Merge pull request #58 from cadenmyers13/skpkg-migration

sbillinge · web-flow · commit 724018c20f18 · 2025-06-25T20:01:45.000-04:00
skpkg: final skpkg migration of files
diff --git a/.codespell/ignore_words.txt b/.codespell/ignore_words.txt
@@ -4,9 +4,6 @@
 ;; abbreviation for "materials" often used in a journal title
 mater
 
-;; alternative use of socioeconomic
-socio-economic
-
 ;; Frobenius norm used in np.linalg.norm
 fro
 
diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md b/.github/ISSUE_TEMPLATE/release_checklist.md
@@ -13,30 +13,30 @@ assignees: ""
 - [ ] 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.
-- [ ] Installation instructions in the README, documentation, and the website (e.g., diffpy.org) are updated.
+- [ ] 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.
 
-Please mention @sbillinge here when you are ready for PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here:
+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:
 
 ### PyPI/GitHub full-release preparation checklist:
 
 - [ ] Create a new conda environment and install the rc from PyPI (`pip install <package-name>==??`)
 - [ ] License information on PyPI is correct.
-- [ ] Docs are deployed successfully to `https://www.diffpy.org/<package-name>`.
+- [ ] Docs are deployed successfully to `https://<github-username-or-orgname>/<package-name>`.
 - [ ] Successfully run all tests, tutorial examples or do functional testing.
 
-Please let @sbillinge know that all checks are done and the package is ready for full release.
+Please let the maintainer know that all checks are done and the package is ready for full release.
 
 ### conda-forge release preparation checklist:
 
-<!-- After @sbillinge releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
+<!-- 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.
-- [ ] Close any open issues on the feedstock. Reach out to @bobleesj if you have questions.
-- [ ] Tag @sbillinge and @bobleesj for conda-forge release.
+- [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions.
+- [ ] Tag the maintainer for conda-forge release.
 
 ### Post-release checklist
 
diff --git a/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md b/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md
@@ -0,0 +1,15 @@
+### What problem does this PR address?
+
+<!-- Provide a brief overview and link to the issue. Attach outputs, including screenshots (before/after), if helpful for the reviewer. -->
+
+### What should the reviewer(s) do?
+
+<!-- Merge the code, provide feedback, initiate a discussion, etc. -->
+
+<!--
+Use the following checklist items when applicable (select only what applies):
+- [ ] This PR introduces a public-facing change (e.g., figures, CLI input/output, API).
+    - [ ] Documentation (e.g., tutorials, examples, README) has been updated.
+    - [ ] A tracking issue or plan to update documentation exists.
+- [ ] This PR affects internal functionality only (no user-facing change).
+-->
diff --git a/.github/workflows/build-wheel-release-upload.yml b/.github/workflows/build-wheel-release-upload.yml
@@ -8,11 +8,11 @@ on:
 
 jobs:
   release:
-    uses: Billingegroup/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
       project: diffpy.srreal
       c_extension: true
-      github_admin_username: sbillinge
+      maintainer_GITHUB_username: sbillinge
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}
diff --git a/.github/workflows/check-news-item.yml b/.github/workflows/check-news-item.yml
@@ -7,6 +7,6 @@ on:
 
 jobs:
   check-news-item:
-    uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
       project: diffpy.srreal
diff --git a/.github/workflows/matrix-and-codecov-on-merge-to-main.yml b/.github/workflows/matrix-and-codecov-on-merge-to-main.yml
@@ -12,7 +12,7 @@ on:
 
 jobs:
   matrix-coverage:
-    uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
       project: diffpy.srreal
       c_extension: true
diff --git a/.github/workflows/publish-docs-on-release.yml b/.github/workflows/publish-docs-on-release.yml
@@ -5,7 +5,7 @@ on:
 
 jobs:
   docs:
-    uses: Billingegroup/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
     with:
       project: diffpy.srreal
       c_extension: true
diff --git a/.github/workflows/tests-on-pr.yml b/.github/workflows/tests-on-pr.yml
@@ -28,22 +28,25 @@ jobs:
       - name: Initialize miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
-          activate-environment: test
           auto-update-conda: true
-          environment-file: environment.yml
           auto-activate-base: false
           python-version: ${{ matrix.python-version }}
-
       - name: Conda config
-        run: >-
-          conda config --set always_yes yes
-          --set changeps1 no
-
+        run: |
+          conda config --add channels conda-forge
       - name: Install diffpy.srreal and requirements
         run: |
-          conda install --file requirements/conda.txt
-          conda install --file requirements/test.txt
+          conda create -n test python=${{ matrix.python-version }} -y
+          source $(conda info --base)/etc/profile.d/conda.sh
+          conda activate test
+          conda install pip -y
+          conda config --set always_yes yes --set changeps1 no
+          conda install --file requirements/conda.txt -y
+          conda install --file requirements/test.txt -y
           python -m pip install . --no-deps
 
       - name: Validate diffpy.pdfgui
-        run: pytest tests
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh
+          conda activate test
+          pytest tests
diff --git a/.gitignore b/.gitignore
@@ -10,6 +10,7 @@ __pycache__/
 .Python
 env/
 build/
+_build/
 develop-eggs/
 dist/
 downloads/
diff --git a/.prettierignore b/.prettierignore
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,13 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "latest"
+
+python:
+  install:
+    - requirements: requirements/docs.txt
+
+sphinx:
+  configuration: doc/source/conf.py
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,5 +1,5 @@
 =============
-Release Notes
+Release notes
 =============
 
 .. current developments
diff --git a/CODE_OF_CONDUCT.rst b/CODE_OF_CONDUCT.rst
@@ -8,7 +8,7 @@ Our Pledge
 We as members, contributors, and leaders pledge to make participation in our
 community a harassment-free experience for everyone, regardless of age, body
 size, visible or invisible disability, ethnicity, sex characteristics, gender
-identity and expression, level of experience, education, socio-economic status,
+identity and expression, level of experience, education, socioeconomic status,
 nationality, personal appearance, race, caste, color, religion, or sexual
 identity and orientation.
 
diff --git a/README.rst b/README.rst
@@ -8,7 +8,7 @@
         :target: https://diffpy.github.io/diffpy.srreal
         :height: 100px
 
-|PyPi| |Forge| |PythonVersion| |PR|
+|PyPI| |Forge| |PythonVersion| |PR|
 
 |CI| |Codecov| |Black| |Tracking|
 
@@ -26,7 +26,7 @@
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
 
-.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.srreal
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.srreal
         :target: https://pypi.org/project/diffpy.srreal/
 
 .. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.srreal
@@ -149,4 +149,9 @@ 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 Prof. Simon Billinge at  sb2896@columbia.edu.
+For more information on diffpy.srreal please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at sb2896@columbia.edu.
+
+Acknowledgements
+----------------
+
+``diffpy.srreal`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -18,6 +18,12 @@
 from importlib.metadata import version
 from pathlib import Path
 
+# Attempt to import the version dynamically from GitHub tag.
+try:
+    fullversion = version("diffpy.srreal")
+except Exception:
+    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.
@@ -43,6 +49,7 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
     "sphinx_rtd_theme",
+    "sphinx_copybutton",
     "m2r",
 ]
 
@@ -68,7 +75,6 @@
 # |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.
@@ -88,6 +94,11 @@
 # substitute YEAR in the copyright string
 copyright = copyright.replace("%Y", year)
 
+# For sphinx_copybutton extension.
+# Do not copy "$" for shell commands in code-blocks.
+copybutton_prompt_text = r"^\$ "
+copybutton_prompt_is_regexp = True
+
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 exclude_patterns = ["build"]
@@ -123,6 +134,14 @@
 #
 html_theme = "sphinx_rtd_theme"
 
+html_context = {
+    "display_github": True,
+    "github_user": "diffpy",
+    "github_repo": "diffpy.srreal",
+    "github_version": "main",
+    "conf_py_path": "/doc/source/",
+}
+
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -4,9 +4,9 @@
 
 .. |title| replace:: diffpy.srreal documentation
 
-diffpy.srreal - Calculators for PDF, bond valence sum, and other quantities based on atom pair interaction.
+``diffpy.srreal`` - Calculators for PDF, bond valence sum, and other quantities based on atom pair interaction.
 
-| Software version |release|.
+| Software version |release|
 | Last updated |today|.
 
 The diffpy.srreal package provides calculators for atomic pair distribution
@@ -66,6 +66,12 @@ Installation
 See the `README <https://github.com/diffpy/diffpy.srreal#installation>`_
 file included with the distribution.
 
+================
+Acknowledgements
+================
+
+``diffpy.srreal`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
+
 =================
 Table of contents
 =================
diff --git a/doc/source/license.rst b/doc/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) 2024, The Trustees of Columbia University in the City of New York.
+Copyright (c) 2025, 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:
diff --git a/environment.yml b/environment.yml
diff --git a/news/skpkg-migration.rst b/news/skpkg-migration.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Support ``scikit-package`` Level 5 standard (https://scikit-package.github.io/scikit-package/).
+
+**Security:**
+
+* <news item>
diff --git a/pyproject.toml b/pyproject.toml
@@ -6,10 +6,10 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.srreal"
 dynamic=['version', 'dependencies']
 authors = [
-  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+  { name="Simon Billinge", email="sb2896@columbia.edu" },
 ]
 maintainers = [
-  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+  { name="Simon Billinge", email="sb2896@columbia.edu" },
 ]
 description = "Calculators for PDF, bond valence sum, and other quantities based on atom pair interaction."
 keywords = ['PDF', 'BVS', 'atom', 'overlap', 'calculator', 'real-space']
@@ -56,6 +56,11 @@ exclude-file = ".codespell/ignore_lines.txt"
 ignore-words = ".codespell/ignore_words.txt"
 skip = "*.cif,*.dat"
 
+[tool.docformatter]
+recursive = true
+wrap-summaries = 72
+wrap-descriptions = 72
+
 [tool.black]
 line-length = 79
 include = '\.pyi?$'
@@ -78,8 +83,3 @@ exclude = '''
   | tests/data
 )/
 '''
-
-[tool.docformatter]
-recursive = true
-wrap-summaries = 72
-wrap-descriptions = 72
diff --git a/requirements/docs.txt b/requirements/docs.txt
@@ -1,4 +1,5 @@
 sphinx
 sphinx_rtd_theme
+sphinx-copybutton
 doctr
 m2r
