From b2d000e09ee53ef20caa9b1a8dc4de274036831f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20M=C3=BCller?= <mueller.seb@posteo.de>
Date: Thu, 22 Jun 2023 11:32:53 +0200
Subject: [PATCH 1/8] fix cython-lint complains

---
 src/gstools/field/summator.pyx      | 13 +++--
 src/gstools/krige/krigesum.pyx      |  3 +-
 src/gstools/variogram/estimator.pyx | 82 ++++++++++++++---------------
 3 files changed, 48 insertions(+), 50 deletions(-)

diff --git a/src/gstools/field/summator.pyx b/src/gstools/field/summator.pyx
index cad20e1d8..c66f1027b 100644
--- a/src/gstools/field/summator.pyx
+++ b/src/gstools/field/summator.pyx
@@ -1,12 +1,10 @@
-#cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
+# cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
 """
 This is the randomization method summator, implemented in cython.
 """
 
 import numpy as np
 
-cimport cython
-
 from cython.parallel import prange
 
 cimport numpy as np
@@ -18,7 +16,7 @@ def summate(
     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]
@@ -53,7 +51,7 @@ def summate_incompr(
     const double[:] z_1,
     const double[:] z_2,
     const double[:, :] pos
-    ):
+):
     cdef int i, j, d
     cdef double phase
     cdef double k_2
@@ -76,6 +74,7 @@ def summate_incompr(
                 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))
-
+                summed_modes[d, i] += (
+                    proj[d] * (z_1[j] * cos(phase) + z_2[j] * sin(phase))
+                )
     return np.asarray(summed_modes)
diff --git a/src/gstools/krige/krigesum.pyx b/src/gstools/krige/krigesum.pyx
index de3a43b1e..3b9848442 100644
--- a/src/gstools/krige/krigesum.pyx
+++ b/src/gstools/krige/krigesum.pyx
@@ -1,11 +1,10 @@
-#cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
+# cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
 """
 This is a summator for the kriging routines
 """
 
 import numpy as np
 
-cimport cython
 from cython.parallel import prange
 cimport numpy as np
 
diff --git a/src/gstools/variogram/estimator.pyx b/src/gstools/variogram/estimator.pyx
index 528004feb..7f1a32a25 100644
--- a/src/gstools/variogram/estimator.pyx
+++ b/src/gstools/variogram/estimator.pyx
@@ -1,4 +1,4 @@
-#cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
+# cython: language_level=3, boundscheck=False, wraparound=False, cdivision=True
 # distutils: language = c++
 """
 This is the variogram estimater, implemented in cython.
@@ -6,8 +6,6 @@ This is the variogram estimater, implemented in cython.
 
 import numpy as np
 
-cimport cython
-
 from cython.parallel import parallel, prange
 
 cimport numpy as np
@@ -16,20 +14,20 @@ 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 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]))
+        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 double[:, :] pos,
     const int i,
     const int j,
 ) nogil:
@@ -48,7 +46,7 @@ cdef inline double dist_haversine(
 
 ctypedef double (*_dist_func)(
     const int,
-    const double[:,:],
+    const double[:, :],
     const int,
     const int,
 ) nogil
@@ -56,9 +54,9 @@ ctypedef double (*_dist_func)(
 
 cdef inline bint dir_test(
     const int dim,
-    const double[:,:] pos,
+    const double[:, :] pos,
     const double dist,
-    const double[:,:] direction,
+    const double[:, :] direction,
     const double angles_tol,
     const double bandwidth,
     const int i,
@@ -74,12 +72,12 @@ cdef inline bint dir_test(
 
     # 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]
+        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]
+            tmp = (pos[k, i] - pos[k, j]) - s_prod * direction[d, k]
             b_dist += tmp * tmp
         in_band = sqrt(b_dist) < bandwidth
 
