Tests and issue #90

Author: maroba

findiff/findiff.py

@@ -88,6 +88,9 @@ def __init__(self, axis, order, spacing, acc):
 
     def __call__(self, f):
         self.validate_f(f)
+        if np.issubdtype(f.dtype, np.integer):
+            f = f.astype(np.float64)
+
         npts = f.shape[self.axis]
         fd = np.zeros_like(f)
         num_bndry_points = len(self.center["coefficients"]) // 2
@@ -177,6 +180,12 @@ def __init__(self, axis, order, spacing, acc):
 
     def __call__(self, f):
         self.validate_f(f)
+        if np.issubdtype(f.dtype, np.integer):
+            f = f.astype(np.float64)
+
+        if np.issubdtype(f.dtype, np.integer):
+            f = f.astype(np.float64)
+
         fd = np.zeros_like(f)
         for off, coef in zip(self.coefs["offsets"], self.coefs["coefficients"]):
             fd += coef * np.roll(f, -off, axis=self.axis)
@@ -212,7 +221,11 @@ def __init__(self, axis, order, coords, acc):
     def __call__(self, y):
         """The core function to take a partial derivative on a non-uniform grid"""
 
+        if np.issubdtype(y.dtype, np.integer):
+            y = y.astype(np.float64)
+
         order, dim = self.order, self.axis
+
         yd = np.zeros_like(y)
 
         ndims = len(y.shape)

pyproject.toml

@@ -5,14 +5,14 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "findiff"
 authors = [
-    {name = "Matthias Baer"},
+    { name = "Matthias Baer" },
 ]
 maintainers = [
-    {name = "Matthias Baer", email="[email protected]"},
+    { name = "Matthias Baer", email = "[email protected]" },
 ]
 description = "A Python package for finite difference derivatives in any number of dimensions."
 readme = "README.md"
-license = {text = "MIT"}
+license = { text = "MIT" }
 dependencies = [
     "numpy",
     "scipy",
@@ -47,6 +47,20 @@ include = ["findiff"]
 [tool.setuptools.dynamic]
 version = { attr = "findiff.__version__" }
 
+[tool.pytest.ini_options]
+addopts = [
+    "--strict-markers"
+]
+testpaths = "tests"
+markers = [
+    "functional: Functional tests for stuff that the user would do",
+    "one_dimensional: Tests in 1D",
+    "periodic: Tests for periodic boundary conditions",
+    "invalid_args: Tests for invalid argument handling",
+    "default_args: Tests for default argument handling",
+    "grid_spec: Marker to construct grid data by fixtures"
+]
+
 [tool.coverage]
 run.source_pkgs = ["findiff", "tests"]
 run.branch = true
@@ -96,9 +110,9 @@ commands = [
 [tool.ruff]
 line-length = 88
 lint.extend-select = [
-    "B",  # flake8-bugbear
-    "I",  # isort
-    "UP",  # pyupgrade
+    "B", # flake8-bugbear
+    "I", # isort
+    "UP", # pyupgrade
 ]
 extend-exclude = [
     "docs/source/**/*.ipynb",

pytest.ini

@@ -9,14 +9,18 @@ def grid_data(request):
         raise ValueError("Grid data marker not defined")
     shape = m.kwargs["shape"]
     edges = m.kwargs["edges"]
+    endpoints = m.kwargs.get("endpoints", [True] * len(shape))
 
     if len(shape) == 1:
-        x = np.linspace(*edges, shape[0])
+        x = np.linspace(*edges, shape[0], endpoint=endpoints[0])
         dx = x[1] - x[0]
         return x, dx
 
     axes = tuple(
-        [np.linspace(edges[k][0], edges[k][1], shape[k]) for k in range(len(shape))]
+        [
+            np.linspace(edges[k][0], edges[k][1], shape[k], endpoint=endpoints[k])
+            for k in range(len(shape))
+        ]
     )
     coords = np.meshgrid(*axes, indexing="ij")
     spacings = [axes[k][1] - axes[k][0] for k in range(len(shape))]

