Re-cookiecut

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

@@ -0,0 +1,12 @@
+name: Check for News
+
+on:
+  pull_request_target:
+    branches:
+    - main
+
+jobs:
+  build:
+    uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
+    with:
+      project: diffpy.structure

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

@@ -0,0 +1,21 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - prereleased
+      - published
+  workflow_dispatch: null
+
+jobs:
+  coverage:
+    uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+    with:
+      project: diffpy.structure
+      c_extension: false
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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

@@ -0,0 +1,14 @@
+name: Build and Deploy Docs
+
+on:
+  release:
+    types:
+      - published
+  workflow_dispatch:
+
+jobs:
+  docs:
+    uses: Billingegroup/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
+    with:
+      project: diffpy.structure
+      c_extension: false

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

@@ -0,0 +1,16 @@
+name: Tests on PR
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  validate:
+    uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
+    with:
+      project: diffpy.structure
+      c_extension: false
+      headless: false

.pre-commit-config.yaml

@@ -16,7 +16,10 @@ repos:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-        exclude: '\.(rst|txt)$'
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-added-large-files
   - repo: https://github.com/psf/black
     rev: 24.4.2
     hooks:

AUTHORS.rst

@@ -1,6 +1,7 @@
 Authors
 =======
 
+Billinge Group and community contributors,
 Pavol Juhas,
 Christopher L. Farrow,
 Xiaohao Yang,

LICENSE.rst

@@ -15,7 +15,7 @@ Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP")
 
 Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National Laboratory
 
-Copyright (c) 2024, The Trustees of Columbia University in the City of New York. 
+Copyright (c) 2024, The Trustees of Columbia University in the City of New York.
 All rights reserved.
 
 The "DiffPy-CMI" is distributed subject to the following license conditions:

LICENSE_DANSE.rst

@@ -9,13 +9,13 @@ Copyright 2006-2007, Board of Trustees of Michigan State University,
 Copyright 2008-2012, The Trustees of Columbia University in the
 City of New York.  (Copyright holder indicated in each source file).
 
-Copyright (c) 2024, The Trustees of Columbia University in the City of New York. 
+Copyright (c) 2024, The Trustees of Columbia University in the City of New York.
 All rights reserved.
 
 For more information please visit the project web-page:
 
     http://www.diffpy.org/
-    
+
 or email Prof. Simon Billinge at sb2896@columbia.edu
 
 Redistribution and use in source and binary forms, with or without

LICENSE_pymmlib.rst

@@ -1,5 +1,5 @@
 .. code-block:: text
-        
+
                         The Artistic License 2.0
 
                 Copyright (c) 2000-2006, The Perl Foundation.

README.rst

@@ -15,8 +15,8 @@
 .. |Black| image:: https://img.shields.io/badge/code_style-black-black
         :target: https://github.com/psf/black
 
-.. |CI| image:: https://github.com/diffpy/diffpy.structure/actions/workflows/main.yml/badge.svg
-        :target: https://github.com/diffpy/diffpy.structure/actions/workflows/main.yml
+.. |CI| image:: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.structure/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.structure
@@ -47,6 +47,7 @@ of symmetry constraints for atom positions and displacement parameters.
 diffpy.structure includes definitions of all space groups in over 500
 symmetry settings.
 
+
 For more information about the diffpy.structure library, please consult our `online documentation <https://diffpy.github.io/diffpy.structure>`_.
 
 Citation
@@ -86,11 +87,7 @@ Then, to fully install ``diffpy.structure`` in our active environment, run ::
 
 Another option is to use ``pip`` to download and install the latest release from
 `Python Package Index <https://pypi.python.org>`_.
-To install using ``pip`` into your ``diffpy.structure_env`` environment, we will also have to install dependencies ::
-
-        pip install -r https://raw.githubusercontent.com/diffpy/diffpy.structure/main/requirements/run.txt
-
-and then install the package ::
+To install using ``pip`` into your ``diffpy.structure_env`` environment, type ::
 
         pip install diffpy.structure
 
@@ -105,7 +102,7 @@ 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.structure. Please join the diffpy.structure users community by joining the Google group. The diffpy.structure 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.structure/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.structure/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.structure/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.structure/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.structure
 in a development mode, with its sources being directly used by Python