skpkg: change README, license coverage year, and other files to scikit level-5 standard

AUTHORS.rst

@@ -0,0 +1,10 @@
+Authors
+=======
+
+Simon Billinge, Billinge Group members
+
+Contributors
+------------
+
+For a list of contributors, visit
+https://github.com/diffpy/diffpy.srxplanar/graphs/contributors

CHANGELOG.rst

@@ -0,0 +1,5 @@
+=============
+Release notes
+=============
+
+.. current developments

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 <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

@@ -0,0 +1,30 @@
+BSD 3-Clause License
+
+Copyright (c) 2008-2025, The Trustees of Columbia University in the City of New York.
+Copyright (c) 1994-2025, Christoph Gohlke
+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.

MANIFEST.in

@@ -1,5 +1,12 @@
-recursive-include diffpy *
-include AUTHORS.txt LICENSE.txt README.md
-include setup.cfg
-exclude MANIFEST.in
-recursive-exclude diffpy *.pyc
+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

@@ -1,5 +1,36 @@
-diffpy.srxplanar
-========================================================================
+|Icon| |title|_
+===============
+
+.. |title| replace:: diffpy.srxplanar
+.. _title: https://diffpy.github.io/diffpy.srxplanar
+
+.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
+        :target: https://diffpy.github.io/diffpy.srxplanar
+        :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.srxplanar/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/diffpy/diffpy.srxplanar
+
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.srxplanar/pulls
+
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.srxplanar
+        :target: https://pypi.org/project/diffpy.srxplanar/
+
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.srxplanar
+        :target: https://pypi.org/project/diffpy.srxplanar/
+
+.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
+        :target: https://github.com/diffpy/diffpy.srxplanar/issues
+
+Distance Printer, calculate the inter atomic distances. Part of xPDFsuite
 
 diffpy.srxplanar package provides 2D diffraction image integration using
 non splitting pixel algorithm. And it can estimate and propagate statistic
@@ -17,79 +48,72 @@ included in this distribution or the API documentation at
 
 http://diffpy.github.io/diffpy.srxplanar/
 
-REQUIREMENTS
-------------------------------------------------------------------------
+For more information about the diffpy.srxplanar library, please consult our `online documentation <https://diffpy.github.io/diffpy.srxplanar>`_.
+
+Citation
+--------
+
+If you use diffpy.srxplanar in a scientific publication, we would like you to cite this package as
 
-The diffpy.srxplanar requires Python 2.6 or 2.7 and the following software:
+        diffpy.srxplanar Package, https://github.com/diffpy/diffpy.srxplanar
 
-* `setuptools`  >=0.61(https://pypi.python.org/pypi/setuptools)
-* `numpy`       >=1.60(http://www.numpy.org/)
-* `scipy`       >=1.10(www.scipy.org/)
-* `FabIO`       >=0.80(http://sourceforge.net/projects/fable/files/fabio/)
+Installation
+------------
 
-If your python version < 2.7 (these two packages are included in 2.7 but not in 2.6)
+The preferred method is to be installed with `xpdfsuite` package or the wheel file.
 
-* `ordereddict` https://pypi.python.org/pypi/ordereddict
-* `argparse`    https://pypi.python.org/pypi/argparse
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
 
-On Ubuntu Linux the part of required software can be easily installed using
-the system package manager::
+        diffpy.srxplanar --version
 
-    sudo aptitude install \
-        python-setuptools python-numpy python-scipy
+You can also type the following command to verify the installation. ::
 
-For Mac OS X machine with the MacPorts package manager one could do::
+        python -c "import diffpy.srxplanar; print(diffpy.srxplanar.__version__)"
 
-    sudo port install \
-        python27 py27-setuptools py27-numpy py27-scipy
 
-When installing with MacPorts, make sure the MacPorts bin directory is the
-first in the system PATH and that python27 is selected as the default
-Python version in MacPorts::
+To view the basic usage and available commands, type ::
 
-    sudo port select --set python python27
+        diffpy.srxplanar -h
 
-For other Linux distributions use their respective package manager; note
-the packages may have slightly different names. diffpy.srxplanar should work
-on other Unix-like operating systems as well.  Please, search the
-web for instructions how to install external dependencies on your particular
-system.
+Getting Started
+---------------
 
-For other packages, please go to the webpage list above to download and install.
+You may consult our `online documentation <https://diffpy.github.io/diffpy.srxplanar>`_ for tutorials and API references.
 
+Support and Contribute
+----------------------
 
-INSTALLATION
-------------------------------------------------------------------------
+If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.srxplanar/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.srxplanar/pulls>`_.
 
-To install the diffpy.srxplanar package::
+Feel free to fork the project. To install diffpy.srxplanar
+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 ::
 
-    python setup.py install
+        pip install -e .
 
-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
-different location.  Note that installation to non-standard directories may
-require adjustments to the PATH and PYTHONPATH environment variables.
+To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit
+hooks.
 
-DEVELOPMENT
-------------------------------------------------------------------------
+1. Install pre-commit in your working environment by running ``conda install pre-commit``.
 
-diffpy.srxplanar is an open-source software developed at the Columbia University
-The diffpy.srxplanar sources are hosted at
+2. Initialize pre-commit (one time only) ``pre-commit install``.
 
-https://github.com/diffpy/diffpy.srxplanar
+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.
 
-Feel free to fork the project and contribute.  To install diffpy.srxplanar
-in a development mode, where the sources are directly used by Python
-rather than copied to a system directory, use::
+Improvements and fixes are always appreciated.
 
-    python setup.py develop --user
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.srxplanar/blob/main/CODE-OF-CONDUCT.rst>`_.
 
-CONTACTS
-------------------------------------------------------------------------
+Contact
+-------
 
-For more information on diffpy.srxplanar please visit the project web-page:
+For more information on diffpy.srxplanar 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.srxplanar`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.

news/TEMPLATE.rst

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+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>