Merge pull request #15 from dabeycorn/doc

skpkg: migrate documentation, README, and public static files

Author: sbillinge

.github/workflows/build-wheel-release.yml

@@ -227,4 +227,4 @@ jobs:
     needs: [test-wheels]
     uses: ./.github/workflows/release-github.yml
     secrets:
-      PAT_TOKEN: ${{ secrets.PAT_TOKEN }}
+      PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

.github/workflows/release-github.yml

@@ -160,4 +160,4 @@ jobs:
           curl --silent --fail --data-binary @"$FILE" \
             -H "Content-Type: application/zip" \
             -H "Authorization: Bearer $PAT_TOKEN" \
-            "${{ steps.create_release.outputs.upload_url }}?name=$(basename "$FILE")"
+            "${{ steps.create_release.outputs.upload_url }}?name=$(basename "$FILE")"

AUTHORS.rst

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

AUTHORS.txt

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

CHANGELOG.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>`_

CODE-OF-CONDUCT.rst

@@ -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

LICENSENOTICE.txt

@@ -1,34 +1,102 @@
-DistancePrinter
-========================================================================
+|Icon| |title|_
+===============
 
-Software for calculating inter-atomic distance for given structure
+.. |title| replace:: diffpy.distanceprinter
+.. _title: https://diffpy.github.io/diffpy.distanceprinter
 
+.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
+        :target: https://diffpy.github.io/diffpy.distanceprinter
+        :height: 100px
 
-REQUIREMENTS
-------------------------------------------------------------------------
+|PythonVersion| |PR|
 
-The DistancePrinter requires Python 2.7 and the following software:
+|Black| |Tracking|
 
-* ``diffpy.pdffit``
+.. |Black| image:: https://img.shields.io/badge/code_style-black-black
+        :target: https://github.com/psf/black
 
-INSTALLATION
-------------------------------------------------------------------------
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.distanceprinter/pulls
 
-To install the DistancePrinter package:
+.. |PythonVersion| image:: https://img.shields.io/badge/python-3.11%20|%203.12%20|%203.13-blue
+        :target: https://pypi.org/project/diffpy.distanceprinter/
 
-    python setup.py install
+.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
+        :target: https://github.com/diffpy/diffpy.distanceprinter/issues
 
-By default the files are installed in the system directories, which are
-usually only writeable by the root.  See the usage info "./setup.py install
---help" for options to install as a normal user under a different location.
-Note that installation to non-standard directories you may require adjustments
-to the PATH and PYTHONPATH environment variables.
+Distance Printer, calculate the inter atomic distances. Part of xPDFsuite
 
-CONTACTS
-------------------------------------------------------------------------
+Citation
+--------
 
-For more information on diffpy.Structure please visit the project web-page
+If you use diffpy.distanceprinter in a scientific publication, we would like you to cite this package as
 
-http://www.diffpy.org/
+        Xiaohao Yang, Pavol Juhas, Christopher L. Farrow and Simon J. L. Billinge, xPDFsuite: an end-to-end
+        software solution for high throughput pair distribution function transformation, visualization and
+        analysis, arXiv 1402.3163 (2025)
 
-or email Prof. Simon Billinge at sb2896@columbia.edu.
+Installation
+------------
+``diffpy.distanceprinter`` is normally installed as part of the ``xpdfsuite`` software, so please refer to the
+installation instructions detailed in the ``README.rst`` file of ``xpdfsuite`` `here <https://github.com/diffpy/diffpy.xpdfsuite/blob/main/README.rst>`_.
+
+Independent Installation
+------------------------
+You can also install ``diffpy.distanceprinter`` independently for yourself.
+
+Assuming you have a wheel file in the current working directory, in an active conda environment please type
+
+    pip install ./diffpy.distanceprinter-VERSION.whl
+
+where you replace VERSION with the actual version you have so the command matches the filename of the
+wheel file you have.
+
+The commands to create and activate the conda environment with name "distanceprinter-env" is
+
+    conda create -n distanceprinter-env python=3.13
+    conda activate distanceprinter-env
+
+If you don't have conda installed, we recomment you install `miniconda
+<https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_
+To install this software from a Python wheel distribution format execute
+
+    pip install ./diffpy.distanceprinter-VERSION.whl
+
+If you are a developer, you can also install this package from sources. First, obtain the source archive
+from `GitHub <https://github.com/diffpy/diffpy.distanceprinter/>`_.
+Install the packages in ``./requirements/conda.txt`` and ``./requirements/tests.txt``
+using the `--file`` command:
+
+    conda activate distanceprinter-env
+    conda install --file ./requirements/conda.txt
+    conda install --file ./requirements/tests.txt
+    pip install -e .    # assuming you are in the top level directory of the package
+
+After installing the dependencies, ``cd`` into your ``diffpy.distanceprinter`` directory
+and run the following ::
+
+        pip install .
+
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.distanceprinter --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.distanceprinter; print(diffpy.distanceprinter.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.distanceprinter -h
+
+
+Contact
+-------
+
+For more information on diffpy.distanceprinter please visit the project `web-page <https://www.diffpy.org>`_ or email Simon J.L. Billinge Group at sb2896@columbia.edu.
+
+Acknowledgements
+----------------
+
+``diffpy.distanceprinter`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.