skpkg: migrate documentation, README, and public static files

AUTHORS.rst

@@ -1,7 +1,7 @@
 Authors
 =======
 
-Billinge Group and community contributors.
+Simon J.L. Billinge group
 
 Contributors
 ------------

CHANGELOG.rst

@@ -1,52 +1,5 @@
 =============
-Release Notes
+Release notes
 =============
 
 .. current developments
-
-0.1.3
-=====
-
-**Fixed:**
-
-* Updated README instructions for pip and conda-forge install
-* Updated README instructions to check for successful installation
-
-
-0.1.2
-=====
-
-**Added:**
-
-* Use GitHub Actions to build, release, upload to PyPI
-* Added issue template for PyPI/GitHub release
-
-**Changed:**
-
-* Added tag check for release
-* citation from arXiv to npj Comput Mater in docs
-
-**Fixed:**
-
-* Python version from 3.9 to 3.12 in CI news item
-* tests folder at the root of the repo
-* re-cookiecuter repo to groupd's package standard
-* Add pip dependencies under pip.txt and conda dependencies under conda.txt
-
-
-0.1.0
-=====
-
-**Added:**
-
-* Initial release of diffpy.snmf
-
-**Changed:**
-
-* Support Python version 3.12
-* Remove support for Python version 3.9
-
-**Fixed:**
-
-* Repo structure modified to the new diffpy standard
-* Code linting based on .pre-commit-config.yaml

LICENSE.rst

@@ -1,7 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2023-2024, 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.
 
 Redistribution and use in source and binary forms, with or without

README.rst

@@ -8,7 +8,7 @@
         :target: https://diffpy.github.io/diffpy.snmf
         :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.snmf
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.snmf
         :target: https://pypi.org/project/diffpy.snmf/
 
 .. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.snmf
@@ -35,7 +35,7 @@
 .. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
         :target: https://github.com/diffpy/diffpy.snmf/issues
 
-A python package implementing the stretched NMF algorithm.
+Python package implementing the stretched NMF algorithm.
 
 ``diffpy.snmf`` implements the stretched non negative matrix factorization (sNMF) and sparse stretched NMF
 (ssNMF) algorithms.
@@ -50,14 +50,9 @@ For more information about the diffpy.snmf library, please consult our `online d
 Citation
 --------
 
-If you use this program for a scientific research that leads
-to publication, we ask that you acknowledge use of the program
-by citing the following paper in your publication:
+If you use diffpy.snmf in a scientific publication, we would like you to cite this package as
 
-   Ran Gu, Yevgeny Rakita, Ling Lan, Zach Thatcher, Gabrielle E. Kamm, Daniel O’Nolan, Brennan Mcbride, Allison Wustrow, James R. Neilson, Karena W. Chapman, Qiang Du, and Simon J. L. Billinge,
-   `Stretched Non-negative Matrix Factorization
-   <https://doi.org/10.1038/s41524-024-01377-5>`__,
-   *npj Comput Mater* **10**, 193 (2024).
+        diffpy.snmf Package, https://github.com/diffpy/diffpy.snmf
 
 Installation
 ------------
@@ -104,7 +99,7 @@ Support and Contribute
 
 `Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.snmf. Please join the diffpy.snmf users community by joining the Google group. The diffpy.snmf project welcomes your expertise and enthusiasm!
 
-If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.snmf/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.snmf/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_.
+If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.snmf/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.snmf/pulls>`_.
 
 Feel free to fork the project and contribute. To install diffpy.snmf
 in a development mode, with its sources being directly used by Python
@@ -132,4 +127,9 @@ Before contributing, please read our `Code of Conduct <https://github.com/diffpy
 Contact
 -------
 
-For more information on diffpy.snmf please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at [email protected].
+For more information on diffpy.snmf please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon J.L. Billinge group at [email protected].
+
+Acknowledgements
+----------------
+
+``diffpy.snmf`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.

doc/source/api/diffpy.snmf.rst

@@ -1,68 +1,30 @@
 :tocdepth: -1
 
-diffpy.snmf package
-===================
+|title|
+=======
 
-.. automodule:: diffpy.snmf
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-Submodules
-----------
-
-diffpy.snmf.subroutines module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.snmf.subroutines
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-diffpy.snmf.containers module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.snmf.containers
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-diffpy.snmf.io module
-^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.snmf.io
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. |title| replace:: diffpy.snmf package
 
-diffpy.snmf.polynomials module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.snmf.polynomials
+.. automodule:: diffpy.snmf
     :members:
     :undoc-members:
     :show-inheritance:
 
-diffpy.snmf.optimizers module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Subpackages
+-----------
 
-.. automodule:: diffpy.snmf.optimizers
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. toctree::
+   diffpy.snmf.example_package
 
-diffpy.snmf.factorizers module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Submodules
+----------
 
-.. automodule:: diffpy.snmf.factorizers
-    :members:
-    :undoc-members:
-    :show-inheritance:
+|module|
+--------
 
-diffpy.snmf.stretchednmfapp module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. |module| replace:: diffpy.snmf.example_submodule module
 
-.. automodule:: diffpy.snmf.stretchednmfapp
+.. automodule:: diffpy.snmf.example_submodule
     :members:
     :undoc-members:
     :show-inheritance:

doc/source/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# diffpy.snmf documentation build configuration file, created by
+# diffpy.snmf documentation build configuration file, created by  # noqa: E501
 # sphinx-quickstart on Thu Jan 30 15:49:41 2014.
 #
 # This file is execfile()d with the current directory set to its
@@ -18,15 +18,21 @@
 from importlib.metadata import version
 from pathlib import Path
 
+# Attempt to import the version dynamically from GitHub tag.
+try:
+    fullversion = version("diffpy.snmf")
+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.
+# documentation root, use Path().resolve() to make it absolute, like shown here.  # noqa: E501
 # sys.path.insert(0, str(Path(".").resolve()))
 sys.path.insert(0, str(Path("../..").resolve()))
 sys.path.insert(0, str(Path("../../src").resolve()))
 
 # abbreviations
-ab_authors = "Billinge Group members and community contributors"
+ab_authors = "Simon J.L. Billinge group"
 
 # -- General configuration ------------------------------------------------
 
@@ -43,6 +49,7 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
     "sphinx_rtd_theme",
+    "sphinx_copybutton",
     "m2r",
 ]
 
@@ -62,13 +69,12 @@
 
 # General information about the project.
 project = "diffpy.snmf"
-copyright = "2023-%Y, The Trustees of Columbia University in the City of New York"
+copyright = "%Y, The Trustees of Columbia University in the City of New York"
 
 # The version info for the project you're documenting, acts as replacement for
 # |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.snmf",
+    "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 +240,13 @@
 # (source start file, target name, title,
 # author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    ("index", "diffpy.snmf.tex", "diffpy.snmf Documentation", ab_authors, "manual"),
+    (
+        "index",
+        "diffpy.snmf.tex",
+        "diffpy.snmf Documentation",
+        ab_authors,
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -249,7 +274,15 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [("index", "diffpy.snmf", "diffpy.snmf Documentation", ab_authors, 1)]
+man_pages = [
+    (
+        "index",
+        "diffpy.snmf",
+        "diffpy.snmf Documentation",
+        ab_authors,
+        1,
+    )
+]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False