skpkg: Migration

.codespell/ignore_words.txt

@@ -4,11 +4,5 @@
 ;; abbreviation for "materials" often used in a journal title
 mater
 
-;; alternative use of socioeconomic
-socio-economic
-
 ;; Frobenius norm used in np.linalg.norm
 fro
-
-;; cutted used as attribute in unit_test.py and fourigui.py
-cutted

.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

@@ -8,11 +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.fourigui
       c_extension: false
-      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.fourigui

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

@@ -12,7 +12,7 @@ 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.fourigui
       c_extension: false

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

@@ -5,7 +5,7 @@ on:
 
 jobs:
   docs:
-    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.fourigui
       c_extension: false

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

@@ -1,15 +1,12 @@
 name: Tests on PR
 
 on:
-  push:
-    branches:
-      - main
   pull_request:
   workflow_dispatch:
 
 jobs:
   tests-on-pr:
-    uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0
     with:
       project: diffpy.fourigui
       c_extension: false

.gitignore

@@ -10,6 +10,7 @@ __pycache__/
 .Python
 env/
 build/
+_build/
 develop-eggs/
 dist/
 downloads/

.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

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.
 

README.rst

@@ -8,7 +8,7 @@
         :target: https://diffpy.github.io/diffpy.fourigui
         :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.fourigui
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.fourigui
         :target: https://pypi.org/project/diffpy.fourigui/
 
 .. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.fourigui
@@ -129,4 +129,9 @@ Before contributing, please read our `Code of Conduct <https://github.com/diffpy
 Contact
 -------
 
-For more information on diffpy.fourigui please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at sb2896@columbia.edu.
+For more information on diffpy.fourigui please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at sb2896@columbia.edu.
+
+Acknowledgements
+----------------
+
+``diffpy.fourigui`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.

doc/make.bat

@@ -1,36 +1,36 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-set SPHINXPROJ=PackagingScientificPython
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=PackagingScientificPython
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

doc/source/api/diffpy.fourigui.rst

@@ -8,6 +8,12 @@ diffpy.fourigui package
     :undoc-members:
     :show-inheritance:
 
+Subpackages
+-----------
+
+.. toctree::
+   diffpy.fourigui.example_package
+
 Submodules
 ----------
 

doc/source/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# diffpy.fourigui documentation build configuration file, created by
+# diffpy.fourigui 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
@@ -18,9 +18,15 @@
 from importlib.metadata import version
 from pathlib import Path
 
+# Attempt to import the version dynamically from GitHub tag.
+try:
+    fullversion = version("diffpy.fourigui")
+except Exception:
+    fullversion = "No version found. The correct version will appear in the released version."  # noqa: E501
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
-# documentation root, use Path().resolve() to make it absolute, like shown here.
+# documentation root, use Path().resolve() to make it absolute, like shown here.  # noqa: E501
 # sys.path.insert(0, str(Path(".").resolve()))
 sys.path.insert(0, str(Path("../..").resolve()))
 sys.path.insert(0, str(Path("../../src").resolve()))
@@ -43,6 +49,7 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
     "sphinx_rtd_theme",
+    "sphinx_copybutton",
     "m2r",
 ]
 
@@ -90,6 +97,11 @@
 # substitute YEAR in the copyright string
 copyright = copyright.replace("%Y", year)
 
+# For sphinx_copybutton extension.
+# Do not copy "$" for shell commands in code-blocks.
+copybutton_prompt_text = r"^\$ "
+copybutton_prompt_is_regexp = True
+
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 exclude_patterns = ["build"]
@@ -125,6 +137,14 @@
 #
 html_theme = "sphinx_rtd_theme"
 
+html_context = {
+    "display_github": True,
+    "github_user": "diffpy",
+    "github_repo": "diffpy.fourigui",
+    "github_version": "main",
+    "conf_py_path": "/doc/source/",
+}
+
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.

doc/source/index.rst

@@ -4,19 +4,25 @@
 
 .. |title| replace:: diffpy.fourigui documentation
 
-diffpy.fourigui - Tool for visualizing 3D diffraction and PDF images.
+``diffpy.fourigui`` - Tool for visualizing 3D diffraction and PDF images.
 
-| Software version |release|.
+| Software version |release|
 | Last updated |today|.
 
+===============
+Getting started
+===============
+
+Welcome to the ``diffpy.fourigui`` documentation!
+
+To get started, please visit the :ref:`Getting started <getting-started>` page.
+
 =======
 Authors
 =======
 
-diffpy.fourigui is developed by Billinge Group
-and its community contributors.
-
-For a detailed list of contributors see
+``diffpy.fourigui`` is developed by Billinge Group
+and its community contributors. For a detailed list of contributors see
 https://github.com/diffpy/diffpy.fourigui/graphs/contributors.
 
 ============
@@ -26,16 +32,23 @@ Installation
 See the `README <https://github.com/diffpy/diffpy.fourigui#installation>`_
 file included with the distribution.
 
+================
+Acknowledgements
+================
+
+``diffpy.fourigui`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
+
 =================
 Table of contents
 =================
 .. toctree::
-   :titlesonly:
+   :maxdepth: 2
 
+   getting-started
    tutorial
-   license
-   release
    Package API <api/diffpy.fourigui>
+   release
+   license
 
 =======
 Indices