Add support for Python v3.13

.github/workflows/main.yml

@@ -22,10 +22,10 @@ jobs:
         with:
           fetch-depth: "0"
 
-      - name: Set up Python 3.9
+      - name: Set up Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
 
       - name: Install dependencies
         run: |
@@ -47,7 +47,7 @@ jobs:
 
       - name: pylint check
         run: |
-          python -m pylint --max-positional-arguments 20 src/gstools/
+          python -m pylint src/gstools/
 
       - name: cython-lint check
         run: |
@@ -75,13 +75,14 @@ jobs:
           fetch-depth: "0"
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.18.0
+        uses: pypa/cibuildwheel@v2.22.0
         with:
-          output-dir: dist
+          output-dir: dist-wheel-${{ matrix.os }}
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          path: ./dist/*.whl
+          name: dist-wheel-${{ matrix.os }}
+          path: ./dist-wheel-${{ matrix.os }}/*.whl
 
   build_sdist:
     name: sdist on ${{ matrix.os }} with py ${{ matrix.ver.py }} numpy${{ matrix.ver.np }} scipy${{ matrix.ver.sp }}
@@ -92,12 +93,13 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-13, macos-14]
         # https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
         ver:
-          - { py: "3.8", np: "==1.20.0", sp: "==1.5.4" }
-          - { py: "3.9", np: "==1.20.0", sp: "==1.5.4" }
-          - { py: "3.10", np: "==1.21.6", sp: "==1.7.2" }
-          - { py: "3.11", np: "==1.23.2", sp: "==1.9.2" }
-          - { py: "3.12", np: "==1.26.2", sp: "==1.11.2" }
-          - { py: "3.12", np: ">=2.0.0rc1", sp: ">=1.13.0" }
+          - {py: '3.8', np: '==1.20.0', sp: '==1.5.4'}
+          - {py: '3.9', np: '==1.20.0', sp: '==1.5.4'}
+          - {py: '3.10', np: '==1.21.6', sp: '==1.7.2'}
+          - {py: '3.11', np: '==1.23.2', sp: '==1.9.2'}
+          - {py: '3.12', np: '==1.26.2', sp: '==1.11.2'}
+          - {py: '3.13', np: '==2.1.0', sp: '==1.14.1'}
+          - {py: '3.13', np: '>=2.1.0', sp: '>=1.14.1'}
         exclude:
           - os: macos-14
             ver: { py: "3.8", np: "==1.20.0", sp: "==1.5.4" }
@@ -134,21 +136,23 @@ jobs:
       - name: Build sdist
         run: |
           # PEP 517 package builder from pypa
-          python -m build --sdist --outdir dist .
+          python -m build --sdist --outdir dist-sdist .
 
-      - uses: actions/upload-artifact@v3
-        if: matrix.os == 'ubuntu-latest' && matrix.ver.py == '3.9'
+      - uses: actions/upload-artifact@v4
+        if: matrix.os == 'ubuntu-latest' && matrix.ver.py == '3.11'
         with:
-          path: dist/*.tar.gz
+          name: dist-sdist
+          path: dist-sdist/*.tar.gz
 
   upload_to_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          pattern: dist-*
+          merge-multiple: true
           path: dist
 
       - name: Publish to Test PyPI

AUTHORS.md

@@ -1,10 +1,10 @@
-# GSTools
+# Authors
 
 GSTools is available on [GitHub](https://github.com/GeoStat-Framework/GSTools)
 and was created by following people.
 
 
-## Main Authors
+## Core developers
 
 - Sebastian Müller, GitHub: [@MuellerSeb](https://github.com/MuellerSeb), Email:  <[email protected]>
 - Lennart Schüler, GitHub: [@LSchueler](https://github.com/LSchueler), Email:  <[email protected]>
@@ -14,4 +14,4 @@ and was created by following people.
 
 - Falk Heße, GitHub: [@fhesze](https://github.com/fhesze), Email: <[email protected]>
 - Bane Sullivan, GitHub: [@banesullivan](https://github.com/banesullivan)
-- Tobias Glaubach, GitHub: [@TobiasGlaubach](https://github.com/TobiasGlaubach)
+- Tobias Glaubach, GitHub: [@TobiasGlaubach](https://github.com/TobiasGlaubach)

README.md

@@ -33,7 +33,7 @@
 
 <img align="right" width="450" src="https://raw.githubusercontent.com/GeoStat-Framework/GSTools/main/docs/source/pics/demonstrator.png" alt="">
 
-GeoStatTools provides geostatistical tools for various purposes:
+GSTools provides geostatistical tools for various purposes:
 - random field generation, including periodic boundaries
 - simple, ordinary, universal and external drift kriging
 - conditioned field generation
@@ -369,7 +369,7 @@ You can contact us via <[email protected]>.
 
 ## License
 
-[LGPLv3][license_link] © 2018-2024
+[LGPLv3][license_link] © 2018-2025
 
 [pip_link]: https://pypi.org/project/gstools
 [conda_link]: https://docs.conda.io/en/latest/miniconda.html

docs/Makefile

@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = python3 -msphinx
-SPHINXPROJ    = GeoStatTools
+SPHINXPROJ    = GSTools
 SOURCEDIR     = source
 BUILDDIR      = build
 

docs/source/authors.rst

@@ -0,0 +1,2 @@
+.. include:: ../../AUTHORS.md
+   :parser: myst_parser.docutils_

docs/source/changelog.rst

@@ -1 +1,2 @@
-.. mdinclude:: ../../CHANGELOG.md
+.. include:: ../../CHANGELOG.md
+   :parser: myst_parser.docutils_

docs/source/conf.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-# GeoStatTools documentation build configuration file, created by
+# GSTools documentation build configuration file, created by
 # sphinx-quickstart on Fri Jan  5 14:20:43 2018.
 #
 # This file is execfile()d with the current directory set to its
@@ -67,7 +67,7 @@ def setup(app):
     "sphinx.ext.napoleon",  # parameters look better than with numpydoc only
     "numpydoc",
     "sphinx_gallery.gen_gallery",
-    "m2r2",
+    "myst_parser",
     "sphinxcontrib.youtube",
 ]
 
@@ -98,7 +98,11 @@ def setup(app):
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
-source_suffix = [".rst", ".md"]
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".md": "markdown",
+}
+# source_suffix = [".rst", ".md"]
 # source_suffix = ".rst"
 
 # The master toctree document.
@@ -152,7 +156,7 @@ def setup(app):
     #    'canonical_url': '',
     #    'analytics_id': '',
     "logo_only": False,
-    "display_version": True,
+    "version_selector": True,
     "prev_next_buttons_location": "top",
     #    'style_external_links': False,
     #    'vcs_pageview_mode': '',
@@ -188,7 +192,7 @@ def setup(app):
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "GeoStatToolsdoc"
+htmlhelp_basename = "GSToolsdoc"
 # logos for the page
 html_logo = "pics/gstools_150.png"
 html_favicon = "pics/gstools.ico"
@@ -217,8 +221,8 @@ def setup(app):
 latex_documents = [
     (
         master_doc,
-        "GeoStatTools.tex",
-        "GeoStatTools Documentation",
+        "GSTools.tex",
+        "GSTools Documentation",
         "Sebastian Müller, Lennart Schüler",
         "manual",
     )
@@ -229,9 +233,7 @@ def setup(app):
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, "geostattools", "GeoStatTools Documentation", [author], 1)
-]
+man_pages = [(master_doc, "GSTools", "GSTools Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -242,10 +244,10 @@ def setup(app):
 texinfo_documents = [
     (
         master_doc,
-        "GeoStatTools",
-        "GeoStatTools Documentation",
+        "GSTools",
+        "GSTools Documentation",
         author,
-        "GeoStatTools",
+        "GSTools",
         "Geo-statistical toolbox.",
         "Miscellaneous",
     )
@@ -320,7 +322,7 @@ def setup(app):
     # Sort gallery example by file name instead of number of lines (default)
     "within_subsection_order": FileNameSortKey,
     # directory where function granular galleries are stored
-    "backreferences_dir": None,
+    "backreferences_dir": "examples/backreferences",
     # Modules for which function level galleries are created.  In
     "doc_module": "gstools",
     # "first_notebook_cell": (

