Merge pull request #242 from GeoStat-Framework/202208_build_update

Build: update setuptools config, package structure and CI

.github/workflows/main.yml

@@ -23,18 +23,53 @@ 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
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install black
+          pip install black 'isort[colors]<6'
 
       - name: black check
         run: |
-          python -m black --check  --diff --color pykrige/ examples/ tests/
+          python -m black --check  --diff --color .
+
+      - name: isort check
+        run: |
+          python -m isort --check --diff --color .
+
+  build_wheels:
+    name: wheels for ${{ matrix.cfg.os }} / ${{ matrix.cfg.arch }}
+    runs-on: ${{ matrix.cfg.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        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@v2.8.1
+        env:
+          CIBW_ARCHS: ${{ matrix.cfg.arch }}
+        with:
+          output-dir: dist
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: ./dist/*.whl
 
   build_sdist:
     name: sdist and coveralls
@@ -48,15 +83,15 @@ jobs:
           fetch-depth: '0'
 
       - name: Set up Python 3.8
-        uses: actions\setup-python@v2
+        uses: actions/setup-python@v2
         with:
           python-version: 3.8
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install build coveralls>=3.0.0
-          pip install --editable .[test]
+          pip install -v --editable .[test]
 
       - name: Run tests
         env:
@@ -74,32 +109,6 @@ jobs:
         with:
           path: dist/*.tar.gz
 
-  build_wheels:
-    name: wheels on ${{matrix.os}}
-    runs-on: ${{matrix.os}}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: '0'
-
-      - name: Build wheels
-        uses: pypa/cibuildwheel@v2.1.1
-        env:
-          CIBW_BUILD: cp36-* cp37-* cp38-* cp39-*
-          CIBW_TEST_EXTRAS: test
-          CIBW_TEST_COMMAND: pytest -v {project}/tests
-        with:
-          output-dir: dist
-
-      - uses: actions/upload-artifact@v2
-        with:
-          path: ./dist/*.whl
-
   upload_to_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest

.gitignore

@@ -16,6 +16,7 @@ downloads/
 eggs/
 .eggs/
 lib/
+!src/pykrige/lib/
 lib64/
 parts/
 sdist/
@@ -108,7 +109,8 @@ tags
 
 # own stuff
 info/
-pykrige/_version.py
+src/pykrige/_version.py
+.vscode/
 
 # Cython generated C code
 *.c

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2015-2021, PyKrige Developers
+Copyright (c) 2015-2022, PyKrige Developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

MANIFEST.in

@@ -1,7 +1,4 @@
-prune *
-graft tests
-recursive-include pykrige *.py *.pyx *.pxd
-recursive-exclude pykrige *.c *.cpp
-include LICENSE README.md pyproject.toml setup.py setup.cfg
-exclude CHANGELOG.md
-global-exclude __pycache__ *.py[cod] .*
+prune **
+recursive-include tests *.py *.txt *.asc
+recursive-include src/pykrige *.py *.pyx *.pxd
+include LICENSE README.md pyproject.toml setup.py

benchmarks/kriging_benchmarks.py

@@ -1,7 +1,9 @@
 # -*- coding: utf-8 -*-
 """Benchmarks."""
 from time import time
+
 import numpy as np
+
 from pykrige.ok import OrdinaryKriging
 
 np.random.seed(19999)

docs/source/_templates/layout.html

@@ -4,17 +4,23 @@
     {{ super() }}
     <br />
     <p class="link caption"><span class="link caption-text">PyKrige Links</span></p>
-    <a href="https://github.com/GeoStat-Framework/PyKrige">PyKrige GitHub</a>
-    <a href="https://doi.org/10.5281/zenodo.3738604">PyKrige Zenodo DOI</a>
-    <a href="https://pypi.org/project/PyKrige/">PyKrige PyPI</a>
+    <ul>
+      <Li><a href="https://github.com/GeoStat-Framework/PyKrige">PyKrige GitHub</a></Li>
+      <Li><a href="https://doi.org/10.5281/zenodo.3738604">PyKrige Zenodo DOI</a></Li>
+      <Li><a href="https://pypi.org/project/PyKrige/">PyKrige PyPI</a></Li>
+    </ul>
     <br />
     <p class="link caption"><span class="link caption-text">GeoStat Framework</span></p>
-    <a href="https://geostat-framework.org">GeoStat Website</a>
-    <a href="https://github.com/GeoStat-Framework">GeoStat Github</a>
-    <a href="https://geostat-framework.readthedocs.io">GeoStat ReadTheDocs</a>
-    <a href="https://pypi.org/user/geostatframework/">GeoStat PyPI</a>
+    <ul>
+      <Li><a href="https://geostat-framework.org">GeoStat Website</a></Li>
+      <Li><a href="https://github.com/GeoStat-Framework">GeoStat Github</a></Li>
+      <Li><a href="https://geostat-framework.readthedocs.io">GeoStat ReadTheDocs</a></Li>
+      <Li><a href="https://pypi.org/user/geostatframework/">GeoStat PyPI</a></Li>
+    </ul>
     <br />
     <br />
-    <a href="genindex.html">Index</a>
-    <a href="contents.html">Sitemap</a>
-  {% endblock %}
+    <ul>
+      <Li><a href="genindex.html">Index</a></Li>
+      <Li><a href="contents.html">Sitemap</a></Li>
+    </ul>
+    {% endblock %}

docs/source/conf.py

@@ -13,11 +13,12 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 import datetime
-import sys
 import os
 import shlex
-import sphinx_rtd_theme
+import sys
+
 import matplotlib
+import sphinx_rtd_theme
 
 matplotlib.use("Agg")
 
