From 0cc899ae853b17362e689e2075626a8407050d93 Mon Sep 17 00:00:00 2001
From: LSchueler <mostem@posteo.de>
Date: Wed, 27 Oct 2021 17:29:29 +0200
Subject: [PATCH 01/10] Remove Cython code & replace it with GSTools-Core
The Github actions still need to be updated.
---
MANIFEST.in | 2 +-
README.md | 1 +
docs/source/index.rst | 1 +
gstools/field/generator.py | 2 +-
gstools/field/summator.pyx | 82 --------
gstools/krige/base.py | 4 +-
gstools/krige/krigesum.pyx | 64 ------
gstools/variogram/estimator.pyx | 346 --------------------------------
gstools/variogram/variogram.py | 17 +-
setup.cfg | 1 +
setup.py | 167 +--------------
11 files changed, 22 insertions(+), 665 deletions(-)
delete mode 100644 gstools/field/summator.pyx
delete mode 100644 gstools/krige/krigesum.pyx
delete mode 100644 gstools/variogram/estimator.pyx
diff --git a/MANIFEST.in b/MANIFEST.in
index 71c3bb1d5..933629618 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,6 +1,6 @@
prune *
graft tests
-recursive-include gstools *.py *.pyx
+recursive-include gstools *.py
recursive-exclude gstools *.c *.cpp
include LICENSE README.md pyproject.toml setup.py setup.cfg
exclude CHANGELOG.md CONTRIBUTING.md AUTHORS.md
diff --git a/README.md b/README.md
index 7ff21bf8f..117ee2eaa 100644
--- a/README.md
+++ b/README.md
@@ -338,6 +338,7 @@ in memory for immediate 3D plotting in Python.
- [NumPy >= 1.14.5](https://www.numpy.org)
- [SciPy >= 1.1.0](https://www.scipy.org/scipylib)
+- [GSTools-Core >= 0.1.0](https://github.com/GeoStat-Framework/GSTools-Core)
- [hankel >= 1.0.2](https://github.com/steven-murray/hankel)
- [emcee >= 3.0.0](https://github.com/dfm/emcee)
- [pyevtk >= 1.1.1](https://github.com/pyscience-projects/pyevtk)
diff --git a/docs/source/index.rst b/docs/source/index.rst
index f66ca738b..1aa563d5f 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -378,6 +378,7 @@ Requirements
- `Numpy >= 1.14.5 <http://www.numpy.org>`_
- `SciPy >= 1.1.0 <http://www.scipy.org>`_
+- `GSTools-Core >= 0.1.0 <https://github.com/GeoStat-Framework/GSTools-Core>`_
- `hankel >= 1.0.2 <https://github.com/steven-murray/hankel>`_
- `emcee >= 3.0.0 <https://github.com/dfm/emcee>`_
- `pyevtk >= 1.1.1 <https://github.com/pyscience-projects/pyevtk>`_
diff --git a/gstools/field/generator.py b/gstools/field/generator.py
index 66f11e99b..f8d7be315 100644
--- a/gstools/field/generator.py
+++ b/gstools/field/generator.py
@@ -16,8 +16,8 @@
import numpy as np
+from gstools_core import summate, summate_incompr
from gstools.covmodel.base import CovModel
-from gstools.field.summator import summate, summate_incompr
from gstools.random.rng import RNG
__all__ = ["RandMeth", "IncomprRandMeth"]
diff --git a/gstools/field/summator.pyx b/gstools/field/summator.pyx
deleted file mode 100644
index ecd7ea58d..000000000
--- a/gstools/field/summator.pyx
+++ /dev/null
@@ -1,82 +0,0 @@
-#cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
-# -*- coding: utf-8 -*-
-"""
-This is the randomization method summator, implemented in cython.
-"""
-
-import numpy as np
-
-cimport cython
-
-from cython.parallel import prange
-
-cimport numpy as np
-from libc.math cimport cos, sin
-
-
-def summate(
- const double[:, :] cov_samples,
- const double[:] z_1,
- const double[:] z_2,
- const double[:, :] pos
- ):
- cdef int i, j, d
- cdef double phase
- cdef int dim = pos.shape[0]
-
- cdef int X_len = pos.shape[1]
- cdef int N = cov_samples.shape[1]
-
- cdef double[:] summed_modes = np.zeros(X_len, dtype=float)
-
- for i in prange(X_len, nogil=True):
- for j in range(N):
- phase = 0.
- for d in range(dim):
- phase += cov_samples[d, j] * pos[d, i]
- summed_modes[i] += z_1[j] * cos(phase) + z_2[j] * sin(phase)
-
- return np.asarray(summed_modes)
-
-
-cdef (double) abs_square(const double[:] vec) nogil:
- cdef int i
- cdef double r = 0.
-
- for i in range(vec.shape[0]):
- r += vec[i]**2
-
- return r
-
-
-def summate_incompr(
- const double[:, :] cov_samples,
- const double[:] z_1,
- const double[:] z_2,
- const double[:, :] pos
- ):
- cdef int i, j, d
- cdef double phase
- cdef double k_2
- cdef int dim = pos.shape[0]
-
- cdef double[:] e1 = np.zeros(dim, dtype=float)
- e1[0] = 1.
- cdef double[:] proj = np.empty(dim)
-
- cdef int X_len = pos.shape[1]
- cdef int N = cov_samples.shape[1]
-
- cdef double[:, :] summed_modes = np.zeros((dim, X_len), dtype=float)
-
- for i in range(X_len):
- for j in range(N):
- k_2 = abs_square(cov_samples[:, j])
- phase = 0.
- for d in range(dim):
- phase += cov_samples[d, j] * pos[d, i]
- for d in range(dim):
- proj[d] = e1[d] - cov_samples[d, j] * cov_samples[0, j] / k_2
- summed_modes[d, i] += proj[d] * (z_1[j] * cos(phase) + z_2[j] * sin(phase))
-
- return np.asarray(summed_modes)
diff --git a/gstools/krige/base.py b/gstools/krige/base.py
index 1e2171856..5558ec7bc 100755
--- a/gstools/krige/base.py
+++ b/gstools/krige/base.py
@@ -16,11 +16,11 @@
import scipy.linalg as spl
from scipy.spatial.distance import cdist
-from gstools.field.base import Field
-from gstools.krige.krigesum import (
+from gstools_core import (
calc_field_krige,
calc_field_krige_and_variance,
)
+from gstools.field.base import Field
from gstools.krige.tools import get_drift_functions, set_condition
from gstools.tools.geometric import rotated_main_axes
from gstools.tools.misc import eval_func
diff --git a/gstools/krige/krigesum.pyx b/gstools/krige/krigesum.pyx
deleted file mode 100644
index 41911cef3..000000000
--- a/gstools/krige/krigesum.pyx
+++ /dev/null
@@ -1,64 +0,0 @@
-#cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
-# -*- coding: utf-8 -*-
-"""
-This is a summator for the kriging routines
-"""
-
-import numpy as np
-
-cimport cython
-from cython.parallel import prange
-cimport numpy as np
-
-
-def calc_field_krige_and_variance(
- 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]
-
- cdef double[:] field = np.zeros(res_i)
- cdef double[:] error = np.zeros(res_i)
- cdef double krig_fac
-
- cdef int i, j, k
-
- # error = krig_vecs * krig_mat * krig_vecs
- # field = cond * krig_mat * krig_vecs
- for k in prange(res_i, nogil=True):
- for i in range(mat_i):
- krig_fac = 0.0
- for j in range(mat_i):
- krig_fac += krig_mat[i, j] * krig_vecs[j, k]
- error[k] += krig_vecs[i, k] * krig_fac
- field[k] += cond[i] * krig_fac
-
- return np.asarray(field), np.asarray(error)
-
-
-def calc_field_krige(
- 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]
-
- cdef double[:] field = np.zeros(res_i)
- cdef double krig_fac
-
- cdef int i, j, k
-
- # field = cond * krig_mat * krig_vecs
- for k in prange(res_i, nogil=True):
- for i in range(mat_i):
- krig_fac = 0.0
- for j in range(mat_i):
- krig_fac += krig_mat[i, j] * krig_vecs[j, k]
- field[k] += cond[i] * krig_fac
-
- return np.asarray(field)
diff --git a/gstools/variogram/estimator.pyx b/gstools/variogram/estimator.pyx
deleted file mode 100644
index 8c149b41b..000000000
--- a/gstools/variogram/estimator.pyx
+++ /dev/null
@@ -1,346 +0,0 @@
-#cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
-# distutils: language = c++
-# -*- coding: utf-8 -*-
-"""
-This is the variogram estimater, implemented in cython.
