adapt to latest pycvodes (#114)

* adapt to latest pycvodes

* bump pycompilation req

* Drop commented code

* Bump pycompilation>=0.4.9 to handle ldflags

.ci/run_ci.sh

@@ -15,17 +15,21 @@ echo -e "[global]\nno-cache-dir = false\ndownload-cache = $(pwd)/ci_cache/pip_ca
 python3 -m pip install symcxx pysym  # unofficial backends, symengine is tested in the conda build
 
 # (cd ./tmp/pycvodes;
-CFLAGS="-isystem $SUNDBASE/include $CFLAGS" LDFLAGS="-Wl,--disable-new-dtags -Wl,-rpath,$SUNDBASE/lib -L$SUNDBASE/lib $LDFLAGS" python3 -m pip install pycvodes # setup.py install )
+SUND_CFLAGS="-isystem $SUNDBASE/include $CFLAGS"
+SUND_LDFLAGS="-Wl,--disable-new-dtags -Wl,-rpath,$SUNDBASE/lib -L$SUNDBASE/lib $LDFLAGS"
+CFLAGS=$SUND_CFLAGS LDFLAGS=$SUND_LDFLAGS python3 -m pip install pycvodes
 git clean -xfd # -e tmp/
 
-export CPATH=$SUNDBASE/include
-export LIBRARY_PATH=$SUNDBASE/lib
-export LD_LIBRARY_PATH=$SUNDBASE/lib
+# export CPATH=$SUNDBASE/include
+# export LIBRARY_PATH=$SUNDBASE/lib
+# export LD_LIBRARY_PATH=$SUNDBASE/lib
 
 python3 setup.py sdist
 PKG_VERSION=$(python3 setup.py --version)
 (cd dist/; python3 -m pip install $PKG_NAME-$PKG_VERSION.tar.gz)
 python3 -m pip install -e .[all]
+export PYODESYS_CVODE_FLAGS=$SUND_CFLAGS
+export PYODESYS_CVODE_LDFLAGS=$SUND_LDFLAGS
 python3 -m pytest -xv -k test_integrate_chained_robertson pyodesys/tests/test_robertson.py
 export PYTHONHASHSEED=$(python3 -c "import random; print(random.randint(1,2**32-1))")
 PYTHON="python3 -R" ./scripts/run_tests.sh --cov $PKG_NAME --cov-report html

.drone.yml

@@ -17,55 +17,55 @@ pipeline:
     ttl: 90  # liftetime in days
 
   # get-pre-reqs:
-  #   image: bjodah/bjodahimg20dev:v1.1.0
+  #   image: bjodah/bjodahimg20dev:v1.2.0
   #   commands:
   #     - mkdir ./tmp
   #     - git clone --recurse-submodules https://github.com/bjodah/pycvodes.git ./tmp/pycvodes
 
   # test-py2:
-  #   image: bjodah/bjodahimg20dev:v1.1.0
+  #   image: bjodah/bjodahimg20dev:v1.2.0
   #   environment:
   #     - CC=gcc-10
   #     - CXX=g++-10
   #     - OMP_NUM_THREADS=1
   #     - ANYODE_NUM_THREADS=2
-  #     - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt/boost_1_72_p/include
+  #     - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt/boost_1_73_p/include
   #     - LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
   #     - LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
-  #     - SUNDBASE=/opt/sundials-5.2.0-klu-lapack
+  #     - SUNDBASE=/opt/sundials-5.3.0-klu-lapack
   #   commands:
   #     - apt-get update && apt-get --assume-yes install python2-dev
   #     - bash -c "ulimit -v 2048000; .ci/test_py2.sh pyodesys $SUNDBASE"
 
-  test-sund-5.2.0-klu:
+  test-sund-5.3.0-klu:
     group: testing
-    image: bjodah/bjodahimg20dev:v1.1.0
+    image: bjodah/bjodahimg20dev:v1.2.0
     environment:
       - CC=gcc-10
       - CXX=g++-10
       - OMP_NUM_THREADS=1
       - ANYODE_NUM_THREADS=2
-      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt/boost_1_72_p/include
+      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt/boost_1_73_p/include
       - LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
       - LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
-      - SUNDBASE=/opt/sundials-5.2.0-klu-lapack
+      - SUNDBASE=/opt/sundials-5.3.0-klu-lapack
     commands:
       - bash -c "ulimit -v 2048000; .ci/run_ci.sh pyodesys $SUNDBASE"
       - ./scripts/prepare_deploy.sh
       - bash -c '[[ $(python3 setup.py --version) =~ ^[0-9]+.* ]]'
 
-  test-sund-5.2.0-nolapack-noklu-extended:
+  test-sund-5.3.0-nolapack-noklu-extended:
     group: testing
-    image: bjodah/bjodahimg20dev:v1.1.0
+    image: bjodah/bjodahimg20dev:v1.2.0
     environment:
       - CC=gcc-10
       - CXX=g++-10
       - OMP_NUM_THREADS=1
       - ANYODE_NUM_THREADS=2
-      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt/boost_1_72_p/include
+      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt/boost_1_73_p/include
       - LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
       - LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
-      - SUNDBASE=/opt/sundials-5.2.0-noklu-nolapack-extended-int64
+      - SUNDBASE=/opt/sundials-5.3.0-noklu-nolapack-extended-int64
       - PYCVODES_NO_LAPACK=1
       - PYCVODES_NO_KLU=1
     commands:

