skpkg: Update project 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.srxplanargui
+      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.srxplanargui
       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.srxplanargui
+  #     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.srxplanargui
+  #     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.srxplanargui
+      c_extension: false
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

AUTHORS.rst

@@ -3,7 +3,7 @@ Authors
 
 Xiaohao Yang
 
-Billinge Group members
+Billinge Group members and the DiffPy Team
 
 Contributors
 ------------

CHANGELOG.rst

@@ -12,4 +12,3 @@ Release notes
 * Change "diffpy.srxplanargui" from python 2 to python 3 architecture.
 * Support ``scikit-package`` Level 5 standard (https://scikit-package.github.io/scikit-package/).
 * Change documentation for diffpy.srxplanargui to successfully display.
-

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

@@ -1,6 +1,7 @@
 BSD 3-Clause License
 
 Copyright (c) 2009-2025, The Trustees of Columbia University in the City of New York.
+Copyright (c) 2026, The DiffPy Team.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.rst

@@ -38,7 +38,9 @@
 
 xPDFsuite, a software for PDF transformation and visualization.
 
-GUI for diffpy.srxplanar
+GUI for diffpy.srxplanar; subpart for xPDFsuite, a software for PDF transformation and visualization
+
+For more information about the diffpy.srxplanargui library, please consult our `online documentation <https://diffpy.github.io/diffpy.srxplanargui>`_.
 
 Citation
 --------
@@ -129,7 +131,7 @@ Before contributing, please read our `Code of Conduct <https://github.com/diffpy
 Contact
 -------
 
-For more information on diffpy.srxplanargui please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at sb2896@columbia.edu.
+For more information on diffpy.srxplanargui please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainers ``Simon Billinge(sbillinge@ucsb.edu)``.
 
 Acknowledgements
 ----------------

cookiecutter.json

@@ -1,15 +1,17 @@
 {
-  "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": "Xiaohao Yang and Billinge Group members and the DiffPy Team",
   "project_name": "diffpy.srxplanargui",
+  "license_holders": "The DiffPy Team",
   "github_username_or_orgname": "diffpy",
   "github_repo_name": "diffpy.srxplanargui",
   "conda_pypi_package_dist_name": "diffpy.srxplanargui",
   "package_dir_name": "diffpy.srxplanargui",
-  "project_short_description": "xPDFsuite, a software for PDF transformation and visualization.",
+  "project_short_description": "GUI for diffpy.srxplanar; subpart for xPDFsuite",
   "project_keywords": "diffpy, pdf, data interpretation",
   "minimum_supported_python_version": "3.11",
   "maximum_supported_python_version": "3.13",

docs/source/conf.py

@@ -32,7 +32,7 @@
 sys.path.insert(0, str(Path("../../src").resolve()))
 
 # abbreviations
-ab_authors = "Rundong Hua, Simon Billinge, Billinge Group members"
+ab_authors = "Billinge Group members and the DiffPy Team"
 
 # -- 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.

docs/source/index.rst

@@ -4,7 +4,8 @@
 
 .. |title| replace:: diffpy.srxplanargui documentation
 
-``diffpy.srxplanargui`` - xPDFsuite, a software for PDF transformation and visualization.
+``diffpy.srxplanargui`` - GUI for diffpy.srxplanar; subpart for xPDFsuite,
+a software for PDF transformation and visualization
 
 | Software version |release|
 | Last updated |today|.
@@ -22,7 +23,7 @@ for getting the whole xpdfsuite package and download the package there.
 Authors
 =======
 
-``diffpy.srxplanargui`` is developed by Xiaohao Yang, Simon Billinge, Billinge Group members. The maintainer for this project is Simon Billinge. For a detailed list of contributors see
+``diffpy.srxplanargui`` is developed by Xiaohao Yang, Simon Billinge, Billinge Group members, and the DiffPy Team. This project is maintained by Simon Billinge. For a detailed list of contributors see
 https://github.com/diffpy/diffpy.srxplanargui/graphs/contributors.
 
 ============

docs/source/license.rst

@@ -10,6 +10,7 @@ OPEN SOURCE LICENSE AGREEMENT
 BSD 3-Clause License
 
 Copyright (c) 2025, The Trustees of Columbia University in the City of New York.
+Copyright (c) 2026, The DiffPy Team.
 All Rights Reserved.
 
 Redistribution and use in source and binary forms, with or without

news/update-scikit-package.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Update package scaffolding to the latest ``scikit-package`` standard.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -6,12 +6,15 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.srxplanargui"
 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 = "xPDFsuite, a software for PDF transformation and visualization."
+description = """
+GUI for diffpy.srxplanar; subpart for xPDFsuite, a software \
+for PDF transformation and visualization\
+"""
 keywords = ['diffpy', 'pdf', 'data interpretation']
 readme = "README.rst"
 requires-python = ">=3.11, <3.14"

requirements/docs.txt

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

src/diffpy/__init__.py

@@ -2,9 +2,11 @@
 ##############################################################################
 #
 # (c) 2012-2025 The Trustees of Columbia University in the City of New York.
+# (c) 2026 The DiffPy Team.
 # All rights reserved.
 #
-# File coded by: Xiaohao Yang and Billinge Group members.
+# File coded by: Xiaohao Yang,
+# Billinge Group members, and community contributors.
 #
 # See GitHub contributions for a more detailed list of contributors.
 # https://github.com/diffpy/diffpy.srxplanargui/graphs/contributors

src/diffpy/srxplanargui/__init__.py

@@ -2,17 +2,19 @@
 ##############################################################################
 #
 # (c) 2012-2025 The Trustees of Columbia University in the City of New York.
+# (c) 2026 The DiffPy Team.
 # All rights reserved.
 #
-# File coded by: Xiaohao Yang, Billinge Group members.
+# File coded by: Xiaohao Yang, Billinge Group members and the DiffPy Team.
 #
 # See GitHub contributions for a more detailed list of contributors.
 # https://github.com/diffpy/diffpy.srxplanargui/graphs/contributors
 #
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-"""XPDFsuite, a software for PDF transformation and visualization."""
+"""GUI for diffpy.srxplanar; subpart for xPDFsuite, a software for PDF
+transformation and visualization."""
 
 # package version
 from diffpy.srxplanargui.version import __version__  # noqa

src/diffpy/srxplanargui/srxplanargui_app.py

@@ -7,8 +7,9 @@ def main():
     parser = argparse.ArgumentParser(
         prog="diffpy.srxplanargui",
         description=(
-            "xPDFsuite, a software for PDF transformation"
-            " and visualization.\n\n For more information, visit: "
+            "GUI for diffpy.srxplanar; subpart for xPDFsuite,"
+            "a software for PDF transformation and visualization\n\n"
+            "For more information, visit: "
             "https://github.com/diffpy/diffpy.srxplanargui/"
         ),
         formatter_class=argparse.RawDescriptionHelpFormatter,

src/diffpy/srxplanargui/version.py

@@ -2,9 +2,10 @@
 ##############################################################################
 #
 # (c) 2012-2025 The Trustees of Columbia University in the City of New York.
+# (c) 2026 The DiffPy Team.
 # All rights reserved.
 #
-# File coded by: Xiaohao Yang, Billinge Group members.
+# File coded by: Xiaohao Yang, Billinge Group members and the DiffPy Team.
 #
 # See GitHub contributions for a more detailed list of contributors.
 # https://github.com/diffpy/diffpy.srxplanargui/graphs/contributors  # noqa: E501

tests/conftest.py

@@ -12,10 +12,7 @@ def user_filesystem(tmp_path):
     cwd_dir = base_dir / "cwd_dir"
     cwd_dir.mkdir(parents=True, exist_ok=True)
 
-    home_config_data = {
-        "username": "home_username",
-        "email": "home@email.com",
-    }
+    home_config_data = {"username": "home_username", "email": "home@email.com"}
     with open(home_dir / "diffpyconfig.json", "w") as f:
         json.dump(home_config_data, f)