refactor: merge john-development to main

.codespell/ignore_words.txt

@@ -6,3 +6,6 @@ mater
 
 ;; Frobenius norm used in np.linalg.norm
 fro
+
+;; alternative spelling of socioeconomic used in code of conduct
+socio-economic

.flake8

@@ -6,8 +6,8 @@ exclude =
     __pycache__,
     build,
     dist,
-    doc/source/conf.py
-max-line-length = 115
+    docs/source/conf.py
+max-line-length = 79
 # Ignore some style 'errors' produced while formatting by 'black'
 # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
 extend-ignore = E203

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -34,7 +34,7 @@ Please let the maintainer know that all checks are done and the package is ready
 <!-- After the maintainer releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
 
 - [ ] Ensure that the full release has appeared on PyPI successfully.
-- [ ] New package dependencies listed in `conda.txt` and `test.txt` are added to `meta.yaml` in the feedstock.
+- [ ] New package dependencies listed in `conda.txt` and `tests.txt` are added to `meta.yaml` in the feedstock.
 - [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions.
 - [ ] Tag the maintainer for conda-forge release.
 

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

@@ -7,10 +7,10 @@ on:
       - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
 
 jobs:
-  release:
+  build-release:
     uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
-      project: diffpy.snmf
+      project: diffpy.stretched-nmf
       c_extension: false
       maintainer_GITHUB_username: sbillinge
     secrets:

.github/workflows/check-news-item.yml

@@ -9,4 +9,4 @@ jobs:
   check-news-item:
     uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
-      project: diffpy.snmf
+      project: diffpy.stretched-nmf

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -14,7 +14,7 @@ jobs:
   matrix-coverage:
     uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
-      project: diffpy.snmf
+      project: diffpy.stretched-nmf
       c_extension: false
       headless: false
     secrets:

.github/workflows/publish-docs-on-release.yml

@@ -7,6 +7,6 @@ jobs:
   docs:
     uses: scikit-package/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
     with:
-      project: diffpy.snmf
+      project: diffpy.stretched-nmf
       c_extension: false
       headless: false

.github/workflows/tests-on-pr.yml

@@ -8,7 +8,7 @@ jobs:
   tests-on-pr:
     uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0
     with:
-      project: diffpy.snmf
+      project: diffpy.stretched-nmf
       c_extension: false
       headless: false
     secrets:

.readthedocs.yaml

@@ -10,4 +10,4 @@ python:
     - requirements: requirements/docs.txt
 
 sphinx:
-  configuration: doc/source/conf.py
+  configuration: docs/source/conf.py

AUTHORS.rst

@@ -1,7 +1,7 @@
 Authors
 =======
 
-Billinge Group and community contributors.
+Simon Billinge, John Halloran, Billinge Group members
 
 Contributors
 ------------

CHANGELOG.rst

@@ -2,8 +2,6 @@
 Release notes
 =============
 
-.. current developments
-
 0.1.3
 =====
 

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

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2023-2025, The Trustees of Columbia University in the City of New York.
+Copyright (c) 2026, 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

README.rst

@@ -1,11 +1,11 @@
 |Icon| |title|_
 ===============
 
-.. |title| replace:: diffpy.snmf
-.. _title: https://diffpy.github.io/diffpy.snmf
+.. |title| replace:: diffpy.stretched-nmf
+.. _title: https://diffpy.github.io/diffpy.stretched-nmf
 
 .. |Icon| image:: https://avatars.githubusercontent.com/diffpy
-        :target: https://diffpy.github.io/diffpy.snmf
+        :target: https://diffpy.github.io/diffpy.stretched-nmf
         :height: 100px
 
 |PyPI| |Forge| |PythonVersion| |PR|
@@ -15,46 +15,42 @@
 .. |Black| image:: https://img.shields.io/badge/code_style-black-black
         :target: https://github.com/psf/black
 
-.. |CI| image:: https://github.com/diffpy/diffpy.snmf/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
-        :target: https://github.com/diffpy/diffpy.snmf/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+.. |CI| image:: https://github.com/diffpy/diffpy.stretched-nmf/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.stretched-nmf/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
 
-.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.snmf/branch/main/graph/badge.svg
-        :target: https://codecov.io/gh/diffpy/diffpy.snmf
+.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.stretched-nmf/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/diffpy/diffpy.stretched-nmf
 
-.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.snmf
-        :target: https://anaconda.org/conda-forge/diffpy.snmf
+.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.stretched-nmf
+        :target: https://anaconda.org/conda-forge/diffpy.stretched-nmf
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.stretched-nmf/pulls
 
-.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.snmf
-        :target: https://pypi.org/project/diffpy.snmf/
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.stretched-nmf
+        :target: https://pypi.org/project/diffpy.stretched-nmf/
 
-.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.snmf
-        :target: https://pypi.org/project/diffpy.snmf/
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.stretched-nmf
+        :target: https://pypi.org/project/diffpy.stretched-nmf/
 
 .. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
-        :target: https://github.com/diffpy/diffpy.snmf/issues
+        :target: https://github.com/diffpy/diffpy.stretched-nmf/issues
 
 A python package implementing the stretched NMF algorithm.
 
-``diffpy.snmf`` implements the stretched non negative matrix factorization (sNMF) and sparse stretched NMF
-(ssNMF) algorithms.
-
 This algorithm is designed to do an NMF factorization on a set of signals ignoring any uniform stretching of the signal
 on the independent variable axis. For example, for powder diffraction data taken from samples containing multiple
 chemical phases where the measurements were done at different temperatures and the materials were undergoing thermal
 expansion.
 
-For more information about the diffpy.snmf library, please consult our `online documentation <https://diffpy.github.io/diffpy.snmf>`_.
+For more information about the diffpy.stretched-nmf library, please consult our `online documentation <https://diffpy.github.io/diffpy.stretched-nmf>`_.
 
 Citation
 --------
 
-If you use this program for a scientific research that leads
-to publication, we ask that you acknowledge use of the program
-by citing the following paper in your publication:
+If you use diffpy.stretched-nmf in a scientific publication, we would like you to cite this package as
 
-   Ran Gu, Yevgeny Rakita, Ling Lan, Zach Thatcher, Gabrielle E. Kamm, Daniel O’Nolan, Brennan Mcbride, Allison Wustrow, James R. Neilson, Karena W. Chapman, Qiang Du, and Simon J. L. Billinge,
+        Ran Gu, Yevgeny Rakita, Ling Lan, Zach Thatcher, Gabrielle E. Kamm, Daniel O’Nolan, Brennan Mcbride, Allison Wustrow, James R. Neilson, Karena W. Chapman, Qiang Du, and Simon J. L. Billinge,
    `Stretched Non-negative Matrix Factorization
    <https://doi.org/10.1038/s41524-024-01377-5>`__,
    *npj Comput Mater* **10**, 193 (2024).
@@ -71,42 +67,49 @@ 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.snmf_env`` ::
-
-        conda create -n diffpy.snmf_env diffpy.snmf
-        conda activate diffpy.snmf_env
-
-To confirm that the installation was successful, type ::
+The following creates and activates a new environment named ``diffpy.stretched-nmf_env`` ::
 
-        python -c "import diffpy.snmf; print(diffpy.snmf.__version__)"
+        conda create -n diffpy.stretched-nmf_env diffpy.stretched-nmf
+        conda activate diffpy.stretched-nmf_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 <https://pypi.python.org>`_.
-To install using ``pip`` into your ``diffpy.snmf_env`` environment, type ::
+To install using ``pip`` into your ``diffpy.stretched-nmf_env`` environment, type ::
 
-        pip install diffpy.snmf
+        pip install diffpy.stretched-nmf
 
 If you prefer to install from sources, after installing the dependencies, obtain the source archive from
-`GitHub <https://github.com/diffpy/diffpy.snmf/>`_. Once installed, ``cd`` into your ``diffpy.snmf`` directory
+`GitHub <https://github.com/diffpy/diffpy.stretched-nmf/>`_. Once installed, ``cd`` into your ``diffpy.stretched-nmf`` directory
 and run the following ::
 
         pip install .
 
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.stretched-nmf --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.stretched_nmf; print(diffpy.stretched_nmf.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.stretched-nmf -h
+
 Getting Started
 ---------------
 
-You may consult our `online documentation <https://diffpy.github.io/diffpy.snmf>`_ for tutorials and API references.
+You may consult our `online documentation <https://diffpy.github.io/diffpy.stretched-nmf>`_ for tutorials and API references.
 
 Support and Contribute
 ----------------------
 
-`Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.snmf. Please join the diffpy.snmf users community by joining the Google group. The diffpy.snmf project welcomes your expertise and enthusiasm!
-
-If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.snmf/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.snmf/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_.
+If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.stretched-nmf/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.stretched-nmf/pulls>`_.
 
-Feel free to fork the project and contribute. To install diffpy.snmf
+Feel free to fork the project and contribute. To install diffpy.stretched-nmf
 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 ::
@@ -127,14 +130,14 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.snmf/blob/main/CODE_OF_CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.stretched-nmf/blob/main/CODE-OF-CONDUCT.rst>`_.
 
 Contact
 -------
 
-For more information on diffpy.snmf please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon J.L. Billinge group at sb2896@columbia.edu.
+For more information on diffpy.stretched-nmf please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at sb2896@columbia.edu.
 
 Acknowledgements
 ----------------
 
-``diffpy.snmf`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
+``diffpy.stretched-nmf`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.