-"""
-
-import numpy as np
-
-cimport cython
-
-from cython.parallel import parallel, prange
-
-cimport numpy as np
-from libc.math cimport M_PI, acos, atan2, cos, fabs, isnan, pow, sin, sqrt
-
-
-cdef inline double dist_euclid(
- const int dim,
- const double[:,:] pos,
- const int i,
- const int j,
-) nogil:
- cdef int d
- cdef double dist_squared = 0.0
- for d in range(dim):
- dist_squared += ((pos[d,i] - pos[d,j]) * (pos[d,i] - pos[d,j]))
- return sqrt(dist_squared)
-
-
-cdef inline double dist_haversine(
- const int dim,
- const double[:,:] pos,
- const int i,
- const int j,
-) nogil:
- # pos holds lat-lon in deg
- cdef double deg_2_rad = M_PI / 180.0
- cdef double diff_lat = (pos[0, j] - pos[0, i]) * deg_2_rad
- cdef double diff_lon = (pos[1, j] - pos[1, i]) * deg_2_rad
- cdef double arg = (
- pow(sin(diff_lat/2.0), 2) +
- cos(pos[0, i]*deg_2_rad) *
- cos(pos[0, j]*deg_2_rad) *
- pow(sin(diff_lon/2.0), 2)
- )
- return 2.0 * atan2(sqrt(arg), sqrt(1.0-arg))
-
-
-ctypedef double (*_dist_func)(
- const int,
- const double[:,:],
- const int,
- const int,
-) nogil
-
-
-cdef inline bint dir_test(
- const int dim,
- const double[:,:] pos,
- const double dist,
- const double[:,:] direction,
- const double angles_tol,
- const double bandwidth,
- const int i,
- const int j,
- const int d,
-) nogil:
- cdef double s_prod = 0.0 # scalar product
- cdef double b_dist = 0.0 # band-distance
- cdef double tmp # temporary variable
- cdef int k
- cdef bint in_band = True
- cdef bint in_angle = True
-
- # scalar-product calculation for bandwidth projection and angle calculation
- for k in range(dim):
- s_prod += (pos[k,i] - pos[k,j]) * direction[d,k]
-
- # calculate band-distance by projection of point-pair-vec to direction line
- if bandwidth > 0.0:
- for k in range(dim):
- tmp = (pos[k,i] - pos[k,j]) - s_prod * direction[d,k]
- b_dist += tmp * tmp
- in_band = sqrt(b_dist) < bandwidth
-
- # allow repeating points (dist = 0)
- if dist > 0.0:
- # use smallest angle by taking absolute value for arccos angle formula
- tmp = fabs(s_prod) / dist
- if tmp < 1.0: # else same direction (prevent numerical errors)
- in_angle = acos(tmp) < angles_tol
-
- return in_band and in_angle
-
-
-cdef inline double estimator_matheron(const double f_diff) nogil:
- return f_diff * f_diff
-
-cdef inline double estimator_cressie(const double f_diff) nogil:
- return sqrt(fabs(f_diff))
-
-ctypedef double (*_estimator_func)(const double) nogil
-
-cdef inline void normalization_matheron(
- double[:] variogram,
- long[:] counts,
-):
- cdef int i
- for i in range(variogram.shape[0]):
- # avoid division by zero
- variogram[i] /= (2. * max(counts[i], 1))
-
-cdef inline void normalization_cressie(
- double[:] variogram,
- long[:] counts,
-):
- cdef int i
- cdef long cnt
- for i in range(variogram.shape[0]):
- # avoid division by zero
- cnt = max(counts[i], 1)
- variogram[i] = (
- 0.5 * (1./cnt * variogram[i])**4 /
- (0.457 + 0.494 / cnt + 0.045 / cnt**2)
- )
-
-ctypedef void (*_normalization_func)(
- double[:],
- long[:],
-)
-
-cdef inline void normalization_matheron_vec(
- double[:,:] variogram,
- long[:,:] counts,
-):
- cdef int d, i
- for d in range(variogram.shape[0]):
- normalization_matheron(variogram[d, :], counts[d, :])
-
-cdef inline void normalization_cressie_vec(
- double[:,:] variogram,
- long[:,:] counts,
-):
- cdef int d, i
- cdef long cnt
- for d in range(variogram.shape[0]):
- normalization_cressie(variogram[d, :], counts[d, :])
-
-ctypedef void (*_normalization_func_vec)(
- double[:,:],
- long[:,:],
-)
-
-cdef _estimator_func choose_estimator_func(str estimator_type):
- cdef _estimator_func estimator_func
- if estimator_type == 'm':
- estimator_func = estimator_matheron
- elif estimator_type == 'c':
- estimator_func = estimator_cressie
- return estimator_func
-
-cdef _normalization_func choose_estimator_normalization(str estimator_type):
- cdef _normalization_func normalization_func
- if estimator_type == 'm':
- normalization_func = normalization_matheron
- elif estimator_type == 'c':
- normalization_func = normalization_cressie
- return normalization_func
-
-cdef _normalization_func_vec choose_estimator_normalization_vec(str estimator_type):
- cdef _normalization_func_vec normalization_func_vec
- if estimator_type == 'm':
- normalization_func_vec = normalization_matheron_vec
- elif estimator_type == 'c':
- normalization_func_vec = normalization_cressie_vec
- return normalization_func_vec
-
-
-def directional(
- const int dim,
- const double[:,:] f,
- const double[:] bin_edges,
- const double[:,:] pos,
- const double[:,:] direction, # should be normed
- const double angles_tol=M_PI/8.0,
- const double bandwidth=-1.0, # negative values to turn of bandwidth search
- const bint separate_dirs=False, # whether the direction bands don't overlap
- str estimator_type='m',
-):
- if pos.shape[1] != f.shape[1]:
- raise ValueError('len(pos) = {0} != len(f) = {1} '.
- format(pos.shape[1], f.shape[1]))
-
- if bin_edges.shape[0] < 2:
- raise ValueError('len(bin_edges) too small')
-
- if angles_tol <= 0:
- raise ValueError('tolerance for angle search masks must be > 0')
-
- cdef _estimator_func estimator_func = choose_estimator_func(estimator_type)
- cdef _normalization_func_vec normalization_func_vec = (
- choose_estimator_normalization_vec(estimator_type)
- )
-
- cdef int d_max = direction.shape[0]
- cdef int i_max = bin_edges.shape[0] - 1
- cdef int j_max = pos.shape[1] - 1
- cdef int k_max = pos.shape[1]
- cdef int f_max = f.shape[0]
-
- cdef double[:,:] variogram = np.zeros((d_max, len(bin_edges)-1))
- cdef long[:,:] counts = np.zeros((d_max, len(bin_edges)-1), dtype=long)
- cdef int i, j, k, m, d
- cdef double dist
-
- for i in prange(i_max, nogil=True):
- for j in range(j_max):
- for k in range(j+1, k_max):
- dist = dist_euclid(dim, pos, j, k)
- if dist < bin_edges[i] or dist >= bin_edges[i+1]:
- continue # skip if not in current bin
- for d in range(d_max):
- if not dir_test(dim, pos, dist, direction, angles_tol, bandwidth, k, j, d):
- continue # skip if not in current direction
- for m in range(f_max):
- # skip no data values
- if not (isnan(f[m,k]) or isnan(f[m,j])):
- counts[d, i] += 1
- variogram[d, i] += estimator_func(f[m,k] - f[m,j])
- # once we found a fitting direction
- # break the search if directions are separated
- if separate_dirs:
- break
-
- normalization_func_vec(variogram, counts)
- return np.asarray(variogram), np.asarray(counts)
-
-def unstructured(
- const int dim,
- const double[:,:] f,
- const double[:] bin_edges,
- const double[:,:] pos,
- str estimator_type='m',
- str distance_type='e',
-):
- cdef _dist_func distance
-
- if distance_type == 'e':
- distance = dist_euclid
- else:
- distance = dist_haversine
- if dim != 2:
- raise ValueError('Haversine: dim = {0} != 2'.format(dim))
-
- if pos.shape[1] != f.shape[1]:
- raise ValueError('len(pos) = {0} != len(f) = {1} '.
- format(pos.shape[1], f.shape[1]))
-
- if bin_edges.shape[0] < 2:
- raise ValueError('len(bin_edges) too small')
-
- cdef _estimator_func estimator_func = choose_estimator_func(estimator_type)
- cdef _normalization_func normalization_func = (
- choose_estimator_normalization(estimator_type)
- )
-
- cdef int i_max = bin_edges.shape[0] - 1
- cdef int j_max = pos.shape[1] - 1
- cdef int k_max = pos.shape[1]
- cdef int f_max = f.shape[0]
-
- cdef double[:] variogram = np.zeros(len(bin_edges)-1)
- cdef long[:] counts = np.zeros(len(bin_edges)-1, dtype=long)
- cdef int i, j, k, m
- cdef double dist
-
- for i in prange(i_max, nogil=True):
- for j in range(j_max):
- for k in range(j+1, k_max):
- dist = distance(dim, pos, j, k)
- if dist < bin_edges[i] or dist >= bin_edges[i+1]:
- continue # skip if not in current bin
- for m in range(f_max):
- # skip no data values
- if not (isnan(f[m,k]) or isnan(f[m,j])):
- counts[i] += 1
- variogram[i] += estimator_func(f[m,k] - f[m,j])
-
- normalization_func(variogram, counts)
- return np.asarray(variogram), np.asarray(counts)
-
-
-def structured(const double[:,:] f, str estimator_type='m'):
- cdef _estimator_func estimator_func = choose_estimator_func(estimator_type)
- cdef _normalization_func normalization_func = (
- choose_estimator_normalization(estimator_type)
- )
-
- cdef int i_max = f.shape[0] - 1
- cdef int j_max = f.shape[1]
- cdef int k_max = i_max + 1
-
- cdef double[:] variogram = np.zeros(k_max)
- cdef long[:] counts = np.zeros(k_max, dtype=long)
- cdef int i, j, k
-
- with nogil, parallel():
- for i in range(i_max):
- for j in range(j_max):
- for k in prange(1, k_max-i):
- counts[k] += 1
- variogram[k] += estimator_func(f[i,j] - f[i+k,j])
-
- normalization_func(variogram, counts)
- return np.asarray(variogram)
-
-
-def ma_structured(
- const double[:,:] f,
- const bint[:,:] mask,
- str estimator_type='m',
-):
- cdef _estimator_func estimator_func = choose_estimator_func(estimator_type)
- cdef _normalization_func normalization_func = (
- choose_estimator_normalization(estimator_type)
- )
-
- cdef int i_max = f.shape[0] - 1
- cdef int j_max = f.shape[1]
- cdef int k_max = i_max + 1
-
- cdef double[:] variogram = np.zeros(k_max)
- cdef long[:] counts = np.zeros(k_max, dtype=long)
- cdef int i, j, k
-
- with nogil, parallel():
- for i in range(i_max):
- for j in range(j_max):
- for k in prange(1, k_max-i):
- if not mask[i,j] and not mask[i+k,j]:
- counts[k] += 1
- variogram[k] += estimator_func(f[i,j] - f[i+k,j])
-
- normalization_func(variogram, counts)
- return np.asarray(variogram)
diff --git a/gstools/variogram/variogram.py b/gstools/variogram/variogram.py
index 7c1076959..d758e3b40 100644
--- a/gstools/variogram/variogram.py
+++ b/gstools/variogram/variogram.py
@@ -12,6 +12,12 @@
"""
import numpy as np
+from gstools_core import (
+ variogram_directional as directional,
+ variogram_ma_structured as ma_structured,
+ variogram_structured as structured,
+ variogram_unstructured as unstructured,
+)
from gstools.normalizer.tools import remove_trend_norm_mean
from gstools.tools.geometric import (
ang2dir,
@@ -20,12 +26,6 @@
generate_grid,
)
from gstools.variogram.binning import standard_bins
-from gstools.variogram.estimator import (
- directional,
- ma_structured,
- structured,
- unstructured,
-)
__all__ = [
"vario_estimate",
@@ -59,7 +59,8 @@ def _separate_dirs_test(direction, angles_tol):
for j in range(i + 1, direction.shape[0]):
s_prod = np.minimum(np.abs(np.dot(direction[i], direction[j])), 1)
separate_dirs &= np.arccos(s_prod) >= 2 * angles_tol
- return separate_dirs
+ # gstools-core doesn't like the type `numpy.bool_`
+ return bool(separate_dirs)
def vario_estimate(
@@ -441,7 +442,7 @@ def vario_estimate_axis(
field = np.ma.array(field, ndmin=1, dtype=np.double)
if missing:
field.mask = np.logical_or(field.mask, missing_mask)
- mask = np.asarray(np.ma.getmaskarray(field), dtype=np.int32)
+ mask = np.ma.getmaskarray(field)
else:
field = np.array(field, ndmin=1, dtype=np.double, copy=False)
missing_mask = None # free space
diff --git a/setup.cfg b/setup.cfg
index efc2fd4c5..d533120b0 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -39,6 +39,7 @@ project_urls =
packages = find:
install_requires =
emcee>=3.0.0,<4
+ gstools_core>=0.1.2,<1
hankel>=1.0.2,<2
meshio>=4.0.3,<6
numpy>=1.14.5,<2
diff --git a/setup.py b/setup.py
index 1bbc7fafa..291d34a54 100644
--- a/setup.py
+++ b/setup.py
@@ -1,169 +1,14 @@
# -*- coding: utf-8 -*-
"""GSTools: A geostatistical toolbox."""
-import glob
import os
-import subprocess
-import sys
-import tempfile
-from distutils.ccompiler import new_compiler
-from distutils.errors import CompileError, LinkError
-from distutils.sysconfig import customize_compiler
import numpy as np
-from Cython.Build import cythonize
-from setuptools import Extension, setup
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-
-
-# openmp finder ###############################################################
-# This code is adapted for a large part from the scikit-learn openmp_helpers.py
-# which can be found at:
-# https://github.com/scikit-learn/scikit-learn/blob/0.24.0/sklearn/_build_utils
-
-
-CCODE = """
-#include <omp.h>
-#include <stdio.h>
-int main(void) {
-#pragma omp parallel
-printf("nthreads=%d\\n", omp_get_num_threads());
-return 0;
-}
-"""
-
-
-def get_openmp_flag(compiler):
- """Get the compiler dependent openmp flag."""
- if hasattr(compiler, "compiler"):
- compiler = compiler.compiler[0]
- else:
- compiler = compiler.__class__.__name__
-
- if sys.platform == "win32" and ("icc" in compiler or "icl" in compiler):
- return ["/Qopenmp"]
- if sys.platform == "win32":
- return ["/openmp"]
- if sys.platform == "darwin" and ("icc" in compiler or "icl" in compiler):
- return ["-openmp"]
- if sys.platform == "darwin" and "openmp" in os.getenv("CPPFLAGS", ""):
- return []
- # Default flag for GCC and clang:
- return ["-fopenmp"]
-
-
-def check_openmp_support():
- """Check whether OpenMP test code can be compiled and run."""
- ccompiler = new_compiler()
- customize_compiler(ccompiler)
-
- with tempfile.TemporaryDirectory() as tmp_dir:
- try:
- os.chdir(tmp_dir)
- # Write test program
- with open("test_openmp.c", "w") as cfile:
- cfile.write(CCODE)
- os.mkdir("objects")
- # Compile, test program
- openmp_flags = get_openmp_flag(ccompiler)
- ccompiler.compile(
- ["test_openmp.c"],
- output_dir="objects",
- extra_postargs=openmp_flags,
- )
- # Link test program
- extra_preargs = os.getenv("LDFLAGS", None)
- if extra_preargs is not None:
- extra_preargs = extra_preargs.split(" ")
- else:
- extra_preargs = []
- objects = glob.glob(
- os.path.join("objects", "*" + ccompiler.obj_extension)
- )
- ccompiler.link_executable(
- objects,
- "test_openmp",
- extra_preargs=extra_preargs,
- extra_postargs=openmp_flags,
- )
- # Run test program
- output = subprocess.check_output("./test_openmp")
- output = output.decode(sys.stdout.encoding or "utf-8").splitlines()
- # Check test program output
- if "nthreads=" in output[0]:
- nthreads = int(output[0].strip().split("=")[1])
- openmp_supported = len(output) == nthreads
- else:
- openmp_supported = False
- openmp_flags = []
- except (CompileError, LinkError, subprocess.CalledProcessError):
- openmp_supported = False
- openmp_flags = []
- finally:
- os.chdir(HERE)
- return openmp_supported, openmp_flags
-
-
-# openmp ######################################################################
-
-
-# you can set GSTOOLS_BUILD_PARALLEL=0 or GSTOOLS_BUILD_PARALLEL=1
-GS_PARALLEL = os.getenv("GSTOOLS_BUILD_PARALLEL")
-USE_OPENMP = bool(int(GS_PARALLEL)) if GS_PARALLEL else False
-
-if USE_OPENMP:
- # just check if wanted
- CAN_USE_OPENMP, FLAGS = check_openmp_support()
- if CAN_USE_OPENMP:
- print("## GSTOOLS setup: OpenMP found.")
- print("## OpenMP flags:", FLAGS)
- else:
- print("## GSTOOLS setup: OpenMP not found.")
-else:
- print("## GSTOOLS setup: OpenMP not wanted by the user.")
- FLAGS = []
-
-
-# cython extensions ###########################################################
-
-
-CY_MODULES = []
-CY_MODULES.append(
- Extension(
- "gstools.field.summator",
- [os.path.join("gstools", "field", "summator.pyx")],
- include_dirs=[np.get_include()],
- extra_compile_args=FLAGS,
- extra_link_args=FLAGS,
- )
-)
-CY_MODULES.append(
- Extension(
- "gstools.variogram.estimator",
- [os.path.join("gstools", "variogram", "estimator.pyx")],
- language="c++",
- include_dirs=[np.get_include()],
- extra_compile_args=FLAGS,
- extra_link_args=FLAGS,
- )
-)
-CY_MODULES.append(
- Extension(
- "gstools.krige.krigesum",
- [os.path.join("gstools", "krige", "krigesum.pyx")],
- include_dirs=[np.get_include()],
- extra_compile_args=FLAGS,
- extra_link_args=FLAGS,
- )
-)
-EXT_MODULES = cythonize(CY_MODULES) # annotate=True
-
-# embed signatures for sphinx
-for ext_m in EXT_MODULES:
- ext_m.cython_directives = {"embedsignature": True}
-
+from setuptools import setup
+import sys
+import site
-# setup #######################################################################
+site.ENABLE_USER_SITE = "--user" in sys.argv[1:]
+HERE = os.path.abspath(os.path.dirname(__file__))
-setup(ext_modules=EXT_MODULES, include_dirs=[np.get_include()])
+setup(include_dirs=[np.get_include()])
From 41cb5d5aea03dfee001fcee36c18af1eeb20edb5 Mon Sep 17 00:00:00 2001
From: LSchueler <mostem@posteo.de>
Date: Tue, 9 Nov 2021 19:51:44 +0100
Subject: [PATCH 02/10] Restore Cython code and make Rust impl. optional
Now, the GSTools-Core is used, if the package can be imported, but it
can also be switched off, by setting the global var.
`gstools.config.USE_RUST=False` during the runtime.
---
MANIFEST.in | 2 +-
README.md | 2 +-
docs/source/index.rst | 2 +-
gstools/__init__.py | 1 +
gstools/config.py | 14 ++
gstools/field/generator.py | 11 +-
gstools/field/summator.pyx | 82 ++++++++
gstools/krige/base.py | 16 +-
gstools/krige/krigesum.pyx | 64 ++++++
gstools/variogram/estimator.pyx | 346 ++++++++++++++++++++++++++++++++
gstools/variogram/variogram.py | 25 ++-
setup.cfg | 3 +-
setup.py | 167 ++++++++++++++-
13 files changed, 712 insertions(+), 23 deletions(-)
create mode 100644 gstools/config.py
create mode 100644 gstools/field/summator.pyx
create mode 100644 gstools/krige/krigesum.pyx
create mode 100644 gstools/variogram/estimator.pyx
diff --git a/MANIFEST.in b/MANIFEST.in
index 933629618..71c3bb1d5 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,6 +1,6 @@
prune *
graft tests
-recursive-include gstools *.py
+recursive-include gstools *.py *.pyx
recursive-exclude gstools *.c *.cpp
include LICENSE README.md pyproject.toml setup.py setup.cfg
exclude CHANGELOG.md CONTRIBUTING.md AUTHORS.md
diff --git a/README.md b/README.md
index 117ee2eaa..c0488480f 100644
--- a/README.md
+++ b/README.md
@@ -338,7 +338,6 @@ in memory for immediate 3D plotting in Python.
- [NumPy >= 1.14.5](https://www.numpy.org)
- [SciPy >= 1.1.0](https://www.scipy.org/scipylib)
-- [GSTools-Core >= 0.1.0](https://github.com/GeoStat-Framework/GSTools-Core)
- [hankel >= 1.0.2](https://github.com/steven-murray/hankel)
- [emcee >= 3.0.0](https://github.com/dfm/emcee)
- [pyevtk >= 1.1.1](https://github.com/pyscience-projects/pyevtk)
@@ -346,6 +345,7 @@ in memory for immediate 3D plotting in Python.
### Optional
+- [GSTools-Core >= 0.1.0](https://github.com/GeoStat-Framework/GSTools-Core)
- [matplotlib](https://matplotlib.org)
- [pyvista](https://docs.pyvista.org/)
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 1aa563d5f..b36965352 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -378,7 +378,6 @@ Requirements
- `Numpy >= 1.14.5 <http://www.numpy.org>`_
- `SciPy >= 1.1.0 <http://www.scipy.org>`_
-- `GSTools-Core >= 0.1.0 <https://github.com/GeoStat-Framework/GSTools-Core>`_
- `hankel >= 1.0.2 <https://github.com/steven-murray/hankel>`_
- `emcee >= 3.0.0 <https://github.com/dfm/emcee>`_
- `pyevtk >= 1.1.1 <https://github.com/pyscience-projects/pyevtk>`_
@@ -388,6 +387,7 @@ Requirements
Optional
--------
+- `GSTools-Core >= 0.1.0 <https://github.com/GeoStat-Framework/GSTools-Core>`_
- `matplotlib <https://matplotlib.org>`_
- `pyvista <https://docs.pyvista.org>`_
diff --git a/gstools/__init__.py b/gstools/__init__.py
index 77281d8d4..a82839cc7 100644
--- a/gstools/__init__.py
+++ b/gstools/__init__.py
@@ -127,6 +127,7 @@
"""
# Hooray!
from gstools import (
+ config,
covmodel,
field,
krige,
diff --git a/gstools/config.py b/gstools/config.py
new file mode 100644
index 000000000..ebbd571cd
--- /dev/null
+++ b/gstools/config.py
@@ -0,0 +1,14 @@
+# -*- coding: utf-8 -*-
+"""
+GStools subpackage providing global variables.
+
+.. currentmodule:: gstools.config
+
+"""
+# pylint: disable=W0611
+try:
+ import gstools_core
+
+ USE_RUST = True
+except ImportError:
+ USE_RUST = False
diff --git a/gstools/field/generator.py b/gstools/field/generator.py
index f8d7be315..91408e884 100644
--- a/gstools/field/generator.py
+++ b/gstools/field/generator.py
@@ -10,16 +10,23 @@
RandMeth
IncomprRandMeth
"""
-# pylint: disable=C0103, W0222
+# pylint: disable=C0103, W0222, C0412
import warnings
from copy import deepcopy as dcp
import numpy as np
-from gstools_core import summate, summate_incompr
+from gstools import config
from gstools.covmodel.base import CovModel
from gstools.random.rng import RNG
+if config.USE_RUST:
+ # pylint: disable=E0401
+ from gstools_core import summate, summate_incompr
+else:
+ # pylint: disable=C0412
+ from gstools.field.summator import summate, summate_incompr
+
__all__ = ["RandMeth", "IncomprRandMeth"]
diff --git a/gstools/field/summator.pyx b/gstools/field/summator.pyx
new file mode 100644
index 000000000..ecd7ea58d
--- /dev/null
+++ b/gstools/field/summator.pyx
@@ -0,0 +1,82 @@
+#cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
+# -*- coding: utf-8 -*-
+"""
+This is the randomization method summator, implemented in cython.
+"""
+
+import numpy as np
+
+cimport cython
+
+from cython.parallel import prange
+
+cimport numpy as np
+from libc.math cimport cos, sin
+
+
+def summate(
+ const double[:, :] cov_samples,
+ const double[:] z_1,
+ const double[:] z_2,
+ const double[:, :] pos
+ ):
+ cdef int i, j, d
+ cdef double phase
+ cdef int dim = pos.shape[0]
+
+ cdef int X_len = pos.shape[1]
+ cdef int N = cov_samples.shape[1]
+
+ cdef double[:] summed_modes = np.zeros(X_len, dtype=float)
+
+ for i in prange(X_len, nogil=True):
+ for j in range(N):
+ phase = 0.
+ for d in range(dim):
+ phase += cov_samples[d, j] * pos[d, i]
+ summed_modes[i] += z_1[j] * cos(phase) + z_2[j] * sin(phase)
+
+ return np.asarray(summed_modes)
+
+
+cdef (double) abs_square(const double[:] vec) nogil:
+ cdef int i
+ cdef double r = 0.
+
+ for i in range(vec.shape[0]):
+ r += vec[i]**2
+
+ return r
+
+
+def summate_incompr(
+ const double[:, :] cov_samples,
+ const double[:] z_1,
+ const double[:] z_2,
+ const double[:, :] pos
+ ):
+ cdef int i, j, d
+ cdef double phase
+ cdef double k_2
+ cdef int dim = pos.shape[0]
+
+ cdef double[:] e1 = np.zeros(dim, dtype=float)
+ e1[0] = 1.
+ cdef double[:] proj = np.empty(dim)
+
+ cdef int X_len = pos.shape[1]
+ cdef int N = cov_samples.shape[1]
+
+ cdef double[:, :] summed_modes = np.zeros((dim, X_len), dtype=float)
+
+ for i in range(X_len):
+ for j in range(N):
+ k_2 = abs_square(cov_samples[:, j])
+ phase = 0.
+ for d in range(dim):
+ phase += cov_samples[d, j] * pos[d, i]
+ for d in range(dim):
+ proj[d] = e1[d] - cov_samples[d, j] * cov_samples[0, j] / k_2
+ summed_modes[d, i] += proj[d] * (z_1[j] * cos(phase) + z_2[j] * sin(phase))
+
+ return np.asarray(summed_modes)
diff --git a/gstools/krige/base.py b/gstools/krige/base.py
index 5558ec7bc..e3922d335 100755
--- a/gstools/krige/base.py
+++ b/gstools/krige/base.py
@@ -9,23 +9,29 @@
.. autosummary::
Krige
"""
-# pylint: disable=C0103, W0221, E1102, R0201
+# pylint: disable=C0103, W0221, E1102, R0201, C0412
import collections
import numpy as np
import scipy.linalg as spl
from scipy.spatial.distance import cdist
-from gstools_core import (
- calc_field_krige,
- calc_field_krige_and_variance,
-)
+from gstools import config
from gstools.field.base import Field
from gstools.krige.tools import get_drift_functions, set_condition
from gstools.tools.geometric import rotated_main_axes
from gstools.tools.misc import eval_func
from gstools.variogram import vario_estimate
+if config.USE_RUST:
+ # pylint: disable=E0401
+ from gstools_core import calc_field_krige, calc_field_krige_and_variance
+else:
+ from gstools.krige.krigesum import (
+ calc_field_krige,
+ calc_field_krige_and_variance,
+ )
+
__all__ = ["Krige"]
diff --git a/gstools/krige/krigesum.pyx b/gstools/krige/krigesum.pyx
new file mode 100644
index 000000000..41911cef3
--- /dev/null
+++ b/gstools/krige/krigesum.pyx
@@ -0,0 +1,64 @@
+#cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
+# -*- coding: utf-8 -*-
+"""
+This is a summator for the kriging routines
+"""
+
+import numpy as np
+
+cimport cython
+from cython.parallel import prange
+cimport numpy as np
+
+
+def calc_field_krige_and_variance(
+ 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]
+
+ cdef double[:] field = np.zeros(res_i)
+ cdef double[:] error = np.zeros(res_i)
+ cdef double krig_fac
+
+ cdef int i, j, k
+
+ # error = krig_vecs * krig_mat * krig_vecs
+ # field = cond * krig_mat * krig_vecs
+ for k in prange(res_i, nogil=True):
+ for i in range(mat_i):
+ krig_fac = 0.0
+ for j in range(mat_i):
+ krig_fac += krig_mat[i, j] * krig_vecs[j, k]
+ error[k] += krig_vecs[i, k] * krig_fac
+ field[k] += cond[i] * krig_fac
+
+ return np.asarray(field), np.asarray(error)
+
+
+def calc_field_krige(
+ 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]
+
+ cdef double[:] field = np.zeros(res_i)
+ cdef double krig_fac
+
+ cdef int i, j, k
+
+ # field = cond * krig_mat * krig_vecs
+ for k in prange(res_i, nogil=True):
+ for i in range(mat_i):
+ krig_fac = 0.0
+ for j in range(mat_i):
+ krig_fac += krig_mat[i, j] * krig_vecs[j, k]
+ field[k] += cond[i] * krig_fac
+
+ return np.asarray(field)
diff --git a/gstools/variogram/estimator.pyx b/gstools/variogram/estimator.pyx
new file mode 100644
index 000000000..8c149b41b
--- /dev/null
+++ b/gstools/variogram/estimator.pyx
@@ -0,0 +1,346 @@
+#cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
+# distutils: language = c++
+# -*- coding: utf-8 -*-
+"""
+This is the variogram estimater, implemented in cython.
+"""
+
+import numpy as np
+
+cimport cython
+
+from cython.parallel import parallel, prange
+
+cimport numpy as np
+from libc.math cimport M_PI, acos, atan2, cos, fabs, isnan, pow, sin, sqrt
+
+
+cdef inline double dist_euclid(
+ const int dim,
+ const double[:,:] pos,
+ const int i,
+ const int j,
+) nogil:
+ cdef int d
+ cdef double dist_squared = 0.0
+ for d in range(dim):
+ dist_squared += ((pos[d,i] - pos[d,j]) * (pos[d,i] - pos[d,j]))
+ return sqrt(dist_squared)
+
+
+cdef inline double dist_haversine(
+ const int dim,
+ const double[:,:] pos,
+ const int i,
+ const int j,
+) nogil:
+ # pos holds lat-lon in deg
+ cdef double deg_2_rad = M_PI / 180.0
+ cdef double diff_lat = (pos[0, j] - pos[0, i]) * deg_2_rad
+ cdef double diff_lon = (pos[1, j] - pos[1, i]) * deg_2_rad
+ cdef double arg = (
+ pow(sin(diff_lat/2.0), 2) +
+ cos(pos[0, i]*deg_2_rad) *
+ cos(pos[0, j]*deg_2_rad) *
+ pow(sin(diff_lon/2.0), 2)
+ )
+ return 2.0 * atan2(sqrt(arg), sqrt(1.0-arg))
+
+
+ctypedef double (*_dist_func)(
+ const int,
+ const double[:,:],
+ const int,
+ const int,
+) nogil
+
+
+cdef inline bint dir_test(
+ const int dim,
+ const double[:,:] pos,
+ const double dist,
+ const double[:,:] direction,
+ const double angles_tol,
+ const double bandwidth,
+ const int i,
+ const int j,
+ const int d,
+) nogil:
+ cdef double s_prod = 0.0 # scalar product
+ cdef double b_dist = 0.0 # band-distance
+ cdef double tmp # temporary variable
+ cdef int k
+ cdef bint in_band = True
+ cdef bint in_angle = True
+
+ # scalar-product calculation for bandwidth projection and angle calculation
+ for k in range(dim):
+ s_prod += (pos[k,i] - pos[k,j]) * direction[d,k]
+
+ # calculate band-distance by projection of point-pair-vec to direction line
+ if bandwidth > 0.0:
+ for k in range(dim):
+ tmp = (pos[k,i] - pos[k,j]) - s_prod * direction[d,k]
+ b_dist += tmp * tmp
+ in_band = sqrt(b_dist) < bandwidth
+
+ # allow repeating points (dist = 0)
+ if dist > 0.0:
+ # use smallest angle by taking absolute value for arccos angle formula
+ tmp = fabs(s_prod) / dist
+ if tmp < 1.0: # else same direction (prevent numerical errors)
+ in_angle = acos(tmp) < angles_tol
+
+ return in_band and in_angle
+
+
+cdef inline double estimator_matheron(const double f_diff) nogil:
+ return f_diff * f_diff
+
+cdef inline double estimator_cressie(const double f_diff) nogil:
+ return sqrt(fabs(f_diff))
+
+ctypedef double (*_estimator_func)(const double) nogil
+
+cdef inline void normalization_matheron(
+ double[:] variogram,
+ long[:] counts,
+):
+ cdef int i
+ for i in range(variogram.shape[0]):
+ # avoid division by zero
+ variogram[i] /= (2. * max(counts[i], 1))
+
+cdef inline void normalization_cressie(
+ double[:] variogram,
+ long[:] counts,
+):
+ cdef int i
+ cdef long cnt
+ for i in range(variogram.shape[0]):
+ # avoid division by zero
+ cnt = max(counts[i], 1)
+ variogram[i] = (
+ 0.5 * (1./cnt * variogram[i])**4 /
+ (0.457 + 0.494 / cnt + 0.045 / cnt**2)
+ )
+
+ctypedef void (*_normalization_func)(
+ double[:],
+ long[:],
+)
+
+cdef inline void normalization_matheron_vec(
+ double[:,:] variogram,
+ long[:,:] counts,
+):
+ cdef int d, i
+ for d in range(variogram.shape[0]):
+ normalization_matheron(variogram[d, :], counts[d, :])
+
+cdef inline void normalization_cressie_vec(
+ double[:,:] variogram,
+ long[:,:] counts,
+):
+ cdef int d, i
+ cdef long cnt
+ for d in range(variogram.shape[0]):
+ normalization_cressie(variogram[d, :], counts[d, :])
+
+ctypedef void (*_normalization_func_vec)(
+ double[:,:],
+ long[:,:],
+)
+
+cdef _estimator_func choose_estimator_func(str estimator_type):
+ cdef _estimator_func estimator_func
+ if estimator_type == 'm':
+ estimator_func = estimator_matheron
+ elif estimator_type == 'c':
+ estimator_func = estimator_cressie
+ return estimator_func
+
+cdef _normalization_func choose_estimator_normalization(str estimator_type):
+ cdef _normalization_func normalization_func
+ if estimator_type == 'm':
+ normalization_func = normalization_matheron
+ elif estimator_type == 'c':
+ normalization_func = normalization_cressie
+ return normalization_func
+
+cdef _normalization_func_vec choose_estimator_normalization_vec(str estimator_type):
+ cdef _normalization_func_vec normalization_func_vec
+ if estimator_type == 'm':
+ normalization_func_vec = normalization_matheron_vec
+ elif estimator_type == 'c':
+ normalization_func_vec = normalization_cressie_vec
+ return normalization_func_vec
+
+
+def directional(
+ const int dim,
+ const double[:,:] f,
+ const double[:] bin_edges,
+ const double[:,:] pos,
+ const double[:,:] direction, # should be normed
+ const double angles_tol=M_PI/8.0,
+ const double bandwidth=-1.0, # negative values to turn of bandwidth search
+ const bint separate_dirs=False, # whether the direction bands don't overlap
+ str estimator_type='m',
+):
+ if pos.shape[1] != f.shape[1]:
+ raise ValueError('len(pos) = {0} != len(f) = {1} '.
+ format(pos.shape[1], f.shape[1]))
+
+ if bin_edges.shape[0] < 2:
+ raise ValueError('len(bin_edges) too small')
+
+ if angles_tol <= 0:
+ raise ValueError('tolerance for angle search masks must be > 0')
+
+ cdef _estimator_func estimator_func = choose_estimator_func(estimator_type)
+ cdef _normalization_func_vec normalization_func_vec = (
+ choose_estimator_normalization_vec(estimator_type)
+ )
+
+ cdef int d_max = direction.shape[0]
+ cdef int i_max = bin_edges.shape[0] - 1
+ cdef int j_max = pos.shape[1] - 1
+ cdef int k_max = pos.shape[1]
+ cdef int f_max = f.shape[0]
+
+ cdef double[:,:] variogram = np.zeros((d_max, len(bin_edges)-1))
+ cdef long[:,:] counts = np.zeros((d_max, len(bin_edges)-1), dtype=long)
+ cdef int i, j, k, m, d
+ cdef double dist
+
+ for i in prange(i_max, nogil=True):
+ for j in range(j_max):
+ for k in range(j+1, k_max):
+ dist = dist_euclid(dim, pos, j, k)
+ if dist < bin_edges[i] or dist >= bin_edges[i+1]:
+ continue # skip if not in current bin
+ for d in range(d_max):
+ if not dir_test(dim, pos, dist, direction, angles_tol, bandwidth, k, j, d):
+ continue # skip if not in current direction
+ for m in range(f_max):
+ # skip no data values
+ if not (isnan(f[m,k]) or isnan(f[m,j])):
+ counts[d, i] += 1
+ variogram[d, i] += estimator_func(f[m,k] - f[m,j])
+ # once we found a fitting direction
+ # break the search if directions are separated
+ if separate_dirs:
+ break
+
+ normalization_func_vec(variogram, counts)
+ return np.asarray(variogram), np.asarray(counts)
+
+def unstructured(
+ const int dim,
+ const double[:,:] f,
+ const double[:] bin_edges,
+ const double[:,:] pos,
+ str estimator_type='m',
+ str distance_type='e',
+):
+ cdef _dist_func distance
+
+ if distance_type == 'e':
+ distance = dist_euclid
+ else:
+ distance = dist_haversine
+ if dim != 2:
+ raise ValueError('Haversine: dim = {0} != 2'.format(dim))
+
+ if pos.shape[1] != f.shape[1]:
+ raise ValueError('len(pos) = {0} != len(f) = {1} '.
