Merge pull request #140 from diffpy/migration

skpkg: pdffit2 up to scikit-package 0.1.0 standards

Author: sbillinge

.codespell/ignore_words.txt

@@ -4,14 +4,24 @@
 ;; abbreviation for "materials" often used in a journal title
 mater
 
-;; alternative use of socioeconomic
-socio-economic
-
 ;; Frobenius norm used in np.linalg.norm
 fro
 
 ;; class name within distutils module
 ccompiler
 
+;; dum as a C variable
+dum
+
+;; gaus used for gaussian
+gaus
+
 ;; structure file format
-discus
+DISCUS
+
+;; Periodic table elements
+Te
+Nd
+
+;; Ois
+Ois

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -13,30 +13,30 @@ assignees: ""
 - [ ] 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.
-- [ ] Installation instructions in the README, documentation, and the website (e.g., diffpy.org) are updated.
+- [ ] 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.
 
-Please mention @sbillinge here when you are ready for PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here:
+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:
 
 ### PyPI/GitHub full-release preparation checklist:
 
 - [ ] Create a new conda environment and install the rc from PyPI (`pip install <package-name>==??`)
 - [ ] License information on PyPI is correct.
-- [ ] Docs are deployed successfully to `https://www.diffpy.org/<package-name>`.
+- [ ] Docs are deployed successfully to `https://<github-username-or-orgname>/<package-name>`.
 - [ ] Successfully run all tests, tutorial examples or do functional testing.
 
-Please let @sbillinge know that all checks are done and the package is ready for full release.
+Please let the maintainer know that all checks are done and the package is ready for full release.
 
 ### conda-forge release preparation checklist:
 
-<!-- After @sbillinge releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
+<!-- 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.
-- [ ] Close any open issues on the feedstock. Reach out to @bobleesj if you have questions.
-- [ ] Tag @sbillinge and @bobleesj for conda-forge release.
+- [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions.
+- [ ] Tag the maintainer for conda-forge release.
 
 ### Post-release checklist
 

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -0,0 +1,15 @@
+### What problem does this PR address?
+
+<!-- Provide a brief overview and link to the issue. Attach outputs, including screenshots (before/after), if helpful for the reviewer. -->
+
+### What should the reviewer(s) do?
+
+<!-- Merge the code, provide feedback, initiate a discussion, etc. -->
+
+<!--
+Use the following checklist items when applicable (select only what applies):
+- [ ] This PR introduces a public-facing change (e.g., figures, CLI input/output, API).
+    - [ ] Documentation (e.g., tutorials, examples, README) has been updated.
+    - [ ] A tracking issue or plan to update documentation exists.
+- [ ] This PR affects internal functionality only (no user-facing change).
+-->

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

@@ -8,12 +8,11 @@ on:
 
 jobs:
   release:
-    uses: Billingegroup/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
       project: diffpy.pdffit2
       c_extension: true
-      github_admin_username: sbillinge
-
+      maintainer_GITHUB_username: sbillinge
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

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

@@ -7,6 +7,6 @@ on:
 
 jobs:
   check-news-item:
-    uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
       project: diffpy.pdffit2

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

@@ -12,10 +12,9 @@ on:
 
 jobs:
   matrix-coverage:
-    uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
       project: diffpy.pdffit2
-      python_versions: "3.11, 3.12, 3.13"
       c_extension: true
       headless: false
     secrets:

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

@@ -1,17 +1,12 @@
 name: Deploy Documentation on Release
 
 on:
-  release:
-    types: [published]
   workflow_dispatch:
 
 jobs:
   docs:
-    permissions:
-      contents: write
-    uses: Billingegroup/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
     with:
       project: diffpy.pdffit2
       c_extension: true
       headless: false
-      python_version: 3.13

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

@@ -1,19 +1,15 @@
 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
+  tests-on-pr:
+    uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0
     with:
-      project: diffpy.pdffi2
+      project: diffpy.pdffit2
       c_extension: true
       headless: false
-      python_version: 3.13
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -10,6 +10,7 @@ __pycache__/
 .Python
 env/
 build/
+_build/
 develop-eggs/
 dist/
 downloads/
@@ -90,10 +91,3 @@ target/
 
 # Ipython Notebook
 .ipynb_checkpoints
-
-# version information
-setup.cfg
-/src/diffpy/*/version.cfg
-
-# Rever
-rever/

.readthedocs.yaml

@@ -0,0 +1,13 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "latest"
+
+python:
+  install:
+    - requirements: requirements/docs.txt
+
+sphinx:
+  configuration: doc/source/conf.py

CHANGELOG.rst

@@ -1,5 +1,5 @@
 =============
-Release Notes
+Release notes
 =============
 
 .. current developments
@@ -65,7 +65,7 @@ Release Notes
 * No notable functional changes from 1.4.1
 
 1.4.4rc0
-=====
+========
 
 **Fixed:**
 

CODE_OF_CONDUCT.rst

@@ -8,7 +8,7 @@ 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, socio-economic status,
+identity and expression, level of experience, education, socioeconomic status,
 nationality, personal appearance, race, caste, color, religion, or sexual
 identity and orientation.
 

