Update cython

CHANGELOG.md

@@ -6,11 +6,13 @@ All notable changes to **GSTools** will be documented in this file.
 ## [Unreleased]
 
 ### Enhancements
+- different variogram estimator functions can now be used #51
 
 ### Changes
 - Python versions 2.7 and 3.4 are no longer supported #40 #43
 
 ### Bugfixes
+- a race condition in the structured variogram estimation has been fixed #51
 
 
 ## [1.1.1] - Reverberating Red - 2019-11-08

README.md

@@ -49,22 +49,8 @@ running. Install the package by typing the following command in a command termin
 
     pip install gstools
 
-To get the latest development version you can install it directly from GitHub:
-
-    pip install https://github.com/GeoStat-Framework/GSTools/archive/develop.zip
-
-To enable the OpenMP support, you have to provide a C compiler, Cython and OpenMP.
-To get all other dependencies, it is recommended to first install gstools once
-in the standard way just decribed.
-Then use the following command:
-
-    pip install --global-option="--openmp" gstools
-
-Or for the development version:
-
-    pip install --global-option="--openmp" https://github.com/GeoStat-Framework/GSTools/archive/develop.zip
-
-If something went wrong during installation, try the [``-I`` flag from pip][pipiflag].
+To install the latest development version via pip, see the
+[documentation][doc_install_link].
 
 
 ## Citation
@@ -336,6 +322,7 @@ You can contact us via <info@geostat-framework.org>.
 [cov_link]: https://geostat-framework.readthedocs.io/projects/gstools/en/latest/covmodel.base.html#gstools.covmodel.base.CovModel
 [stable_link]: https://en.wikipedia.org/wiki/Stable_distribution
 [doc_link]: https://geostat-framework.readthedocs.io/projects/gstools/en/latest/
+[doc_install_link]: https://gstools.readthedocs.io/en/stable/#pip
 [tut_link]: https://geostat-framework.readthedocs.io/projects/gstools/en/latest/tutorials.html
 [tut1_link]: https://geostat-framework.readthedocs.io/projects/gstools/en/latest/tutorial_01_srf.html
 [tut2_link]: https://geostat-framework.readthedocs.io/projects/gstools/en/latest/tutorial_02_cov.html

gstools/field/summator.pyx

@@ -1,10 +1,8 @@
-#!python
-#cython: language_level=2
+#cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
 # -*- coding: utf-8 -*-
 """
 This is the variogram estimater, implemented in cython.
 """
-from __future__ import division, absolute_import, print_function
 
 import numpy as np
 
@@ -18,14 +16,11 @@ DTYPE = np.double
 ctypedef np.double_t DTYPE_t
 
 
-@cython.boundscheck(False)
-@cython.wraparound(False)
-@cython.cdivision(True)
 def summate_unstruct(
-    double[:,:] cov_samples,
-    double[:] z_1,
-    double[:] z_2,
-    double[:,:] pos
+    const double[:,:] cov_samples,
+    const double[:] z_1,
+    const double[:] z_2,
+    const double[:,:] pos
     ):
     cdef int i, j, d, X_len, N
     cdef double phase
@@ -46,16 +41,13 @@ def summate_unstruct(
 
     return np.asarray(summed_modes)
 
-@cython.boundscheck(False)
-@cython.wraparound(False)
-@cython.cdivision(True)
 def summate_struct(
-    double[:,:] cov_samples,
-    double[:] z_1,
-    double[:] z_2,
-    double[:] x,
-    double[:] y=None,
-    double[:] z=None,
+    const double[:,:] cov_samples,
+    const double[:] z_1,
+    const double[:] z_2,
+    const double[:] x,
+    const double[:] y=None,
+    const double[:] z=None,
 ):
     if y == None and z == None:
         return summate_struct_1d(cov_samples, z_1, z_2, x)
@@ -64,14 +56,11 @@ def summate_struct(
     else:
         return summate_struct_3d(cov_samples, z_1, z_2, x, y, z)
 
-@cython.boundscheck(False)
-@cython.wraparound(False)
-@cython.cdivision(True)
 def summate_struct_1d(
-    double[:,:] cov_samples,
-    double[:] z_1,
-    double[:] z_2,
-    double[:] x,
+    const double[:,:] cov_samples,
+    const double[:] z_1,
+    const double[:] z_2,
+    const double[:] x,
     ):
 
     cdef int i, j, X_len, N
@@ -89,15 +78,12 @@ def summate_struct_1d(
 
     return np.asarray(summed_modes)
 
