn
-
-    int CVodeSetJacFn(void *cvode_mem, CVodeJacFn jac)
-    int CVodeGetWorkSpace(void *cvode_mem, long int *lenrwLS, long int *leniwLS)
-    int CVodeGetNumJacEvals(void *cvode_mem, long int *njevals)
-    int CVodeGetNumRhsEvals(void *cvode_mem, long int *nfevalsLS)
-    int CVodeGetLastFlag(void *cvode_mem, long int *flag)
-    char *CVodeGetReturnFlagName(long int flag)
 
 cdef extern from "cvode/cvode_bandpre.h":
     int CVBandPrecInit(void *cvode_mem, sunindextype N, sunindextype mu,
@@ -203,6 +196,7 @@ cdef extern from "cvode/cvode_bandpre.h":
                                long int *leniwLS)
     int CVBandPrecGetNumRhsEvals(void *cvode_mem, long int *nfevalsBP)
 
+
 cdef extern from "cvode/cvode_diag.h":
     # CVDIAG return values
     enum: CVDIAG_SUCCESS         #  0
@@ -221,6 +215,7 @@ cdef extern from "cvode/cvode_diag.h":
     int CVDiagGetLastFlag(void *cvode_mem, long int *flag)
     char *CVDiagGetReturnFlagName(long int flag)
 
+
 cdef extern from "cvode/cvode_bbdpre.h":
     ctypedef int (*CVLocalFn)(sunindextype Nlocal, sunrealtype t, N_Vector y,
                               N_Vector g, void *user_data)
@@ -236,27 +231,3 @@ cdef extern from "cvode/cvode_bbdpre.h":
     int CVBBDPrecGetWorkSpace(void *cvode_mem, long int *lenrwBBDP, 
                               long int *leniwBBDP)
     int CVBBDPrecGetNumGfnEvals(void *cvode_mem, long int *ngevalsBBDP)
-
-cdef extern from "cvode/cvode_spils.h":
-
-    ctypedef CVLsPrecSetupFn CVodePrecSetupFn
-    ctypedef CVLsPrecSolveFn CVodePrecSolveFn
-    ctypedef CVLsJacTimesSetupFn CVodeJacTimesSetupFn
-    ctypedef CVLsJacTimesVecFn CVodeJacTimesVecFn
-
-    int CVodeSetEpsLin(void *cvode_mem, sunrealtype eplifac)
-    int CVodeSetPreconditioner(void *cvode_mem, CVodePrecSetupFn pset,
-                                 CVodePrecSolveFn psolve)
-    int CVodeSetJacTimes(void *cvode_mem, CVodeJacTimesSetupFn jtsetup,
-                           CVodeJacTimesVecFn jtimes)
-
-    int CVodeGetWorkSpace(void *cvode_mem, long int *lenrwLS, long int *leniwLS)
-    int CVodeGetNumPrecEvals(void *cvode_mem, long int *npevals)
-    int CVodeGetNumPrecSolves(void *cvode_mem, long int *npsolves)
-    int CVodeGetNumLinIters(void *cvode_mem, long int *nliters)
-    int CVodeGetNumConvFails(void *cvode_mem, long int *nlcfails)
-    int CVodeGetNumJTSetupEvals(void *cvode_mem, long int *njtsetups)
-    int CVodeGetNumJtimesEvals(void *cvode_mem, long int *njvevals)
-    int CVodeGetNumRhsEvals(void *cvode_mem, long int *nfevalsLS)
-    int CVodeGetLastFlag(void *cvode_mem, long int *flag)
-    char *CVodeGetReturnFlagName(long int flag)