Merge pull request #152 from stevenhua0320/skpkg-update

skpkg: redo scikit-package with latest version with minimal fix

Author: sbillinge

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -11,12 +11,13 @@ assignees: ""
 - [ ] All PRs/issues attached to the release are merged.
 - [ ] All the badges on the README are passing.
 - [ ] License information is verified as correct. If you are unsure, please comment below.
-- [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are
-      missing), tutorials, and other human-written text is up-to-date with any changes in the code.
+- [ ] Locally rendered documentation contains all appropriate pages, tutorials, and other human-written text is up-to-date with any changes in the code.
+- [ ] All API references are included. To check this, run `conda install scikit-package` and then `package build api-doc`. Review any edits made by rerendering the docs locally.
 - [ ] Installation instructions in the README, documentation, and the website are updated.
 - [ ] Successfully run any tutorial examples or do functional testing with the latest Python version.
 - [ ] Grammar and writing quality are checked (no typos).
 - [ ] Install `pip install build twine`, run `python -m build` and `twine check dist/*` to ensure that the package can be built and is correctly formatted for PyPI release.
+- [ ] Dispatch matrix testing to test the release on all Python versions and systems. If you do not have permission to run this workflow, tag the maintainer and say `@maintainer, please dispatch matrix testing workflow`.
 
 Please tag the maintainer (e.g., @username) in the comment here when you are ready for the PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here:
 

.github/workflows/build-and-publish-docs-on-dispatch.yml

@@ -0,0 +1,18 @@
+name: Build and Publish Docs on Dispatch
+
+on:
+  workflow_dispatch:
+
+jobs:
+  get-python-version:
+    uses: scikit-package/release-scripts/.github/workflows/_get-python-version-latest.yml@v0
+    with:
+      python_version: 0
+
+  docs:
+    uses: scikit-package/release-scripts/.github/workflows/_release-docs.yml@v0
+    with:
+      project: diffpy.structure
+      c_extension: false
+      headless: false
+      python_version: ${{ fromJSON(needs.get-python-version.outputs.latest_python_version) }}

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

@@ -1,4 +1,4 @@
-name: Release (GitHub/PyPI) and Deploy Docs
+name: Build Wheel, Release on GitHub/PyPI, and Deploy Docs
 
 on:
   workflow_dispatch:
@@ -7,7 +7,7 @@ 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.structure

.github/workflows/matrix-and-codecov.yml

@@ -0,0 +1,21 @@
+name: Matrix and Codecov
+
+on:
+  # push:
+  #   branches:
+  #     - main
+  release:
+    types:
+      - prereleased
+      - published
+  workflow_dispatch:
+
+jobs:
+  matrix-coverage:
+    uses: scikit-package/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 }}

CODE-OF-CONDUCT.rst

@@ -67,7 +67,7 @@ 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.
+sbillinge@ucsb.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.

README.rst

@@ -25,6 +25,7 @@
         :target: https://anaconda.org/conda-forge/diffpy.structure
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.structure/pulls
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.structure
         :target: https://pypi.org/project/diffpy.structure/
@@ -99,6 +100,19 @@ and run the following ::
 
         pip install .
 
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.structure --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.structure; print(diffpy.structure.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.structure -h
+
 Getting Started
 ---------------
 
@@ -134,8 +148,15 @@ Improvements and fixes are always appreciated.
 
 Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE-OF-CONDUCT.rst>`_.
 
-Acknowledgement
----------------
+Contact
+-------
+
+For more information on diffpy.structure please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainer``Simon Billinge(sbillinge@ucsb.edu)``.
+
+Acknowledgements
+----------------
+
+``diffpy.structure`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
 
 Space group codes in *spacegroupmod.py* and *mmlibspacegroups.py*
 originate from the `pymmlib project <http://pymmlib.sourceforge.net>`_.
@@ -144,8 +165,3 @@ Less common settings of space groups were generating using the
 `Computational Crystallography Toolbox <http://cctbx.sourceforge.net>`_.
 
