chore: add back necessary lines from the files

Author: zmx27

AUTHORS.rst

@@ -1,7 +1,7 @@
 Authors
 =======
 
-Simon J.L. Billinge group
+Billinge Group and community contributors.
 
 Contributors
 ------------

CHANGELOG.rst

@@ -3,3 +3,50 @@ Release notes
 =============
 
 .. current developments
+
+0.1.3
+=====
+
+**Fixed:**
+
+* Updated README instructions for pip and conda-forge install
+* Updated README instructions to check for successful installation
+
+
+0.1.2
+=====
+
+**Added:**
+
+* Use GitHub Actions to build, release, upload to PyPI
+* Added issue template for PyPI/GitHub release
+
+**Changed:**
+
+* Added tag check for release
+* citation from arXiv to npj Comput Mater in docs
+
+**Fixed:**
+
+* Python version from 3.9 to 3.12 in CI news item
+* tests folder at the root of the repo
+* re-cookiecuter repo to groupd's package standard
+* Add pip dependencies under pip.txt and conda dependencies under conda.txt
+
+
+0.1.0
+=====
+
+**Added:**
+
+* Initial release of diffpy.snmf
+
+**Changed:**
+
+* Support Python version 3.12
+* Remove support for Python version 3.9
+
+**Fixed:**
+
+* Repo structure modified to the new diffpy standard
+* Code linting based on .pre-commit-config.yaml

LICENSE.rst

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2025, The Trustees of Columbia University in the City of New York.
+Copyright (c) 2024-2025, 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

@@ -99,7 +99,7 @@ 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>`_.
+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>`_.
 
 Feel free to fork the project and contribute. To install diffpy.snmf
 in a development mode, with its sources being directly used by Python

doc/source/api/diffpy.snmf.rst

@@ -1,30 +1,68 @@
 :tocdepth: -1
 
-|title|
-=======
-
-.. |title| replace:: diffpy.snmf package
+diffpy.snmf package
+===================
 
 .. automodule:: diffpy.snmf
     :members:
     :undoc-members:
     :show-inheritance:
 
-Subpackages
------------
-
-.. toctree::
-   diffpy.snmf.example_package
-
 Submodules
 ----------
 
-|module|
---------
+diffpy.snmf.subroutines module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.snmf.subroutines
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.snmf.containers module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.snmf.containers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.snmf.io module
+^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.snmf.io
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.snmf.polynomials module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.snmf.polynomials
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.snmf.optimizers module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.snmf.optimizers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.snmf.factorizers module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.snmf.factorizers
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
-.. |module| replace:: diffpy.snmf.example_submodule module
+diffpy.snmf.stretchednmfapp module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.snmf.example_submodule
+.. automodule:: diffpy.snmf.stretchednmfapp
     :members:
     :undoc-members:
     :show-inheritance:

doc/source/conf.py

@@ -32,7 +32,7 @@
 sys.path.insert(0, str(Path("../../src").resolve()))
 
 # abbreviations
-ab_authors = "Simon J.L. Billinge group"
+ab_authors = "Billinge Group members and community contributors"
 
 # -- General configuration ------------------------------------------------
 

doc/source/license.rst

@@ -9,7 +9,7 @@ OPEN SOURCE LICENSE AGREEMENT
 =============================
 BSD 3-Clause License
 
-Copyright (c) 2025, The Trustees of Columbia University in the City of New York.
+Copyright (c) 2024-2025, 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