README.rst

@@ -92,7 +92,7 @@ the solvers and then their python bindings. The 3rd party requirements are as fo
 
 - pygslodeiv2_ (requires GSL_ >=1.16)
 - pyodeint_ (requires boost_ >=1.72.0)
-- pycvodes_ (requires SUNDIALS_ >=5.2.0)
+- pycvodes_ (requires SUNDIALS_ >=5.3.0)
 
 .. _GSL: https://www.gnu.org/software/gsl/
 .. _boost: http://www.boost.org/

conda-recipe/meta.yaml

@@ -29,7 +29,7 @@ requirements:
     - pyodeint >=0.10.1
     - pygslodeiv2 >=0.9.1
     - pycvodes >=0.11.12
-    - pycompilation >=0.4.6
+    - pycompilation >=0.4.9
     - pycodeexport >=0.1.2
     - cython
     - python-symengine

pyodesys/_release.py

@@ -1 +1 @@
-__version__ = '0.13.0.dev0+git'
+__version__ = '0.13.1.dev0+git'

pyodesys/native/_base.py

@@ -80,6 +80,10 @@ class _NativeCodeBase(Cpp_Code):
     # `namespace_extend` is set in init
 
     def __init__(self, odesys, *args, **kwargs):
+        if Cpp_Code is object:
+            raise ModuleNotFoundError("failed to import Cpp_Code from pycodeexport")
+        if compile_sources is None:
+            raise ModuleNotFoundError("failed to import compile_sources from pycompilation")
         if odesys.nroots > 0 and not self._support_roots:
             raise ValueError("%s does not support nroots > 0" % self.__class__.__name__)
         self.namespace_override = kwargs.pop('namespace_override', {})

pyodesys/native/cvode.py

@@ -8,7 +8,7 @@
 from ..util import import_
 from ._base import _NativeCodeBase, _NativeSysBase, _compile_kwargs
 
-_config, get_include, _libs = import_('pycvodes', 'config', 'get_include', "_libs")
+get_include, config, _libs = import_("pycvodes", "get_include", "config", "_libs")
 
 if sys.version_info < (3, 6, 0):
     class ModuleNotFoundError(ImportError):
@@ -19,8 +19,8 @@ class NativeCvodeCode(_NativeCodeBase):
     wrapper_name = '_cvode_wrapper'
 
     try:
-        _realtype = _config['REAL_TYPE']
-        _indextype = _config['INDEX_TYPE']
+        _realtype = config['REAL_TYPE']
+        _indextype = config['INDEX_TYPE']
     except ModuleNotFoundError:
         _realtype = '#error "realtype_failed-to-import-pycvodes-or-too-old-version"'
         _indextype = '#error "indextype_failed-to-import-pycvodes-or-too-old-version"'
@@ -37,13 +37,15 @@ class NativeCvodeCode(_NativeCodeBase):
 
     def __init__(self, *args, **kwargs):
         self.compile_kwargs = copy.deepcopy(_compile_kwargs)
-        self.compile_kwargs['define'] = ['PYCVODES_NO_KLU={}'.format("0" if _config.get('KLU', True) else "1"),
-                                         'PYCVODES_NO_LAPACK={}'.format("0" if _config.get('LAPACK', True) else "1"),
-                                         'ANYODE_NO_LAPACK={}'.format("0" if _config.get('LAPACK', True) else "1")]
+        self.compile_kwargs['define'] = ['PYCVODES_NO_KLU={}'.format("0" if config.get('KLU', True) else "1"),
+                                         'PYCVODES_NO_LAPACK={}'.format("0" if config.get('LAPACK', True) else "1"),
+                                         'ANYODE_NO_LAPACK={}'.format("0" if config.get('LAPACK', True) else "1")]
         self.compile_kwargs['include_dirs'].append(get_include())
         self.compile_kwargs['libraries'].extend(_libs.get_libs().split(','))
         self.compile_kwargs['libraries'].extend([l for l in os.environ.get(
-            'PYODESYS_LAPACK', "lapack,blas" if _config["LAPACK"] else "").split(",") if l != ""])
+            'PYODESYS_LAPACK', "lapack,blas" if config["LAPACK"] else "").split(",") if l != ""])
+        self.compile_kwargs['flags'] = [f for f in os.environ.get("PYODESYS_CVODE_FLAGS", "").split() if f]
+        self.compile_kwargs['ldflags'] = [f for f in os.environ.get("PYODESYS_CVODE_LDFLAGS", "").split() if f]
         super(NativeCvodeCode, self).__init__(*args, **kwargs)
 
 

setup.py

@@ -77,8 +77,8 @@ def _path_under_setup(*args):
 _author, _author_email = open(_path_under_setup('AUTHORS'), 'rt').readline().split('<')
 
 extras_req = {
-    'integrators': ['pyodeint>=0.10.3', 'pycvodes>=0.13', 'pygslodeiv2>=0.9.3'],
-    'native': ['pycompilation>=0.4.3', 'pycodeexport>=0.1.2', 'appdirs'],
+    'integrators': ['pyodeint>=0.10.3', 'pycvodes>=0.13.1', 'pygslodeiv2>=0.9.3'],
+    'native': ['pycompilation>=0.4.9', 'pycodeexport>=0.1.2', 'appdirs'],
     'docs': ['Sphinx', 'sphinx_rtd_theme', 'numpydoc'],
     'testing': ['pytest', 'pytest-cov', 'pytest-flakes', 'pytest-pep8', 'rstcheck']
 }