chore: skpkg update

.github/workflows/build-and-publish-docs-on-dispatch.yml

@@ -0,0 +1,18 @@
+name: Build and Publish Docs on Dispatch
+
+on:
+  workflow_dispatch:
+
+jobs:
+  get-python-version:
+    uses: scikit-package/release-scripts/.github/workflows/_get-python-version-latest.yml@v0
+    with:
+      python_version: 0
+
+  docs:
+    uses: scikit-package/release-scripts/.github/workflows/_release-docs.yml@v0
+    with:
+      project: diffpy.apps
+      c_extension: false
+      headless: false
+      python_version: ${{ fromJSON(needs.get-python-version.outputs.latest_python_version) }}

.github/workflows/build-wheel-release-upload.yml

@@ -1,18 +1,76 @@
-name: Release (GitHub/PyPI) and Deploy Docs
+name: Build Wheel and Release
 
+# Trigger on tag push or manual dispatch.
+# Tag and release privilege are verified inside the reusable workflow.
 on:
   workflow_dispatch:
   push:
     tags:
-      - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
+      - "*"
+
+# ── Release modality ──────────────────────────────────────────────────────────
+# Three options are provided below. Only ONE job should be active at a time.
+# To switch: comment out the active job and uncomment your preferred option,
+# then commit the change to main before tagging a release.
+# ─────────────────────────────────────────────────────────────────────────────
 
 jobs:
+  # Option 1 (default): Release to GitHub, publish to PyPI, and deploy docs.
+  #
+  # The wheel is uploaded to PyPI so users can install with `pip install`.
+  # A GitHub release is created with the changelog as the release body, and
+  # the Sphinx documentation is rebuilt and deployed to GitHub Pages.
+  #
+  # Choose this for open-source packages distributed via PyPI and/or
+  # conda-forge where broad public availability is the goal.
   build-release:
     uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
       project: diffpy.apps
       c_extension: false
-      maintainer_GITHUB_username: sbillinge
+      maintainer_github_username: sbillinge
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}
+
+  # Option 2: Release to GitHub and deploy docs, without publishing to PyPI.
+  #
+  # A GitHub release is created and the Sphinx docs are deployed, but the
+  # wheel is not uploaded to PyPI. The source code remains publicly visible
+  # on GitHub and can be installed directly from there.
+  #
+  # Choose this when the package is public but you prefer to keep it off the
+  # default pip index — for example, if you distribute via conda-forge only,
+  # or if the package is not yet ready for a permanent PyPI presence.
+  #
+  # To use: comment out Option 1 above and uncomment the lines below.
+  # build-release-no-pypi:
+  #   uses: scikit-package/release-scripts/.github/workflows/_build-release-github-no-pypi.yml@v0
+  #   with:
+  #     project: diffpy.apps
+  #     c_extension: false
+  #     maintainer_github_username: sbillinge
+  #   secrets:
+  #     PAT_TOKEN: ${{ secrets.PAT_TOKEN }}
+
+  # Option 3: Release to GitHub with wheel, license, and instructions bundled
+  # as a downloadable zip attached to the GitHub release asset.
+  #
+  # The wheel is built and packaged together with INSTRUCTIONS.txt and the
+  # LICENSE file into a zip that is attached directly to the GitHub release.
+  # Users with access to the (private) repo download the zip, follow the
+  # instructions inside, and install locally with pip. No PyPI or conda-forge
+  # upload occurs, and no docs are deployed.
+  #
+  # Choose this for private or restricted packages where distribution must be
+  # controlled: only users with repo access can download the release asset,
+  # making the GitHub release itself the distribution channel.
+  #
+  # To use: comment out Option 1 above and uncomment the lines below.
+  # build-release-private:
+  #   uses: scikit-package/release-scripts/.github/workflows/_build-release-github-private-pure.yml@v0
+  #   with:
+  #     project: diffpy.apps
+  #     maintainer_github_username: sbillinge
+  #   secrets:
+  #     PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

.github/workflows/check-news-item.yml

@@ -3,7 +3,7 @@ name: Check for News
 on:
   pull_request_target:
     branches:
-      - main
+      - main # GitHub does not evaluate expressions in trigger filters; edit this value if your base branch is not main
 
 jobs:
   check-news-item:

.github/workflows/matrix-and-codecov-on-merge-to-main.yml → .github/workflows/matrix-and-codecov.yml

@@ -1,6 +1,9 @@
-name: CI
+name: Matrix and Codecov
 
 on:
+  # push:
+  #   branches:
+  #     - main
   release:
     types:
       - prereleased
@@ -14,6 +17,5 @@ jobs:
       project: diffpy.apps
       c_extension: false
       headless: false
-      python_versions: 3.12, 3.13
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -1,5 +1,5 @@
 default_language_version:
-  python: python3
+  python: python3.13
 ci:
   autofix_commit_msg: |
     [pre-commit.ci] auto fixes from pre-commit hooks
@@ -29,7 +29,7 @@ repos:
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
-    rev: 8.0.1
+    rev: 9.0.0a3
     hooks:
       - id: isort
         args: ["--profile", "black"]
@@ -57,10 +57,11 @@ repos:
       - id: prettier
         additional_dependencies:
           - "prettier@^3.2.4"
-        types: [yaml, markdown, json]
-  # ruff - An extremely fast Python linter and code formatter, written in Rust.
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.12
+  # docformatter - PEP 257 compliant docstring formatter
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.8
     hooks:
-      - id: ruff-check
-        args: [--fix, --config=pyproject.toml]
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]
+        exclude: ^tests/test_runmacro\.py$

