uMigration

.flake8

@@ -1,3 +1,5 @@
+# As of now, flake8 does not natively support configuration via pyproject.toml
+# https://github.com/microsoft/vscode-flake8/issues/135
 [flake8]
 exclude =
     .git,

.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.pdfgui
       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.pdfgui

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

@@ -11,62 +11,11 @@ on:
   workflow_dispatch:
 
 jobs:
-  coverage:
-    defaults:
-      run:
-        shell: bash -l {0}
-
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
-        python-version: ["3.11", "3.12", "3.13"]
-    env:
-      LATEST_PYTHON_VERSION: "3.13"
-    steps:
-      - name: Check out diffpy.pdfgui
-        uses: actions/checkout@v4
-
-      - name: Initialize miniconda
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          activate-environment: test
-          miniforge-version: latest
-          environment-file: environment.yml
-          auto-activate-base: false
-          python-version: ${{ matrix.python-version }}
-
-      - name: Conda config
-        run: >-
-          conda config --set always_yes yes
-          --set changeps1 no
-
-      - name: Install diffpy.pdfgui and requirements
-        run: |
-          conda install --file requirements/test.txt
-          conda install wxpython diffpy.utils matplotlib-base
-          pip install diffpy.pdffit2==1.5.0rc1
-          python -m pip install . --no-deps
-
-      - name: Start Xvfb for ubuntu-latest only
-        if: matrix.os == 'ubuntu-latest'
-        run: |
-          sudo apt-get install -y xvfb
-          export DISPLAY=:99
-          Xvfb :99 -screen 0 1024x768x16 &
-
-      - name: Validate diffpy.pdfgui
-        run: |
-          if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
-            export DISPLAY=:99
-          fi
-          pytest --cov
-          coverage report -m
-          codecov
-
-      - name: Upload coverage to Codecov
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == env.LATEST_PYTHON_VERSION
-        uses: codecov/codecov-action@v4
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+  matrix-coverage:
+    uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+    with:
+      project: diffpy.pdfgui
+      c_extension: false
+      headless: true
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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

@@ -7,7 +7,7 @@ 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.pdfgui
       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.pdfgui
         :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.pdfgui
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.pdfgui
         :target: https://pypi.org/project/diffpy.pdfgui/
 
 .. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.pdfgui
@@ -35,7 +35,7 @@
 .. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
         :target: https://github.com/diffpy/diffpy.pdfgui/issues
 
-Graphical user interface program for structure refinements to atomic
+Graphical user interface program for structure refinements to the atomic
 pair distribution function.
 
 For users who do not have the expertise or necessity for command
@@ -167,4 +167,9 @@ Before contributing, please read our `Code of Conduct <https://github.com/diffpy
 Contact
 -------
 
-For more information on diffpy.pdfgui please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at [email protected].
+For more information on diffpy.pdfgui please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at [email protected].
+
+Acknowledgements
+----------------
+
+``diffpy.pdfgui`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.

doc/source/conf.py

@@ -13,6 +13,12 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
+# Attempt to import the version dynamically from GitHub tag.
+try:
+    fullversion = version("diffpy.pdfgui")
+except Exception:
+    fullversion = "No version found. The correct version will appear in the released version."  # noqa: E501
+
 import sys
 import time
 from importlib.metadata import version
@@ -42,6 +48,7 @@
     "sphinx.ext.todo",
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
+    "sphinx_copybutton",
     "sphinx_rtd_theme",
     "m2r",
 ]
@@ -64,6 +71,11 @@
 project = "diffpy.pdfgui"
 copyright = "%Y, The Trustees of Columbia University in the City of New York"
 
+# For sphinx_copybutton extension.
+# Do not copy "$" for shell commands in code-blocks.
+copybutton_prompt_text = r"^\$ "
+copybutton_prompt_is_regexp = True
+
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
@@ -123,6 +135,14 @@
 #
 html_theme = "sphinx_rtd_theme"
 
+html_context = {
+    "display_github": True,
+    "github_user": "diffpy",
+    "github_repo": "diffpy.pdfgui",
+    "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.
@@ -158,7 +178,7 @@
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
 # directly to the root of the documentation.
-html_extra_path = ["../manual"]
+html_extra_path = []
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
@@ -221,7 +241,13 @@
 # (source start file, target name, title,
 # author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    ("index", "diffpy.pdfgui.tex", "diffpy.pdfgui Documentation", ab_authors, "manual"),
+    (
+        "index",
+        "diffpy.pdfgui.tex",
+        "diffpy.pdfgui Documentation",
+        ab_authors,
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -249,7 +275,15 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [("index", "diffpy.pdfgui", "diffpy.pdfgui Documentation", ab_authors, 1)]
+man_pages = [
+    (
+        "index",
+        "diffpy.pdfgui",
+        "diffpy.pdfgui Documentation",
+        ab_authors,
+        1,
+    )
+]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False

doc/source/examples.rst

@@ -313,7 +313,7 @@ approx- imately 3nm in size.
 
 Input files:
 
-- :download:`Doping data series <manual_resources/Nanoparticle structure.zip>` containing:
+- :download:`Nanoparticle structure<manual_resources/Nanoparticle structure.zip>` containing:
 
   1. two PDF data collected from the bulk and naoparticle material.
   2. a project named ``CdSe-nano.ddp``

doc/source/index.rst

@@ -4,7 +4,7 @@
 
 .. |title| replace:: diffpy.pdfgui documentation
 
-diffpy.pdfgui - GUI for PDF simulation and structure refinement.
+``diffpy.pdfgui`` - Graphical user interface program for structure refinements to the atomic pair distribution function.
 
 | Software version |release|
 | Last updated |today|

doc/source/manual_resources/tui_mno_bond_lengths.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
-"""Extract the shortest Mn-O bond lengths from all fits in PDFgui project.
+"""Extract the shortest Mn-O bond lengths from all fits in PDFgui
+project.
 
 This script loops through all refined phases in PDFgui project and
 calculates their shortest Mn-O bond lengths using diffpy.pdffit2

doc/source/tutorial.rst

@@ -123,7 +123,7 @@ Procedure:
    factor, and a set of parameters intended to be used to account for
    correlated atomic motion effects that typically sharpen the nearest
    neighbor PDF peak. These are ``delta1``, ``delta2``, ``sratio``, and
-   ``rcut ``. The ``spdiameter`` and ``stepcut`` parameters include scatterer
+   ``rcut``. The ``spdiameter`` and ``stepcut`` parameters include scatterer
    size effects in the PDF. These parameters will be described later. The
    bottom part of the panel contains standard unit cell content related
    information such as atomic species, their fractional coordinates,

news/doc.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Support ``scikit-package`` Level 5 standard (https://scikit-package.github.io/scikit-package/).
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -6,12 +6,12 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.pdfgui"
 dynamic=['version', 'dependencies']
 authors = [
-  { name="Simon J.L. Billinge group", email="[email protected]" },
+  { name="Simon J.L. Billinge group", email="[email protected]" },
 ]
 maintainers = [
-  { name="Simon J.L. Billinge group", email="[email protected]" },
+  { name="Simon J.L. Billinge group", email="[email protected]" },
 ]
-description = "GUI for PDF simulation and structure refinement."
+description = "Graphical user interface program for structure refinements to the atomic pair distribution function."
 keywords = ['PDF structure refinement GUI']
 readme = "README.rst"
 requires-python = ">=3.11, <3.14"
@@ -81,3 +81,7 @@ exclude = '''
   | tests/data
 )/
 '''
+[tool.docformatter]
+recursive = true
+wrap-summaries = 72
+wrap-descriptions = 72

requirements/docs.txt

@@ -1,4 +1,5 @@
 sphinx
 sphinx_rtd_theme
+sphinx-copybutton
 doctr
 m2r

src/diffpy/pdfgui/applications/pdfgui.py

@@ -54,9 +54,9 @@ def version():
 
 
 def processArguments(argv1):
-    """Process command line arguments and store results in pdfguiglobals. This
-    method updates cmdopts, cmdargs and dbopts attributes in the pdfguiglobals
-    module.
+    """Process command line arguments and store results in
+    pdfguiglobals. This method updates cmdopts, cmdargs and dbopts
+    attributes in the pdfguiglobals module.
 
     argv1   -- list of command line arguments excluding the executable