 ``diffpy.structure`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
-
-Contact
--------
-
-For more information on diffpy.structure please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at sb2896@columbia.edu.

cookiecutter.json

@@ -0,0 +1,20 @@
+{
+  "author_names": "Simon Billinge, Sangjoon Bob Lee",
+  "author_emails": "sbillinge@ucsb.edu, sl5400@columbia.edu",
+  "maintainer_names": "Simon Billinge, Sangjoon Bob Lee",
+  "maintainer_emails": "sbillinge@ucsb.edu, sl5400@columbia.edu",
+  "maintainer_github_usernames": "sbillinge, bobleesj",
+  "contributors": "Chris Farrow, Pavol Juhas, Simon Billinge, Billinge Group members",
+  "license_holders": "The Trustees of Columbia University in the City of New York",
+  "project_name": "diffpy.structure",
+  "github_username_or_orgname": "diffpy",
+  "github_repo_name": "diffpy.structure",
+  "conda_pypi_package_dist_name": "diffpy.structure",
+  "package_dir_name": "diffpy.structure",
+  "project_short_description": "Crystal structure container and parsers for structure formats.",
+  "project_keywords": "diffpy, crystal structure data storage, CIF, PDB",
+  "minimum_supported_python_version": "3.12",
+  "maximum_supported_python_version": "3.14",
+  "project_needs_c_code_compiled": "No",
+  "project_has_gui_tests": "No"
+}

docs/source/api/diffpy.structure.rst

@@ -1,7 +1,9 @@
 :tocdepth: -1
 
-diffpy.structure package
-========================
+|title|
+=======
+
+.. |title| replace:: diffpy.structure package
 
 .. automodule:: diffpy.structure
     :members:

docs/source/conf.py

@@ -32,7 +32,7 @@
 sys.path.insert(0, str(Path("../../src").resolve()))
 
 # abbreviations
-ab_authors = "Chris Farrow, Pavol Juhas,  Simon Billinge, Billinge Group members"
+ab_authors = "Chris Farrow, Pavol Juhas, Simon Billinge, Billinge Group members"
 
 # -- General configuration ------------------------------------------------
 
@@ -50,7 +50,7 @@
     "sphinx.ext.intersphinx",
     "sphinx_rtd_theme",
     "sphinx_copybutton",
-    "m2r",
+    "m2r2",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -222,7 +222,7 @@
 
 # Output file base name for HTML help builder.
 basename = "diffpy.structure".replace(" ", "").replace(".", "")
-htmlhelp_basename = basename + "docs"
+htmlhelp_basename = basename + "doc"
 
 
 # -- Options for LaTeX output ---------------------------------------------

docs/source/index.rst

@@ -4,11 +4,15 @@
 
 .. |title| replace:: diffpy.structure documentation
 
-diffpy.structure - Crystal structure container and parsers for structure formats.
+``diffpy.structure`` - Crystal structure container and parsers for structure formats.
 
-| Software version |release|.
+| Software version |release|
 | Last updated |today|.
 
+===============
+Getting started
+===============
+
 The diffpy.structure package provides objects for storing atomic
 coordinates, displacement parameters and other crystal structure data.
 diffpy.structure supports import and export of structure data in several
@@ -22,16 +26,19 @@ includes definitions of all space groups in over 500 symmetry settings.
 Authors
 =======
 
-diffpy.structure is developed by members of the Billinge Group at
-Columbia University and at Brookhaven National Laboratory including
-Pavol Juhás, Christopher L. Farrow, Xiaohao Yang, Simon J.L. Billinge.
-
-For a detailed list of contributors see
+``diffpy.structure`` is developed by Chris Farrow, Pavol Juhas, Simon Billinge, Billinge Group members. This project is maintained by Simon Billinge. For a detailed list of contributors see
 https://github.com/diffpy/diffpy.structure/graphs/contributors.
 
-===============
-Acknowledgments
-===============
+============
+Installation
+============
+
+See the `README <https://github.com/diffpy/diffpy.structure#installation>`_
+file included with the distribution.
+
+================
+Acknowledgements
+================
 
 Space group codes in *spacegroupmod.py* and *mmlibspacegroups.py*
 originate from the pymmlib project, http://pymmlib.sourceforge.net.
@@ -58,23 +65,15 @@ by citing the following paper in your publication:
    <http://dx.doi.org/10.1107/S2053273315014473>`__,
    *Acta Crystallogr. A* **71**, 562-568 (2015).
 
-============
-Installation
-============
-
-See the `README <https://github.com/diffpy/diffpy.structure#installation>`_
-file included with the distribution.
-
 =================
 Table of contents
 =================
-
 .. toctree::
-   :titlesonly:
+   :maxdepth: 2
 
-   license
-   release
    Package API <api/diffpy.structure>
+   release
+   license
 
 =======
 Indices