skpkg: use package update to run skpkg on files

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -11,12 +11,13 @@ assignees: ""
 - [ ] 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.
-- [ ] 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:
 
@@ -34,7 +35,7 @@ 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.
 

.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.srreal
+      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:
-  release:
+  # 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.srreal
       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.srreal
+  #     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.srreal
+  #     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

@@ -1,9 +1,9 @@
-name: CI
+name: Matrix and Codecov
 
 on:
-  push:
-    branches:
-      - main
+  # push:
+  #   branches:
+  #     - main
   release:
     types:
       - prereleased

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.

README.rst

@@ -25,6 +25,7 @@
         :target: https://anaconda.org/conda-forge/diffpy.srreal
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.srreal/pulls
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.srreal
         :target: https://pypi.org/project/diffpy.srreal/
@@ -111,6 +112,19 @@ and run the following ::
 
         pip install .
 
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.srreal --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.srreal; print(diffpy.srreal.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.srreal -h
+
 Getting Started
 ---------------
 
@@ -149,7 +163,7 @@ Before contributing, please read our `Code of Conduct <https://github.com/diffpy
 Contact
 -------
 
-For more information on diffpy.srreal please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at sb2896@columbia.edu.
+For more information on diffpy.srreal please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainers ``Simon Billinge(sbillinge@ucsb.edu)``.
 
 Acknowledgements
 ----------------

cookiecutter.json

@@ -0,0 +1,20 @@
+{
+  "author_names": "Simon Billinge",
+  "author_emails": "sbillinge@ucsb.edu",
+  "maintainer_names": "Simon Billinge",
+  "maintainer_emails": "sbillinge@ucsb.edu",
+  "maintainer_github_usernames": "sbillinge",
+  "contributors": "Billinge Group members and community contributors",
+  "license_holders": "The Trustees of Columbia University in the City of New York",
+  "project_name": "diffpy.srreal",
+  "github_username_or_orgname": "diffpy",
+  "github_repo_name": "diffpy.srreal",
+  "conda_pypi_package_dist_name": "diffpy.srreal",
+  "package_dir_name": "diffpy.srreal",
+  "project_short_description": "Calculators for PDF, bond valence sum, and other quantities based on atom pair interaction.",
+  "project_keywords": "PDF, BVS, atom, overlap, calculator, real-space",
+  "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

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# diffpy.srreal documentation build configuration file, created by
+# diffpy.srreal documentation build configuration file, created by  # noqa: E501
 # sphinx-quickstart on Thu Jan 30 15:49:41 2014.
 #
 # This file is execfile()d with the current directory set to its
@@ -26,7 +26,7 @@
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
-# documentation root, use Path().resolve() to make it absolute, like shown here.
+# documentation root, use Path().resolve() to make it absolute, like shown here.  # noqa: E501
 # sys.path.insert(0, str(Path(".").resolve()))
 sys.path.insert(0, str(Path("../..").resolve()))
 sys.path.insert(0, str(Path("../../src").resolve()))
@@ -50,7 +50,7 @@
     "sphinx.ext.intersphinx",
     "sphinx_rtd_theme",
     "sphinx_copybutton",
-    "m2r",
+    "m2r2",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -319,7 +319,4 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {
-    "numpy": ("https://numpy.org/doc/stable/", None),
-    "python": ("https://docs.python.org/3", None),
-}
+# intersphinx_mapping = {'http://docs.python.org/': None}

docs/source/index.rst

@@ -9,6 +9,12 @@
 | Software version |release|
 | Last updated |today|.
 
+===============
+Getting started
+===============
+
+Welcome to the ``diffpy.srreal`` documentation!
+
 The diffpy.srreal package provides calculators for atomic pair distribution
 function (PDF), bond valence sums (BVS), atom overlaps for a hard-sphere
 model, bond distances and directions up to specified maximum distance.   The
@@ -43,11 +49,11 @@ pairs, by defining only the function that processes atom-pair contributions.
 Authors
 =======
 
-diffpy.srreal is developed by members of the Billinge Group at
+``diffpy.srreal`` 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.
 
-For a detailed list of contributors see
+This project is maintained by Simon Billinge. For a detailed list of contributors see
 https://github.com/diffpy/diffpy.srreal/graphs/contributors.
 
 Reference
@@ -76,12 +82,12 @@ Acknowledgements
 Table of contents
 =================
 .. toctree::
-   :titlesonly:
+   :maxdepth: 2
 
-   license
-   release
    examples
    Package API <api/diffpy.srreal>
+   release
+   license
 
 =======
 Indices

docs/source/license.rst

@@ -22,7 +22,7 @@ Copyright (c) 2008-2012, The Trustees of Columbia University in the City of New
 
 Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National Laboratory
 
-Copyright (c) 2025, The Trustees of Columbia University in the City of New York.
+Copyright (c) 2025-2026, The Trustees of Columbia University in the City of New York.
 All rights reserved.
 
 The "DiffPy-CMI" is distributed subject to the following license conditions:

news/package-update.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Add support for python 3.14 and remove support for python 3.11
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -1,20 +1,20 @@
 [build-system]
-requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0", "numpy"]
+requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "diffpy.srreal"
 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 = "Calculators for PDF, bond valence sum, and other quantities based on atom pair interaction."
 keywords = ['PDF', 'BVS', 'atom', 'overlap', 'calculator', 'real-space']
 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',
 ]
@@ -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-srreal = "diffpy.srreal.srreal_app:main"
+
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}
 

requirements/docs.txt

@@ -2,4 +2,4 @@ sphinx
 sphinx_rtd_theme
 sphinx-copybutton
 doctr
-m2r
+m2r2