@@ -130,32 +128,31 @@ ctypedef void (*_normalization_func)(
 )
 
 cdef inline void normalization_matheron_vec(
-    double[:,:] variogram,
-    long[:,:] counts,
+    double[:, :] variogram,
+    long[:, :] counts,
 ):
-    cdef int d, i
+    cdef int d
     for d in range(variogram.shape[0]):
         normalization_matheron(variogram[d, :], counts[d, :])
 
 cdef inline void normalization_cressie_vec(
-    double[:,:] variogram,
-    long[:,:] counts,
+    double[:, :] variogram,
+    long[:, :] counts,
 ):
-    cdef int d, i
-    cdef long cnt
+    cdef int d
     for d in range(variogram.shape[0]):
         normalization_cressie(variogram[d, :], counts[d, :])
 
 ctypedef void (*_normalization_func_vec)(
-    double[:,:],
-    long[:,:],
+    double[:, :],
+    long[:, :],
 )
 
 cdef _estimator_func choose_estimator_func(str estimator_type):
     cdef _estimator_func estimator_func
     if estimator_type == 'm':
         estimator_func = estimator_matheron
-    else: # estimator_type == 'c'
+    else:  # estimator_type == 'c'
         estimator_func = estimator_cressie
     return estimator_func
 
@@ -163,7 +160,7 @@ cdef _normalization_func choose_estimator_normalization(str estimator_type):
     cdef _normalization_func normalization_func
     if estimator_type == 'm':
         normalization_func = normalization_matheron
-    else: # estimator_type == 'c'
+    else:  # estimator_type == 'c'
         normalization_func = normalization_cressie
     return normalization_func
 
@@ -171,16 +168,16 @@ cdef _normalization_func_vec choose_estimator_normalization_vec(str estimator_ty
     cdef _normalization_func_vec normalization_func_vec
     if estimator_type == 'm':
         normalization_func_vec = normalization_matheron_vec
-    else: # estimator_type == 'c'
+    else:  # estimator_type == 'c'
         normalization_func_vec = normalization_cressie_vec
     return normalization_func_vec
 
 
 def directional(
-    const double[:,:] f,
+    const double[:, :] f,
     const double[:] bin_edges,
-    const double[:,:] pos,
-    const double[:,:] direction,  # should be normed
+    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
@@ -207,8 +204,8 @@ def directional(
     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 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
 
@@ -219,13 +216,15 @@ def directional(
                 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):
+                    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])):
+                        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])
+                            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:
@@ -234,10 +233,11 @@ def directional(
     normalization_func_vec(variogram, counts)
     return np.asarray(variogram), np.asarray(counts)
 
+
 def unstructured(
-    const double[:,:] f,
+    const double[:, :] f,
     const double[:] bin_edges,
-    const double[:,:] pos,
+    const double[:, :] pos,
     str estimator_type='m',
     str distance_type='e',
 ):
@@ -280,15 +280,15 @@ def unstructured(
                     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])):
+                    if not (isnan(f[m, k]) or isnan(f[m, j])):
                         counts[i] += 1
-                        variogram[i] += estimator_func(f[m,k] - f[m,j])
+                        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'):
+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)
@@ -307,15 +307,15 @@ def structured(const double[:,:] f, str estimator_type='m'):
             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])
+                    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,
+    const double[:, :] f,
+    const bint[:, :] mask,
     str estimator_type='m',
 ):
     cdef _estimator_func estimator_func = choose_estimator_func(estimator_type)
@@ -335,9 +335,9 @@ def ma_structured(
         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]:
+                    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])
+                        variogram[k] += estimator_func(f[i, j] - f[i+k, j])
 
     normalization_func(variogram, counts)
     return np.asarray(variogram)

From b2583e05cb81e5c180cf4c2ef974c542337e535c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20M=C3=BCller?= <mueller.seb@posteo.de>
Date: Thu, 22 Jun 2023 11:41:51 +0200
Subject: [PATCH 2/8] add lint opt deps; add cython-lint check in CI

---
 .github/workflows/main.yml | 11 +++++++----
 pyproject.toml             |  6 ++++++
 2 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index c3bf56e0d..a48126fb8 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -32,20 +32,23 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install black 'pylint<3' 'isort[colors]<6'
-          pip install -v --editable .
+          pip install -v --editable .[lint]
 
       - name: black check
         run: |
           python -m black --check --diff --color .
 
