skpkg: use package update to run skpkg on files

.flake8

@@ -6,7 +6,7 @@ exclude =
     __pycache__,
     build,
     dist,
-    doc/source/conf.py
+    docs/source/conf.py
 # huge loops in crystal.py
 max-line-length = 99
 # Ignore some style 'errors' produced while formatting by 'black'

.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: pyobjcryst
+      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: pyobjcryst
       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: pyobjcryst
+  #     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: pyobjcryst
+  #     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

.github/workflows/tests-on-pr.yml

@@ -2,8 +2,6 @@ name: Tests on PR
 
 on:
   pull_request:
-    branches:
-      - "**"
   workflow_dispatch:
 
 jobs:

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-DANSE.rst

@@ -4,14 +4,14 @@ LICENSE
 This program is part of the DiffPy and DANSE open-source projects
 and is available subject to the conditions and terms laid out below.
 
-Copyright (c) 2009-2012, The Trustees of Columbia University in
+Copyright (c) 2009-Present, The Trustees of Columbia University in
 the City of New York.  All rights reserved.
 
 For more information please visit the project web-page:
 
     http://www.diffpy.org/
 
-or email Prof. Simon Billinge at sb2896@columbia.edu
+or email Prof. Simon Billinge at sbillinge@ucsb.edu
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions

LICENSE.rst

@@ -15,7 +15,7 @@ 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) 2024-2025, The Trustees of Columbia University in the City of New York.
+Copyright (c) 2024-Present, 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:

README.rst

@@ -219,7 +219,7 @@ Before contributing, please read our `Code of Conduct <https://github.com/diffpy
 Contact
 -------
 
-For more information on pyobjcryst please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at sb2896@columbia.edu.
+For more information on pyobjcryst please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at sbillinge@ucsb.edu.
 
 You can also contact Vincent Favre-Nicolin (favre@esrf.fr) if you are using pyobjcryst outside diffpy, e.g. to display structures in a notebook, refine powder patterns or solve structures using the global optimisation algorithms, etc..
 

cookiecutter.json

@@ -1,8 +1,10 @@
 {
-  "maintainer_name": "Simon J.L. Billinge group",
-  "maintainer_email": "sb2896@columbia.edu",
-  "maintainer_github_username": "sbillinge",
-  "contributors": "Billinge Group members",
+  "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 ccommunity contributors",
   "license_holders": "The Trustees of Columbia University in the City of New York",
   "project_name": "pyobjcryst",
   "github_username_or_orgname": "diffpy",
@@ -11,8 +13,8 @@
   "package_dir_name": "pyobjcryst",
   "project_short_description": "Python bindings to the ObjCryst++ library.",
   "project_keywords": "objcryst, atom structure crystallography, powder diffraction",
-  "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

@@ -72,9 +72,10 @@ def setup(app):
     "sphinx.ext.todo",
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
+    "sphinx_rtd_theme",
     "sphinx_copybutton",
     "nbsphinx",
-    "m2r",
+    "m2r2",
 ]
 
 # Add any paths that contain templates here, relative to this directory.

docs/source/index.rst

@@ -79,12 +79,12 @@ Table of contents
 .. toctree::
    :maxdepth: 2
 
-   getting-started
    Examples <examples/examples>
    Package API <api/pyobjcryst>
    release
    license
 
+=======
 Indices
 =======