Merge pull request #369 from stevenhua0320/scikit-package-1

sbillinge · web-flow · commit 64ad577850cc · 2025-12-18T13:32:10.000-05:00
scikit:recut diffpy.utils using latest scikit-package.
diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md b/.github/ISSUE_TEMPLATE/release_checklist.md
@@ -34,7 +34,7 @@ Please let the maintainer know that all checks are done and the package is ready
 <!-- After the maintainer releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
 
 - [ ] Ensure that the full release has appeared on PyPI successfully.
-- [ ] New package dependencies listed in `conda.txt` and `test.txt` are added to `meta.yaml` in the feedstock.
+- [ ] New package dependencies listed in `conda.txt` and `tests.txt` are added to `meta.yaml` in the feedstock.
 - [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions.
 - [ ] Tag the maintainer for conda-forge release.
 
diff --git a/.github/workflows/build-wheel-release-upload.yml b/.github/workflows/build-wheel-release-upload.yml
@@ -7,7 +7,7 @@ on:
       - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
 
 jobs:
-  release:
+  build-release:
     uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
       project: diffpy.utils
diff --git a/README.rst b/README.rst
@@ -25,6 +25,7 @@
         :target: https://anaconda.org/conda-forge/diffpy.utils
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.utils/pulls
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.utils
         :target: https://pypi.org/project/diffpy.utils/
@@ -35,8 +36,7 @@
 .. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
         :target: https://github.com/diffpy/diffpy.utils/issues
 
-diffpy.utils Package
-========================================================================
+Shared utilities for diffpy packages.
 
 General utilities for analyzing diffraction data
 
diff --git a/cookiecutter.json b/cookiecutter.json
@@ -0,0 +1,18 @@
+{
+  "maintainer_name": "Simon Billinge",
+  "maintainer_email": "sb2896@columbia.edu",
+  "maintainer_github_username": "sbillinge",
+  "contributors": "Timur Davis, Chris Farrow, Pavol Juhas",
+  "license_holders": "The Trustees of Columbia University in the City of New York",
+  "project_name": "diffpy.utils",
+  "github_username_or_orgname": "diffpy",
+  "github_repo_name": "diffpy.utils",
+  "conda_pypi_package_dist_name": "diffpy.utils",
+  "package_dir_name": "diffpy.utils",
+  "project_short_description": "Shared utilities for diffpy packages.",
+  "project_keywords": "text data parsers, wx grid, diffraction objects",
+  "minimum_supported_python_version": "3.11",
+  "maximum_supported_python_version": "3.13",
+  "project_needs_c_code_compiled": "No",
+  "project_has_gui_tests": "No"
+}
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -6,7 +6,7 @@
 
 diffpy.utils - General utilities for analyzing diffraction data
 
-| Software version |release|.
+| Software version |release|
 | Last updated |today|.
 
 The diffpy.utils package provides a number of functions and classes designed to help
@@ -33,7 +33,7 @@ Illustrations of when and how one would use various diffpy.utils functions.
 Authors
 =======
 
-diffpy.utils is developed by members of the Billinge Group at
+``diffpy.utils`` is developed by members of the Billinge Group at
 Columbia University and at Brookhaven National Laboratory including
 Pavol Juhás, Christopher L. Farrow, Simon J. L. Billinge, Andrew Yang,
 with contributions from many Billinge Group members and
diff --git a/news/scikit-package.rst b/news/scikit-package.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* No News Added: recut diffpy.utils using latest scikit-package
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/pyproject.toml b/pyproject.toml
@@ -48,6 +48,9 @@ include = ["*"]  # package names should match these glob patterns (["*"] by defa
 exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
+[project.scripts]
+diffpy-utils = "diffpy.utils_app:main"
+
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}
 
@@ -56,6 +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?$'
diff --git a/src/diffpy/utils/_deprecator.py b/src/diffpy/utils/_deprecator.py
@@ -11,8 +11,8 @@
 
 
 def deprecated(message, *, category=DeprecationWarning, stacklevel=1):
-    """Deprecation decorator for functions and classes that is compatible with
-    Python versions prior to 3.13.
+    """Deprecation decorator for functions and classes that is
+    compatible with Python versions prior to 3.13.
 
     Examples
     --------
diff --git a/src/diffpy/utils/diffraction_objects.py b/src/diffpy/utils/diffraction_objects.py
@@ -211,8 +211,8 @@ def __eq__(self, other):
         return True
 
     def __add__(self, other):
-        """Add a scalar value or another DiffractionObject to the yarray of the
-        DiffractionObject.
+        """Add a scalar value or another DiffractionObject to the yarray
+        of the DiffractionObject.
 
         Parameters
         ----------
@@ -262,8 +262,8 @@ def __add__(self, other):
     __radd__ = __add__
 
     def __sub__(self, other):
-        """Subtract scalar value or another DiffractionObject to the yarray of
-        the DiffractionObject.
+        """Subtract scalar value or another DiffractionObject to the
+        yarray of the DiffractionObject.
 
         This method behaves similarly to the `__add__` method, but performs
         subtraction instead of addition. For details on parameters, returns
@@ -290,8 +290,8 @@ def __sub__(self, other):
     __rsub__ = __sub__
 
     def __mul__(self, other):
-        """Multiply a scalar value or another DiffractionObject with the yarray
-        of this DiffractionObject.
+        """Multiply a scalar value or another DiffractionObject with the
+        yarray of this DiffractionObject.
 
         This method behaves similarly to the `__add__` method, but performs
         multiplication instead of addition. For details on parameters,
@@ -318,8 +318,8 @@ def __mul__(self, other):
     __rmul__ = __mul__
 
     def __truediv__(self, other):
-        """Divide the yarray of this DiffractionObject by a scalar value or
-        another DiffractionObject.
+        """Divide the yarray of this DiffractionObject by a scalar value
+        or another DiffractionObject.
 
         This method behaves similarly to the `__add__` method, but performs
         division instead of addition. For details on parameters, returns,
@@ -474,7 +474,8 @@ def _get_original_array(self):
             return self.on_d(), "d"
 
     def on_q(self):
-        """Return the tuple of two 1D numpy arrays containing q and y data.
+        """Return the tuple of two 1D numpy arrays containing q and y
+        data.
 
         Returns
         -------
@@ -484,7 +485,8 @@ def on_q(self):
         return [self.all_arrays[:, 1], self.all_arrays[:, 0]]
 
     def on_tth(self):
-        """Return the tuple of two 1D numpy arrays containing tth and y data.
+        """Return the tuple of two 1D numpy arrays containing tth and y
+        data.
 
         Returns
         -------
@@ -494,7 +496,8 @@ def on_tth(self):
         return [self.all_arrays[:, 2], self.all_arrays[:, 0]]
 
     def on_d(self):
-        """Return the tuple of two 1D numpy arrays containing d and y data.
+        """Return the tuple of two 1D numpy arrays containing d and y
+        data.
 
         Returns
         -------
@@ -506,8 +509,8 @@ def on_d(self):
     def scale_to(
         self, target_diff_object, q=None, tth=None, d=None, offset=None
     ):
-        """Return a new diffraction object which is the current object but
-        rescaled in y to the target.
+        """Return a new diffraction object which is the current object
+        but rescaled in y to the target.
 
         By default, if `q`, `tth`, or `d` are not provided, scaling is
         based on the max intensity from each object. Otherwise, y-value in
@@ -568,7 +571,8 @@ def scale_to(
         return scaled_do
 
     def on_xtype(self, xtype):
-        """Return a tuple of two 1D numpy arrays containing x and y data.
+        """Return a tuple of two 1D numpy arrays containing x and y
+        data.
 
         Parameters
         ----------
@@ -597,8 +601,9 @@ def on_xtype(self, xtype):
             raise ValueError(_xtype_wmsg(xtype))
 
     def dump(self, filepath, xtype=None):
-        """Dump the xarray and yarray of the diffraction object to a two-column
-        file, with the associated information included in the header.
+        """Dump the xarray and yarray of the diffraction object to a
+        two-column file, with the associated information included in the
+        header.
 
         Parameters
         ----------
diff --git a/src/diffpy/utils/parsers/serialization.py b/src/diffpy/utils/parsers/serialization.py
@@ -33,8 +33,9 @@ def serialize_data(
     show_path=True,
     serial_file=None,
 ):
-    """Serialize file data into a dictionary. Can also save dictionary into a
-    serial language file. Dictionary is formatted as {filename: data}.
+    """Serialize file data into a dictionary. Can also save dictionary
+    into a serial language file. Dictionary is formatted as {filename:
+    data}.
 
     Requires hdata and data_table (can be generated by loadData).
 
diff --git a/src/diffpy/utils/resampler.py b/src/diffpy/utils/resampler.py
@@ -80,8 +80,8 @@ def wsinterp(x, xp, fp, left=None, right=None):
 
 
 def nsinterp(xp, fp, qmin=0, qmax=25, left=None, right=None):
-    """One-dimensional Whittaker-Shannon interpolation onto the Nyquist-Shannon
-    grid.
+    """One-dimensional Whittaker-Shannon interpolation onto the Nyquist-
+    Shannon grid.
 
     Takes a band-limited function fp and original grid xp and resamples fp on
     the NS grid. Uses the minimum number of points N required by the Nyquist
diff --git a/src/diffpy/utils/tools.py b/src/diffpy/utils/tools.py
@@ -51,8 +51,8 @@ def _load_config(file_path):
 
 
 def get_user_info(owner_name=None, owner_email=None, owner_orcid=None):
-    """Get name, email, and ORCID of the owner/user from various sources and
-    return it as a metadata dictionary.
+    """Get name, email, and ORCID of the owner/user from various sources
+    and return it as a metadata dictionary.
 
     The function looks for information in JSON configuration files named
     ``diffpyconfig.json``. These can be in the user's home directory and in
@@ -109,8 +109,8 @@ def get_user_info(owner_name=None, owner_email=None, owner_orcid=None):
 
 
 def check_and_build_global_config(skip_config_creation=False):
-    """Check for a global diffpu config file in user's home directory and
-    creates one if it is missing.
+    """Check for a global diffpu config file in user's home directory
+    and creates one if it is missing.
 
     The file it looks for is called diffpyconfig.json.  This can contain
     anything in json format, but minimally contains information about the
@@ -234,7 +234,8 @@ def get_density_from_cloud(sample_composition, mp_token=""):
 def compute_mu_using_xraydb(
     sample_composition, energy, sample_mass_density=None, packing_fraction=None
 ):
-    """Compute the attenuation coefficient (mu) using the XrayDB database.
+    """Compute the attenuation coefficient (mu) using the XrayDB
+    database.
 
     Computes mu based on the sample composition and energy.
     User should provide a sample mass density or a packing fraction.
@@ -287,8 +288,8 @@ def compute_mu_using_xraydb(
 
 
 def _top_hat(z, half_slit_width):
-    """Create a top-hat function, return 1.0 for values within the specified
-    slit width and 0 otherwise."""
+    """Create a top-hat function, return 1.0 for values within the
+    specified slit width and 0 otherwise."""
     return np.where((z >= -half_slit_width) & (z <= half_slit_width), 1.0, 0.0)
 
