Ci fix and drop of Py35 support

.github/workflows/main.yml

@@ -13,14 +13,6 @@ on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
-env:
-  # needed by coveralls
-  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  CIBW_BUILD: "cp35-* cp36-* cp37-* cp38-* cp39-*"
-  CIBW_BEFORE_BUILD: 'pip install "numpy<=1.19.4" "scipy<=1.5.4" "cython>=0.29.14" setuptools'
-  CIBW_TEST_REQUIRES: "pytest scikit-learn"
-  CIBW_TEST_COMMAND: "pytest -v {project}/tests"
-
 jobs:
   format_check:
     name: format check
@@ -67,17 +59,19 @@ jobs:
           pip install -r requirements_setup.txt
           pip install -r requirements.txt
           pip install -r requirements_test.txt
-          pip install coveralls>=2.0.0
+          pip install coveralls>=3.0.0
 
       - name: Build sdist
         run: |
           python setup.py sdist -d dist
           python setup.py build_ext --inplace
 
       - name: Run tests
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           python -m pytest --cov pykrige --cov-report term-missing -v tests/
-          python -m coveralls
+          python -m coveralls --service=github
 
       - uses: actions/upload-artifact@v2
         with:
@@ -96,18 +90,15 @@ jobs:
         with:
           fetch-depth: '0'
 
-      - name: Set up Python
-        uses: actions\setup-python@v2
-        with:
-          python-version: "3.8"
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install cibuildwheel==1.7.0
       - name: Build wheels
-        run: |
-          python -m cibuildwheel --output-dir dist
+        uses: joerick/[email protected]
+        env:
+          CIBW_BUILD: cp36-* cp37-* cp38-* cp39-*
+          CIBW_BEFORE_BUILD: pip install numpy==1.19.* scipy==1.5.* cython==0.29.* setuptools
+          CIBW_TEST_REQUIRES: pytest scikit-learn
+          CIBW_TEST_COMMAND: pytest -v {project}/tests
+        with:
+          output-dir: dist
 
       - uses: actions/upload-artifact@v2
         with:
@@ -125,7 +116,7 @@ jobs:
 
       - name: Publish to Test PyPI
         if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop'
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.test_pypi_password }}
@@ -135,7 +126,7 @@ jobs:
       - name: Publish to PyPI
         # only if tagged
         if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

benchmarks/kriging_benchmarks.py

@@ -3,11 +3,11 @@
 from time import time
 import numpy as np
 from pykrige.ok import OrdinaryKriging
+
 np.random.seed(19999)
 
-VARIOGRAM_MODELS = ['power', 'gaussian', 'spherical',
-                    'exponential', 'linear']
-BACKENDS = ['vectorized', 'loop', 'C']
+VARIOGRAM_MODELS = ["power", "gaussian", "spherical", "exponential", "linear"]
+BACKENDS = ["vectorized", "loop", "C"]
 N_MOVING_WINDOW = [None, 10, 50, 100]
 
 
@@ -36,23 +36,32 @@ def make_benchark(n_train, n_test, n_dim=2):
 
     for variogram_model in VARIOGRAM_MODELS:
         tic = time()
-        OK = OrdinaryKriging(X_train[:, 0], X_train[:, 1], y_train,
-                             variogram_model='linear',
-                             verbose=False, enable_plotting=False)
-        res['t_train_{}'.format(variogram_model)] = time() - tic
+        OK = OrdinaryKriging(
+            X_train[:, 0],
+            X_train[:, 1],
+            y_train,
+            variogram_model="linear",
+            verbose=False,
+            enable_plotting=False,
+        )
+        res["t_train_{}".format(variogram_model)] = time() - tic
 
     # All the following tests are performed with the linear variogram model
     for backend in BACKENDS:
         for n_closest_points in N_MOVING_WINDOW:
 
-            if backend == 'vectorized' and n_closest_points is not None:
+            if backend == "vectorized" and n_closest_points is not None:
                 continue  # this is not supported
 
             tic = time()
-            OK.execute('points', X_test[:, 0], X_test[:, 1],
-                       backend=backend,
-                       n_closest_points=n_closest_points)
-            res['t_test_{}_{}'.format(backend, n_closest_points)] = time() - tic
+            OK.execute(
+                "points",
+                X_test[:, 0],
+                X_test[:, 1],
+                backend=backend,
+                n_closest_points=n_closest_points,
+            )
+            res["t_test_{}_{}".format(backend, n_closest_points)] = time() - tic
 
     return res
 
@@ -71,34 +80,40 @@ def print_benchmark(n_train, n_test, n_dim, res):
     res : dict
       a dictionary with the timing results
     """
-    print('='*80)
-    print(' '*10, 'N_dim={}, N_train={}, N_test={}'.format(n_dim,
-                                                           n_train, n_test))
-    print('='*80)
-    print('\n', '# Training the model', '\n')
-    print('|'.join(['{:>11} '.format(el) for el in ['t_train (s)'] +
-                    VARIOGRAM_MODELS]))
-    print('-' * (11 + 2) * (len(VARIOGRAM_MODELS) + 1))
-    print('|'.join(['{:>11} '.format('Training')] +
-                   ['{:>11.2} '.format(el) for el in
-                    [res['t_train_{}'.format(mod)]
-                     for mod in VARIOGRAM_MODELS]]))
-
-    print('\n', '# Predicting kriging points', '\n')
-    print('|'.join(['{:>11} '.format(el) for el in ['t_test (s)'] + BACKENDS]))
-    print('-' * (11 + 2) * (len(BACKENDS) + 1))
+    print("=" * 80)
+    print(" " * 10, "N_dim={}, N_train={}, N_test={}".format(n_dim, n_train, n_test))
+    print("=" * 80)
+    print("\n", "# Training the model", "\n")
+    print("|".join(["{:>11} ".format(el) for el in ["t_train (s)"] + VARIOGRAM_MODELS]))
+    print("-" * (11 + 2) * (len(VARIOGRAM_MODELS) + 1))
+    print(
+        "|".join(
+            ["{:>11} ".format("Training")]
+            + [
+                "{:>11.2} ".format(el)
+                for el in [res["t_train_{}".format(mod)] for mod in VARIOGRAM_MODELS]
+            ]
+        )
+    )
+
+    print("\n", "# Predicting kriging points", "\n")
+    print("|".join(["{:>11} ".format(el) for el in ["t_test (s)"] + BACKENDS]))
+    print("-" * (11 + 2) * (len(BACKENDS) + 1))
 
     for n_closest_points in N_MOVING_WINDOW:
-        timing_results = [res.get(
-            't_test_{}_{}'.format(mod, n_closest_points), '')
-                          for mod in BACKENDS]
-        print('|'.join(['{:>11} '.format('N_nn=' + str(n_closest_points))] +
-                       ['{:>11.2} '.format(el) for el in timing_results]))
-
-
-if __name__ == '__main__':
-    for no_train, no_test in [(400, 1000),
-                              (400, 2000),
-                              (800, 2000)]:
+        timing_results = [
+            res.get("t_test_{}_{}".format(mod, n_closest_points), "")
+            for mod in BACKENDS
+        ]
+        print(
+            "|".join(
+                ["{:>11} ".format("N_nn=" + str(n_closest_points))]
+                + ["{:>11.2} ".format(el) for el in timing_results]
+            )
+        )
+
+
+if __name__ == "__main__":
+    for no_train, no_test in [(400, 1000), (400, 2000), (800, 2000)]:
         results = make_benchark(no_train, no_test)
         print_benchmark(no_train, no_test, 2, results)

pykrige/ok.py

@@ -958,7 +958,12 @@ def execute(
                 zvalues, sigmasq = self._exec_loop_moving_window(a, bd, mask, bd_idx)
             elif backend == "C":
                 zvalues, sigmasq = _c_exec_loop_moving_window(
-                    a, bd, mask.astype("int8"), bd_idx, self.X_ADJUSTED.shape[0], c_pars
+                    a,
+                    bd,
+                    mask.astype("int8"),
+                    bd_idx.astype(int),
+                    self.X_ADJUSTED.shape[0],
+                    c_pars,
                 )
             else:
                 raise ValueError(

setup.py

@@ -64,7 +64,6 @@
     "Operating System :: Unix",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.5",
     "Programming Language :: Python :: 3.6",
     "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
@@ -89,7 +88,7 @@
     classifiers=CLASSIFIERS,
     platforms=["Windows", "Linux", "Solaris", "Mac OS-X", "Unix"],
     include_package_data=True,
-    python_requires=">=3.5",
+    python_requires=">=3.6",
     use_scm_version={
         "relative_to": __file__,
         "write_to": "pykrige/_version.py",