Fix cython syntax and port to more recent numpy.pxd

python/_cosmomath.pyx

@@ -12,7 +12,7 @@ cdef extern from "numpy/npy_common.h":
    ctypedef npy_intp
 
 cdef extern from "special_math.hpp" namespace "CosmoTool":
-   T log_modified_bessel_first_kind[T](T v, T z) nogil except +
+   T log_modified_bessel_first_kind[T](T v, T z) except + nogil
 
 cdef extern from "numpy_adaptors.hpp" namespace "CosmoTool":
    void parallel_ufunc_dd_d[T,IT](char **args, IT* dimensions, IT* steps, void *func)

python/_cosmotool.pyx

@@ -39,7 +39,7 @@ cdef extern from "loadSimu.hpp" namespace "CosmoTool":
 
 cdef extern from "loadGadget.hpp" namespace "CosmoTool":
 
-  SimuData *loadGadgetMulti(const char *fname, int id, int flags, int gformat) nogil except +
+  SimuData *loadGadgetMulti(const char *fname, int id, int flags, int gformat) except + nogil
   void cxx_writeGadget "CosmoTool::writeGadget" (const char * s, SimuData *data) except +
 
 cdef extern from "safe_gadget.hpp":
@@ -313,6 +313,13 @@ tries to get an array from the object."""
 references to the object are gone. """
         pass
 
+
+cdef extern from "numpy/arrayobject.h":
+    # a little bit awkward: the reference to obj will be stolen
+    # using PyObject*  to signal that Cython cannot handle it automatically
+    int PyArray_SetBaseObject(np.ndarray arr, PyObject *obj) except -1 # -1 means there was an error
+
+
 cdef object wrap_array(void *p, np.uint64_t s, int typ):
     cdef np.ndarray ndarray
     cdef ArrayWrapper wrapper
@@ -320,7 +327,8 @@ cdef object wrap_array(void *p, np.uint64_t s, int typ):
     wrapper = ArrayWrapper()
     wrapper.set_data(s, typ, p)
     ndarray = np.array(wrapper, copy=False)
-    ndarray.base = <PyObject*> wrapper
+    #ndarray.base = <PyObject*> wrapper
+    PyArray_SetBaseObject(ndarray, <PyObject*> wrapper)
     Py_INCREF(wrapper)
 
     return ndarray

python/_project.pyx

@@ -727,7 +727,7 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density,
     cdef int iu0[3]
     cdef int i
     cdef int N = density.shape[0]
-    cdef int half_N = density.shape[0]/2
+    cdef int half_N = density.shape[0]//2
     cdef int completed
     cdef DTYPE_t I0, d, dist2, delta, s, max_distance2
     cdef int jumper[1]