+ format(pos.shape[1], f.shape[1]))
+
+ if bin_edges.shape[0] < 2:
+ raise ValueError('len(bin_edges) too small')
+
+ cdef _estimator_func estimator_func = choose_estimator_func(estimator_type)
+ cdef _normalization_func normalization_func = (
+ choose_estimator_normalization(estimator_type)
+ )
+
+ cdef int i_max = bin_edges.shape[0] - 1
+ cdef int j_max = pos.shape[1] - 1
+ cdef int k_max = pos.shape[1]
+ cdef int f_max = f.shape[0]
+
+ cdef double[:] variogram = np.zeros(len(bin_edges)-1)
+ cdef long[:] counts = np.zeros(len(bin_edges)-1, dtype=long)
+ cdef int i, j, k, m
+ cdef double dist
+
+ for i in prange(i_max, nogil=True):
+ for j in range(j_max):
+ for k in range(j+1, k_max):
+ dist = distance(dim, pos, j, k)
+ if dist < bin_edges[i] or dist >= bin_edges[i+1]:
+ continue # skip if not in current bin
+ for m in range(f_max):
+ # skip no data values
+ if not (isnan(f[m,k]) or isnan(f[m,j])):
+ counts[i] += 1
+ variogram[i] += estimator_func(f[m,k] - f[m,j])
+
+ normalization_func(variogram, counts)
+ return np.asarray(variogram), np.asarray(counts)
+
+
+def structured(const double[:,:] f, str estimator_type='m'):
+ cdef _estimator_func estimator_func = choose_estimator_func(estimator_type)
+ cdef _normalization_func normalization_func = (
+ choose_estimator_normalization(estimator_type)
+ )
+
+ cdef int i_max = f.shape[0] - 1
+ cdef int j_max = f.shape[1]
+ cdef int k_max = i_max + 1
+
+ cdef double[:] variogram = np.zeros(k_max)
+ cdef long[:] counts = np.zeros(k_max, dtype=long)
+ cdef int i, j, k
+
+ with nogil, parallel():
+ for i in range(i_max):
+ for j in range(j_max):
+ for k in prange(1, k_max-i):
+ counts[k] += 1
+ variogram[k] += estimator_func(f[i,j] - f[i+k,j])
+
+ normalization_func(variogram, counts)
+ return np.asarray(variogram)
+
+
+def ma_structured(
+ const double[:,:] f,
+ const bint[:,:] mask,
+ str estimator_type='m',
+):
+ cdef _estimator_func estimator_func = choose_estimator_func(estimator_type)
+ cdef _normalization_func normalization_func = (
+ choose_estimator_normalization(estimator_type)
+ )
+
+ cdef int i_max = f.shape[0] - 1
+ cdef int j_max = f.shape[1]
+ cdef int k_max = i_max + 1
+
+ cdef double[:] variogram = np.zeros(k_max)
+ cdef long[:] counts = np.zeros(k_max, dtype=long)
+ cdef int i, j, k
+
+ with nogil, parallel():
+ for i in range(i_max):
+ for j in range(j_max):
+ for k in prange(1, k_max-i):
+ if not mask[i,j] and not mask[i+k,j]:
+ counts[k] += 1
+ variogram[k] += estimator_func(f[i,j] - f[i+k,j])
+
+ normalization_func(variogram, counts)
+ return np.asarray(variogram)
diff --git a/gstools/variogram/variogram.py b/gstools/variogram/variogram.py
index d758e3b40..e24255ebd 100644
--- a/gstools/variogram/variogram.py
+++ b/gstools/variogram/variogram.py
@@ -10,14 +10,10 @@
vario_estimate
vario_estimate_axis
"""
+# pylint: disable=C0412
import numpy as np
-from gstools_core import (
- variogram_directional as directional,
- variogram_ma_structured as ma_structured,
- variogram_structured as structured,
- variogram_unstructured as unstructured,
-)
+from gstools import config
from gstools.normalizer.tools import remove_trend_norm_mean
from gstools.tools.geometric import (
ang2dir,
@@ -27,6 +23,21 @@
)
from gstools.variogram.binning import standard_bins
+if config.USE_RUST:
+ # pylint: disable=E0401
+ from gstools_core import variogram_directional as directional
+ from gstools_core import variogram_ma_structured as ma_structured
+ from gstools_core import variogram_structured as structured
+ from gstools_core import variogram_unstructured as unstructured
+else:
+ # pylint: disable=C0412
+ from gstools.variogram.estimator import (
+ directional,
+ ma_structured,
+ structured,
+ unstructured,
+ )
+
__all__ = [
"vario_estimate",
"vario_estimate_axis",
@@ -443,6 +454,8 @@ def vario_estimate_axis(
if missing:
field.mask = np.logical_or(field.mask, missing_mask)
mask = np.ma.getmaskarray(field)
+ if not config.USE_RUST:
+ mask = np.asarray(mask, dtype=np.int32)
else:
field = np.array(field, ndmin=1, dtype=np.double, copy=False)
missing_mask = None # free space
diff --git a/setup.cfg b/setup.cfg
index d533120b0..116b51ba9 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -39,7 +39,6 @@ project_urls =
packages = find:
install_requires =
emcee>=3.0.0,<4
- gstools_core>=0.1.2,<1
hankel>=1.0.2,<2
meshio>=4.0.3,<6
numpy>=1.14.5,<2
@@ -67,6 +66,8 @@ doc =
plotting =
matplotlib>=3,<4
pyvista>=0.29,<1
+rust =
+ gstools_core>=0.1.2,<1
test =
coverage[toml]>=5.2.1,<6
pytest>=6.0,<7
diff --git a/setup.py b/setup.py
index 291d34a54..1bbc7fafa 100644
--- a/setup.py
+++ b/setup.py
@@ -1,14 +1,169 @@
# -*- coding: utf-8 -*-
"""GSTools: A geostatistical toolbox."""
+import glob
import os
-
-import numpy as np
-from setuptools import setup
+import subprocess
import sys
-import site
+import tempfile
+from distutils.ccompiler import new_compiler
+from distutils.errors import CompileError, LinkError
+from distutils.sysconfig import customize_compiler
-site.ENABLE_USER_SITE = "--user" in sys.argv[1:]
+import numpy as np
+from Cython.Build import cythonize
+from setuptools import Extension, setup
HERE = os.path.abspath(os.path.dirname(__file__))
-setup(include_dirs=[np.get_include()])
+
+# openmp finder ###############################################################
+# This code is adapted for a large part from the scikit-learn openmp_helpers.py
+# which can be found at:
+# https://github.com/scikit-learn/scikit-learn/blob/0.24.0/sklearn/_build_utils
+
+
+CCODE = """
+#include <omp.h>
+#include <stdio.h>
+int main(void) {
+#pragma omp parallel
+printf("nthreads=%d\\n", omp_get_num_threads());
+return 0;
+}
+"""
+
+
+def get_openmp_flag(compiler):
+ """Get the compiler dependent openmp flag."""
+ if hasattr(compiler, "compiler"):
+ compiler = compiler.compiler[0]
+ else:
+ compiler = compiler.__class__.__name__
+
+ if sys.platform == "win32" and ("icc" in compiler or "icl" in compiler):
+ return ["/Qopenmp"]
+ if sys.platform == "win32":
+ return ["/openmp"]
+ if sys.platform == "darwin" and ("icc" in compiler or "icl" in compiler):
+ return ["-openmp"]
+ if sys.platform == "darwin" and "openmp" in os.getenv("CPPFLAGS", ""):
+ return []
+ # Default flag for GCC and clang:
+ return ["-fopenmp"]
+
+
+def check_openmp_support():
+ """Check whether OpenMP test code can be compiled and run."""
+ ccompiler = new_compiler()
+ customize_compiler(ccompiler)
+
+ with tempfile.TemporaryDirectory() as tmp_dir:
+ try:
+ os.chdir(tmp_dir)
+ # Write test program
+ with open("test_openmp.c", "w") as cfile:
+ cfile.write(CCODE)
+ os.mkdir("objects")
+ # Compile, test program
+ openmp_flags = get_openmp_flag(ccompiler)
+ ccompiler.compile(
+ ["test_openmp.c"],
+ output_dir="objects",
+ extra_postargs=openmp_flags,
+ )
+ # Link test program
+ extra_preargs = os.getenv("LDFLAGS", None)
+ if extra_preargs is not None:
+ extra_preargs = extra_preargs.split(" ")
+ else:
+ extra_preargs = []
+ objects = glob.glob(
+ os.path.join("objects", "*" + ccompiler.obj_extension)
+ )
+ ccompiler.link_executable(
+ objects,
+ "test_openmp",
+ extra_preargs=extra_preargs,
+ extra_postargs=openmp_flags,
+ )
+ # Run test program
+ output = subprocess.check_output("./test_openmp")
+ output = output.decode(sys.stdout.encoding or "utf-8").splitlines()
+ # Check test program output
+ if "nthreads=" in output[0]:
+ nthreads = int(output[0].strip().split("=")[1])
+ openmp_supported = len(output) == nthreads
+ else:
+ openmp_supported = False
+ openmp_flags = []
+ except (CompileError, LinkError, subprocess.CalledProcessError):
+ openmp_supported = False
+ openmp_flags = []
+ finally:
+ os.chdir(HERE)
+ return openmp_supported, openmp_flags
+
+
+# openmp ######################################################################
+
+
+# you can set GSTOOLS_BUILD_PARALLEL=0 or GSTOOLS_BUILD_PARALLEL=1
+GS_PARALLEL = os.getenv("GSTOOLS_BUILD_PARALLEL")
+USE_OPENMP = bool(int(GS_PARALLEL)) if GS_PARALLEL else False
+
+if USE_OPENMP:
+ # just check if wanted
+ CAN_USE_OPENMP, FLAGS = check_openmp_support()
+ if CAN_USE_OPENMP:
+ print("## GSTOOLS setup: OpenMP found.")
+ print("## OpenMP flags:", FLAGS)
+ else:
+ print("## GSTOOLS setup: OpenMP not found.")
+else:
+ print("## GSTOOLS setup: OpenMP not wanted by the user.")
+ FLAGS = []
+
+
+# cython extensions ###########################################################
+
+
+CY_MODULES = []
+CY_MODULES.append(
+ Extension(
+ "gstools.field.summator",
+ [os.path.join("gstools", "field", "summator.pyx")],
+ include_dirs=[np.get_include()],
+ extra_compile_args=FLAGS,
+ extra_link_args=FLAGS,
+ )
+)
+CY_MODULES.append(
+ Extension(
+ "gstools.variogram.estimator",
+ [os.path.join("gstools", "variogram", "estimator.pyx")],
+ language="c++",
+ include_dirs=[np.get_include()],
+ extra_compile_args=FLAGS,
+ extra_link_args=FLAGS,
+ )
+)
+CY_MODULES.append(
+ Extension(
+ "gstools.krige.krigesum",
+ [os.path.join("gstools", "krige", "krigesum.pyx")],
+ include_dirs=[np.get_include()],
+ extra_compile_args=FLAGS,
+ extra_link_args=FLAGS,
+ )
+)
+EXT_MODULES = cythonize(CY_MODULES) # annotate=True
+
+# embed signatures for sphinx
+for ext_m in EXT_MODULES:
+ ext_m.cython_directives = {"embedsignature": True}
+
+
+# setup #######################################################################
+
+
+setup(ext_modules=EXT_MODULES, include_dirs=[np.get_include()])
From e1bd45c1a09fdbb13393390676a99ef7ba455b67 Mon Sep 17 00:00:00 2001
From: LSchueler <mostem@posteo.de>
Date: Tue, 9 Nov 2021 20:12:46 +0100
Subject: [PATCH 03/10] Remove unnecessary `dim` arg. in Cython code
This makes the Cython code compatible to GSTools-Core v0.1.2 again.
---
gstools/variogram/estimator.pyx | 4 ++--
gstools/variogram/variogram.py | 2 --
2 files changed, 2 insertions(+), 4 deletions(-)
diff --git a/gstools/variogram/estimator.pyx b/gstools/variogram/estimator.pyx
index 8c149b41b..6c5a67dff 100644
--- a/gstools/variogram/estimator.pyx
+++ b/gstools/variogram/estimator.pyx
@@ -178,7 +178,6 @@ cdef _normalization_func_vec choose_estimator_normalization_vec(str estimator_ty
def directional(
- const int dim,
const double[:,:] f,
const double[:] bin_edges,
const double[:,:] pos,
@@ -203,6 +202,7 @@ def directional(
choose_estimator_normalization_vec(estimator_type)
)
+ cdef int dim = pos.shape[0]
cdef int d_max = direction.shape[0]
cdef int i_max = bin_edges.shape[0] - 1
cdef int j_max = pos.shape[1] - 1
@@ -237,13 +237,13 @@ def directional(
return np.asarray(variogram), np.asarray(counts)
def unstructured(
- const int dim,
const double[:,:] f,
const double[:] bin_edges,
const double[:,:] pos,
str estimator_type='m',
str distance_type='e',
):
+ cdef int dim = pos.shape[0]
cdef _dist_func distance
if distance_type == 'e':
diff --git a/gstools/variogram/variogram.py b/gstools/variogram/variogram.py
index e24255ebd..e9c00536b 100644
--- a/gstools/variogram/variogram.py
+++ b/gstools/variogram/variogram.py
@@ -353,7 +353,6 @@ def vario_estimate(
# "h"aversine or "e"uclidean distance type
distance_type = "h" if latlon else "e"
estimates, counts = unstructured(
- dim,
field,
bin_edges,
pos,
@@ -362,7 +361,6 @@ def vario_estimate(
)
else:
estimates, counts = directional(
- dim,
field,
bin_edges,
pos,
From 872570fe537a0913106ac4d1de3298628c0008dc Mon Sep 17 00:00:00 2001
From: LSchueler <mostem@posteo.de>
Date: Tue, 9 Nov 2021 20:22:27 +0100
Subject: [PATCH 04/10] Satify coveralls
---
gstools/config.py | 2 +-
gstools/field/generator.py | 2 +-
gstools/krige/base.py | 5 ++++-
gstools/variogram/variogram.py | 16 ++++++++++++----
4 files changed, 18 insertions(+), 7 deletions(-)
diff --git a/gstools/config.py b/gstools/config.py
index ebbd571cd..090b6154f 100644
--- a/gstools/config.py
+++ b/gstools/config.py
@@ -9,6 +9,6 @@
try:
import gstools_core
- USE_RUST = True
+ USE_RUST = True #pragma: no cover
except ImportError:
USE_RUST = False
diff --git a/gstools/field/generator.py b/gstools/field/generator.py
index 91408e884..c13d71a79 100644
--- a/gstools/field/generator.py
+++ b/gstools/field/generator.py
@@ -22,7 +22,7 @@
if config.USE_RUST:
# pylint: disable=E0401
- from gstools_core import summate, summate_incompr
+ from gstools_core import summate, summate_incompr # pragma: no cover
else:
# pylint: disable=C0412
from gstools.field.summator import summate, summate_incompr
diff --git a/gstools/krige/base.py b/gstools/krige/base.py
index e3922d335..d2ef1042c 100755
--- a/gstools/krige/base.py
+++ b/gstools/krige/base.py
@@ -25,7 +25,10 @@
if config.USE_RUST:
# pylint: disable=E0401
- from gstools_core import calc_field_krige, calc_field_krige_and_variance
+ from gstools_core import (
+ calc_field_krige,
+ calc_field_krige_and_variance,
+ ) # pragma: no cover
else:
from gstools.krige.krigesum import (
calc_field_krige,
diff --git a/gstools/variogram/variogram.py b/gstools/variogram/variogram.py
index e9c00536b..26f41054f 100644
--- a/gstools/variogram/variogram.py
+++ b/gstools/variogram/variogram.py
@@ -25,10 +25,18 @@
if config.USE_RUST:
# pylint: disable=E0401
- from gstools_core import variogram_directional as directional
- from gstools_core import variogram_ma_structured as ma_structured
- from gstools_core import variogram_structured as structured
- from gstools_core import variogram_unstructured as unstructured
+ from gstools_core import (
+ variogram_directional as directional,
+ ) # pragma: no cover
+ from gstools_core import (
+ variogram_ma_structured as ma_structured,
+ ) # pragma: no cover
+ from gstools_core import (
+ variogram_structured as structured,
+ ) # pragma: no cover
+ from gstools_core import (
+ variogram_unstructured as unstructured,
+ ) # pragma: no cover
else:
# pylint: disable=C0412
from gstools.variogram.estimator import (
From 1ff09ed620f1600e4de7fcf593f37deb576c01c1 Mon Sep 17 00:00:00 2001
From: LSchueler <mostem@posteo.de>
Date: Tue, 9 Nov 2021 20:39:15 +0100
Subject: [PATCH 05/10] Update changelog
---
CHANGELOG.md | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 95ad2e2c6..82b9afd46 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,15 @@
All notable changes to **GSTools** will be documented in this file.
+## [1.3.4] - Pure Pink ?
+
+### Enhancements
+- add GStools-Core as optional dependency [#215](https://github.com/GeoStat-Framework/GSTools/pull/215)
+
+### Changes
+- remove unnecessary `dim` argument in Cython code [#216](https://github.com/GeoStat-Framework/GSTools/issues/216)
+
+
## [1.3.3] - Pure Pink - 2021-08
### Enhancements
From 60325f0b798c50f856528fa5a396b414da9985b0 Mon Sep 17 00:00:00 2001
From: LSchueler <mostem@posteo.de>
Date: Tue, 9 Nov 2021 20:56:10 +0100
Subject: [PATCH 06/10] Update installation part of doc.
---
docs/source/index.rst | 27 +++++++++++++++++++++++++++
gstools/config.py | 2 +-
gstools/krige/base.py | 4 ++--
gstools/variogram/variogram.py | 16 ++++++++--------
4 files changed, 38 insertions(+), 11 deletions(-)
diff --git a/docs/source/index.rst b/docs/source/index.rst
index b36965352..28e6c34de 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -70,6 +70,8 @@ To get the latest development version you can install it directly from GitHub:
If something went wrong during installation, try the :code:`-I` `flag from pip <https://pip-python3.readthedocs.io/en/latest/reference/pip_install.html?highlight=i#cmdoption-i>`_.
+**Speeding up GSTools by parallelization**
+
To enable the OpenMP support, you have to provide a C compiler and OpenMP.
Parallel support is controlled by an environment variable ``GSTOOLS_BUILD_PARALLEL``,
that can be ``0`` or ``1`` (interpreted as ``0`` if not present).
@@ -89,6 +91,31 @@ For the development version, you can do almost the same:
export GSTOOLS_BUILD_PARALLEL=1
pip install git+git://github.com/GeoStat-Framework/GSTools.git@main
+**Using experimental GSTools-Core for even more speed**
+
+You can install the optional dependency `GSTools-Core <https://github.com/GeoStat-Framework/GSTools-Core>`_,
+which is a re-implementation of the main algorithms used in GSTools. The new
+package uses the language Rust and it should be faster (in some cases by orders
+of magnitude), safer, and it will potentially completely replace the current
+standard implementation in Cython. Once the package GSTools-Core is available
+on your machine, it will be used by default. In case you want to switch back to
+the Cython implementation, you can set :code:`gstools.config.USE_RUST=False` in
+your code. This also works at runtime. You can install the optional dependency
+e.g. by
+
+.. code-block:: none
+
+ pip install gstools[rust]
+
+or by manually installing the package
+
+.. code-block:: none
+
+ pip install gstools-core
+
+GSTools-Core will automatically use all your cores in parallel, without having
+to use OpenMP or a local C compiler.
+
Citation
========
diff --git a/gstools/config.py b/gstools/config.py
index 090b6154f..4186a259c 100644
--- a/gstools/config.py
+++ b/gstools/config.py
@@ -9,6 +9,6 @@
try:
import gstools_core
- USE_RUST = True #pragma: no cover
+ USE_RUST = True # pragma: no cover
except ImportError:
USE_RUST = False
diff --git a/gstools/krige/base.py b/gstools/krige/base.py
index d2ef1042c..0ffc482cb 100755
--- a/gstools/krige/base.py
+++ b/gstools/krige/base.py
@@ -25,10 +25,10 @@
if config.USE_RUST:
# pylint: disable=E0401
- from gstools_core import (
+ from gstools_core import ( # pragma: no cover
calc_field_krige,
calc_field_krige_and_variance,
- ) # pragma: no cover
+ )
else:
from gstools.krige.krigesum import (
calc_field_krige,
diff --git a/gstools/variogram/variogram.py b/gstools/variogram/variogram.py
index 26f41054f..77b9a2c20 100644
--- a/gstools/variogram/variogram.py
+++ b/gstools/variogram/variogram.py
@@ -26,17 +26,17 @@
if config.USE_RUST:
# pylint: disable=E0401
from gstools_core import (
- variogram_directional as directional,
- ) # pragma: no cover
+ variogram_directional as directional, # pragma: no cover
+ )
from gstools_core import (
- variogram_ma_structured as ma_structured,
- ) # pragma: no cover
+ variogram_ma_structured as ma_structured, # pragma: no cover
+ )
from gstools_core import (
- variogram_structured as structured,
- ) # pragma: no cover
+ variogram_structured as structured, # pragma: no cover
+ )
from gstools_core import (
- variogram_unstructured as unstructured,
- ) # pragma: no cover
+ variogram_unstructured as unstructured, # pragma: no cover
+ )
else:
# pylint: disable=C0412
from gstools.variogram.estimator import (
From 164b6872167ccb20c89b969c22ad35937a8be404 Mon Sep 17 00:00:00 2001
From: LSchueler <mostem@posteo.de>
Date: Tue, 9 Nov 2021 21:20:04 +0100
Subject: [PATCH 07/10] Mention RAYON_NUM_THREADS in readme
---
docs/source/index.rst | 2 ++
1 file changed, 2 insertions(+)
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 28e6c34de..3880d412e 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -115,6 +115,8 @@ or by manually installing the package
GSTools-Core will automatically use all your cores in parallel, without having
to use OpenMP or a local C compiler.
+In case you want to restrict the number of threads used, you can set the
+environment variable ``RAYON_NUM_THREADS`` to the desired amount.
Citation
From c0777e394c07c3cad60aaa682b031e6b2334dbdc Mon Sep 17 00:00:00 2001
From: LSchueler <mostem@posteo.de>
Date: Tue, 9 Nov 2021 21:27:03 +0100
Subject: [PATCH 08/10] Use correct version of GSTools-Core
---
README.md | 2 +-
docs/source/index.rst | 2 +-
setup.cfg | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index c0488480f..f68e49a91 100644
--- a/README.md
+++ b/README.md
@@ -345,7 +345,7 @@ in memory for immediate 3D plotting in Python.
### Optional
-- [GSTools-Core >= 0.1.0](https://github.com/GeoStat-Framework/GSTools-Core)
+- [GSTools-Core >= 0.2.0](https://github.com/GeoStat-Framework/GSTools-Core)
- [matplotlib](https://matplotlib.org)
- [pyvista](https://docs.pyvista.org/)
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 3880d412e..8ead50563 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -416,7 +416,7 @@ Requirements
Optional
--------
-- `GSTools-Core >= 0.1.0 <https://github.com/GeoStat-Framework/GSTools-Core>`_
+- `GSTools-Core >= 0.2.0 <https://github.com/GeoStat-Framework/GSTools-Core>`_
- `matplotlib <https://matplotlib.org>`_
- `pyvista <https://docs.pyvista.org>`_
diff --git a/setup.cfg b/setup.cfg
index 116b51ba9..5a59f87c9 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -67,7 +67,7 @@ plotting =
matplotlib>=3,<4
pyvista>=0.29,<1
rust =
- gstools_core>=0.1.2,<1
+ gstools_core>=0.2.0,<1
test =
coverage[toml]>=5.2.1,<6
pytest>=6.0,<7
From 774c73034c41f47c0e4f97cfbdb13fbe57081472 Mon Sep 17 00:00:00 2001
From: LSchueler <mostem@posteo.de>
Date: Wed, 10 Nov 2021 16:58:03 +0100
Subject: [PATCH 09/10] Improve import situation
---
gstools/variogram/variogram.py | 19 +++++--------------
1 file changed, 5 insertions(+), 14 deletions(-)
diff --git a/gstools/variogram/variogram.py b/gstools/variogram/variogram.py
index 77b9a2c20..7acce928a 100644
--- a/gstools/variogram/variogram.py
+++ b/gstools/variogram/variogram.py
@@ -23,22 +23,13 @@
)
from gstools.variogram.binning import standard_bins
-if config.USE_RUST:
+if config.USE_RUST: # pragma: no cover
# pylint: disable=E0401
- from gstools_core import (
- variogram_directional as directional, # pragma: no cover
- )
- from gstools_core import (
- variogram_ma_structured as ma_structured, # pragma: no cover
- )
- from gstools_core import (
- variogram_structured as structured, # pragma: no cover
- )
- from gstools_core import (
- variogram_unstructured as unstructured, # pragma: no cover
- )
+ from gstools_core import variogram_directional as directional
+ from gstools_core import variogram_ma_structured as ma_structured
+ from gstools_core import variogram_structured as structured
+ from gstools_core import variogram_unstructured as unstructured
else:
- # pylint: disable=C0412
from gstools.variogram.estimator import (
directional,
ma_structured,
From 0049a31e3fce1c866ea006e1be131ad5617a35eb Mon Sep 17 00:00:00 2001
From: LSchueler <mostem@posteo.de>
Date: Wed, 10 Nov 2021 17:04:18 +0100
Subject: [PATCH 10/10] Clean up some linter flags
---
gstools/config.py | 4 ++--
gstools/field/generator.py | 5 ++---
gstools/krige/base.py | 7 ++-----
3 files changed, 6 insertions(+), 10 deletions(-)
diff --git a/gstools/config.py b/gstools/config.py
index 4186a259c..38f3e7faa 100644
--- a/gstools/config.py
+++ b/gstools/config.py
@@ -6,9 +6,9 @@
"""
# pylint: disable=W0611
-try:
+try: # pragma: no cover
import gstools_core
- USE_RUST = True # pragma: no cover
+ USE_RUST = True
except ImportError:
USE_RUST = False
diff --git a/gstools/field/generator.py b/gstools/field/generator.py
index c13d71a79..31cc7eea2 100644
--- a/gstools/field/generator.py
+++ b/gstools/field/generator.py
@@ -20,11 +20,10 @@
from gstools.covmodel.base import CovModel
from gstools.random.rng import RNG
-if config.USE_RUST:
+if config.USE_RUST: # pragma: no cover
# pylint: disable=E0401
- from gstools_core import summate, summate_incompr # pragma: no cover
+ from gstools_core import summate, summate_incompr
else:
- # pylint: disable=C0412
from gstools.field.summator import summate, summate_incompr
__all__ = ["RandMeth", "IncomprRandMeth"]
diff --git a/gstools/krige/base.py b/gstools/krige/base.py
index 0ffc482cb..8accf5080 100755
--- a/gstools/krige/base.py
+++ b/gstools/krige/base.py
@@ -23,12 +23,9 @@
from gstools.tools.misc import eval_func
from gstools.variogram import vario_estimate
-if config.USE_RUST:
+if config.USE_RUST: # pragma: no cover
# pylint: disable=E0401
- from gstools_core import ( # pragma: no cover
- calc_field_krige,
- calc_field_krige_and_variance,
- )
+ from gstools_core import calc_field_krige, calc_field_krige_and_variance
else:
from gstools.krige.krigesum import (
calc_field_krige,