LICENSE.rst

@@ -13,7 +13,7 @@ the following paper in your publication:
         in crystals (https://stacks.iop.org/0953-8984/19/335219), *J. Phys.: Condens. Matter*, 19, 335219 (2007)
 
 Copyright 2006-2007, Board of Trustees of Michigan State University,
-Copyright 2008-2024, Board of Trustees of Columbia University in the
+Copyright 2008-2025, Board of Trustees of Columbia University in the
 city of New York.  (Copyright holder indicated in each source file).
 
 For more information please visit the project web-page:

README.rst

@@ -8,7 +8,7 @@
         :target: https://diffpy.github.io/diffpy.pdffit2
         :height: 100px
 
-|PyPi| |Forge| |PythonVersion| |PR|
+|PyPI| |Forge| |PythonVersion| |PR|
 
 |CI| |Codecov| |Black| |Tracking|
 
@@ -26,7 +26,7 @@
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
 
-.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.pdffit2
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.pdffit2
         :target: https://pypi.org/project/diffpy.pdffit2/
 
 .. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.pdffit2
@@ -87,19 +87,17 @@ The preferred method is to use `Miniconda Python
 <https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_
 and install from the "conda-forge" channel of Conda packages.
 
-Add the "conda-forge" channel by running the following command in a terminal: ::
+To add "conda-forge" to the conda channels, run the following in a terminal. ::
 
         conda config --add channels conda-forge
 
-Create a new environment named ``diffpy.pdffit2_env`` and install ``diffpy.pdffit2``: ::
+We want to install our packages in a suitable conda environment.
+The following creates and activates a new environment named ``diffpy.pdffit2_env`` ::
 
         conda create -n diffpy.pdffit2_env diffpy.pdffit2
-
-Activate the environment: ::
-
         conda activate diffpy.pdffit2_env
 
-Confirm that the installation was successful: ::
+To confirm that the installation was successful, type ::
 
         python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)"
 
@@ -118,25 +116,20 @@ Install pdffit2 using ``pip`` to download and install the latest version from `P
 
         pip install diffpy.pdffit2
 
-Confirm that the installation was successful: ::
+To confirm that the installation was successful, type ::
 
         python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)"
 
-Build from source
-~~~~~~~~~~~~~~~~~
+If you prefer to install from sources, after installing the dependencies, obtain the source archive from
+`GitHub <https://github.com/diffpy/diffpy.pdffit2/>`_. Once installed, ``cd`` into your ``diffpy.pdffit2`` directory
+and run the following ::
 
-For advanced users, obtain the source archive, and in the ``diffpy.pdffit2`` directory, run ::
+        pip install .
 
-        conda create -n diffpy.pdffit2_env python=3.13 \
-                --file requirements/test.txt \
-                --file requirements/conda.txt \
-                --file requirements/build.txt
+Getting Started
+---------------
 
-Activate the environment, build the package, and run unit tests by following commands sequentially: ::
-
-        conda activate diffpy.pdffit2_env
-        pip install . --no-deps
-        pytest
+You may consult our `online documentation <https://diffpy.github.io/diffpy.pdffit2>`_ for tutorials and API references.
 
 Support and Contribute
 ----------------------
@@ -182,4 +175,9 @@ Before contributing, please read our `Code of Conduct <https://github.com/diffpy
 Contact
 -------
 
-For more information on diffpy.pdffit2 please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at [email protected].
+For more information on diffpy.pdffit2 please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at [email protected].
+
+Acknowledgements
+----------------
+
+``diffpy.pdffit2`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.

doc/source/api/diffpy.pdffit2.rst

@@ -1,7 +1,9 @@
 :tocdepth: -1
 
-diffpy.pdffit2 package
-======================
+|title|
+=======
+
+.. |title| replace:: diffpy.pdffit2 package
 
 .. automodule:: diffpy.pdffit2
     :members: