From 635d035c72f94a395fecd32143e485b045b07b4c Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:50:53 -0500 Subject: [PATCH 1/9] skpkg: create temp doc directory Signed-off-by: Dasun Abeykoon --- docs/Makefile | 194 ++++++++++++ docs/make.bat | 36 +++ docs/source/_static/.placeholder | 0 docs/source/api/diffpy.distanceprinter.rst | 30 ++ docs/source/conf.py | 324 +++++++++++++++++++++ docs/source/release.rst | 5 + 6 files changed, 589 insertions(+) create mode 100644 docs/Makefile create mode 100644 docs/make.bat create mode 100644 docs/source/_static/.placeholder create mode 100644 docs/source/api/diffpy.distanceprinter.rst create mode 100644 docs/source/conf.py create mode 100644 docs/source/release.rst diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..9d60f49 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,194 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = build +BASENAME = $(subst .,,$(subst $() $(),,diffpy.distanceprinter)) + +# User-friendly check for sphinx-build +ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) +$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) +endif + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/$(BASENAME).qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/$(BASENAME).qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/$(BASENAME)" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/$(BASENAME)" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +latexpdfja: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through platex and dvipdfmx..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." + +# Manual publishing to the gh-pages branch + +GITREPOPATH = $(shell cd $(CURDIR) && git rev-parse --git-dir) +GITREMOTE = origin +GITREMOTEURL = $(shell git config --get remote.$(GITREMOTE).url) +GITLASTCOMMIT = $(shell git rev-parse --short HEAD) + +publish: + @test -d build/html || \ + ( echo >&2 "Run 'make html' first!"; false ) + git show-ref --verify --quiet refs/heads/gh-pages || \ + git branch --track gh-pages $(GITREMOTE)/gh-pages + test -d build/gh-pages || \ + git clone -s -b gh-pages $(GITREPOPATH) build/gh-pages + cd build/gh-pages && \ + git pull $(GITREMOTEURL) gh-pages + rsync -acv --delete --exclude=.git --exclude=.rsync-exclude \ + --exclude-from=build/gh-pages/.rsync-exclude \ + --link-dest=$(CURDIR)/build/html build/html/ build/gh-pages/ + cd build/gh-pages && \ + git add --all . && \ + git diff --cached --quiet || \ + git commit -m "Sync with the source at $(GITLASTCOMMIT)." + cd build/gh-pages && \ + git push origin gh-pages diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..2be8306 --- /dev/null +++ b/docs/make.bat @@ -0,0 +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 diff --git a/docs/source/_static/.placeholder b/docs/source/_static/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/docs/source/api/diffpy.distanceprinter.rst b/docs/source/api/diffpy.distanceprinter.rst new file mode 100644 index 0000000..ae0bb79 --- /dev/null +++ b/docs/source/api/diffpy.distanceprinter.rst @@ -0,0 +1,30 @@ +:tocdepth: -1 + +|title| +======= + +.. |title| replace:: diffpy.distanceprinter package + +.. automodule:: diffpy.distanceprinter + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + diffpy.distanceprinter.example_package + +Submodules +---------- + +|module| +-------- + +.. |module| replace:: diffpy.distanceprinter.example_submodule module + +.. automodule:: diffpy.distanceprinter.example_submodule + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..e797146 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,324 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +# +# diffpy.distanceprinter 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 +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys +import time +from importlib.metadata import version +from pathlib import Path + +# Attempt to import the version dynamically from GitHub tag. +try: + fullversion = version("diffpy.distanceprinter") +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. # 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 = ( + "Xiaohao Yang, Sangjoon Lee, Simon Billinge, Billinge Group members" +) + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", + "sphinx.ext.todo", + "sphinx.ext.viewcode", + "sphinx.ext.intersphinx", + "sphinx_rtd_theme", + "sphinx_copybutton", + "m2r", +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +source_suffix = [".rst", ".md"] + +# The encoding of source files. +# source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = "index" + +# General information about the project. +project = "diffpy.distanceprinter" +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. + +# The short X.Y version. +version = "".join(fullversion.split(".post")[:1]) +# The full version, including alpha/beta/rc tags. +release = fullversion + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +# today = '' +today = time.strftime("%B %d, %Y", time.localtime()) +year = today.split()[-1] +# Else, today_fmt is used as the format for a strftime call. +# today_fmt = '%B %d, %Y' +# 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"] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +# default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +# add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +# add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +# show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = "sphinx" + +# A list of ignored prefixes for module index sorting. +modindex_common_prefix = ["diffpy.distanceprinter"] + +# Display all warnings for missing links. +nitpicky = True + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = "sphinx_rtd_theme" + +html_context = { + "display_github": True, + "github_user": "diffpy", + "github_repo": "diffpy.distanceprinter", + "github_version": "main", + "conf_py_path": "/docs/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. +# +html_theme_options = { + "navigation_with_keys": "true", +} + +# Add any paths that contain custom themes here, relative to this directory. +# html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +# html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +# html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +# html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +# html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +# html_static_path = ['_static'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +# html_extra_path = [] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +# html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +# html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +# html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +# html_additional_pages = {} + +# If false, no module index is generated. +# html_domain_indices = True + +# If false, no index is generated. +# html_use_index = True + +# If true, the index is split into individual pages for each letter. +# html_split_index = False + +# If true, links to the reST sources are added to the pages. +# html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +# html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +# html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +# html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +# html_file_suffix = None + +# Output file base name for HTML help builder. +basename = "diffpy.distanceprinter".replace(" ", "").replace(".", "") +htmlhelp_basename = basename + "doc" + + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { + # The paper size ('letterpaper' or 'a4paper'). + # 'papersize': 'letterpaper', + # The font size ('10pt', '11pt' or '12pt'). + # 'pointsize': '10pt', + # Additional stuff for the LaTeX preamble. + # 'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + ( + "index", + "diffpy.distanceprinter.tex", + "diffpy.distanceprinter Documentation", + ab_authors, + "manual", + ), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +# latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +# latex_use_parts = False + +# If true, show page references after internal links. +# latex_show_pagerefs = False + +# If true, show URL addresses after external links. +# latex_show_urls = False + +# Documents to append as an appendix to all manuals. +# latex_appendices = [] + +# If false, no module index is generated. +# latex_domain_indices = True + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ( + "index", + "diffpy.distanceprinter", + "diffpy.distanceprinter Documentation", + ab_authors, + 1, + ) +] + +# If true, show URL addresses after external links. +# man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ( + "index", + "diffpy.distanceprinter", + "diffpy.distanceprinter Documentation", + ab_authors, + "diffpy.distanceprinter", + "One line description of project.", + "Miscellaneous", + ), +] + +# Documents to append as an appendix to all manuals. +# texinfo_appendices = [] + +# If false, no module index is generated. +# texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +# texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +# texinfo_no_detailmenu = False + + +# Example configuration for intersphinx: refer to the Python standard library. +# intersphinx_mapping = {'http://docs.python.org/': None} diff --git a/docs/source/release.rst b/docs/source/release.rst new file mode 100644 index 0000000..27cd0cc --- /dev/null +++ b/docs/source/release.rst @@ -0,0 +1,5 @@ +:tocdepth: -1 + +.. index:: release notes + +.. include:: ../../CHANGELOG.rst From f561d7218159052014ecc0d17605afcb94bd68ac Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:51:40 -0500 Subject: [PATCH 2/9] skpkg: replace AUTHORS.txt with AUTHORS.rst Signed-off-by: Dasun Abeykoon --- AUTHORS.rst | 10 ++++++++++ AUTHORS.txt | 1 - 2 files changed, 10 insertions(+), 1 deletion(-) create mode 100644 AUTHORS.rst delete mode 100644 AUTHORS.txt diff --git a/AUTHORS.rst b/AUTHORS.rst new file mode 100644 index 0000000..68e8471 --- /dev/null +++ b/AUTHORS.rst @@ -0,0 +1,10 @@ +Authors +======= + +Xiaohao Yang and Billinge Group members + +Contributors +------------ + +For a list of contributors, visit +https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors diff --git a/AUTHORS.txt b/AUTHORS.txt deleted file mode 100644 index e36df7d..0000000 --- a/AUTHORS.txt +++ /dev/null @@ -1 +0,0 @@ -Xiaohao Yang From 4c43dee8825b834c4f38f2617e944e4eedadcd2c Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:52:47 -0500 Subject: [PATCH 3/9] skpkg: add CHANGELOG.rst and CODE-OF-CONDUCT.rst Signed-off-by: Dasun Abeykoon --- CHANGELOG.rst | 5 ++ CODE-OF-CONDUCT.rst | 133 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 138 insertions(+) create mode 100644 CHANGELOG.rst create mode 100644 CODE-OF-CONDUCT.rst diff --git a/CHANGELOG.rst b/CHANGELOG.rst new file mode 100644 index 0000000..f29d3b5 --- /dev/null +++ b/CHANGELOG.rst @@ -0,0 +1,5 @@ +============= +Release notes +============= + +.. current developments diff --git a/CODE-OF-CONDUCT.rst b/CODE-OF-CONDUCT.rst new file mode 100644 index 0000000..e8199ca --- /dev/null +++ b/CODE-OF-CONDUCT.rst @@ -0,0 +1,133 @@ +===================================== + Contributor Covenant Code of Conduct +===================================== + +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, socioeconomic status, +nationality, personal appearance, race, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +Our Standards +------------- + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or advances of + any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email address, + without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +Enforcement Responsibilities +---------------------------- + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +Scope +----- + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official email address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +Enforcement +----------- + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +sb2896@columbia.edu. All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +Enforcement Guidelines +---------------------- + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +1. Correction +**************** + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +2. Warning +************* + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +3. Temporary Ban +****************** + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +4. Permanent Ban +****************** + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +Attribution +----------- + +This Code of Conduct is adapted from the `Contributor Covenant `_. + +Community Impact Guidelines were inspired by `Mozilla's code of conduct enforcement ladder `_. + +For answers to common questions about this code of conduct, see the `FAQ `_. `Translations are available `_ From dabccd621052d1ff2668724b2ab630bddcd5f529 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:53:44 -0500 Subject: [PATCH 4/9] doc: update README.rst with updated installation instructions, badges, and citations Signed-off-by: Dasun Abeykoon --- README.rst | 110 +++++++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 89 insertions(+), 21 deletions(-) diff --git a/README.rst b/README.rst index 15b7d2a..63b9120 100644 --- a/README.rst +++ b/README.rst @@ -1,34 +1,102 @@ -DistancePrinter -======================================================================== +|Icon| |title|_ +=============== -Software for calculating inter-atomic distance for given structure +.. |title| replace:: diffpy.distanceprinter +.. _title: https://diffpy.github.io/diffpy.distanceprinter +.. |Icon| image:: https://avatars.githubusercontent.com/diffpy + :target: https://diffpy.github.io/diffpy.distanceprinter + :height: 100px -REQUIREMENTS ------------------------------------------------------------------------- +|PythonVersion| |PR| -The DistancePrinter requires Python 2.7 and the following software: +|Black| |Tracking| -* ``diffpy.pdffit`` +.. |Black| image:: https://img.shields.io/badge/code_style-black-black + :target: https://github.com/psf/black -INSTALLATION ------------------------------------------------------------------------- +.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff + :target: https://github.com/diffpy/diffpy.distanceprinter/pulls -To install the DistancePrinter package: +.. |PythonVersion| image:: https://img.shields.io/badge/python-3.11%20|%203.12%20|%203.13-blue + :target: https://pypi.org/project/diffpy.distanceprinter/ - python setup.py install +.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue + :target: https://github.com/diffpy/diffpy.distanceprinter/issues -By default the files are installed in the system directories, which are -usually only writeable by the root. See the usage info "./setup.py install ---help" for options to install as a normal user under a different location. -Note that installation to non-standard directories you may require adjustments -to the PATH and PYTHONPATH environment variables. +Distance Printer, calculate the inter atomic distances. Part of xPDFsuite -CONTACTS ------------------------------------------------------------------------- +Citation +-------- -For more information on diffpy.Structure please visit the project web-page +If you use diffpy.distanceprinter in a scientific publication, we would like you to cite this package as -http://www.diffpy.org/ + Xiaohao Yang, Pavol Juhas, Christopher L. Farrow and Simon J. L. Billinge, xPDFsuite: an end-to-end + software solution for high throughput pair distribution function transformation, visualization and + analysis, arXiv 1402.3163 (2014) -or email Prof. Simon Billinge at sb2896@columbia.edu. +Installation +------------ +``diffpy.distanceprinter`` is normally installed as part of the ``xpdfsuite`` software, so please refer to the +installation instructions detailed in the ``README.rst`` file of ``xpdfsuite`` `here `_. + +Independent Installation +------------------------ +You can also install ``diffpy.distanceprinter`` independently for yourself. + +Assuming you have a wheel file in the current working directory, in an active conda environment please type + + pip install ./diffpy.distanceprinter-VERSION.whl + +where you replace VERSION with the actual version you have so the command matches the filename of the +wheel file you have. + +The commands to create and activate the conda environment with name "conf-env" is + + conda create -n conf-env python=3.13 + conda activate conf-env + +If you don't have conda installed, we recomment you install `miniconda +`_ +To install this software from a Python wheel distribution format execute + + pip install ./diffpy.distanceprinter-VERSION.whl + +If you are a developer, you can also install this package from sources. First, obtain the source archive +from `GitHub `_. +Install the packages in ``./requirements/conda.txt`` and ``./requirements/tests.txt`` +using the `--file`` command: + + conda activate conf-env + conda install --file ./requirements/conda.txt + conda install --file ./requirements/tests.txt + pip install -e . # assuming you are in the top level directory of the package + +After installing the dependencies, ``cd`` into your ``diffpy.distanceprinter`` directory +and run the following :: + + pip install . + +This package also provides command-line utilities. To check the software has been installed correctly, type :: + + diffpy.distanceprinter --version + +You can also type the following command to verify the installation. :: + + python -c "import diffpy.distanceprinter; print(diffpy.distanceprinter.__version__)" + + +To view the basic usage and available commands, type :: + + diffpy.distanceprinter -h + + +Contact +------- + +For more information on diffpy.distanceprinter please visit the project `web-page `_ or email Simon J.L. Billinge Group at sb2896@columbia.edu. + +Acknowledgements +---------------- + +``diffpy.distanceprinter`` is built and maintained with `scikit-package `_. From ae732560b4fb19fbab9320bb0e896c8047392cbd Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:54:26 -0500 Subject: [PATCH 5/9] skpkg: add news files Signed-off-by: Dasun Abeykoon --- news/TEMPLATE.rst | 23 +++++++++++++++++++++++ news/doc.rst | 24 ++++++++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 news/TEMPLATE.rst create mode 100644 news/doc.rst diff --git a/news/TEMPLATE.rst b/news/TEMPLATE.rst new file mode 100644 index 0000000..790d30b --- /dev/null +++ b/news/TEMPLATE.rst @@ -0,0 +1,23 @@ +**Added:** + +* + +**Changed:** + +* + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* diff --git a/news/doc.rst b/news/doc.rst new file mode 100644 index 0000000..35c29f4 --- /dev/null +++ b/news/doc.rst @@ -0,0 +1,24 @@ +**Added:** + +* + +**Changed:** + +* Updated from Python 2.6-2.7 to Python 3.11-3.13 +* Support ``scikit-package`` Level 5 standard (https://scikit-package.github.io/scikit-package/). + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* From c2caa4eac7acced0563d1cce25869b6ea0395696 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:55:27 -0500 Subject: [PATCH 6/9] pre-commit: format workflow files Signed-off-by: Dasun Abeykoon --- .github/workflows/build-wheel-release.yml | 2 +- .github/workflows/release-github.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-wheel-release.yml b/.github/workflows/build-wheel-release.yml index 7691787..14c1dc3 100644 --- a/.github/workflows/build-wheel-release.yml +++ b/.github/workflows/build-wheel-release.yml @@ -227,4 +227,4 @@ jobs: needs: [test-wheels] uses: ./.github/workflows/release-github.yml secrets: - PAT_TOKEN: ${{ secrets.PAT_TOKEN }} \ No newline at end of file + PAT_TOKEN: ${{ secrets.PAT_TOKEN }} diff --git a/.github/workflows/release-github.yml b/.github/workflows/release-github.yml index 204d34c..be9c891 100644 --- a/.github/workflows/release-github.yml +++ b/.github/workflows/release-github.yml @@ -160,4 +160,4 @@ jobs: curl --silent --fail --data-binary @"$FILE" \ -H "Content-Type: application/zip" \ -H "Authorization: Bearer $PAT_TOKEN" \ - "${{ steps.create_release.outputs.upload_url }}?name=$(basename "$FILE")" \ No newline at end of file + "${{ steps.create_release.outputs.upload_url }}?name=$(basename "$FILE")" From 225bcef0d40597f9ca9ccc89722c6ab22047c674 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:58:02 -0500 Subject: [PATCH 7/9] doc: replace copyright year ranges to 2009-2025 Signed-off-by: Dasun Abeykoon --- LICENSENOTICE.txt | 2 +- README.rst | 2 +- docs/source/conf.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/LICENSENOTICE.txt b/LICENSENOTICE.txt index 68ada6a..c5cdb02 100644 --- a/LICENSENOTICE.txt +++ b/LICENSENOTICE.txt @@ -5,6 +5,6 @@ prohibited. If you don’t know whether or not your anticipated use is under a license, you must contact Prof. Simon Billinge at sb2896@columbia.edu. Use of this software without a license is prohibited. -Copyright 2009-2014, Trustees of Columbia University in the City of New York. +Copyright 2009-2025, Trustees of Columbia University in the City of New York. For more information please email Prof. Simon Billinge at sb2896@columbia.edu diff --git a/README.rst b/README.rst index 63b9120..bff2696 100644 --- a/README.rst +++ b/README.rst @@ -33,7 +33,7 @@ If you use diffpy.distanceprinter in a scientific publication, we would like you Xiaohao Yang, Pavol Juhas, Christopher L. Farrow and Simon J. L. Billinge, xPDFsuite: an end-to-end software solution for high throughput pair distribution function transformation, visualization and - analysis, arXiv 1402.3163 (2014) + analysis, arXiv 1402.3163 (2025) Installation ------------ diff --git a/docs/source/conf.py b/docs/source/conf.py index e797146..451aec0 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -2,7 +2,7 @@ # -*- coding: utf-8 -*- # # diffpy.distanceprinter documentation build configuration file, created by # noqa: E501 -# sphinx-quickstart on Thu Jan 30 15:49:41 2014. +# sphinx-quickstart on Thu Jan 30 15:49:41 2025. # # This file is execfile()d with the current directory set to its # containing dir. From 65ed969a61c0242b299f42a523c631dc4658a68d Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 18:35:30 -0500 Subject: [PATCH 8/9] tests: remove irrelevant whitespace from strings before comparing --- tests/test_distanceprinter.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/tests/test_distanceprinter.py b/tests/test_distanceprinter.py index c58d41b..f4c987a 100644 --- a/tests/test_distanceprinter.py +++ b/tests/test_distanceprinter.py @@ -49,4 +49,9 @@ def test_distanceprinter(monkeypatch): # Remove stru file path when comparing as it may differ between machines resultstr = resultstr.split("\n", 2)[2] teststr = teststr.split("\n", 2)[2] + + # Remove irrelevant whitespace when comparing + resultstr = "".join(resultstr.split()) + teststr = "".join(teststr.split()) + assert resultstr == teststr From 7c8e5e9989848e32d936a6c3aeae83eec04c5ca6 Mon Sep 17 00:00:00 2001 From: "Dasun L. Abeykoon" Date: Sun, 19 Oct 2025 19:37:15 -0500 Subject: [PATCH 9/9] doc: rename example conda env name to "distanceprinter-env" in install instructions --- README.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.rst b/README.rst index bff2696..90cf3c6 100644 --- a/README.rst +++ b/README.rst @@ -51,10 +51,10 @@ Assuming you have a wheel file in the current working directory, in an active co where you replace VERSION with the actual version you have so the command matches the filename of the wheel file you have. -The commands to create and activate the conda environment with name "conf-env" is +The commands to create and activate the conda environment with name "distanceprinter-env" is - conda create -n conf-env python=3.13 - conda activate conf-env + conda create -n distanceprinter-env python=3.13 + conda activate distanceprinter-env If you don't have conda installed, we recomment you install `miniconda `_ @@ -67,7 +67,7 @@ from `GitHub `_. Install the packages in ``./requirements/conda.txt`` and ``./requirements/tests.txt`` using the `--file`` command: - conda activate conf-env + conda activate distanceprinter-env conda install --file ./requirements/conda.txt conda install --file ./requirements/tests.txt pip install -e . # assuming you are in the top level directory of the package