Added reporting of code coverage by test suite.

Code coverage by the test suite is measured via pyTest and its
pyTest-cov plug-in. The script `coverage.py` runs the coverage
test, renders the coverage report, and also creates the coverage
badge, unless that file already exists in the `tests` folder.

.gitignore

@@ -1,6 +1,8 @@
 /develop/
 /deploy/docs/
 /deploy/dist/
+/deploy/coverage/
+/deploy/coverage.sqlite
 /dist/
 **/__pycache__
 **/.pytest_cache

ReadMe.md

@@ -1,4 +1,5 @@
-Kernel density estimation via diffusion in 1d and 2d.
+# KDE-diffusion
+*Kernel density estimation via diffusion in 1d and 2d*
 
 Provides the fast, adaptive kernel density estimator based on linear
 diffusion processes for one-dimensional and two-dimensional input data
@@ -9,15 +10,14 @@ in Python, with added test coverage.
 
 Find the full [documentation on Read-the-Docs][docs].
 
-[![citation](https://zenodo.org/badge/263433787.svg)](https://zenodo.org/badge/latestdoi/263433787)
-[![license](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
-[![release](https://img.shields.io/pypi/v/kde-diffusion.svg)](https://pypi.python.org/pypi/kde-diffusion)
-[![downloads](https://pepy.tech/badge/kde-diffusion)](https://pepy.tech/project/kde-diffusion)
-[![documentation](https://readthedocs.org/projects/kde-diffusion/badge/?version=latest)](https://kde-diffusion.readthedocs.io/en/latest/?badge=latest)
-
 [paper]: https://dx.doi.org/10.1214/10-AOS799
 [kde1d]: https://mathworks.com/matlabcentral/fileexchange/14034
 [kde2d]: https://mathworks.com/matlabcentral/fileexchange/17204
 [docs]:  https://kde-diffusion.readthedocs.io
 
-
+[![citation](https://zenodo.org/badge/263433787.svg)](https://zenodo.org/badge/latestdoi/263433787)
+[![license](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
+[![release](https://img.shields.io/pypi/v/kde-diffusion.svg)](https://pypi.python.org/pypi/kde-diffusion)
+[![downloads](https://pepy.tech/badge/kde-diffusion)](https://pepy.tech/project/kde-diffusion)
+![coverage](tests/coverage.svg?raw=true)
+[![documentation](https://readthedocs.org/projects/kde-diffusion/badge/?version=latest)](https://kde-diffusion.readthedocs.io/en/latest/?badge=latest)

deploy/build.py

@@ -1,16 +1,11 @@
-"""Builds documentation and installation package."""
+"""Builds the installation package."""
 __license__ = 'MIT'
 
 from subprocess import run
 from pathlib import Path
 from shutil import rmtree
 
 root = Path(__file__).resolve().parent.parent
-
-process = run(['sphinx-build', 'docs', 'deploy/docs'], cwd=root)
-if process.returncode:
-    raise RuntimeError('Error while building documentation.')
-
 process = run(['flit', 'build', '--format', 'wheel'], cwd=root)
 if process.returncode:
     raise RuntimeError('Error while building wheel.')

deploy/clean.py

@@ -4,13 +4,13 @@
 from pathlib import Path
 from shutil import rmtree
 
-root = Path(__file__).absolute().parent.parent
+root = Path(__file__).resolve().parent.parent
 
 for folder in root.rglob('__pycache__'):
-    rmtree(folder)
+    rmtree(folder, ignore_errors=True)
 
 for folder in root.rglob('.pytest_cache'):
     rmtree(folder)
 
-for folder in (root/'deploy'/'dist', root/'deploy'/'docs'):
-    rmtree(folder, ignore_errors=True)
+for folder in ('docs', 'dist', 'coverage'):
+    rmtree(root/'deploy'/folder, ignore_errors=True)

deploy/coverage.py

@@ -0,0 +1,24 @@
+"""Measures code coverage by test suite."""
+__license__ = 'MIT'
+
+
+from subprocess import run
+from pathlib import Path
+
+
+here = Path(__file__).resolve().parent
+root = here.parent
+file = here/'coverage.sqlite'
+
+run(['pytest', '--cov'], cwd=root)
+
+print('Rendering coverage report.')
+folder = (here/'coverage').relative_to(root)
+run(['coverage', 'html', f'--directory={folder}'], cwd=root)
+
+badge = root/'tests'/file.with_suffix('.svg').name
+if badge.exists():
+    print('Coverage badge already exists.')
+else:
+    print('Rendering coverage badge.')
+    run(['coverage-badge', '-f', '-o', str(badge)], cwd=root)

deploy/publish.py

@@ -5,7 +5,6 @@
 from pathlib import Path
 
 root = Path(__file__).resolve().parent.parent
-
 process = run(['flit', 'publish', '--format', 'wheel'], cwd=root)
 if process.returncode:
-    raise RuntimeError('Error while publishing to PyPI.')
+    raise RuntimeError('Error while publishing on PyPI.')

deploy/release.md

@@ -0,0 +1,11 @@
+Steps to take when releasing a new version:
+* Bump version number and enter current date in `__init__.py`.
+* Add a dedicated commit for the version bump.
+* Tag the commit with the version number, for example: `git tag -a v1.0.3`.
+* Enter the release notes as an annotation.
+* Push the commit (but not the tag): `git push origin main`.
+* Check that documentation built successfully on Read-the-Docs.
+* Publish on PyPI by running `deploy/publish.py`.
+* Check that meta information is correct on PyPI.
+* Then push the tag: `git push --tags`.
+* Create a new release on GitHub and add the release notes.

deploy/render.py

@@ -0,0 +1,10 @@
+"""Renders the documentation."""
+__license__ = 'MIT'
+
+from subprocess import run
+from pathlib import Path
+
+root = Path(__file__).resolve().parent.parent
+process = run(['sphinx-build', 'docs', 'deploy/docs'], cwd=root)
+if process.returncode:
+    raise RuntimeError('Error while rendering documentation.')

pyproject.toml

@@ -22,8 +22,8 @@ classifiers = [
     'License :: OSI Approved :: MIT License']
 
 [tool.flit.metadata.requires-extra]
-test = ['pyTest']
-doc = ['Sphinx', 'Sphinx-RTD-theme', 'reCommonMark']
+doc = ['Sphinx', 'Sphinx-RTD-theme', 'MyST-parser', 'CommonMark']
+test = ['pyTest', 'pyTest-cov', 'coverage-badge', 'flake8']
 
 [tool.flit.metadata.urls]
 Documentation = 'https://kde-diffusion.readthedocs.io'

tests/test_1d.py

@@ -27,7 +27,7 @@ def setup_module():
 # Tests                                #
 ########################################
 
-def test_density():
+def test_reference():
     x = reference['x']
     N = reference['N']
     assert N == len(x)
@@ -40,11 +40,27 @@ def test_density():
     assert isclose(bandwidth, reference['bandwidth']).all()
 
 
+def test_arguments():
+    (density, grid, bandwidth) = kde1d([-2, -1, 0, +1, +2]*20, 4)
+    assert len(grid) == 4
+    assert isclose(grid.min(), -2.4)
+    assert isclose(grid.max(), +1.2)
+    (density, grid, bandwidth) = kde1d([-2, -1, 0, +1, +2]*20, 4, 2)
+    assert isclose(grid.min(), -2)
+    assert isclose(grid.max(), +1)
+    try:
+        kde1d([-2, -1, 0, +1, +2]*10, 4)
+        raised_error = False
+    except ValueError:
+        raised_error = True
+    assert raised_error
+
+
 ########################################
 # Main                                 #
 ########################################
 
 if __name__ == '__main__':
-    # Runs if test script is executed directly, and not via pytest.
     setup_module()
-    test_density()
+    test_reference()
+    test_arguments()

tests/test_2d.py

@@ -27,7 +27,7 @@ def setup_module():
 # Test                                 #
 ########################################
 
-def test_density():
+def test_reference():
     x = reference['x']
     y = reference['y']
     N = reference['N']
@@ -47,11 +47,49 @@ def test_density():
     assert isclose(bandwidth, reference['bandwidth']).all()
 
 
+def test_arguments():
+    samples = [-2, -1, 0, +1, +2]
+    (density, grid, bandwith) = kde2d(samples*5, samples*5, 16)
+    assert len(grid[0]) == 16
+    assert len(grid[1]) == 16
+    assert isclose(grid[0].min(), -3.0)
+    assert isclose(grid[0].max(), +2.625)
+    assert isclose(grid[1].min(), -3.0)
+    assert isclose(grid[1].max(), +2.625)
+    (density, grid, bandwidth) = kde2d(samples*5, samples*5, 16, (2, None))
+    assert isclose(grid[0].min(), -2)
+    assert isclose(grid[0].max(), +1.75)
+    assert isclose(grid[1].min(), -3)
+    assert isclose(grid[1].max(), +2.625)
+    (density, grid, bandwidth) = kde2d(samples*5, samples*5, 16, (None, 2))
+    assert isclose(grid[0].min(), -3)
+    assert isclose(grid[0].max(), +2.625)
+    assert isclose(grid[1].min(), -2)
+    assert isclose(grid[1].max(), +1.75)
+    (density, grid, bandwidth) = kde2d(samples*5, samples*5, 16, 2)
+    assert isclose(grid[0].min(), -2)
+    assert isclose(grid[0].max(), +1.75)
+    assert isclose(grid[1].min(), -2)
+    assert isclose(grid[1].max(), +1.75)
+    try:
+        kde2d(samples, samples*2, 16)
+        raised_error = False
+    except ValueError:
+        raised_error = True
+    assert raised_error
+    try:
+        kde2d(samples, samples, 16)
+        raised_error = False
+    except ValueError:
+        raised_error = True
+    assert raised_error
+
+
 ########################################
 # Main                                 #
 ########################################
 
 if __name__ == '__main__':
-    # Runs if test script is executed directly, and not via pytest.
     setup_module()
-    test_density()
+    test_reference()
+    test_arguments()

tox.ini

@@ -18,3 +18,16 @@ ignore =
     E741
 per-file-ignores =
     kde_diffusion/__init__.py:F401
+
+
+[pytest]
+addopts = --verbose
+testpaths =
+    tests
+filterwarnings =
+    ignore::UserWarning
+
+
+[coverage:run]
+source = kde_diffusion/
+data_file = deploy/coverage.sqlite