docs/source/contents.rst

@@ -9,4 +9,5 @@ Contents
    index
    tutorials
    api
+   authors
    changelog

docs/source/index.rst

@@ -22,7 +22,7 @@ GSTools Quickstart
 Purpose
 =======
 
-GeoStatTools provides geostatistical tools for various purposes:
+GSTools provides geostatistical tools for various purposes:
 
 - random field generation, including periodic boundaries
 - simple, ordinary, universal and external drift kriging

docs/source/tutorials.rst

@@ -30,3 +30,12 @@ explore its whole beauty and power.
 
    .. youtube:: qZBJ-AZXq6Q
       :width: 100%
+
+   |
+
+   Gallery
+   =======
+
+   .. minigallery::
+
+      ../../examples/**/*.py

pyproject.toml

@@ -38,6 +38,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering",
     "Topic :: Scientific/Engineering :: GIS",
     "Topic :: Scientific/Engineering :: Hydrology",
@@ -56,15 +57,15 @@ dependencies = [
 
 [project.optional-dependencies]
 doc = [
-    "m2r2>=0.2.8",
+    "myst_parser",
     "matplotlib>=3.7",
     "meshzoo>=0.7",
     "numpydoc>=1.1",
     "pykrige>=1.5,<2",
     "pyvista>=0.40",
     "sphinx>=7",
     "sphinx-gallery>=0.8",
-    "sphinx-rtd-theme>=2",
+    "sphinx-rtd-theme>=3",
     "sphinxcontrib-youtube>=1.1",
 ]
 plotting = [
@@ -110,6 +111,7 @@ target-version = [
     "py310",
     "py311",
     "py312",
+    "py313",
 ]
 
 [tool.coverage]
@@ -157,11 +159,12 @@ target-version = [
     max-statements = 85
     max-attributes = 25
     max-public-methods = 80
+    max-positional-arguments=20
 
 [tool.cibuildwheel]
 # Switch to using build
 build-frontend = "build"
-# Disable building PyPy wheels on all platforms, 32bit for py3.10/11/12, musllinux builds, py3.6/7
+# Disable building PyPy wheels on all platforms, 32bit for py3.10/11/12/13, musllinux builds, py3.6/7
 skip = ["cp36-*", "cp37-*", "pp*", "*-win32", "*-manylinux_i686", "*-musllinux_*"]
 # Run the package tests using `pytest`
 test-extras = "test"

src/gstools/__init__.py

@@ -2,7 +2,7 @@
 Purpose
 =======
 
-GeoStatTools is a library providing geostatistical tools
+GSTools is a library providing geostatistical tools
 for random field generation, conditioned field generation,
 kriging and variogram estimation
 based on a list of provided or even user-defined covariance models.

src/gstools/normalizer/base.py

@@ -13,10 +13,14 @@
 import warnings
 
 import numpy as np
-import scipy.misc as spm
 import scipy.optimize as spo
 
 
+def _derivative(f, x, dx=1e-6):
+    """Central difference formula."""
+    return (f(x + dx) - f(x - dx)) / (2 * dx)
+
+
 class Normalizer:
     """Normalizer class.
 
@@ -57,7 +61,7 @@ def _normalize(self, data):
         return data
 
     def _derivative(self, data):
-        return spm.derivative(self._normalize, data, dx=self._dx)
+        return _derivative(self._normalize, data, dx=self._dx)
 
     def _loglikelihood(self, data):
         add = -0.5 * np.size(data) * (np.log(2 * np.pi) + 1)