Merge pull request #20 from ajdawson/modernize

Modernize

.github/dependabot.yml

@@ -0,0 +1,8 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "Bot"

.github/workflows/docs.yml

@@ -0,0 +1,49 @@
+name: Documentation
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: checkout
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Setup Micromamba
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-name: DOCS
+        init-shell: bash
+        create-args: >-
+          python=3 pip iris numpy sphinx sphinx-rtd-theme --channel conda-forge
+
+    - name: Install gridfill
+      shell: bash -l {0}
+      run: |
+        python -m pip install -e . --no-deps --force-reinstall
+
+    - name: Build documentation
+      shell: bash -l {0}
+      run: |
+        set -e
+        micromamba activate DOCS
+        pushd doc
+        make clean html linkcheck
+        popd
+
+    - name: Deploy
+      if: success() && github.event_name == 'release'
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: doc/_build/html

.github/workflows/tests_iris.yml

@@ -0,0 +1,37 @@
+name: Tests (with iris)
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  run:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [windows-latest, ubuntu-latest, macos-latest]
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup Micromamba Python ${{ matrix.python-version }}
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=${{ matrix.python-version }} pip pytest iris numpy --channel conda-forge
+
+
+    - name: Install gridfill
+      shell: bash -l {0}
+      run: |
+        python -m pip install -e . --no-deps --force-reinstall
+
+    - name: Tests
+      shell: bash -l {0}
+      run: |
+        python -m pytest -vrsx gridfill/tests

.github/workflows/tests_numpy.yml

@@ -0,0 +1,37 @@
+name: Tests (numpy only)
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  run:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        os: [windows-latest, ubuntu-latest, macos-latest]
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup Micromamba Python ${{ matrix.python-version }}
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=${{ matrix.python-version }} pip pytest numpy --channel conda-forge
+
+
+    - name: Install gridfill
+      shell: bash -l {0}
+      run: |
+        python -m pip install -e . --no-deps --force-reinstall
+
+    - name: Tests
+      shell: bash -l {0}
+      run: |
+        python -m pytest -vrsx gridfill/tests

.gitignore

@@ -21,3 +21,4 @@ dist
 ## Ignore build output
 gridfill/_gridfill.c
 *.so
+gridfill/_version.py

MANIFEST.in

@@ -1,4 +1,3 @@
-include COPYING
-include README.rst
-recursive-include lib *.py
-recursive-include lib *.pyx
+include COPYING README.rst
+recursive-include gridfill *.py *.pyx *.npy
+recursive-include doc *.py *.rst Makefile

README.rst

@@ -33,6 +33,22 @@ gridfill can also operate on `iris` cubes, which requires the iris_
 package to be installed.
 
 
-.. _conda: http://conda.pydata.org
+Developers
+----------
+
+For development the pytest package is required in order to run tests. In order
+to run all tests you should also install iris_.
+
+Tests can be run in-place but you must first compile the extension module::
+
+    python setup.py build_ext --inplace
+    python -m pytest
+
+Tests can also be run against the installed version::
+
+    python -m pytest --pyargs gridfill.tests
+
+
+.. _conda: https://docs.conda.io/en/latest/
 .. _Github: https://github.com/ajdawson/gridfill
-.. _iris: http://scitools.org.uk/iris
+.. _iris: https://scitools-iris.readthedocs.io/en/stable/

doc/conf.py

@@ -73,7 +73,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -147,7 +147,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = []
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -299,5 +299,5 @@
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
     'numpy': ('http://docs.scipy.org/doc/numpy', None),
-    'iris': ('http://scitools.org.uk/iris/docs/latest', None),
+    'iris': ('https://scitools-iris.readthedocs.io/en/latest/', None),
 }

doc/index.rst

@@ -13,7 +13,7 @@ Gridfill
 Gridfill is a Python package for filling in missing values in gridded data.
 Missing values are filled by solving Poisson's equation using an iterative relaxation scheme at the missing values, resulting in a smooth filling.
 
-The core package runs on Python 2 or 3, on Linux and OSX (maybe on Windows too), and requires numpy_.
+The core package runs on Python 3, on Linux and OSX (maybe on Windows too), and requires numpy_.
 Gridfill has an optional interface for working with iris_ cubes.
 
 
@@ -64,10 +64,10 @@ Bug reports and feature requests should be made using the repository issues_ pag
 Pull requests for new features and bug fixes are welcome!
 
 
-.. _numpy: http://www.numpy.org
-.. _iris: http://scitools.org.uk/iris
-.. _conda: http://conda.pydata.org/docs/
-.. _setuptools: https://pypi.python.org/pypi/setuptools
-.. _cython: http://cython.org
-.. _Github: http://github.com/ajdawson/gridfill
-.. _issues: http://github.com/ajdawson/gridfill/issues
+.. _numpy: https://numpy.org
+.. _iris: https://scitools-iris.readthedocs.io/en/stable/
+.. _conda: https://docs.conda.io/en/latest/
+.. _setuptools: https://setuptools.pypa.io/en/latest/
+.. _cython: https://cython.org
+.. _Github: https://github.com/ajdawson/gridfill
+.. _issues: https://github.com/ajdawson/gridfill/issues

gridfill/__init__.py

@@ -22,9 +22,10 @@
 
 from .gridfill import fill, fill_cube
 
-
-# Define a version string.
-__version__ = '1.0.dev2'
+try:
+    from ._version import __version__
+except ImportError:
+    __version__ == "unknown"
 
 # Define the objects to be imported by imports of the form:
 #   from gridfill import *

gridfill/_gridfill.pyx

@@ -1,4 +1,4 @@
-#cython: boundscheck=False, wraparound=False, initializedcheck=False
+#cython: language_level=3, boundscheck=False, wraparound=False, initializedcheck=False
 """Fill missing values in grids using an iterative relaxation scheme."""
 # Copyright (c) 2016 Andrew Dawson
 #

gridfill/tests/test_fill.py

@@ -20,7 +20,7 @@
 # THE SOFTWARE.
 import os
 
-from nose.tools import raises
+import pytest
 import numpy as np
 import numpy.ma as ma
 
@@ -72,12 +72,17 @@ def test_multi_grid(self):
                          cyclic=self.cyclic, verbose=False)
         self.assert_array_almost_equal(filled, self.soln)
 
-    @raises(TypeError)
     def test_not_masked(self):
-        filled, c = fill(self.grid.filled(fill_value=np.nan), self.eps,
-                         relax=self.relax, itermax=self.itermax,
-                         initzonal=self.initzonal, cyclic=self.cyclic,
-                         verbose=False)
+        with pytest.raises(TypeError):
+            fill(
+                self.grid.filled(fill_value=np.nan),
+                self.eps,
+                relax=self.relax,
+                itermax=self.itermax,
+                initzonal=self.initzonal,
+                cyclic=self.cyclic,
+                verbose=False,
+            )
 
     def assert_array_almost_equal(self, a, b):
         np.testing.assert_array_almost_equal(a, b)

gridfill/tests/test_fill_cube.py

@@ -20,13 +20,12 @@
 # THE SOFTWARE.
 import warnings
 
-from nose import SkipTest
-from nose.tools import raises
-
+import pytest
 try:
-    import iris
+    import iris.coords
+    import iris.cube
 except ImportError:
-    raise SkipTest('Cannot import iris, fill_cube() will not be tested')
+    pytest.skip('Cannot import iris, fill_cube() will not be tested', allow_module_level=True)
 import numpy as np
 
 from gridfill import fill_cube
@@ -83,11 +82,13 @@ def test_multi_grid_inplace(self):
         assert not hasattr(filled.data, 'mask')
         assert not hasattr(cube.data, 'mask')
 
-    @raises(TypeError)
     def test_not_masked(self):
         cube = self.cube.copy(data=self.cube.data.filled(fill_value=np.nan))
-        fill_cube(cube, self.eps, relax=self.relax, itermax=self.itermax,
-                  initzonal=self.initzonal, verbose=False)
+        with pytest.raises(TypeError):
+            fill_cube(
+                cube, self.eps, relax=self.relax, itermax=self.itermax,
+                initzonal=self.initzonal, verbose=False
+            )
 
     def test_not_converged_warning(self):
         with warnings.catch_warnings(record=True) as w: