From 27e9d673d90568626feabebd4383693d9a7fcca2 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Wed, 8 Oct 2025 08:52:32 -0500 Subject: [PATCH 01/14] skpkg: create template 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 | 322 +++++++++++++++++++++ docs/source/license.rst | 38 +++ docs/source/release.rst | 5 + 7 files changed, 625 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/license.rst 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..46258b4 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,322 @@ +#!/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/license.rst b/docs/source/license.rst new file mode 100644 index 0000000..5e751f7 --- /dev/null +++ b/docs/source/license.rst @@ -0,0 +1,38 @@ +:tocdepth: -1 + +.. index:: license + +License +####### + +OPEN SOURCE LICENSE AGREEMENT +============================= +BSD 3-Clause License + +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 +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 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 21d5c354ef5e26fbbfc65b372910969eb5137327 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Wed, 8 Oct 2025 08:58:17 -0500 Subject: [PATCH 02/14] skpkg: add config files for authors, changelog, code of conduct, license Signed-off-by: Dasun Abeykoon --- AUTHORS.rst | 10 ++++ CHANGELOG.rst | 5 ++ CODE-OF-CONDUCT.rst | 133 ++++++++++++++++++++++++++++++++++++++++++++ LICENSE.rst | 29 ++++++++++ 4 files changed, 177 insertions(+) create mode 100644 AUTHORS.rst create mode 100644 CHANGELOG.rst create mode 100644 CODE-OF-CONDUCT.rst create mode 100644 LICENSE.rst diff --git a/AUTHORS.rst b/AUTHORS.rst new file mode 100644 index 0000000..3f23ab7 --- /dev/null +++ b/AUTHORS.rst @@ -0,0 +1,10 @@ +Authors +======= + +Xiaohao Yang, Sangjoon Lee, Simon Billinge, Billinge Group members + +Contributors +------------ + +For a list of contributors, visit +https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors 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 `_ diff --git a/LICENSE.rst b/LICENSE.rst new file mode 100644 index 0000000..9cc6a9d --- /dev/null +++ b/LICENSE.rst @@ -0,0 +1,29 @@ +BSD 3-Clause License + +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 +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its contributors + may be used to endorse or promote products derived from this software + without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. From 3750189972c8a53ccbe92ef8e1daab51673026ab Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Wed, 8 Oct 2025 08:58:31 -0500 Subject: [PATCH 03/14] skpkg: add MANIFEST.in Signed-off-by: Dasun Abeykoon --- MANIFEST.in | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/MANIFEST.in b/MANIFEST.in index 0ecc683..f1a78ee 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,3 +1,12 @@ -recursive-include DistancePrinter * -prune doc -exclude MANIFEST.in +graft src +graft tests +graft requirements + +include AUTHORS.rst LICENSE*.rst README.rst + +# Exclude all bytecode files and __pycache__ directories +global-exclude *.py[cod] # Exclude all .pyc, .pyo, and .pyd files. +global-exclude .DS_Store # Exclude Mac filesystem artifacts. +global-exclude __pycache__ # Exclude Python cache directories. +global-exclude .git* # Exclude git files and directories. +global-exclude .idea # Exclude PyCharm project settings. From 72005737755a79485d2b1530666f84cbf4827cea Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Wed, 8 Oct 2025 08:58:40 -0500 Subject: [PATCH 04/14] skpkg: add README.rst Signed-off-by: Dasun Abeykoon --- README.rst | 143 +++++++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 122 insertions(+), 21 deletions(-) diff --git a/README.rst b/README.rst index 15b7d2a..3e813be 100644 --- a/README.rst +++ b/README.rst @@ -1,34 +1,135 @@ -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 ------------------------------------------------------------------------- +|PyPI| |Forge| |PythonVersion| |PR| -The DistancePrinter requires Python 2.7 and the following software: +|CI| |Codecov| |Black| |Tracking| -* ``diffpy.pdffit`` +.. |Black| image:: https://img.shields.io/badge/code_style-black-black + :target: https://github.com/psf/black -INSTALLATION ------------------------------------------------------------------------- +.. |CI| image:: https://github.com/diffpy/diffpy.distanceprinter/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg + :target: https://github.com/diffpy/diffpy.distanceprinter/actions/workflows/matrix-and-codecov-on-merge-to-main.yml -To install the DistancePrinter package: +.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.distanceprinter/branch/main/graph/badge.svg + :target: https://codecov.io/gh/diffpy/diffpy.distanceprinter - python setup.py install +.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.distanceprinter + :target: https://anaconda.org/conda-forge/diffpy.distanceprinter -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. +.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff + :target: https://github.com/diffpy/diffpy.distanceprinter/pulls -CONTACTS ------------------------------------------------------------------------- +.