CODE-OF-CONDUCT.rst

@@ -67,7 +67,7 @@ Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-yx2924@columbia.edu and sbillinge@ucsb.edu. All complaints will be reviewed and investigated promptly and fairly.
+sbillinge@ucsb.edu. All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the
 reporter of any incident.

cookiecutter.json

@@ -1,12 +1,12 @@
 {
   "author_names": "Yuchen Xiao, Simon Billinge",
-  "author_emails": "yx2924@columbia.edu, sbillinge@ucsb.edu",
-  "maintainer_names": "Yuchen Xiao, Simon Billinge",
-  "maintainer_emails": "yx2924@columbia.edu, sbillinge@ucsb.edu",
+  "author_emails": "xiaoyuch@msu.edu, sbillinge@ucsb.edu",
+  "maintainer_names": "Simon Billinge",
+  "maintainer_emails": "sbillinge@ucsb.edu",
   "maintainer_github_usernames": "sbillinge",
   "contributors": "Yuchen Xiao, Simon Billinge and members of the Billinge group",
-  "license_holders": "diffpy.apps contributors",
   "project_name": "diffpy.apps",
+  "license_holders": "diffpy.apps contributors",
   "github_username_or_orgname": "diffpy",
   "github_repo_name": "diffpy.apps",
   "conda_pypi_package_dist_name": "diffpy.apps",

docs/make.bat

@@ -1,36 +1,36 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-set SPHINXPROJ=PackagingScientificPython
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=PackagingScientificPython
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/source/index.rst

@@ -21,7 +21,7 @@ To get started, please visit the :ref:`Getting started <getting-started>` page.
 Authors
 =======
 
-``diffpy.apps`` is developed by Yuchen Xiao, Simon Billinge and members of the Billinge group. This project is maintained by Yuchen Xiao and Simon Billinge. For a detailed list of contributors see
+``diffpy.apps`` is developed by Yuchen Xiao, Simon Billinge and members of the Billinge group. This project is maintained by Simon Billinge. For a detailed list of contributors see
 https://github.com/diffpy/diffpy.apps/graphs/contributors.
 
 ============

news/skpkg-update.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added: scikit-package update this repo.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -6,11 +6,10 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.apps"
 dynamic=['version', 'dependencies']
 authors = [
-  {name='Yuchen Xiao', email='yx2924@columbia.edu'},
+  {name='Yuchen Xiao', email='xiaoyuch@msu.edu'},
   {name='Simon Billinge', email='sbillinge@ucsb.edu'},
 ]
 maintainers = [
-  {name='Yuchen Xiao', email='yx2924@columbia.edu'},
   {name='Simon Billinge', email='sbillinge@ucsb.edu'},
 ]
 description = "User applications to help with tasks using diffpy packages"

src/diffpy/__init__.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2026 diffpy.apps contributors.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.apps/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################

src/diffpy/apps/pdfadapter.py

@@ -202,7 +202,6 @@ def initialize_recipe(
         delta1 and delta2 variables, and structure parameters
         constrained by the space group.
         """
-
         recipe = FitRecipe()
         recipe.add_contribution(self.contribution)
         qdamp = recipe.create_new_variable("qdamp", fixed=False, value=0.04)

src/diffpy/apps/refinebase/parametric_model.py

@@ -199,8 +199,7 @@ def residual(self):
 
 class ParametricModelFunction(ParametricModel):
     def __init__(self, name, function, argnames=None):
-        """
-        Initialize a ParametricModelFunction instance.
+        """Initialize a ParametricModelFunction instance.
 
         function can be either a callable or a string representing
         the pre-defined function.
@@ -254,8 +253,7 @@ def __init__(
         finite=False,
         run_parallel=True,
     ):
-        """
-        Create a ParametricModelPDF instance from a structure object.
+        """Create a ParametricModelPDF instance from a structure object.
 
         structure can be a raw diffpy.structure/pyobjcryst structure, or
         an existing DiffpyStructureParSet/ObjCrystCrystalParSet phase
@@ -615,10 +613,11 @@ def create_pdf_model_from_code(
     finite=False,
     run_parallel=True,
 ):
-    """Create a ParametricModelPDF by executing code that builds a structure.
+    """Create a ParametricModelPDF by executing code that builds a
+    structure.
 
-    The code must assign the structure/crystal object to a variable named
-    structure_name (default "structure") in its local namespace.
+    The code must assign the structure/crystal object to a variable
+    named structure_name (default "structure") in its local namespace.
     """
     local_namespace = {}
     exec(code, global_namespace, local_namespace)