chore: move necessary files over to scaffold

.codecov.yml

@@ -1,14 +1,14 @@
 coverage:
   status:
-    project:  # more options at https://docs.codecov.com/docs/commit-status
+    project: # more options at https://docs.codecov.com/docs/commit-status
       default:
         target: auto # use the coverage from the base commit, fail if coverage is lower
-        threshold: 0%  # allow the coverage to drop by
+        threshold: 0% # allow the coverage to drop by
 
 comment:
   layout: " diff, flags, files"
   behavior: default
   require_changes: false
-  require_base: false  # [true :: must have a base report to post]
-  require_head: false  # [true :: must have a head report to post]
+  require_base: false # [true :: must have a base report to post]
+  require_head: false # [true :: must have a head report to post]
   hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage]

.codespell/ignore_words.txt

@@ -4,8 +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

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -6,30 +6,41 @@ labels: "release"
 assignees: ""
 ---
 
-### PyPI/GitHub release checklist:
+### PyPI/GitHub rc-release preparation checklist:
 
 - [ ] 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.
-- [ ] Installation instructions in the README, documentation and on the website (e.g., diffpy.org) are updated.
+      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 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:
 
-### conda-forge release checklist:
+### PyPI/GitHub full-release preparation checklist:
 
-<!-- After @sbillinge releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
+- [ ] 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://<github-username-or-orgname>/<package-name>`.
+- [ ] Successfully run all tests, tutorial examples or do functional testing.
 
+Please let the maintainer know that all checks are done and the package is ready for full release.
+
+### conda-forge release preparation checklist:
+
+<!-- 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.
-- [ ] All relevant issues in the feedstock are addressed in the release PR.
+- [ ] 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
 
 <!-- Before closing this issue, please complete the following: -->
 
-- [ ]  Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
-- [ ]  Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.
+- [ ] Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
+- [ ] Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.

.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

@@ -4,13 +4,15 @@ on:
   workflow_dispatch:
   push:
     tags:
-      - '*'  # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
+      - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
 
 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.srmise
+      c_extension: false
+      maintainer_GITHUB_username: sbillinge
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

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

@@ -3,10 +3,10 @@ name: Check for News
 on:
   pull_request_target:
     branches:
-    - main
+      - main
 
 jobs:
-  build:
-    uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
+  check-news-item:
+    uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
       project: diffpy.srmise

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

@@ -11,8 +11,8 @@ on:
   workflow_dispatch:
 
 jobs:
-  coverage:
-    uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+  matrix-coverage:
+    uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
       project: diffpy.srmise
       c_extension: false

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

@@ -0,0 +1,12 @@
+name: Deploy Documentation on Release
+
+on:
+  workflow_dispatch:
+
+jobs:
+  docs:
+    uses: scikit-package/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
+    with:
+      project: diffpy.srmise
+      c_extension: false
+      headless: false

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

@@ -1,15 +1,12 @@
 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.srmise
       c_extension: false

.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 default_language_version:
-    python: python3
+  python: python3
 ci:
-    autofix_commit_msg: |
-        [pre-commit.ci] auto fixes from pre-commit hooks
-    autofix_prs: true
-    autoupdate_branch: 'pre-commit-autoupdate'
-    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
-    autoupdate_schedule: monthly
-    skip: [no-commit-to-branch]
-    submodules: false
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit hooks
+  autofix_prs: true
+  autoupdate_branch: "pre-commit-autoupdate"
+  autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate"
+  autoupdate_schedule: monthly
+  skip: [no-commit-to-branch]
+  submodules: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
@@ -47,6 +47,20 @@ repos:
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0
     hooks:
-    - id: codespell
-      additional_dependencies:
-        - tomli
+      - id: codespell
+        additional_dependencies:
+          - tomli
+  # prettier - multi formatter for .json, .yml, and .md files
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - "prettier@^3.2.4"
+  # docformatter - PEP 257 compliant docstring formatter
+  - repo: https://github.com/s-weigand/docformatter
+    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]

.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.
 

