skpkg: run package update on the repository and support python 3.14 while dropping 3.11

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -1,23 +1,25 @@
----
+    ---
+
 name: Release
 about: Checklist and communication channel for PyPI and GitHub release
 title: "Ready for <version-number> PyPI/GitHub release"
 labels: "release"
 assignees: ""
+
 ---
 
 ### PyPI/GitHub rc-release preparation checklist:
 
 - [ ] All PRs/issues attached to the release are merged.
 - [ ] All the badges on the README are passing.
 - [ ] License information is verified as correct. If you are unsure, please comment below.
-- [ ] The `FALLBACK_VERSION` in `setup.py` has been updated to the latest version on PyPI.
-- [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are
-      missing), tutorials, and other human-written text is up-to-date with any changes in the code.
+- [ ] Locally rendered documentation contains all appropriate pages, tutorials, and other human-written text is up-to-date with any changes in the code.
+- [ ] All API references are included. To check this, run `conda install scikit-package` and then `package build api-doc`. Review any edits made by rerendering the docs locally.
 - [ ] Installation instructions in the README, documentation, and the website are updated.
 - [ ] Successfully run any tutorial examples or do functional testing with the latest Python version.
 - [ ] Grammar and writing quality are checked (no typos).
 - [ ] Install `pip install build twine`, run `python -m build` and `twine check dist/*` to ensure that the package can be built and is correctly formatted for PyPI release.
+- [ ] Dispatch matrix testing to test the release on all Python versions and systems. If you do not have permission to run this workflow, tag the maintainer and say `@maintainer, please dispatch matrix testing workflow`.
 
 Please tag the maintainer (e.g., @username) in the comment here when you are ready for the PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here:
 

.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.pdffit2
+      c_extension: true
+      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.pdffit2
       c_extension: true
-      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.pdffit2
+  #     c_extension: true
+  #     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.pdffit2
+  #     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.yml

@@ -0,0 +1,21 @@
+name: Matrix and Codecov
+
+on:
+  # push:
+  #   branches:
+  #     - main
+  release:
+    types:
+      - prereleased
+      - published
+  workflow_dispatch:
+
+jobs:
+  matrix-coverage:
+    uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+    with:
+      project: diffpy.pdffit2
+      c_extension: true
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

AUTHORS.rst

@@ -23,7 +23,7 @@ contributors.  This is an open-source project and we hope and expect
 that the list of contributors will expand with time.  Many thanks to
 all current and future contributors!
 
-For more information on the DiffPy project email sb2896@columbia.edu
+For more information on the DiffPy project email sbillinge@ucsb.edu
 
 DiffPy was initiated as part of the Distributed Data Analysis of Neutron
 Scattering Experiments (DANSE) project, funded by the National Science

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
-sb2896@columbia.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.

LICENSE.rst

@@ -13,7 +13,7 @@ the following paper in your publication:
         in crystals (https://stacks.iop.org/0953-8984/19/335219), *J. Phys.: Condens. Matter*, 19, 335219 (2007)
 
 Copyright 2006-2007, Board of Trustees of Michigan State University,
-Copyright 2008-2025, Board of Trustees of Columbia University in the
+Copyright 2008-2026, Board of Trustees of Columbia University in the
 city of New York.  (Copyright holder indicated in each source file).
 
 For more information please visit the project web-page:

README.rst

@@ -79,7 +79,7 @@ If you use diffpy.pdffit2 in a scientific publication, we would like you to cite
 Installation
 ------------
 
-diffpy.pdffit2 supports Python 3.11, 3.12, and 3.13.
+diffpy.pdffit2 supports Python 3.12, 3.13, and 3.14.
 
 Windows, macOS (non-Arm64), Linux
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

cookiecutter.json

@@ -1,7 +1,9 @@
 {
-  "maintainer_name": "Simon Billinge",
-  "maintainer_email": "sb2896@columbia.edu",
-  "maintainer_github_username": "sbillinge",
+  "author_names": "Simon Billinge",
+  "author_emails": "sbillinge@ucsb.edu",
+  "maintainer_names": "Simon Billinge",
+  "maintainer_emails": "sbillinge@ucsb.edu",
+  "maintainer_github_usernames": "sbillinge",
   "contributors": "Pavol Juhas, Chris Farrow, Simon Billinge, Billinge Group members",
   "license_holders": "The Trustees of Columbia University in the City of New York",
   "project_name": "diffpy.pdffit2",
@@ -11,8 +13,8 @@
   "package_dir_name": "diffpy.pdffit2",
   "project_short_description": "PDFfit2 - real space structure refinement program.",
   "project_keywords": "PDF, structure refinement",
-  "minimum_supported_python_version": "3.11",
-  "maximum_supported_python_version": "3.13",
+  "minimum_supported_python_version": "3.12",
+  "maximum_supported_python_version": "3.14",
   "project_needs_c_code_compiled": "Yes",
   "project_has_gui_tests": "No"
 }

