refactor: change references of snmf to stretched-nmf (#185)

* chore: use new name in scikit-package space

* refactor: rename references throughout program snmf -> stretched-nmf

* refactor: rename project references

* chore: add news item for package-name-update

* chore: CI toml issue

---------

Co-authored-by: John Halloran <jhalloran@oxy.edu>

Author: john-halloran

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

@@ -10,7 +10,7 @@ jobs:
   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:

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|
@@ -15,26 +15,26 @@
 .. |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.snmf/pulls
+        :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.
 
@@ -43,12 +43,12 @@ on the independent variable axis. For example, for powder diffraction data taken
 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 diffpy.snmf in a scientific publication, we would like you to cite this package as
+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,
    `Stretched Non-negative Matrix Factorization
@@ -67,49 +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`` ::
+The following creates and activates a new environment named ``diffpy.stretched-nmf_env`` ::
 
-        conda create -n diffpy.snmf_env diffpy.snmf
-        conda activate diffpy.snmf_env
+        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.snmf --version
+        diffpy.stretched-nmf --version
 
 You can also type the following command to verify the installation. ::
 
-        python -c "import diffpy.snmf; print(diffpy.snmf.__version__)"
+        python -c "import diffpy.stretched_nmf; print(diffpy.stretched_nmf.__version__)"
 
 
 To view the basic usage and available commands, type ::
 
-        diffpy.snmf -h
+        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
 ----------------------
 
-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>`_.
+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 ::
@@ -130,14 +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 Billinge 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/>`_.

cookiecutter.json

@@ -4,11 +4,11 @@
   "maintainer_github_username": "sbillinge",
   "contributors": "Simon Billinge, John Halloran, Billinge Group members",
   "license_holders": "The Trustees of Columbia University in the City of New York",
-  "project_name": "diffpy.snmf",
+  "project_name": "diffpy.stretched-nmf",
   "github_username_or_orgname": "diffpy",
-  "github_repo_name": "diffpy.snmf",
-  "conda_pypi_package_dist_name": "diffpy.snmf",
-  "package_dir_name": "diffpy.snmf",
+  "github_repo_name": "diffpy.stretched-nmf",
+  "conda_pypi_package_dist_name": "diffpy.stretched-nmf",
+  "package_dir_name": "diffpy.stretched_nmf",
   "project_short_description": "A python package implementing the stretched NMF algorithm.",
   "project_keywords": "diffraction, PDF, x-ray, mapping",
   "minimum_supported_python_version": "3.11",

docs/Makefile

@@ -6,7 +6,7 @@ SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = build
-BASENAME      = $(subst .,,$(subst $() $(),,diffpy.snmf))
+BASENAME      = $(subst .,,$(subst $() $(),,diffpy.stretched-nmf))
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)

docs/source/api/snmf_class.rst

@@ -1,7 +1,7 @@
 SNMFOptimizer
 =============
 
-.. autoclass:: diffpy.snmf.snmf_class.SNMFOptimizer
+.. autoclass:: diffpy.stretched_nmf.snmf_class.SNMFOptimizer
    :members: __init__, fit
    :undoc-members:
    :show-inheritance:

docs/source/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# diffpy.snmf documentation build configuration file, created by  # noqa: E501
+# diffpy.stretched-nmf documentation build configuration file, created by  # noqa: E501
 # sphinx-quickstart on Thu Jan 30 15:49:41 2014.
 #
 # This file is execfile()d with the current directory set to its
@@ -20,7 +20,7 @@
 
 # Attempt to import the version dynamically from GitHub tag.
 try:
-    fullversion = version("diffpy.snmf")
+    fullversion = version("diffpy.stretched-nmf")
 except Exception:
     fullversion = "No version found. The correct version will appear in the released version."  # noqa: E501
 
@@ -68,7 +68,7 @@
 master_doc = "index"
 
 # General information about the project.
-project = "diffpy.snmf"
+project = "diffpy.stretched-nmf"
 copyright = "%Y, The Trustees of Columbia University in the City of New York"
 
 # The version info for the project you're documenting, acts as replacement for
@@ -122,7 +122,7 @@
 pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
-modindex_common_prefix = ["diffpy.snmf"]
+modindex_common_prefix = ["diffpy.stretched_nmf"]
 
 # Display all warnings for missing links.
 nitpicky = True
@@ -137,7 +137,7 @@
 html_context = {
     "display_github": True,
     "github_user": "diffpy",
-    "github_repo": "diffpy.snmf",
+    "github_repo": "diffpy.stretched-nmf",
     "github_version": "main",
     "conf_py_path": "/docs/source/",
 }
@@ -221,7 +221,7 @@
 # html_file_suffix = None
 
 # Output file base name for HTML help builder.
-basename = "diffpy.snmf".replace(" ", "").replace(".", "")
+basename = "diffpy.stretched-nmf".replace(" ", "").replace(".", "")
 htmlhelp_basename = basename + "doc"
 
 
@@ -242,8 +242,8 @@
 latex_documents = [
     (
         "index",
-        "diffpy.snmf.tex",
-        "diffpy.snmf Documentation",
+        "diffpy.stretched-nmf.tex",
+        "diffpy.stretched-nmf Documentation",
         ab_authors,
         "manual",
     ),
@@ -277,8 +277,8 @@
 man_pages = [
     (
         "index",
-        "diffpy.snmf",
-        "diffpy.snmf Documentation",
+        "diffpy.stretched-nmf",
+        "diffpy.stretched-nmf Documentation",
         ab_authors,
         1,
     )
@@ -296,10 +296,10 @@
 texinfo_documents = [
     (
         "index",
-        "diffpy.snmf",
-        "diffpy.snmf Documentation",
+        "diffpy.stretched-nmf",
+        "diffpy.stretched-nmf Documentation",
         ab_authors,
-        "diffpy.snmf",
+        "diffpy.stretched-nmf",
         "One line description of project.",
         "Miscellaneous",
     ),