skpkg: updated labpdfproc with scikit-package level 5

stevenhua0320 · Sep 29, 2026 · Sep 30, 2026 · Sep 30, 2026 · Sep 30, 2026 · Sep 30, 2026
commit 428e874cbd05f34743b8adb1d7b96d45a8b313bf
diff --git a/.github/workflows/build-wheel-release-upload.yml b/.github/workflows/build-wheel-release-upload.yml
@@ -1,18 +1,76 @@
-name: Build Wheel, Release on 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.labpdfproc
       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.labpdfproc
+  #     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.labpdfproc
+  #     maintainer_github_username: sbillinge
+  #   secrets:
+  #     PAT_TOKEN: ${{ secrets.PAT_TOKEN }}
diff --git a/.github/workflows/check-news-item.yml b/.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:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,5 +1,5 @@
 default_language_version:
-  python: python3
+  python: python3.14
 ci:
   autofix_commit_msg: |
     [pre-commit.ci] auto fixes from pre-commit hooks
@@ -52,7 +52,7 @@ repos:
           - tomli
   # prettier - multi formatter for .json, .yml, and .md files
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         additional_dependencies:

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -3,112 +3,3 @@ Release notes
 =============
 
 .. current developments
-
-0.3.1
-=====
-
-**Added:**
-
-* Add back support for Python 3.10 and 3.11.
-
-
-0.3.0
-=====
-
-**Added:**
-
-* Functionalities to estimate mu*D theoretically.
-* Added published reference to ``README.rst``.
-* Fast calculation supports values up to muD = 7
-* Recookiecut with updated ``scikit-package`` to enable docs preview in PRs.
-* Updated package standards to scikit-package 0.3.0.
-* Added ``cookiecutter.json`` file for the ``package update`` command.
-* Functionality to read wavelength and anode type directly from a diffpy configuration file.
-* Utility and example documentation for ``tools`` module.
-* Gooey support so that the app can be run with GUI
-* Coverage report in each PR
-* doi in Readme for papers.
-* Support for independent variables other than two-theta.
-* new subcommand ``applymud`` to run the original absorption correction process through CLI.
-* Utility and example documentation for the main module.
-* Added documentation for new CLI updates.
-* Documentation for functions module.
-* Spelling check via Codespell in pre-commit
-* Python 3.13 support
-* Functionality in `load_user_info` to enable user to enter an ORCID.
-
-**Changed:**
-
-* Default to brute-force computation when muD < 0.5 or > 7.
-* Print a warning message instead of error, explicitly stating the input muD value
-* Functions that use DiffractionObject` in `diffpy.utils` to follow the new API.
-* Workflow for loading wavelength - raise an error when both wavelength and anode type are specified.
-* Readme: muD now requires the ``--mud`` flag instead of a required argument.
-* Made muD an optional argument and provided different options (manually entry / z-scan file path) for users to specify muD
-* Increased the number of significant figures for wavelength and separated values for Ka1 and Ka2.
-* hyphens / underscores format according to new scikit-package group standard.
-* GitHub workflows for renamed test file.
-* Return a ``ValueError`` if no wavelength is found on config file or if its not specified.
-* Compartmentalize commands into the subcommands ``mud``, ``zscan``, and ``sample``. See documentation for more info.
-* Changed ``doc`` to ``docs`` and ``CODE_OF_CONDUCT.rst`` to ``CODE-OF-CONDUCT.rst`` to comply with scikit-package standards.
-* All function docstrings and tests to be more informative, incorporating new ORCID function and improving overall clarity.
-
-**Fixed:**
-
-* duplicated wavelength information in output files
-
-**Removed:**
-
-* Remove the import of extend_path from pkgutil in diffpy/__init__.py since we are not strictly following the Python namespace package convention.
-
-
-0.2.0
-=====
-
-**Added:**
-
-* Support for Python 3.13
-
-**Removed:**
-
-* Support for Python 3.10
-
-
-0.1.3
-=====
-
-**Added:**
-
-* generate package API doc
-* redo cookiecutter to add issue templates and update readme
-
-
-0.1.2
-=====
-
-**Added:**
-
-* polynomial interpolation as the default method for cve computation.
-
-**Fixed:**
-
-* add PyPI packages under pip.txt
-
-
-
-0.1.1
-=====
-
-
-
-0.1.1
-=====
-
-
-
-0.1.0
-=====
-
-
-
-Initial release of labPDFproc.  Please see README and documentation for details
diff --git a/LICENSE.rst b/LICENSE.rst
@@ -1,9 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2025-2026, The Trustees of Columbia University in the City of New York.
-All rights reserved.
-
-Copyright (c) 2026-present, diffpy.labpdfproc developers and contributors.
+Copyright (c) 2026, The Trustees of Columbia University in the City of New York.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -3,7 +3,6 @@ graft tests
 graft requirements
 
 include AUTHORS.rst LICENSE*.rst README.rst
-include src/diffpy/labpdfproc/data *
 
 # Exclude all bytecode files and __pycache__ directories
 global-exclude *.py[cod]  # Exclude all .pyc, .pyo, and .pyd files.

diff --git a/README.rst b/README.rst
@@ -38,30 +38,7 @@
 
 Tools for processing x-ray powder diffraction data from laboratory sources.
 
-PDFgetX3 has revolutionized how PDF methods can be applied to solve nanostructure problems.
-However, the program was designed for use with Rapid Acquisition PDF (RAPDF) data from synchrotron sources.
-A key approximation inherent in the use of PDFgetX3 for RAPDF data is that absorption effects are negligible.
-This is typically not the case for laboratory x-ray diffractometers, where absorption effects can be significant.
-
-This app is designed to preprocess data from laboratory x-ray diffractometers before using PDFgetX3 to obtain PDFs.
-The app currently carries out an absorption correction assuming a parallel beam capillary geometry
-which is the most common geometry for lab PDF measurements.
-
-The theory is described in the following paper:
-
-        Chen, Y., Schertenleib, T., Yang, A., Schouwink, P., Queen, W. L., and Billinge, S. J. L.,
-        *Absorption Correction for Reliable Pair Distribution Functions from Low Energy X-ray Sources*.
-        Crystal Growth & Design, 2026, 26 (3), 1036–1047.
-        https://doi.org/10.1021/acs.cgd.5c00551
-
-
-The related experimental data acquisition protocols are described in the following paper:
-
-        Schertenleib, T., Schmuckler, D., Chen, Y., Jin, G. B., Queen, W. L., and Billinge, S. J. L. (2025).
-        *Testing Protocols for Obtaining Reliable Pair Distribution Functions from Laboratory X-Ray Sources Using PDFgetX3*.
-        Chem. Methods, 2500001.
-        https://doi.org/10.1002/cmtd.202500001
-
+* LONGER DESCRIPTION HERE
 
 For more information about the diffpy.labpdfproc library, please consult our `online documentation <https://diffpy.github.io/diffpy.labpdfproc>`_.
 
@@ -70,10 +47,7 @@ Citation
 
 If you use diffpy.labpdfproc in a scientific publication, we would like you to cite this package as
 
-        Chen, Y., Schertenleib, T., Yang, A., Schouwink, P., Queen, W. L., and Billinge, S. J. L.,
-        *Absorption Correction for Reliable Pair Distribution Functions from Low Energy X-ray Sources*.
-        Crystal Growth & Design, 2026, 26 (3), 1036–1047.
-        https://doi.org/10.1021/acs.cgd.5c00551
+        diffpy.labpdfproc Package, https://github.com/diffpy/diffpy.labpdfproc
 
 Installation
 ------------
@@ -108,7 +82,7 @@ and run the following ::
 
 This package also provides command-line utilities. To check the software has been installed correctly, type ::
 
-        labpdfproc --version
+        diffpy.labpdfproc --version
 
 You can also type the following command to verify the installation. ::
 
@@ -117,7 +91,7 @@ You can also type the following command to verify the installation. ::
 
 To view the basic usage and available commands, type ::
 
-        labpdfproc -h
+        diffpy.labpdfproc -h
 
 Getting Started
 ---------------

diff --git a/cookiecutter.json b/cookiecutter.json
@@ -5,8 +5,8 @@
   "maintainer_emails": "sbillinge@ucsb.edu",
   "maintainer_github_usernames": "sbillinge",
   "contributors": "Yucong Chen, Till Schertenleib, Caden Myers, Billinge Group members",
-  "license_holders": "The Trustees of Columbia University in the City of New York",
   "project_name": "diffpy.labpdfproc",
+  "license_holders": "The Trustees of Columbia University in the City of New York",
   "github_username_or_orgname": "diffpy",
   "github_repo_name": "diffpy.labpdfproc",
   "conda_pypi_package_dist_name": "diffpy.labpdfproc",

diff --git a/docs/make.bat b/docs/make.bat
@@ -1,36 +1,36 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-set SPHINXPROJ=PackagingScientificPython
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=PackagingScientificPython
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd