CIBW: add support for py3.10 and Apple Silicon; use CIBWv2

.github/workflows/main.yml

@@ -23,7 +23,7 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Set up Python 3.8
-        uses: actions\setup-python@v2
+        uses: actions/setup-python@v2
         with:
           python-version: 3.8
 
@@ -46,24 +46,29 @@ jobs:
           python -m isort --check --diff --color .
 
   build_wheels:
-    name: wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
+    name: wheels for ${{ matrix.cfg.os }} / ${{ matrix.cfg.arch }}
+    runs-on: ${{ matrix.cfg.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        cfg:
+        - { os: ubuntu-latest, arch: x86_64 }
+        - { os: ubuntu-latest, arch: i686 }
+        - { os: windows-latest, arch: AMD64 }
+        - { os: windows-latest, arch: x86 }
+        - { os: macos-latest, arch: x86_64 }
+        - { os: macos-latest, arch: arm64 }
+        - { os: macos-latest, arch: universal2 }
 
     steps:
       - uses: actions/checkout@v2
         with:
           fetch-depth: '0'
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v1.11.1.post1
+        uses: pypa/cibuildwheel@v2.2.2
         env:
-          CIBW_BUILD: cp36-* cp37-* cp38-* cp39-*
-          CIBW_TEST_EXTRAS: test
-          CIBW_TEST_COMMAND: pytest -v {project}/tests
+          CIBW_ARCHS: ${{ matrix.cfg.arch }}
         with:
           output-dir: dist
 
@@ -78,15 +83,15 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
 
     steps:
       - uses: actions/checkout@v2
         with:
           fetch-depth: '0'
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions\setup-python@v2
+        uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
 

CHANGELOG.md

@@ -3,6 +3,17 @@
 All notable changes to **GSTools** will be documented in this file.
 
 
+## [1.3.4] - Pure Pink - 2021-11
+
+### Enhancements
+- add GStools-Core as optional dependency [#215](https://github.com/GeoStat-Framework/GSTools/pull/215)
+- provide wheels for Python 3.10 [#211](https://github.com/GeoStat-Framework/GSTools/pull/211)
+- provide macOS wheels for Apple Silicon [#211](https://github.com/GeoStat-Framework/GSTools/pull/211)
+
+### 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
@@ -310,7 +321,8 @@ See: [#197](https://github.com/GeoStat-Framework/GSTools/issues/197)
 First release of GSTools.
 
 
-[Unreleased]: https://github.com/GeoStat-Framework/gstools/compare/v1.3.3...HEAD
+[Unreleased]: https://github.com/GeoStat-Framework/gstools/compare/v1.3.4...HEAD
+[1.3.4]: https://github.com/GeoStat-Framework/gstools/compare/v1.3.3...v1.3.4
 [1.3.3]: https://github.com/GeoStat-Framework/gstools/compare/v1.3.2...v1.3.3
 [1.3.2]: https://github.com/GeoStat-Framework/gstools/compare/v1.3.1...v1.3.2
 [1.3.1]: https://github.com/GeoStat-Framework/gstools/compare/v1.3.0...v1.3.1

CITATION.bib

@@ -0,0 +1,10 @@
+@Article{gmd-2021-301,
+AUTHOR = {M\"uller, S. and Sch\"uler, L. and Zech, A. and He{\ss}e, F.},
+TITLE = {GSTools v1.3: A toolbox for geostatistical modelling in Python},
+JOURNAL = {Geoscientific Model Development Discussions},
+VOLUME = {2021},
+YEAR = {2021},
+PAGES = {1--33},
+URL = {https://gmd.copernicus.org/preprints/gmd-2021-301/},
+DOI = {10.5194/gmd-2021-301}
+}

README.md

@@ -66,13 +66,17 @@ To install the latest development version via pip, see the
 
 ## Citation
 
-At the moment you can cite the Zenodo code publication of GSTools:
+If you are using GSTools in your publication please cite our paper:
 
-> Sebastian Müller & Lennart Schüler. GeoStat-Framework/GSTools. Zenodo. https://doi.org/10.5281/zenodo.1313628
+> Müller, S., Schüler, L., Zech, A., and Heße, F.:
+> GSTools v1.3: A toolbox for geostatistical modelling in Python,
+> Geosci. Model Dev. Discuss. [preprint], https://doi.org/10.5194/gmd-2021-301, in review, 2021.
+
+You can cite the Zenodo code publication of GSTools by:
 
-If you want to cite a specific version, have a look at the Zenodo site.
+> Sebastian Müller & Lennart Schüler. GeoStat-Framework/GSTools. Zenodo. https://doi.org/10.5281/zenodo.1313628
 
-A publication for the GeoStat-Framework is in preperation.
+If you want to cite a specific version, have a look at the [Zenodo site](https://doi.org/10.5281/zenodo.1313628).
 
 
 ## Documentation for GSTools
@@ -341,6 +345,7 @@ in memory for immediate 3D plotting in Python.
 
 ### Optional
 
+- [GSTools-Core >= 0.2.0](https://github.com/GeoStat-Framework/GSTools-Core)
 - [matplotlib](https://matplotlib.org)
 - [pyvista](https://docs.pyvista.org/)
 

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).
@@ -89,17 +91,46 @@ 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.
+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
 ========
 
-At the moment you can cite the Zenodo code publication of GSTools:
+If you are using GSTools in your publication please cite our paper:
 
-| *Sebastian Müller & Lennart Schüler. GeoStat-Framework/GSTools. Zenodo. https://doi.org/10.5281/zenodo.1313628*
+| *Müller, S., Schüler, L., Zech, A., and Heße, F.: GSTools v1.3: A toolbox for geostatistical modelling in Python, Geosci. Model Dev. Discuss. [preprint], https://doi.org/10.5194/gmd-2021-301, in review, 2021.*
+
+You can cite the Zenodo code publication of GSTools by:
 
-If you want to cite a specific version, have a look at the Zenodo site.
+| *Sebastian Müller & Lennart Schüler. GeoStat-Framework/GSTools. Zenodo. https://doi.org/10.5281/zenodo.1313628*
 
-A publication for the GeoStat-Framework is in preperation.
+If you want to cite a specific version, have a look at the `Zenodo site <https://doi.org/10.5281/zenodo.1313628)>`__.
 
 
 Tutorials and Examples
@@ -385,6 +416,7 @@ Requirements
 Optional
 --------
 
+- `GSTools-Core >= 0.2.0 <https://github.com/GeoStat-Framework/GSTools-Core>`_
 - `matplotlib <https://matplotlib.org>`_
 - `pyvista <https://docs.pyvista.org>`_
 

gstools/__init__.py

@@ -127,6 +127,7 @@
 """
 # Hooray!
 from gstools import (
+    config,
     covmodel,
     field,
     krige,

gstools/config.py

@@ -0,0 +1,14 @@
+# -*- coding: utf-8 -*-
+"""
+GStools subpackage providing global variables.
+
+.. currentmodule:: gstools.config
+
+"""
+# pylint: disable=W0611
+try:  # pragma: no cover
+    import gstools_core
+
+    USE_RUST = True
+except ImportError:
+    USE_RUST = False

gstools/field/generator.py

@@ -10,16 +10,22 @@
    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 import config
 from gstools.covmodel.base import CovModel
-from gstools.field.summator import summate, summate_incompr
 from gstools.random.rng import RNG
 
+if config.USE_RUST:  # pragma: no cover
+    # pylint: disable=E0401
+    from gstools_core import summate, summate_incompr
+else:
+    from gstools.field.summator import summate, summate_incompr
+
 __all__ = ["RandMeth", "IncomprRandMeth"]
 
 

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 import config
 from gstools.field.base import Field
-from gstools.krige.krigesum import (
-    calc_field_krige,
-    calc_field_krige_and_variance,
-)
 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:  # pragma: no cover
+    # 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"]
 
 

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':

gstools/variogram/variogram.py

@@ -10,8 +10,10 @@
    vario_estimate
    vario_estimate_axis
 """
+# pylint: disable=C0412
 import numpy as np
 
+from gstools import config
 from gstools.normalizer.tools import remove_trend_norm_mean
 from gstools.tools.geometric import (
     ang2dir,
@@ -20,12 +22,20 @@
     generate_grid,
 )
 from gstools.variogram.binning import standard_bins
-from gstools.variogram.estimator import (
-    directional,
-    ma_structured,
-    structured,
-    unstructured,
-)
+
+if config.USE_RUST:  # pragma: no cover
+    # 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:
+    from gstools.variogram.estimator import (
+        directional,
+        ma_structured,
+        structured,
+        unstructured,
+    )
 
 __all__ = [
     "vario_estimate",
@@ -59,7 +69,8 @@ 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(
@@ -341,7 +352,6 @@ 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,
@@ -350,7 +360,6 @@ def vario_estimate(
         )
     else:
         estimates, counts = directional(
-            dim,
             field,
             bin_edges,
             pos,
@@ -441,7 +450,9 @@ 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)
+        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