chore: move over rest of doc and src files (#168)

* chore: move over rest of doc and src files

* chore: run pre-commit

* chore: fix index.rst back to original

Author: kwagoner94

doc/source/api/diffpy.srmise.rst

@@ -1,7 +1,9 @@
 :tocdepth: -1
 
-diffpy.srmise package
-=====================
+|title|
+=======
+
+.. |title| replace:: diffpy.srmise package
 
 .. automodule:: diffpy.srmise
     :members:

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.srmise")
+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 = "Simon Billinge, Billinge Group members"
 
 # -- General configuration ------------------------------------------------
 
@@ -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.srmise",
+    "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.srmise.tex", "diffpy.srmise Documentation", ab_authors, "manual"),
+    (
+        "index",
+        "diffpy.srmise.tex",
+        "diffpy.srmise 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.srmise", "diffpy.srmise Documentation", ab_authors, 1)]
+man_pages = [
+    (
+        "index",
+        "diffpy.srmise",
+        "diffpy.srmise Documentation",
+        ab_authors,
+        1,
+    )
+]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False

doc/source/index.rst

@@ -4,19 +4,24 @@
 
 .. |title| replace:: diffpy.srmise documentation
 
-diffpy.srmise - Peak extraction and peak fitting tool for atomic pair distribution functions..
+``diffpy.srmise`` - Peak extraction and peak fitting tool for atomic pair distribution functions
 
-| Software version |release|.
+| Software version |release|
 | Last updated |today|.
 
+===============
+Getting started
+===============
+
+Welcome to the ``diffpy.srmise`` documentation!
+
+To get started, please visit the :ref:`Getting started <getting-started>` page.
+
 =======
 Authors
 =======
 
-diffpy.srmise is developed by Billinge Group
-and its community contributors.
-
-For a detailed list of contributors see
+``diffpy.srmise`` is developed by Simon Billinge, Billinge Group members. The maintainer for this project is Simon Billinge. For a detailed list of contributors see
 https://github.com/diffpy/diffpy.srmise/graphs/contributors.
 
 ============
@@ -26,6 +31,12 @@ Installation
 See the `README <https://github.com/diffpy/diffpy.srmise#installation>`_
 file included with the distribution.
 
+================
+Acknowledgements
+================
+
+``diffpy.srmise`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
+
 =================
 Table of contents
 =================

doc/source/license.rst

@@ -11,7 +11,7 @@ BSD 3-Clause License
 
 Copyright 2014-2015, Board of Trustees of Michigan State University
 
-Copyright 2016-2024, The Trustees of Columbia University in the City of New York.
+Copyright 2016-2025, The Trustees of Columbia University in the City of New York.
 
 All rights reserved.
 

src/diffpy/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (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/srmise/__init__.py

@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (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.
+# File coded by: Simon Billinge, Billinge Group members.
 #
 # See GitHub contributions for a more detailed list of contributors.
 # https://github.com/diffpy/diffpy.srmise/graphs/contributors
@@ -15,6 +15,7 @@
 """Peak extraction and peak fitting tool for atomic pair distribution
 functions."""
 
+
 # package version
 from diffpy.srmise.version import __version__
 

src/diffpy/srmise/version.py

@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (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.
+# File coded by: Simon Billinge, Billinge Group members.
 #
 # See GitHub contributions for a more detailed list of contributors.
 # https://github.com/diffpy/diffpy.srmise/graphs/contributors