 
@@ -319,9 +320,10 @@ def _model_function(z, diameter, z0, I0, mud, slope):
 
 
 def _extend_z_and_convolve(z, diameter, half_slit_width, z0, I0, mud, slope):
-    """Extend z values and I values for padding (so that we don't have tails in
-    convolution), then perform convolution (note that the convolved I values
-    are the same as modeled I values if slit width is close to 0)"""
+    """Extend z values and I values for padding (so that we don't have
+    tails in convolution), then perform convolution (note that the
+    convolved I values are the same as modeled I values if slit width is
+    close to 0)"""
     n_points = len(z)
     z_left_pad = np.linspace(
         z.min() - n_points * (z[1] - z[0]), z.min(), n_points
@@ -342,8 +344,8 @@ def _extend_z_and_convolve(z, diameter, half_slit_width, z0, I0, mud, slope):
 
 def _objective_function(params, z, observed_data):
     """Compute the objective function for fitting a model to the
-    observed/experimental data by minimizing the sum of squared residuals
-    between the observed data and the convolved model data."""
+    observed/experimental data by minimizing the sum of squared
+    residuals between the observed data and the convolved model data."""
     diameter, half_slit_width, z0, I0, mud, slope = params
     convolved_model_data = _extend_z_and_convolve(
         z, diameter, half_slit_width, z0, I0, mud, slope
@@ -353,7 +355,8 @@ def _objective_function(params, z, observed_data):
 
 
 def _compute_single_mud(z_data, I_data):
-    """Perform dual annealing optimization and extract the parameters."""
+    """Perform dual annealing optimization and extract the
+    parameters."""
     bounds = [
         (
             1e-5,
@@ -382,8 +385,8 @@ def _compute_single_mud(z_data, I_data):
 
 
 def compute_mud(filepath):
-    """Compute the best-fit mu*D value from a z-scan file, removing the sample
-    holder effect.
+    """Compute the best-fit mu*D value from a z-scan file, removing the
+    sample holder effect.
 
     This function loads z-scan data and fits it to a model
     that convolves a top-hat function with I = I0 * e^{-mu * l}.
diff --git a/src/diffpy/utils/transforms.py b/src/diffpy/utils/transforms.py
@@ -76,7 +76,8 @@ def q_to_tth(q, wavelength):
 
 
 def tth_to_q(tth, wavelength):
-    r"""Helper function to convert two-theta to q on independent variable axis.
+    r"""Helper function to convert two-theta to q on independent variable
+    axis.
 
     If wavelength is missing, returns independent variable axis as integer
     indexes.
@@ -124,8 +125,8 @@ def tth_to_q(tth, wavelength):
 
 
 def q_to_d(q):
-    r"""Helper function to convert q to d on independent variable axis, using
-    :math:`d = \frac{2 \pi}{q}`.
+    r"""Helper function to convert q to d on independent variable axis,
+    using :math:`d = \frac{2 \pi}{q}`.
 
     Parameters
     ----------
@@ -144,7 +145,8 @@ def q_to_d(q):
 
 
 def tth_to_d(tth, wavelength):
-    r"""Helper function to convert two-theta to d on independent variable axis.
+    r"""Helper function to convert two-theta to d on independent variable
+    axis.
 
     The formula is ..
     math:: d = \frac{\lambda}{2 \sin\left(\frac{2\theta}{2}\right)}.
@@ -178,7 +180,8 @@ def tth_to_d(tth, wavelength):
 
 
 def d_to_q(d):
-    r"""Helper function to convert q to d using :math:`d = \frac{2 \pi}{q}`.
+    r"""Helper function to convert q to d using :math:`d = \frac{2
+    \pi}{q}`.
 
     Parameters
     ----------
@@ -197,7 +200,8 @@ def d_to_q(d):
 
 
 def d_to_tth(d, wavelength):
-    r"""Helper function to convert d to two-theta on independent variable axis.
+    r"""Helper function to convert d to two-theta on independent variable
+    axis.
 
     The formula is ..
     math:: 2\theta = 2 \arcsin\left(\frac{\lambda}{2d}\right).
diff --git a/src/diffpy/utils/utils_app.py b/src/diffpy/utils/utils_app.py
diff --git a/src/diffpy/utils/version.py b/src/diffpy/utils/version.py
diff --git a/src/diffpy/utils/wx/gridutils.py b/src/diffpy/utils/wx/gridutils.py
