skpkg: Update prokect to latest scikit-package standards

.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:
 

.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.srxplanar
+      c_extension: false
+      headless: false
+      python_version: ${{ fromJSON(needs.get-python-version.outputs.latest_python_version) }}

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

@@ -1,19 +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.srxplanar
       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.srxplanar
+  #     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.srxplanar
+  #     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
@@ -17,6 +17,5 @@ jobs:
       project: diffpy.srxplanar
       c_extension: false
       headless: false
-
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -43,3 +43,6 @@ nosetests.xml
 setup.cfg
 /diffpy/srxplanar/version.cfg
 /diffpy/confutils/version.cfg
+
+# PyCharm / IDEs
+.idea/

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
@@ -21,31 +21,31 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 26.5.1
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.3.0
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 9.0.0a3
     hooks:
       - id: isort
         args: ["--profile", "black"]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.9.1
     hooks:
       - id: nbstripout
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       - id: no-commit-to-branch
         name: Prevent Commit to Main Branch
         args: ["--branch", "main"]
         stages: [pre-commit]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.3
     hooks:
       - id: codespell
         additional_dependencies:
@@ -58,8 +58,8 @@ repos:
         additional_dependencies:
           - "prettier@^3.2.4"
   # docformatter - PEP 257 compliant docstring formatter
-  - repo: https://github.com/s-weigand/docformatter
-    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.8
     hooks:
       - id: docformatter
         additional_dependencies: [tomli]

CHANGELOG.rst

@@ -20,4 +20,3 @@ Release notes
 
 * Remove local clone of srxconfutils and replace with package from pypi
 * Removed glob of user home in load-image
-

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

@@ -2,6 +2,7 @@ BSD 3-Clause License
 
 Copyright (c) 2008-2025, The Trustees of Columbia University in the City of New York.
 Copyright (c) 1994-2014, Christoph Gohlke
+Copyright (c) 2026, Billinge Group Members and The DiffPy Team.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

MANIFEST.in

@@ -1,7 +1,6 @@
 graft src
 graft tests
 graft requirements
-graft docs/examples
 
 include AUTHORS.rst LICENSE*.rst README.rst
 

README.rst

@@ -15,8 +15,8 @@
 .. |Black| image:: https://img.shields.io/badge/code_style-black-black
         :target: https://github.com/psf/black
 
-.. |CI| image:: https://github.com/diffpy/diffpy.cmi/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
-        :target: https://github.com/diffpy/diffpy.srxplanar/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+.. |CI| image:: https://github.com/diffpy/diffpy.srxplanar/actions/workflows/matrix-and-codecov.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.srxplanar/actions/workflows/matrix-and-codecov.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.srxplanar/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.srxplanar
@@ -36,7 +36,7 @@
 .. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
         :target: https://github.com/diffpy/diffpy.srxplanar/issues
 
-This is part of xPDFsuite package.
+2D diffraction image integration using non splitting pixel algorithm
 
 diffpy.srxplanar package provides 2D diffraction image integration using
 non splitting pixel algorithm. And it can estimate and propagate statistic
@@ -118,7 +118,7 @@ Support and Contribute
 
 If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.srxplanar/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.srxplanar/pulls>`_.
 
-Feel free to fork the project. To install diffpy.srxplanar
+Feel free to fork the project and contribute. To install diffpy.srxplanar
 in a development mode, with its sources being directly used by Python
 rather than copied to a package directory, use the following in the root
 directory ::
@@ -144,7 +144,7 @@ Before contributing, please read our `Code of Conduct <https://github.com/diffpy
 Contact
 -------
 
-For more information on diffpy.srxplanar please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at sb2896@columbia.edu.
+For more information on diffpy.srxplanar please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainers ``Simon Billinge(sbillinge@ucsb.edu)``.
 
 Acknowledgements
 ----------------

cookiecutter.json

@@ -1,10 +1,12 @@
 {
-  "maintainer_name": "Simon Billinge",
-  "maintainer_email": "sb2896@columbia.edu",
-  "maintainer_github_username": "sbillinge",
-  "contributors": "Xiaohao Yang and Billinge Group members",
-  "license_holders": "The Trustees of Columbia University in the City of New York",
+  "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",
   "project_name": "diffpy.srxplanar",
+  "license_holders": "Billinge Group Members and The DiffPy Team",
   "github_username_or_orgname": "diffpy",
   "github_repo_name": "diffpy.srxplanar",
   "conda_pypi_package_dist_name": "diffpy.srxplanar",

docs/source/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# diffpy.srxplanar documentation build configuration file, created by
+# diffpy.srxplanar 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
@@ -22,17 +22,17 @@
 try:
     fullversion = version("diffpy.srxplanar")
 except Exception:
-    fullversion = "No version found. The correct version will appear in the released version."
+    fullversion = "No version found. The correct version will appear in the released version."  # noqa: E501
 
 # 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()))
 
 # abbreviations
-ab_authors = "Xiaohao Yang and Billinge Group members"
+ab_authors = "Xiaohao Yang and Billinge Group Members"
 
 # -- General configuration ------------------------------------------------
 
@@ -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.
@@ -69,7 +69,7 @@
 
 # General information about the project.
 project = "diffpy.srxplanar"
-copyright = "%Y, The Trustees of Columbia University in the City of New York"
+copyright = "%Y, Billinge Group Members and The DiffPy Team"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

docs/source/index.rst

@@ -4,25 +4,32 @@
 
 .. |title| replace:: diffpy.srxplanar documentation
 
-| Software version |release|
-| Last updated |today|.
-
-diffpy.srxplanar package provides 2D diffraction image integration using
-non splitting pixel algorithm. And it can estimate and propagate statistic
-uncertainty of raw counts and integrated intensity. If you are using this
-software. If you use this program to do productive scientific research that
+``diffpy.srxplanar`` - The diffpy.srxplanar package provides 2D diffraction image integration using
+non splitting pixel algorithm. It can also estimate and propagate statistic
+uncertainty of raw counts and integrated intensity. If you use this program to do productive scientific research that
 leads to publication, we kindly ask that you acknowledge use of the program
 by citing the following paper in your publication:
 
     Xiaohao Yang, Pavol Juhas, Simon J. L. Billinge, On the estimation of
     statistical uncertainties on powder diffraction and small angle
     scattering data from 2-D x-ray detectors, arXiv:1309.3614
 
+| Software version |release|
+| Last updated |today|.
+
+===============
+Getting started
+===============
+
+Welcome to the ``diffpy.srxplanar`` documentation!
+
+To get started, please visit the :ref:`Getting started <getting-started>` page.
+
 =======
 Authors
 =======
 
-``diffpy.srxplanar`` is developed by Xiaohao Yang and Billinge Group members. The maintainer for this project is Simon Billinge. For a detailed list of contributors see
+``diffpy.srxplanar`` is developed by Xiaohao Yang and Billinge Group Members. This project is maintained by Simon Billinge. For a detailed list of contributors see
 https://github.com/diffpy/diffpy.srxplanar/graphs/contributors.
 
 ============
@@ -44,9 +51,9 @@ Table of contents
 .. toctree::
    :maxdepth: 2
 
+   getting-started
    Package API <api/diffpy.srxplanar>
-   Modules <api/modules>
-   Release notes <release>
+   release
    license
 
 =======