doc/examples/fit_initial.py

@@ -10,14 +10,16 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""Example of peak fitting C60 PDF (unnormalized) with unreliable uncertainties.
-
-Peak fitting in SrMise means fitting a model of initial peaks, which may be
-specified manually or estimated with a clustering-based convenience function,
-just as with specifying initial peaks for peak extraction.  Unlike peak
-extraction, it does not attempt to add or remove peaks, apply termination
-ripples, or otherwise do anything beyond chi-square fitting using the specified
-grid."""
+"""Example of peak fitting C60 PDF (unnormalized) with unreliable
+uncertainties.
+
+Peak fitting in SrMise means fitting a model of initial peaks, which may
+be specified manually or estimated with a clustering-based convenience
+function, just as with specifying initial peaks for peak extraction.
+Unlike peak extraction, it does not attempt to add or remove peaks,
+apply termination ripples, or otherwise do anything beyond chi-square
+fitting using the specified grid.
+"""
 
 import matplotlib.pyplot as plt
 

doc/examples/multimodel_known_dG1.py

@@ -10,8 +10,8 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""Extract multiple models from crystalline PDF with known uncertainties for
-use in later AIC-driven multimodeling analysis.
+"""Extract multiple models from crystalline PDF with known uncertainties
+for use in later AIC-driven multimodeling analysis.
 
 The multimodel approach generates many models of varying complexity by assuming
 a range of experimental uncertainties are physically plausible.  This example

doc/examples/multimodel_known_dG2.py

@@ -10,7 +10,8 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""AIC-driven multimodel analysis of crystalline PDF with known uncertainties.
+"""AIC-driven multimodel analysis of crystalline PDF with known
+uncertainties.
 
 The multimodel approach generates many models of varying complexity by assuming
 a range of experimental uncertainties are physically plausible.  This example

doc/examples/multimodel_unknown_dG1.py

@@ -10,8 +10,8 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""Extract multiple models from nanoparticle PDF with unknown uncertainties for
-use in later AIC-driven multimodeling analysis.
+"""Extract multiple models from nanoparticle PDF with unknown
+uncertainties for use in later AIC-driven multimodeling analysis.
 
 The multimodel approach generates many models of varying complexity by assuming
 a range of experimental uncertainties are physically plausible.  This example

doc/examples/parameter_summary.py

@@ -25,7 +25,8 @@
 nyquist (whether to use Nyquist sampling)
 supersample (minimum amount to oversample during initial stages)
 cres (clustering resolution)
-initial_peaks (peaks already assumed to exist during extraction)"""
+initial_peaks (peaks already assumed to exist during extraction)
+"""
 
 import matplotlib.pyplot as plt
 

doc/examples/query_results.py

@@ -10,7 +10,8 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""Example of extracting multiple peaks and accessing results programmatically.
+"""Example of extracting multiple peaks and accessing results
+programmatically.
 
 This example shows how to extract a range of peaks from a simple crystalline
 PDF using a crystalline baseline obtained from an existing trial.  It shows

pyproject.toml

@@ -67,6 +67,9 @@ skip = "*.cif,*.dat"
 recursive = true
 wrap-summaries = 72
 wrap-descriptions = 72
+exclude = [
+  "src/diffpy/srmise/baselines/arbitrary.py"
+]
 
 [tool.black]
 line-length = 115

requirements/docs.txt

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

src/diffpy/__init__.py

@@ -12,7 +12,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """Blank namespace package for module diffpy."""
 
 

src/diffpy/srmise/__init__.py

@@ -12,8 +12,8 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
-"""Peak extraction and peak fitting tool for atomic pair distribution functions."""
+"""Peak extraction and peak fitting tool for atomic pair distribution
+functions."""
 
 # package version
 from diffpy.srmise.version import __version__

src/diffpy/srmise/applications/plot.py

@@ -11,7 +11,7 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""plot extracted peaks and comparison to ideal distances (if given)"""
+"""Plot extracted peaks and comparison to ideal distances (if given)"""
 
 import optparse
 import sys
@@ -175,7 +175,7 @@ def labelallsubplots():
 
 
 def makeplot(ppe_or_stability, ip=None, **kwds):
-    """Plot stuff"""
+    """Plot stuff."""
     if isinstance(ppe_or_stability, PeakStability):
         stability = ppe_or_stability
         ppe = stability.ppe
@@ -530,7 +530,8 @@ def on_draw(event):
 
 
 def readcompare(filename):
-    """Returns a list of distances read from filename, otherwise None."""
+    """Returns a list of distances read from filename, otherwise
+    None."""
 
     # TODO: Make this safer
     try: