skpkg: line length fixes, GH workflow edits, and other small edits

.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
 

.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).
+-->

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

@@ -8,12 +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.pdffit2
       c_extension: true
-      github_admin_username: sbillinge
-
+      maintainer_GITHUB_username: sbillinge
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

.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.pdffit2

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -12,10 +12,9 @@ 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.pdffit2
-      python_versions: "3.11, 3.12, 3.13"
       c_extension: true
       headless: false
     secrets:

.github/workflows/publish-docs-on-release.yml

@@ -1,17 +1,12 @@
 name: Deploy Documentation on Release
 
 on:
-  release:
-    types: [published]
   workflow_dispatch:
 
 jobs:
   docs:
-    permissions:
-      contents: write
-    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.pdffit2
       c_extension: true
       headless: false
-      python_version: 3.13

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

@@ -1,19 +1,15 @@
 name: Tests on PR
 
 on:
-  push:
-    branches:
-      - main
   pull_request:
   workflow_dispatch:
 
 jobs:
-  validate:
-    uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
+  tests-on-pr:
+    uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0
     with:
-      project: diffpy.pdffi2
+      project: diffpy.pdffit2
       c_extension: true
       headless: false
-      python_version: 3.13
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.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

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.pdffit2")
+except Exception:
+    fullversion = "No version found. The correct version will appear in the released version."
+
 # 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.
@@ -26,7 +32,7 @@
 sys.path.insert(0, str(Path("../../src").resolve()))
 
 # abbreviations
-ab_authors = "Billinge Group members and community contributors"
+ab_authors = "Billinge group and community members."
 
 # -- General configuration ------------------------------------------------
 
@@ -43,6 +49,7 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
     "sphinx_rtd_theme",
+    "sphinx_copybutton",
     "m2r",
 ]
 
@@ -88,6 +95,11 @@
 # 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 +135,14 @@
 #
 html_theme = "sphinx_rtd_theme"
 
+html_context = {
+    "display_github": True,
+    "github_user": "diffpy",
+    "github_repo": "diffpy.pdffit2",
+    "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.
@@ -221,7 +241,13 @@
 # (source start file, target name, title,
 # author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    ("index", "diffpy.pdffit2.tex", "diffpy.pdffit2 Documentation", ab_authors, "manual"),
+    (
+        "index",
+        "diffpy.pdffit2.tex",
+        "diffpy.pdffit2 Documentation",
+        ab_authors,
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -249,7 +275,15 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [("index", "diffpy.pdffit2", "diffpy.pdffit2 Documentation", ab_authors, 1)]
+man_pages = [
+    (
+        "index",
+        "diffpy.pdffit2",
+        "diffpy.pdffit2 Documentation",
+        ab_authors,
+        1,
+    )
+]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False

news/setup-CI.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news needed: line length fixes and other adjustments to copyright year.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -6,13 +6,13 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.pdffit2"
 dynamic=['version', 'dependencies']
 authors = [
-  { name="Simon J.L. Billinge group", email="[email protected]" },
+  { name="Simon Billinge", email="[email protected]" },
 ]
 maintainers = [
-  { name="Simon J.L. Billinge group", email="[email protected]" },
+  { name="Simon Billinge", email="[email protected]" },
 ]
 description = "PDFfit2 - real space structure refinement program."
-keywords = ["PDF", "structure refinement"]
+keywords = ['PDF', 'structure refinement']
 readme = "README.rst"
 requires-python = ">=3.11, <3.14"
 classifiers = [
@@ -57,7 +57,7 @@ ignore-words = ".codespell/ignore_words.txt"
 skip = "*.cif,*.dat,*.cc,*.h"
 
 [tool.black]
-line-length = 115
+line-length = 79
 include = '\.pyi?$'
 exclude = '''
 /(

requirements/conda.txt

@@ -1 +1,2 @@
 diffpy.structure
+numpy

requirements/docs.txt

@@ -1,4 +1,5 @@
 sphinx
 sphinx_rtd_theme
+sphinx-copybutton
 doctr
 m2r

requirements/pip.txt

@@ -1 +1,2 @@
 diffpy.structure
+numpy

setup.py

@@ -62,7 +62,8 @@ def get_gsl_config():
             return rv
         else:
             warnings.warn(
-                f"CONDA_PREFIX is set to {conda_prefix}, " "but GSL not found at those paths. Proceeding..."
+                f"CONDA_PREFIX is set to {conda_prefix}, "
+                "but GSL not found at those paths. Proceeding..."
             )
 
     # 2. Check using GSL_PATH.
@@ -76,7 +77,8 @@ def get_gsl_config():
             return rv
         else:
             raise EnvironmentError(
-                f"GSL_PATH={gsl_path} is set, but {inc} or {lib} not found. " "Please verify your GSL_PATH."
+                f"GSL_PATH={gsl_path} is set, but {inc} or {lib} not found. "
+                "Please verify your GSL_PATH."
             )
 
     # 3. Try using the gsl-config executable (only on Unix-like systems).
@@ -92,8 +94,14 @@ def get_gsl_config():
             lib_match = re.search(r"(?m)^[^#]*\s-L(\S+)", txt)
             if prefix_match:
                 prefix_path = Path(prefix_match.group(1))
-                inc_dir = include_match.group(1) if include_match else (prefix_path / "include")
-                lib_dir = lib_match.group(1) if lib_match else (prefix_path / "lib")
+                inc_dir = (
+                    include_match.group(1)
+                    if include_match
+                    else (prefix_path / "include")
+                )
+                lib_dir = (
+                    lib_match.group(1) if lib_match else (prefix_path / "lib")
+                )
                 rv["include_dirs"].append(str(inc_dir))
                 rv["library_dirs"].append(str(lib_dir))
                 return rv
@@ -164,7 +172,14 @@ def create_extensions():
 
     compiler_type = get_compiler_type()
     if compiler_type in ("unix", "cygwin", "mingw32"):
-        extra_compile_args = ["-std=c++11", "-Wall", "-Wno-write-strings", "-O3", "-funroll-loops", "-ffast-math"]
+        extra_compile_args = [
+            "-std=c++11",
+            "-Wall",
+            "-Wno-write-strings",
+            "-O3",
+            "-funroll-loops",
+            "-ffast-math",
+        ]
         # Check for static GSL libraries and add them if found.
         static_libs = [
             os.path.join(p, "libgsl.a")
@@ -189,15 +204,21 @@ def create_extensions():
         "extra_link_args": extra_link_args,
         "extra_objects": extra_objects,
     }
-    ext = Extension("diffpy.pdffit2.pdffit2", glob.glob("src/extensions/**/*.cc"), **ext_kws)
+    ext = Extension(
+        "diffpy.pdffit2.pdffit2",
+        glob.glob("src/extensions/**/*.cc"),
+        **ext_kws,
+    )
     return [ext]
 
 
+# Extensions not included in pyproject.toml
 setup_args = dict(
     ext_modules=[],
     cmdclass={"build_ext": CustomBuildExt},
 )
 
+
 if __name__ == "__main__":
     setup_args["ext_modules"] = create_extensions()
     setup(**setup_args)

src/diffpy/__init__.py

@@ -3,7 +3,7 @@
 #
 # (c) 2008 trustees of the Michigan State University.
 # All rights reserved.
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.

src/diffpy/pdffit2/__init__.py

@@ -3,7 +3,7 @@
 #
 # (c) 2006 trustees of the Michigan State University.
 # All rights reserved.
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.