@@ -28,9 +29,10 @@
 # sys.path.insert(0, os.path.abspath("../../"))
 sys.path.insert(0, os.path.abspath("sphinxext"))
 
-import pykrige
 from github_link import make_linkcode_resolve
 
+import pykrige
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -45,17 +47,34 @@
     "sphinx.ext.mathjax",
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
-    "sphinxcontrib.napoleon",
+    "sphinx.ext.napoleon",  # parameters look better than with numpydoc only
+    "numpydoc",
     "sphinx_gallery.gen_gallery",
     "sphinx.ext.linkcode",
     "m2r2",
 ]
 
-
-autosummary_generate = True
-
 autodoc_default_flags = ["members", "inherited-members"]
 
+# autosummaries from source-files
+autosummary_generate = True
+# dont show __init__ docstring
+autoclass_content = "class"
+# sort class members
+autodoc_member_order = "groupwise"
+# autodoc_member_order = 'bysource'
+
+# Notes in boxes
+napoleon_use_admonition_for_notes = True
+# Attributes like parameters
+# napoleon_use_ivar = True
+# this is a nice class-doc layout
+numpydoc_show_class_members = True
+# class members have no separate file, so they are not in a toctree
+numpydoc_class_members_toctree = False
+# for the covmodels alot of classmembers show up...
+# maybe switch off with:    :no-inherited-members:
+numpydoc_show_inherited_class_members = True
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -326,7 +345,7 @@
 # The following is used by sphinx.ext.linkcode to provide links to github
 linkcode_resolve = make_linkcode_resolve(
     "pykrige",
-    u"https://github.com/GeoStat-Framework/"
+    "https://github.com/GeoStat-Framework/"
     "PyKrige/blob/{revision}/"
     "{package}/{path}#L{lineno}",
 )

docs/source/sphinxext/github_link.py

@@ -1,11 +1,11 @@
 # Adapted from scikit learn
 
-from operator import attrgetter
 import inspect
-import subprocess
 import os
+import subprocess
 import sys
 from functools import partial
+from operator import attrgetter
 
 REVISION_CMD = "git rev-parse --short HEAD"
 

examples/00_ordinary.py

@@ -6,11 +6,11 @@
 
 """
 
+import matplotlib.pyplot as plt
 import numpy as np
+
 import pykrige.kriging_tools as kt
 from pykrige.ok import OrdinaryKriging
-import matplotlib.pyplot as plt
-
 
 data = np.array(
     [

examples/01_universal.py

@@ -6,10 +6,10 @@
 
 """
 
-from pykrige.uk import UniversalKriging
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
 
+from pykrige.uk import UniversalKriging
 
 data = np.array(
     [

examples/02_kriging3D.py

@@ -4,11 +4,11 @@
 
 """
 
-from pykrige.ok3d import OrdinaryKriging3D
-from pykrige.uk3d import UniversalKriging3D
 import numpy as np
 from matplotlib import pyplot as plt
 
+from pykrige.ok3d import OrdinaryKriging3D
+from pykrige.uk3d import UniversalKriging3D
 
 data = np.array(
     [

examples/03_gstools_covmodel.py

@@ -5,10 +5,11 @@
 
 Example how to use the PyKrige routines with a GSTools CovModel.
 """
+import gstools as gs
 import numpy as np
-from pykrige.ok import OrdinaryKriging
 from matplotlib import pyplot as plt
-import gstools as gs
+
+from pykrige.ok import OrdinaryKriging
 
 # conditioning data
 data = np.array(

examples/04_krige_geometric.py

@@ -7,10 +7,10 @@
 for ordinary kriging on a sphere.
 """
 
-from pykrige.ok import OrdinaryKriging
 import numpy as np
 from matplotlib import pyplot as plt
 
+from pykrige.ok import OrdinaryKriging
 
 # Make this example reproducible:
 np.random.seed(89239413)

examples/05_kriging_1D.py

@@ -4,8 +4,9 @@
 
 An example of 1D kriging with PyKrige
 """
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
+
 from pykrige import OrdinaryKriging
 
 plt.style.use("ggplot")

examples/06_exact_values_example_1D.py

@@ -7,10 +7,11 @@
 as a non-exact interpolator in 1D. 
 """
 
-from pykrige.ok import OrdinaryKriging
 import matplotlib.pyplot as plt
 import numpy as np
 
+from pykrige.ok import OrdinaryKriging
+
 plt.style.use("ggplot")
 
 np.random.seed(42)

examples/07_regression_kriging2d.py

@@ -7,11 +7,11 @@
 
 import sys
 
-from sklearn.svm import SVR
+from sklearn.datasets import fetch_california_housing
 from sklearn.ensemble import RandomForestRegressor
 from sklearn.linear_model import LinearRegression
-from sklearn.datasets import fetch_california_housing
 from sklearn.model_selection import train_test_split
+from sklearn.svm import SVR
 
 from pykrige.rk import RegressionKriging
 

examples/08_krige_cv.py

@@ -7,9 +7,9 @@
 """
 
 import numpy as np
-from pykrige.rk import Krige
 from sklearn.model_selection import GridSearchCV
 
+from pykrige.rk import Krige
 
 # 2D Kring param opt