+      - name: isort check
+        run: |
+          python -m isort --check --diff --color .
+
       - name: pylint check
         run: |
           python -m pylint src/gstools/
 
-      - name: isort check
+      - name: cython-lint check
         run: |
-          python -m isort --check --diff --color .
+          cython-lint src/gstools/
 
   build_wheels:
     name: wheels for ${{ matrix.cfg.os }} / ${{ matrix.cfg.arch }}
diff --git a/pyproject.toml b/pyproject.toml
index 3a6c7ec07..39948c191 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -72,6 +72,12 @@ plotting = [
 ]
 rust = ["gstools_core>=0.2.0,<1"]
 test = ["pytest-cov>=3"]
+lint = [
+    "black",
+    "pylint<3",
+    "isort[colors]<6",
+    "cython-lint",
+]
 
 [project.urls]
 Changelog = "https://github.com/GeoStat-Framework/GSTools/blob/main/CHANGELOG.md"

From 2615b539e753c4642d3f289a071bc1e996c099d8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20M=C3=BCller?= <mueller.seb@posteo.de>
Date: Thu, 22 Jun 2023 11:47:02 +0200
Subject: [PATCH 3/8] apply isort to pyx files

---
 src/gstools/field/summator.pyx      | 1 -
 src/gstools/krige/krigesum.pyx      | 2 +-
 src/gstools/variogram/estimator.pyx | 1 -
 3 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/gstools/field/summator.pyx b/src/gstools/field/summator.pyx
index c66f1027b..29239c074 100644
--- a/src/gstools/field/summator.pyx
+++ b/src/gstools/field/summator.pyx
@@ -4,7 +4,6 @@ This is the randomization method summator, implemented in cython.
 """
 
 import numpy as np
-
 from cython.parallel import prange
 
 cimport numpy as np
diff --git a/src/gstools/krige/krigesum.pyx b/src/gstools/krige/krigesum.pyx
index 3b9848442..2f79d3adb 100644
--- a/src/gstools/krige/krigesum.pyx
+++ b/src/gstools/krige/krigesum.pyx
@@ -4,8 +4,8 @@ This is a summator for the kriging routines
 """
 
 import numpy as np
-
 from cython.parallel import prange
+
 cimport numpy as np
 
 
diff --git a/src/gstools/variogram/estimator.pyx b/src/gstools/variogram/estimator.pyx
index 7f1a32a25..611f5efbd 100644
--- a/src/gstools/variogram/estimator.pyx
+++ b/src/gstools/variogram/estimator.pyx
@@ -5,7 +5,6 @@ This is the variogram estimater, implemented in cython.
 """
 
 import numpy as np
-
 from cython.parallel import parallel, prange
 
 cimport numpy as np

From 1238f81cb7310051ec08c9e262932d2d877c9bcb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20M=C3=BCller?= <mueller.seb@posteo.de>
Date: Fri, 3 Nov 2023 15:45:42 +0100
Subject: [PATCH 4/8] cython: switch to cython >3.0

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 39948c191..daa4c4bd7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,7 +3,7 @@ requires = [
     "setuptools>=64",
     "setuptools_scm>=7",
     "oldest-supported-numpy",
-    "Cython>=0.29.32,<3.0",
+    "Cython>=3.0",
     "extension-helpers>=1",
 ]
 build-backend = "setuptools.build_meta"

From 7d8d6817b19e924cb33c506bff697d30bce90b4b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20M=C3=BCller?= <mueller.seb@posteo.de>
Date: Fri, 3 Nov 2023 15:50:23 +0100
Subject: [PATCH 5/8] lint: remove caps for lint deps

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index daa4c4bd7..cf5048c96 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -74,8 +74,8 @@ rust = ["gstools_core>=0.2.0,<1"]
 test = ["pytest-cov>=3"]
 lint = [
     "black",
-    "pylint<3",
-    "isort[colors]<6",
+    "pylint",
+    "isort[colors]",
     "cython-lint",
 ]
 

From 8e82b3c9445e12265b878d89f5dd551430d19104 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20M=C3=BCller?= <mueller.seb@posteo.de>
Date: Fri, 3 Nov 2023 15:56:31 +0100
Subject: [PATCH 6/8] python: drop py37 and add 312

