skpkg: setup CI after migrating src, tests, requirements, and .github directory

.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]

.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

@@ -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.nmf_mapping
+      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.nmf_mapping

.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.nmf_mapping
       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.nmf_mapping
+      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.nmf_mapping
       c_extension: false

.gitignore

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

.isort.cfg

@@ -1,4 +1,5 @@
 [settings]
+# Keep import statement below line_length character limit
 line_length = 115
 multi_line_output = 3
 include_trailing_comma = True

.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]

pyproject.toml

@@ -6,13 +6,13 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.nmf_mapping"
 dynamic=['version', 'dependencies']
 authors = [
-  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+  { name="Simon J.L. Billinge group", email="sb2896@columbia.edu" },
 ]
 maintainers = [
-  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+  { name="Simon J.L. Billinge group", email="sb2896@columbia.edu" },
 ]
 description = "Python package for running NMF analysis on PDF and XRD data."
-keywords = ['"diffpy"', '"PDF"', '"NMF"']
+keywords = ['diffpy', 'PDF', 'NMF']
 readme = "README.rst"
 requires-python = ">=3.11, <3.14"
 classifiers = [
@@ -42,9 +42,6 @@ template = "{tag}"
 dev_template = "{tag}"
 dirty_template = "{tag}"
 
-[project.scripts]
-snmf = "diffpy.nmf_mapping.main:main"
-
 [tool.setuptools.packages.find]
 where = ["src"]  # list of folders that contain the packages (["."] by default)
 include = ["*"]  # package names should match these glob patterns (["*"] by default)
@@ -59,8 +56,13 @@ exclude-file = ".codespell/ignore_lines.txt"
 ignore-words = ".codespell/ignore_words.txt"
 skip = "*.cif,*.dat"
 
+[tool.docformatter]
+recursive = true
+wrap-summaries = 72
+wrap-descriptions = 72
+
 [tool.black]
-line-length = 115
+line-length = 79
 include = '\.pyi?$'
 exclude = '''
 /(

requirements/docs.txt

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

src/__init__.py

@@ -12,7 +12,6 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
 """nmf_mapping - tools for performing NMF on PDF and XRD data."""
 
 

src/diffpy/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.
@@ -12,7 +12,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """Blank namespace package for module diffpy."""
 
 

src/diffpy/nmf_mapping/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.
@@ -12,11 +12,10 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """Python package for running NMF analysis on PDF and XRD data."""
 
 # package version
-from diffpy.nmf_mapping.version import __version__
+from diffpy.nmf_mapping.version import __version__  # noqa
 
 # silence the pyflakes syntax checker
 assert __version__ or True