tests/conftest.py

@@ -1,8 +1,10 @@
 import numpy as np
 import pytest
+from numpy.testing import assert_array_almost_equal
 
 import findiff
 from findiff import FinDiff
+from findiff.coefs import coefficients_non_uni
 
 
 def test_findiff_should_raise_exception_when_applied_to_unevaluated_function():
@@ -141,3 +143,22 @@ def assert_dict_almost_equal(first, second):
         assert first[k] == pytest.approx(0, abs=1.0e-8)
     for k in set(second) - set(first):
         assert 0 == pytest.approx(second[k], abs=1.0e-8)
+
+
+class TestIssue90:
+
+    def test_reproduce_issue90(self):
+
+        x = np.array([0.0, 1.0, 1.5, 3.5, 4.0, 6.0])
+        f1 = np.array([1, 2, 4, 7, 11, 16])
+        f2 = np.sin(x)
+
+        d_dx = FinDiff(0, x, acc=2)
+        df_dx1 = d_dx(f1)
+        df_dx2 = d_dx(f2)
+
+        grad1 = np.gradient(f1, x, edge_order=2)
+        grad2 = np.gradient(f2, x, edge_order=2)
+
+        assert_array_almost_equal(df_dx2, grad2)
+        assert_array_almost_equal(df_dx1, grad1)

tests/test_bugs.py

@@ -7,16 +7,6 @@
 from findiff import Diff, Identity
 
 
-def test_partial_d_dx_periodic():
-    x = np.linspace(0, 2 * np.pi, 200, endpoint=False)
-    dx = x[1] - x[0]
-    f = np.sin(x)
-    expected = np.cos(x)
-    actual = Diff(0, dx, periodic=True, acc=4)(f)
-
-    assert_array_almost_equal(expected, actual)
-
-
 def test_partial_d2_dx2_matrix_periodic():
     dx = 1
     expected = np.array(

tests/test_diff.py

@@ -11,7 +11,7 @@
 class TestDiff_1D:
 
     @pytest.mark.grid_spec(shape=(101,), edges=(0, 1))
-    def test_diff_1d(self, grid_data):
+    def test_diff(self, grid_data):
         x, dx = grid_data
 
         u = x**2
@@ -23,7 +23,7 @@ def test_diff_1d(self, grid_data):
         assert_array_almost_equal(expected, actual)
 
     @pytest.mark.grid_spec(shape=(101,), edges=(0, 1))
-    def test_diff_1d_deferred(self, grid_data):
+    def test_diff_deferred(self, grid_data):
         x, dx = grid_data
 
         u = x**2
@@ -35,15 +35,15 @@ def test_diff_1d_deferred(self, grid_data):
 
         assert_array_almost_equal(expected, actual)
 
-    def test_diff_1d_deferred_called_too_early(self):
+    def test_diff_deferred_called_too_early(self):
         u = np.zeros(10)
         fd = Diff(0)
         with pytest.raises(TypeError, match="Unknown axis type."):
             fd(u)
 
     @pytest.mark.default_args
     @pytest.mark.grid_spec(shape=(101,), edges=(0, 1))
-    def test_diff_1d_defaults(self, grid_data):
+    def test_diff_defaults(self, grid_data):
         x, dx = grid_data
 
         u = x**2
@@ -56,10 +56,20 @@ def test_diff_1d_defaults(self, grid_data):
         assert_array_almost_equal(expected, actual)
 
     @pytest.mark.invalid_args
-    def test_diff_1d_invalid_args(self):
+    def test_diff_invalid_args(self):
 
         with pytest.raises(ValueError, match="Dimension must be >= 0"):
             Diff(-1, 1)
 
         with pytest.raises(ValueError, match="Spacing must be > 0."):
             Diff(0, -1)
+
+    @pytest.mark.periodic
+    @pytest.mark.grid_spec(shape=[200], edges=(0, 2 * np.pi), endpoints=[False])
+    def test_diff_periodic(self, grid_data):
+        x, dx = grid_data
+        f = np.sin(x)
+
+        actual = Diff(0, dx, periodic=True, acc=4)(f)
+
+        assert_array_almost_equal(np.cos(x), actual)