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.distanceprinter + :target: https://pypi.org/project/diffpy.distanceprinter/ -For more information on diffpy.Structure please visit the project web-page +.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.distanceprinter + :target: https://pypi.org/project/diffpy.distanceprinter/ -http://www.diffpy.org/ +.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue + :target: https://github.com/diffpy/diffpy.distanceprinter/issues -or email Prof. Simon Billinge at sb2896@columbia.edu. +Distance Printer, calculate the inter atomic distances. Part of xPDFsuite + +For more information about the diffpy.distanceprinter library, please consult our `online documentation `_. + +Citation +-------- + +If you use diffpy.distanceprinter in a scientific publication, we would like you to cite this package as + + diffpy.distanceprinter Package, https://github.com/diffpy/diffpy.distanceprinter + +Installation +------------ + +The preferred method is to use `Miniconda Python +`_ +and install from the "conda-forge" channel of Conda packages. + +To add "conda-forge" to the conda channels, run the following in a terminal. :: + + conda config --add channels conda-forge + +We want to install our packages in a suitable conda environment. +The following creates and activates a new environment named ``diffpy.distanceprinter_env`` :: + + conda create -n diffpy.distanceprinter_env diffpy.distanceprinter + conda activate diffpy.distanceprinter_env + +The output should print the latest version displayed on the badges above. + +If the above does not work, you can use ``pip`` to download and install the latest release from +`Python Package Index `_. +To install using ``pip`` into your ``diffpy.distanceprinter_env`` environment, type :: + + pip install diffpy.distanceprinter + +If you prefer to install from sources, after installing the dependencies, obtain the source archive from +`GitHub `_. Once installed, ``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 + +Getting Started +--------------- + +You may consult our `online documentation `_ for tutorials and API references. + +Support and Contribute +---------------------- + +If you see a bug or want to request a feature, please `report it as an issue `_ and/or `submit a fix as a PR `_. + +Feel free to fork the project and contribute. To install diffpy.distanceprinter +in a development mode, with its sources being directly used by Python +rather than copied to a package directory, use the following in the root +directory :: + + pip install -e . + +To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit +hooks. + +1. Install pre-commit in your working environment by running ``conda install pre-commit``. + +2. Initialize pre-commit (one time only) ``pre-commit install``. + +Thereafter your code will be linted by black and isort and checked against flake8 before you can commit. +If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should +pass after they are modified). If the flake8 test fails please see the error messages and fix them manually before +trying to commit again. + +Improvements and fixes are always appreciated. + +Before contributing, please read our `Code of Conduct `_. + +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 c9f24b32d61514004ae32a4411e47474a3699ca4 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Wed, 8 Oct 2025 09:00:32 -0500 Subject: [PATCH 05/14] skpkg: add news files Signed-off-by: Dasun Abeykoon --- news/TEMPLATE.rst | 23 +++++++++++++++++++++++ news/doc.rst | 23 +++++++++++++++++++++++ 2 files changed, 46 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..a50d58c --- /dev/null +++ b/news/doc.rst @@ -0,0 +1,23 @@ +**Added:** + +* + +**Changed:** + +* Support ``scikit-package`` Level 5 standard (https://scikit-package.github.io/scikit-package/). + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* From 30ba4ec0730ac913f529a2c970313f688ec4aa35 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Tue, 14 Oct 2025 18:50:43 -0500 Subject: [PATCH 06/14] delete old author.txt Signed-off-by: Dasun Abeykoon --- AUTHORS.txt | 1 - 1 file changed, 1 deletion(-) delete mode 100644 AUTHORS.txt 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 cca82a73e27a003f5862c3fc4bb927f29e9c98ee Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Tue, 14 Oct 2025 18:51:27 -0500 Subject: [PATCH 07/14] skpkg: simplify author names in AUTHORS.rst Signed-off-by: Dasun Abeykoon --- AUTHORS.rst | 2 +- cookiecutter.json | 18 ++++++++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 cookiecutter.json diff --git a/AUTHORS.rst b/AUTHORS.rst index 3f23ab7..68e8471 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -1,7 +1,7 @@ Authors ======= -Xiaohao Yang, Sangjoon Lee, Simon Billinge, Billinge Group members +Xiaohao Yang and Billinge Group members Contributors ------------ diff --git a/cookiecutter.json b/cookiecutter.json new file mode 100644 index 0000000..d5646d4 --- /dev/null +++ b/cookiecutter.json @@ -0,0 +1,18 @@ +{ + "maintainer_name": "Simon J.L. Billinge Group", + "maintainer_email": "sb2896@columbia.edu", + "maintainer_github_username": "sbillinge", + "contributors": "Xiaohao Yang, Sangjoon Lee, Simon Billinge, Billinge Group members", + "license_holders": "The Trustees of Columbia University in the City of New York", + "project_name": "diffpy.distanceprinter", + "github_username_or_orgname": "diffpy", + "github_repo_name": "diffpy.distanceprinter", + "conda_pypi_package_dist_name": "diffpy.distanceprinter", + "package_dir_name": "diffpy.distanceprinter", + "project_short_description": "Distance Printer, calculate the inter atomic distances. Part of xPDFsuite", + "project_keywords": "diffpy, pdf, data-interpretation", + "minimum_supported_python_version": "3.11", + "maximum_supported_python_version": "3.13", + "project_needs_c_code_compiled": "No", + "project_has_gui_tests": "No" +} From c9f438fd2c769dd65c6c58191a447a8cde3cc2c4 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Tue, 14 Oct 2025 18:55:25 -0500 Subject: [PATCH 08/14] skpkg: delete open source license Signed-off-by: Dasun Abeykoon --- LICENSE.rst | 29 ----------------------------- 1 file changed, 29 deletions(-) delete mode 100644 LICENSE.rst diff --git a/LICENSE.rst b/LICENSE.rst deleted file mode 100644 index 9cc6a9d..0000000 --- a/LICENSE.rst +++ /dev/null @@ -1,29 +0,0 @@ -BSD 3-Clause License - -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 -modification, are permitted provided that the following conditions are met: - -1. Redistributions of source code must retain the above copyright notice, this - list of conditions and the following disclaimer. - -2. Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimer in the documentation - and/or other materials provided with the distribution. - -3. Neither the name of the copyright holder nor the names of its contributors - may be used to endorse or promote products derived from this software - without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE -FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. From ab02bfc45597b6f330ee805f3ac250b9de93c14d Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Tue, 14 Oct 2025 18:55:51 -0500 Subject: [PATCH 09/14] skpkg: change copyright year range in LICENSENOTICE.txt Signed-off-by: Dasun Abeykoon --- LICENSENOTICE.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From a9b16bbd348995c1c9faa686eb68e27be573ebac Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Tue, 14 Oct 2025 18:56:24 -0500 Subject: [PATCH 10/14] skpkg: remove irrelevant README shields Signed-off-by: Dasun Abeykoon --- README.rst | 18 +++--------------- 1 file changed, 3 insertions(+), 15 deletions(-) diff --git a/README.rst b/README.rst index 3e813be..8f8cce7 100644 --- a/README.rst +++ b/README.rst @@ -8,29 +8,17 @@ :target: https://diffpy.github.io/diffpy.distanceprinter :height: 100px -|PyPI| |Forge| |PythonVersion| |PR| +|PythonVersion| |PR| -|CI| |Codecov| |Black| |Tracking| +|Black| |Tracking| .. |Black| image:: https://img.shields.io/badge/code_style-black-black :target: https://github.com/psf/black -.. |CI| image:: https://github.com/diffpy/diffpy.distanceprinter/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg - :target: https://github.com/diffpy/diffpy.distanceprinter/actions/workflows/matrix-and-codecov-on-merge-to-main.yml - -.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.distanceprinter/branch/main/graph/badge.svg - :target: https://codecov.io/gh/diffpy/diffpy.distanceprinter - -.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.distanceprinter - :target: https://anaconda.org/conda-forge/diffpy.distanceprinter - .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff :target: https://github.com/diffpy/diffpy.distanceprinter/pulls -.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.distanceprinter - :target: https://pypi.org/project/diffpy.distanceprinter/ - -.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.distanceprinter +.. |PythonVersion| image:: https://img.shields.io/badge/python-3.11%20|%203.12%20|%203.13-blue :target: https://pypi.org/project/diffpy.distanceprinter/ .. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue From 96dcb022fd544c60d7cc312cb43c69117524e589 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Tue, 14 Oct 2025 19:02:56 -0500 Subject: [PATCH 11/14] skpkg: modify README.rst to include updated install instructions Signed-off-by: Dasun Abeykoon --- README.rst | 81 ++++++++++++++++++++---------------------------------- 1 file changed, 30 insertions(+), 51 deletions(-) diff --git a/README.rst b/README.rst index 8f8cce7..63b9120 100644 --- a/README.rst +++ b/README.rst @@ -26,42 +26,53 @@ Distance Printer, calculate the inter atomic distances. Part of xPDFsuite -For more information about the diffpy.distanceprinter library, please consult our `online documentation `_. - Citation -------- If you use diffpy.distanceprinter in a scientific publication, we would like you to cite this package as - diffpy.distanceprinter Package, https://github.com/diffpy/diffpy.distanceprinter + 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) 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 `_. -The preferred method is to use `Miniconda Python -`_ -and install from the "conda-forge" channel of Conda packages. +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 -To add "conda-forge" to the conda channels, run the following in a terminal. :: +where you replace VERSION with the actual version you have so the command matches the filename of the +wheel file you have. - conda config --add channels conda-forge +The commands to create and activate the conda environment with name "conf-env" is -We want to install our packages in a suitable conda environment. -The following creates and activates a new environment named ``diffpy.distanceprinter_env`` :: + conda create -n conf-env python=3.13 + conda activate conf-env - conda create -n diffpy.distanceprinter_env diffpy.distanceprinter - conda activate diffpy.distanceprinter_env +If you don't have conda installed, we recomment you install `miniconda +`_ +To install this software from a Python wheel distribution format execute -The output should print the latest version displayed on the badges above. + pip install ./diffpy.distanceprinter-VERSION.whl -If the above does not work, you can use ``pip`` to download and install the latest release from -`Python Package Index `_. -To install using ``pip`` into your ``diffpy.distanceprinter_env`` environment, type :: +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: - pip install diffpy.distanceprinter + 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 -If you prefer to install from sources, after installing the dependencies, obtain the source archive from -`GitHub `_. Once installed, ``cd`` into your ``diffpy.distanceprinter`` directory +After installing the dependencies, ``cd`` into your ``diffpy.distanceprinter`` directory and run the following :: pip install . @@ -79,38 +90,6 @@ To view the basic usage and available commands, type :: diffpy.distanceprinter -h -Getting Started ---------------- - -You may consult our `online documentation `_ for tutorials and API references. - -Support and Contribute ----------------------- - -If you see a bug or want to request a feature, please `report it as an issue `_ and/or `submit a fix as a PR `_. - -Feel free to fork the project and contribute. To install diffpy.distanceprinter -in a development mode, with its sources being directly used by Python -rather than copied to a package directory, use the following in the root -directory :: - - pip install -e . - -To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit -hooks. - -1. Install pre-commit in your working environment by running ``conda install pre-commit``. - -2. Initialize pre-commit (one time only) ``pre-commit install``. - -Thereafter your code will be linted by black and isort and checked against flake8 before you can commit. -If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should -pass after they are modified). If the flake8 test fails please see the error messages and fix them manually before -trying to commit again. - -Improvements and fixes are always appreciated. - -Before contributing, please read our `Code of Conduct `_. Contact ------- From 7cd368cee1673cb98c49ff46338078aaee682ccc Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Tue, 14 Oct 2025 19:04:01 -0500 Subject: [PATCH 12/14] doc: remove BSD open source license from blank docs Signed-off-by: Dasun Abeykoon --- docs/source/license.rst | 38 -------------------------------------- 1 file changed, 38 deletions(-) delete mode 100644 docs/source/license.rst diff --git a/docs/source/license.rst b/docs/source/license.rst deleted file mode 100644 index 5e751f7..0000000 --- a/docs/source/license.rst +++ /dev/null @@ -1,38 +0,0 @@ -:tocdepth: -1 - -.. index:: license - -License -####### - -OPEN SOURCE LICENSE AGREEMENT -============================= -BSD 3-Clause License - -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 -modification, are permitted provided that the following conditions are met: - -1. Redistributions of source code must retain the above copyright notice, this - list of conditions and the following disclaimer. - -2. Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimer in the documentation - and/or other materials provided with the distribution. - -3. Neither the name of the copyright holder nor the names of its - contributors may be used to endorse or promote products derived from - this software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE -FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. From c5b967010f80d22e5f976f2b351514d471a48d70 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Tue, 14 Oct 2025 19:21:42 -0500 Subject: [PATCH 13/14] doc: update news to include python 3 migration Signed-off-by: Dasun Abeykoon --- news/doc.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/news/doc.rst b/news/doc.rst index a50d58c..35c29f4 100644 --- a/news/doc.rst +++ b/news/doc.rst @@ -4,6 +4,7 @@ **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:** From da57be501bb505230107d467e4b78d2fa08a9816 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Wed, 15 Oct 2025 19:19:15 -0500 Subject: [PATCH 14/14] doc: run pre-commit on all files Signed-off-by: Dasun Abeykoon --- docs/source/conf.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 46258b4..e797146 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -32,7 +32,9 @@ sys.path.insert(0, str(Path("../../src").resolve())) # abbreviations -ab_authors = "Xiaohao Yang, Sangjoon Lee, Simon Billinge, Billinge Group members" +ab_authors = ( + "Xiaohao Yang, Sangjoon Lee, Simon Billinge, Billinge Group members" +) # -- General configuration ------------------------------------------------