skpkg: setup CI after migrating tests, src, requirements, and .github folder

.gitignore

@@ -10,6 +10,7 @@ __pycache__/
 .Python
 env/
 build/
+_build/
 develop-eggs/
 dist/
 downloads/

pyproject.toml

@@ -59,6 +59,11 @@ exclude-file = ".codespell/ignore_lines.txt"
 ignore-words = ".codespell/ignore_words.txt"
 skip = "*.cif,*.dat"
 
+[tool.docformatter]
+recursive = true
+wrap-summaries = 72
+wrap-descriptions = 72
+
 [tool.black]
 line-length = 79
 include = '\.pyi?$'

requirements/docs.txt

@@ -1,4 +1,5 @@
 sphinx
 sphinx_rtd_theme
+sphinx-copybutton
 doctr
 m2r

src/diffpy/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2022-2025 The Trustees of Columbia University in the City of New York.
+# (c) 2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.
@@ -12,11 +12,3 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-"""Blank namespace package for module diffpy."""
-
-
-from pkgutil import extend_path
-
-__path__ = extend_path(__path__, __name__)
-
-# End of file

src/diffpy/fourigui/__init__.py

@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2022-2025 The Trustees of Columbia University in the City of New York.
+# (c) 2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
-# File coded by: Billinge Group members and community contributors.
+# File coded by: Billinge Group members.
 #
 # See GitHub contributions for a more detailed list of contributors.
 # https://github.com/diffpy/diffpy.fourigui/graphs/contributors
@@ -15,7 +15,7 @@
 """Tool for visualizing 3D diffraction and PDF images."""
 
 # package version
-from diffpy.fourigui.version import __version__
+from diffpy.fourigui.version import __version__  # noqa
 
 # silence the pyflakes syntax checker
 assert __version__ or True

src/diffpy/fourigui/fourigui.py

@@ -285,10 +285,10 @@ def initUI(self):
         )  # , height=HEIGHT//2, width=WIDTH//2)
 
     def load_cube(self):
-        """Loads 3D array in h5py file format from the filename input panel 3D
-        array is expected to be a reconstructed reciprocal scattering volume
-        when executed, one slide perpendicular to the selected axis will be
-        plotted in the plot panel."""
+        """Loads 3D array in h5py file format from the filename input
+        panel 3D array is expected to be a reconstructed reciprocal
+        scattering volume when executed, one slide perpendicular to the
+        selected axis will be plotted in the plot panel."""
 
         filename = self.filename_entry.get()
         f = h5py.File(filename, "r")
@@ -397,8 +397,8 @@ def colorrange_upd(self):
         self.plot_plane()
 
     def intensity_upd_local(self):
-        """Show local intensity minimum, maximum and sum of current plotted
-        plane."""
+        """Show local intensity minimum, maximum and sum of current
+        plotted plane."""
         if self.axis.get() == 0:
             plane = self.cube[self.plane_num.get(), :, :]
         elif self.axis.get() == 1:
@@ -418,7 +418,8 @@ def intensity_upd_local(self):
         self.localnanratio["text"] = f"{round(nan_ratio, 2)}"
 
     def intensity_upd_global(self):
-        """Load global intensity minimum, maximum and sum of 3D array."""
+        """Load global intensity minimum, maximum and sum of 3D
+        array."""
         self.intensity_upd_local()
         nan_ratio = np.count_nonzero(np.isnan(self.cube)) / self.cube.size
         self.globalmax["text"] = (
@@ -433,8 +434,9 @@ def intensity_upd_global(self):
         self.globalnanratio["text"] = "{}".format(round(nan_ratio, 2))
 
     def fft(self):
-        """Fourier transform 3D array from reciprocal to real space the origin
-        of reciprocal and real space is expected to be the central voxel."""
+        """Fourier transform 3D array from reciprocal to real space the
+        origin of reciprocal and real space is expected to be the
+        central voxel."""
 
         def perform_fft(fftholder):
             fftholder = np.nan_to_num(fftholder)
@@ -487,9 +489,9 @@ def perform_fft(fftholder):
         self.intensity_upd_global()
 
     def ifft(self):
-        """Inverse Fourier transform 3D array from real to reciprocal space the
-        origin of real and reciprocal space is expected to be the central
-        voxel."""
+        """Inverse Fourier transform 3D array from real to reciprocal
+        space the origin of real and reciprocal space is expected to be
+        the central voxel."""
         if not self.cutoff.get():
             self.cube_real = self.cube
             self.cube = self.cube_reci
@@ -562,8 +564,8 @@ def applycutoff(self):
             self.intensity_upd_global()
 
     def redocutuff(self):
-        """Redo the cutoff operation depending on the current space (real or
-        reciprocal)."""
+        """Redo the cutoff operation depending on the current space
+        (real or reciprocal)."""
         if self.space.get():  # in real space
             self.cube_realcut = self.cube
             if not self.transformed:
@@ -588,8 +590,8 @@ def newcutoff(self):
         self.applycutoff()
 
     def plot_next_plane(self):
-        """Plot the next plane in the dataset, looping back to the first if at
-        the end."""
+        """Plot the next plane in the dataset, looping back to the first
+        if at the end."""
         n = self.plane_num.get()
         if n == len(self.cube[self.axis.get()]) - 1:
             n = 0
@@ -616,7 +618,8 @@ def animation(self):
         self.plot_next_plane()
 
     def multiple_funcs(*funcs):
-        """Executes multiple functions passed as arguments in sequence."""
+        """Executes multiple functions passed as arguments in
+        sequence."""
         for func in funcs:
             func
 

src/diffpy/fourigui/functions.py

@@ -0,0 +1,31 @@
+import numpy as np
+
+
+def dot_product(a, b):
+    """Compute the dot product of two vectors of any size.
+
+    Ensure that the inputs, a and b, are of the same size.
+    The supported types are "array_like" objects, which can
+    be converted to a NumPy array. Examples include lists and tuples.
+
+    Parameters
+    ----------
+    a : array_like
+        The first input vector.
+    b : array_like
+        The second input vector.
+
+    Returns
+    -------
+    float
+        The dot product of the two vectors.
+
+    Examples
+    --------
+    Compute the dot product of two lists:
+    >>> a = [1, 2, 3]
+    >>> b = [4, 5, 6]
+    >>> dot_product(a, b)
+    32.0
+    """
+    return float(np.dot(a, b))

src/diffpy/fourigui/version.py

@@ -1,13 +1,13 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2022-2025 The Trustees of Columbia University in the City of New York.
+# (c) 2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
-# File coded by: Billinge Group members and community contributors.
+# File coded by: Billinge Group members.
 #
 # See GitHub contributions for a more detailed list of contributors.
-# https://github.com/diffpy/diffpy.fourigui/graphs/contributors
+# https://github.com/diffpy/diffpy.fourigui/graphs/contributors  # noqa: E501
 #
 # See LICENSE.rst for license information.
 #

tests/test_functions.py

@@ -0,0 +1,40 @@
+import numpy as np
+import pytest
+
+from diffpy.fourigui import functions  # noqa
+
+
+def test_dot_product_2D_list():
+    a = [1, 2]
+    b = [3, 4]
+    expected = 11.0
+    actual = functions.dot_product(a, b)
+    assert actual == expected
+
+
+def test_dot_product_3D_list():
+    a = [1, 2, 3]
+    b = [4, 5, 6]
+    expected = 32.0
+    actual = functions.dot_product(a, b)
+    assert actual == expected
+
+
+@pytest.mark.parametrize(
+    "a, b, expected",
+    [
+        # Test whether the dot product function works with 2D and 3D vectors
+        # C1: lists, expect correct float output
+        ([1, 2], [3, 4], 11.0),
+        ([1, 2, 3], [4, 5, 6], 32.0),
+        # C2: tuples, expect correct float output
+        ((1, 2), (3, 4), 11.0),
+        ((1, 2, 3), (4, 5, 6), 32.0),
+        # C3: numpy arrays, expect correct float output
+        (np.array([1, 2]), np.array([3, 4]), 11.0),
+        (np.array([1, 2, 3]), np.array([4, 5, 6]), 32.0),
+    ],
+)
+def test_dot_product(a, b, expected):
+    actual = functions.dot_product(a, b)
+    assert actual == expected

tests/test_version.py

@@ -1,6 +1,6 @@
 """Unit tests for __version__.py."""
 
-import diffpy.fourigui
+import diffpy.fourigui  # noqa
 
 
 def test_package_version():