From b600b458b35b8935db71b05f4bd402d7ad2e3a1d Mon Sep 17 00:00:00 2001 From: stevenhua0320 Date: Wed, 31 Jul 2024 18:05:05 +0800 Subject: [PATCH 1/2] add untrack files and add cookiecut.rst news --- AUTHORS.rst | 11 +++ AUTHORS.txt | 3 - CHANGELOG.rst | 5 ++ CODE_OF_CONDUCT.rst | 133 ++++++++++++++++++++++++++++++ doc/Makefile | 194 ++++++++++++++++++++++++++++++++++++++++++++ doc/make.bat | 36 ++++++++ news/TEMPLATE.rst | 23 ++++++ news/cookiecut.rst | 23 ++++++ 8 files changed, 425 insertions(+), 3 deletions(-) create mode 100644 AUTHORS.rst delete mode 100644 AUTHORS.txt create mode 100644 CHANGELOG.rst create mode 100644 CODE_OF_CONDUCT.rst create mode 100644 doc/Makefile create mode 100644 doc/make.bat create mode 100644 news/TEMPLATE.rst create mode 100644 news/cookiecut.rst diff --git a/AUTHORS.rst b/AUTHORS.rst new file mode 100644 index 0000000..9cef943 --- /dev/null +++ b/AUTHORS.rst @@ -0,0 +1,11 @@ +Authors +======= + +Luke Granlund +Billinge Group and community contibutors. + +Contributors +------------ + +For a list of contributors, visit +https://github.com/diffpy/diffpy.srmise/graphs/contributors diff --git a/AUTHORS.txt b/AUTHORS.txt deleted file mode 100644 index be8310a..0000000 --- a/AUTHORS.txt +++ /dev/null @@ -1,3 +0,0 @@ -SrMise (diffpy.srmise) authors: - -Luke Granlund diff --git a/CHANGELOG.rst b/CHANGELOG.rst new file mode 100644 index 0000000..2669451 --- /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..ff9c356 --- /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, socio-economic 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/doc/Makefile b/doc/Makefile new file mode 100644 index 0000000..798f52b --- /dev/null +++ b/doc/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 $() $(),,diffpy.srmise)) + +# User-friendly check for sphinx-build +ifeq ($(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/doc/make.bat b/doc/make.bat new file mode 100644 index 0000000..2be8306 --- /dev/null +++ b/doc/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/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/cookiecut.rst b/news/cookiecut.rst new file mode 100644 index 0000000..25b8176 --- /dev/null +++ b/news/cookiecut.rst @@ -0,0 +1,23 @@ +**Added:** + +* + +**Changed:** + +* + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* Cookiecuttered diffpy.srmise to new Billingegroup standard. + +**Security:** + +* From 3caee5ea29a3f8eec2d8d40174b3323463668e00 Mon Sep 17 00:00:00 2001 From: stevenhua0320 Date: Wed, 31 Jul 2024 18:06:09 +0800 Subject: [PATCH 2/2] delete README.txt --- requirements/README.txt | 11 ----------- 1 file changed, 11 deletions(-) delete mode 100644 requirements/README.txt diff --git a/requirements/README.txt b/requirements/README.txt deleted file mode 100644 index dc34909..0000000 --- a/requirements/README.txt +++ /dev/null @@ -1,11 +0,0 @@ -# YOU MAY DELETE THIS FILE AFTER SETTING UP DEPENDENCIES! -# -# This directory is where you should place your project dependencies. -# "pip.txt" should contain all required packages not available on conda. -# All other files should contain only packages available to download from conda. -# build.txt should contain all packages required to build (not run) the project. -# run.txt should contain all packages (including optional packages) required for a user to run the program. -# test.txt should contain all packages required for the testing suite and to ensure all tests pass. -# docs.txt should contain all packages required for building the package documentation page. -# -# YOU MAY DELETE THIS FILE AFTER SETTING UP DEPENDENCIES!