---
 .github/workflows/main.yml |  4 ++--
 pyproject.toml             | 10 +++++-----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index a48126fb8..e116c4832 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -71,7 +71,7 @@ jobs:
           fetch-depth: '0'
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.11.2
+        uses: pypa/cibuildwheel@v2.16.2
         env:
           CIBW_ARCHS: ${{ matrix.cfg.arch }}
         with:
@@ -88,7 +88,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v2
diff --git a/pyproject.toml b/pyproject.toml
index cf5048c96..70b7d0a62 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ requires = [
 build-backend = "setuptools.build_meta"
 
 [project]
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 name = "gstools"
 description = "GSTools: A geostatistical toolbox."
 authors = [
@@ -32,11 +32,11 @@ classifiers = [
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering",
     "Topic :: Scientific/Engineering :: GIS",
     "Topic :: Scientific/Engineering :: Hydrology",
@@ -104,11 +104,11 @@ line_length = 79
 [tool.black]
 line-length = 79
 target-version = [
-    "py37",
     "py38",
     "py39",
     "py310",
     "py311",
+    "py312",
 ]
 
 [tool.coverage]
@@ -160,8 +160,8 @@ target-version = [
 [tool.cibuildwheel]
 # Switch to using build
 build-frontend = "build"
-# Disable building PyPy wheels on all platforms, 32bit for py3.10/11 and musllinux builds, py3.6
-skip = ["cp36-*", "pp*", "cp31*-win32", "cp31*-manylinux_i686", "*-musllinux_*"]
+# Disable building PyPy wheels on all platforms, 32bit for py3.10/11/12, musllinux builds, py3.6/7
+skip = ["cp36-*", "cp37-*", "pp*", "cp31*-win32", "cp31*-manylinux_i686", "*-musllinux_*"]
 # Run the package tests using `pytest`
 test-extras = "test"
 test-command = "pytest -v {package}/tests"

From 702e2b90d796b38e5fb1110726a64a8aa36b095e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20M=C3=BCller?= <mueller.seb@posteo.de>
Date: Fri, 3 Nov 2023 16:00:16 +0100
Subject: [PATCH 7/8] update changelog

---
 CHANGELOG.md | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 633b50b4e..00513d23b 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,18 @@
 
 All notable changes to **GSTools** will be documented in this file.
 
+## [1.5.1] - Nifty Neon - 2023-11
+
+### Enhancements
+
+see [#317](https://github.com/GeoStat-Framework/GSTools/pull/317)
+
+- added wheels for Python 3.12
+- dropped support for Python 3.7 (EOL)
+- linted Cython files with cython-lint
+- use Cython 3 to build extensions
+
+
 ## [1.5.0] - Nifty Neon - 2023-06
 
 ### Enhancements
@@ -404,7 +416,8 @@ See: [#197](https://github.com/GeoStat-Framework/GSTools/issues/197)
 First release of GSTools.
 
 
-[Unreleased]: https://github.com/GeoStat-Framework/gstools/compare/v1.5.0...HEAD
+[Unreleased]: https://github.com/GeoStat-Framework/gstools/compare/v1.5.1...HEAD
+[1.5.1]: https://github.com/GeoStat-Framework/gstools/compare/v1.5.0...v1.5.1
 [1.5.0]: https://github.com/GeoStat-Framework/gstools/compare/v1.4.1...v1.5.0
 [1.4.1]: https://github.com/GeoStat-Framework/gstools/compare/v1.4.0...v1.4.1
 [1.4.0]: https://github.com/GeoStat-Framework/gstools/compare/v1.3.5...v1.4.0

From 5638e15f9f30371745ef7895c5da910de794779a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20M=C3=BCller?= <mueller.seb@posteo.de>
Date: Fri, 3 Nov 2023 16:09:05 +0100
Subject: [PATCH 8/8] rtd config fix

---
 .readthedocs.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 2ef05a17d..7dd176079 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -1,12 +1,16 @@
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 sphinx:
   configuration: docs/source/conf.py
 
 formats: all
 
 python:
-  version: 3.8
   install:
     - method: pip
       path: .