docs/source/conf.py

@@ -52,12 +52,9 @@
     "sphinx.ext.intersphinx",
     "sphinx_rtd_theme",
     "sphinx_copybutton",
-    "m2r",
+    "m2r2",
 ]
 
-autodoc_mock_imports = [
-    "diffpy.pdffit2.pdffit2",
-]
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -80,7 +77,6 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 
-fullversion = version(project)
 # The short X.Y version.
 version = "".join(fullversion.split(".post")[:1])
 # The full version, including alpha/beta/rc tags.

docs/source/examples/Ni_refinement.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-"""Perform simple refinement of Ni structure to the experimental x-ray PDF.
+"""Perform simple refinement of Ni structure to the experimental x-ray
+PDF.
 
 Save fitted curve, refined structure and results summary.
 """

docs/source/index.rst

@@ -9,6 +9,12 @@
 | Software version |release|
 | Last updated |today|.
 
+===============
+Getting started
+===============
+
+Welcome to the ``diffpy.pdffit2`` documentation!
+
 The diffpy.pdffit2 package provides functions for the calculation and
 refinement of atomic Pair Distribution Functions (PDF) from crystal
 structure models.  It is used as a computational engine by PDFgui. All
@@ -88,7 +94,7 @@ Acknowledgements
 Table of contents
 =================
 .. toctree::
-   :titlesonly:
+   :maxdepth: 2
 
    examples
    Package API <api/diffpy.pdffit2>

pyproject.toml

@@ -6,15 +6,15 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.pdffit2"
 dynamic=['version', 'dependencies']
 authors = [
-  { name="Simon Billinge", email="sb2896@columbia.edu" },
+  {name='Simon Billinge', email='sbillinge@ucsb.edu'},
 ]
 maintainers = [
-  { name="Simon Billinge", email="sb2896@columbia.edu" },
+  {name='Simon Billinge', email='sbillinge@ucsb.edu'},
 ]
 description = "PDFfit2 - real space structure refinement program."
 keywords = ['PDF', 'structure refinement']
 readme = "README.rst"
-requires-python = ">=3.11, <3.14"
+requires-python = ">=3.12, <3.15"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
@@ -25,9 +25,9 @@ classifiers = [
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX',
         'Operating System :: Unix',
-        'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
         'Programming Language :: Python :: 3.13',
+        'Programming Language :: Python :: 3.14',
         'Topic :: Scientific/Engineering :: Physics',
         'Topic :: Scientific/Engineering :: Chemistry',
 ]
@@ -57,7 +57,12 @@ dependencies = {file = ["requirements/pip.txt"]}
 [tool.codespell]
 exclude-file = ".codespell/ignore_lines.txt"
 ignore-words = ".codespell/ignore_words.txt"
-skip = "*.cif,*.dat,*.cc,*.h"
+skip = "*.cif,*.dat"
+
+[tool.docformatter]
+recursive = true
+wrap-summaries = 72
+wrap-descriptions = 72
 
 [tool.black]
 line-length = 79

src/diffpy/__init__.py

@@ -3,7 +3,7 @@
 #
 # (c) 2008 trustees of the Michigan State University.
 # All rights reserved.
-# (c) 2025 The Trustees of Columbia University in the City of New York.
+# (c) 2025-2026 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.

src/diffpy/pdffit2/__init__.py

@@ -3,10 +3,10 @@
 #
 # (c) 2006 trustees of the Michigan State University.
 # All rights reserved.
-# (c) 2025 The Trustees of Columbia University in the City of New York.
+# (c) 2025-2026 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 and community contributors.
 #
 # See GitHub contributions for a more detailed list of contributors.
 # https://github.com/diffpy/diffpy.pdffit2/graphs/contributors

src/diffpy/pdffit2/ipy_ext.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
-"""This module defines functions within IPython session to simulate the old
-pdffit2 interactive session.
+"""This module defines functions within IPython session to simulate the
+old pdffit2 interactive session.
 
 Usage: %load_ext diffpy.pdffit2.ipy_ext
 """