-@cython.boundscheck(False)
-@cython.wraparound(False)
-@cython.cdivision(True)
 def summate_struct_2d(
-    double[:,:] cov_samples,
-    double[:] z_1,
-    double[:] z_2,
-    double[:] x,
-    double[:] y,
+    const double[:,:] cov_samples,
+    const double[:] z_1,
+    const double[:] z_2,
+    const double[:] x,
+    const double[:] y,
     ):
     cdef int i, j, k, X_len, Y_len, N
     cdef double phase
@@ -116,16 +102,13 @@ def summate_struct_2d(
 
     return np.asarray(summed_modes)
 
-@cython.boundscheck(False)
-@cython.wraparound(False)
-@cython.cdivision(True)
 def summate_struct_3d(
-    double[:,:] cov_samples,
-    double[:] z_1,
-    double[:] z_2,
-    double[:] x,
-    double[:] y,
-    double[:] z,
+    const double[:,:] cov_samples,
+    const double[:] z_1,
+    const double[:] z_2,
+    const double[:] x,
+    const double[:] y,
+    const double[:] z,
     ):
     cdef int i, j, k, l, X_len, Y_len, Z_len, N
     cdef double phase
@@ -150,10 +133,7 @@ def summate_struct_3d(
 
     return np.asarray(summed_modes)
 
-@cython.boundscheck(False)
-@cython.wraparound(False)
-@cython.cdivision(True)
-cdef (double) abs_square(double[:] vec) nogil:
+cdef (double) abs_square(const double[:] vec) nogil:
     cdef int i
     cdef double r = 0.
 
@@ -162,14 +142,11 @@ cdef (double) abs_square(double[:] vec) nogil:
 
     return r
 
-@cython.boundscheck(False)
-@cython.wraparound(False)
-@cython.cdivision(True)
 def summate_incompr_unstruct(
-    double[:,:] cov_samples,
-    double[:] z_1,
-    double[:] z_2,
-    double[:,:] pos
+    const double[:,:] cov_samples,
+    const double[:] z_1,
+    const double[:] z_2,
+    const double[:,:] pos
     ):
     cdef int i, j, d, X_len, N
     cdef double phase
@@ -198,31 +175,25 @@ def summate_incompr_unstruct(
 
     return np.asarray(summed_modes)
 
-@cython.boundscheck(False)
-@cython.wraparound(False)
-@cython.cdivision(True)
 def summate_incompr_struct(
-    double[:,:] cov_samples,
-    double[:] z_1,
-    double[:] z_2,
-    double[:] x,
-    double[:] y=None,
-    double[:] z=None,
+    const double[:,:] cov_samples,
+    const double[:] z_1,
+    const double[:] z_2,
+    const double[:] x,
+    const double[:] y=None,
+    const double[:] z=None,
 ):
     if z == None:
         return summate_incompr_struct_2d(cov_samples, z_1, z_2, x, y)
     else:
         return summate_incompr_struct_3d(cov_samples, z_1, z_2, x, y, z)
 
-@cython.boundscheck(False)
-@cython.wraparound(False)
-@cython.cdivision(True)
 def summate_incompr_struct_2d(
-    double[:,:] cov_samples,
-    double[:] z_1,
-    double[:] z_2,
-    double[:] x,
-    double[:] y,
+    const double[:,:] cov_samples,
+    const double[:] z_1,
+    const double[:] z_2,
+    const double[:] x,
+    const double[:] y,
     ):
     cdef int i, j, k, d, X_len, Y_len, N
     cdef double phase
@@ -250,16 +221,13 @@ def summate_incompr_struct_2d(
 
     return np.asarray(summed_modes)
 
-@cython.boundscheck(False)
-@cython.wraparound(False)
-@cython.cdivision(True)
 def summate_incompr_struct_3d(
-    double[:,:] cov_samples,
-    double[:] z_1,
-    double[:] z_2,
-    double[:] x,
-    double[:] y,
-    double[:] z,
+    const double[:,:] cov_samples,
+    const double[:] z_1,
+    const double[:] z_2,
+    const double[:] x,
+    const double[:] y,
+    const double[:] z,
     ):
     cdef int i, j, k, l, d, X_len, Y_len, Z_len, N
     cdef double phase

gstools/krige/krigesum.pyx

@@ -1,9 +1,8 @@
-# cython: language_level=2
+#cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
 # -*- coding: utf-8 -*-
 """
 This is a summator for the kriging routines
 """
-from __future__ import division, absolute_import, print_function
 
 import numpy as np
 
@@ -12,9 +11,11 @@ from cython.parallel import prange
 cimport numpy as np
 
 
-@cython.boundscheck(False) # turn off bounds-checking for entire function
-@cython.wraparound(False)  # turn off negative index wrapping for entire function
-def krigesum(double[:,:] krig_mat, double[:,:] krig_vecs, double[:] cond):
+def krigesum(
+    const double[:,:] krig_mat,
+    const double[:,:] krig_vecs,
+    const double[:] cond
+):
 
     cdef int mat_i = krig_mat.shape[0]
     cdef int res_i = krig_vecs.shape[1]