Merge pull request #27 from stevenhua0320/doc

Author: sbillinge

AUTHORS.rst

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+Authors
+=======
+
+Xiaohao Yang
+
+Billinge Group members
+
+Contributors
+------------
+
+For a list of contributors, visit
+https://github.com/diffpy/diffpy.srxplanargui/graphs/contributors

CHANGELOG.rst

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+=============
+Release notes
+=============
+
+.. current developments

CODE-OF-CONDUCT.rst

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+=====================================
+ 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 <https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>`_.
+
+Community Impact Guidelines were inspired by `Mozilla's code of conduct enforcement ladder <https://github.com/mozilla/inclusion>`_.
+
+For answers to common questions about this code of conduct, see the `FAQ <https://www.contributor-covenant.org/faq>`_. `Translations are available <https://www.contributor-covenant.org/translations>`_

LICENSE.rst

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+Copyright (c) 2009-2025, The Trustees of Columbia University in the City of New York.
+All rights reserved.
+
+Use of this software is subject to and permitted only under a separate,
+written Use License granted by Columbia University.  If you or your employer
+is not a party to such an agreement, then your use of this software is
+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.
+
+For more information please email Prof. Simon Billinge at sb2896@columbia.edu

MANIFEST.in

@@ -1,3 +1,12 @@
-recursive-include dpx *
-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.

README.rst

@@ -1,45 +1,97 @@
-dpx.srxplanargui
-========================================================================
+|Icon| |title|_
+===============
+
+.. |title| replace:: diffpy.srxplanargui
+.. _title: https://diffpy.github.io/diffpy.srxplanargui
+
+.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
+        :target: https://diffpy.github.io/diffpy.srxplanargui
+        :height: 100px
+
+|PythonVersion| |PR|
+
+|Black| |Tracking|
+
+.. |Black| image:: https://img.shields.io/badge/code_style-black-black
+        :target: https://github.com/psf/black
+
+.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.srxplanargui/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/diffpy/diffpy.srxplanargui
+
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.srxplanargui/pulls
+
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.srxplanargui
+        :target: https://pypi.org/project/diffpy.srxplanargui/
+
+.. |PythonVersion| image:: https://img.shields.io/badge/python-3.11%20|%203.12%20|%203.13-blue
+
+.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
+        :target: https://github.com/diffpy/diffpy.srxplanargui/issues
+
+xPDFsuite, a software for PDF transformation and visualization.
 
 GUI for diffpy.srxplanar
 
-REQUIREMENTS
-------------------------------------------------------------------------
+Citation
+--------
+
+If you use diffpy.srxplanargui in a scientific publication, we would like you to cite this package as
+
+        Yang, X., Juhas, P., Farrow, C. L., & Billinge, S. J. (2014).
+        xPDFsuite: an end-to-end software solution for high throughput pair distribution function transformation,
+        visualization and analysis. arXiv preprint arXiv:1402.3163.
+
+Installation
+------------
+
+The preferred method is to be installed with `xpdfsuite` package or the wheel file.
+
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.srxplanargui --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.srxplanargui; print(diffpy.srxplanargui.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.srxplanargui -h
 
-The dpx.srxplanargui requires Python 2.7 and the following software:
+Support
+----------------------
 
-* ``diffpy.srxplanar``
-* ``dpx.confutils``
-* ``numpy``
-* ``scipy``
-* ``traits``
-* ``traitsui``
-* ``chaco``
+If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.srxplanargui/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.srxplanargui/pulls>`_.
 
-The image integration (diffpy.srxplanargui) requires
+Feel free to fork the project. To install diffpy.srxplanargui
+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 ::
 
-* ``fabio``
-* ``pyfai``
-* ``matplotlib``
+        pip install -e .
 
-INSTALLATION
-------------------------------------------------------------------------
+To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit
+hooks.
 
-We are going to release conda package for all platform. For general user
-please use the installation file and install software. For developor,
-you can install dpx.srxplanargui using
+1. Install pre-commit in your working environment by running ``conda install pre-commit``.
 
-    python setup.py install
+2. Initialize pre-commit (one time only) ``pre-commit install``.
 
-Note: the dependency is not specified in the setup.py. You need to install
-them yourself. You can use Anaconda or other python enviroment.
+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.
 
-CONTACTS
-------------------------------------------------------------------------
+Contact
+-------
 
-For more information on diffpy.Structure please visit the project web-page
+For more information on diffpy.srxplanargui please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at sb2896@columbia.edu.
 
-http://www.diffpy.org/
+Acknowledgements
+----------------
 
-or email Prof. Simon Billinge at sb2896@columbia.edu.
+``diffpy.srxplanargui`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.

docs/source/_static/.placeholder

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+:tocdepth: -1
+
+|title|
+=======
+
+.. |title| replace:: diffpy.srxplanargui package
+
+.. automodule:: diffpy.srxplanargui
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+   diffpy.srxplanargui.example_package
+
+Submodules
+----------
+
+|module|
+--------
+
+.. |module| replace:: diffpy.srxplanargui.example_submodule module
+
+.. automodule:: diffpy.srxplanargui.example_submodule
+    :members:
+    :undoc-members:
+    :show-inheritance: