Cookiecutter - move tests folder, add entry point, conduct functional tests

.codespell/ignore_lines.txt

@@ -0,0 +1,2 @@
+;; Please include filenames and explanations for each ignored line.
+;; See https://docs.openverse.org/meta/codespell.html for docs.

.codespell/ignore_words.txt

@@ -0,0 +1,11 @@
+;; Please include explanations for each ignored word (lowercase).
+;; See https://docs.openverse.org/meta/codespell.html for docs.
+
+;; 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/bug_feature.md

@@ -0,0 +1,16 @@
+---
+name: Bug Report or Feature Request
+about: Report a bug or suggest a new feature!
+title: ""
+labels: ""
+assignees: ""
+---
+
+### Problem
+
+<!--
+For a bug report, please copy and paste any error messages from the application or command-line here.
+For a feature request, please state how the new functionality could benefit the community.
+-->
+
+### Proposed solution

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -0,0 +1,22 @@
+---
+name: Release
+about: Checklist and communication channel for PyPI and GitHub release
+title: "Ready for <version-number> PyPI/GitHub release"
+labels: "release"
+assignees: ""
+---
+
+### Release checklist for GitHub contributors
+
+- [ ] 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 and
+  tested
+- [ ] Successfully run any tutorial examples or do functional testing in some other way.
+- [ ] Grammar and writing quality have been checked (no typos).
+
+Please mention @sbillinge when you are ready for release. Include any additional comments necessary, such as
+version information and details about the pre-release.

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

@@ -0,0 +1,16 @@
+name: Release (GitHub/PyPI) and Deploy Docs
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - '*'  # 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
+    with:
+      project: diffpy.nmf_mapping
+    secrets:
+      PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+      PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

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

@@ -0,0 +1,12 @@
+name: Check for News
+
+on:
+  pull_request_target:
+    branches:
+    - main
+
+jobs:
+  build:
+    uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
+    with:
+      project: diffpy.nmf_mapping

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

@@ -0,0 +1,21 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - prereleased
+      - published
+  workflow_dispatch:
+
+jobs:
+  coverage:
+    uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+    with:
+      project: diffpy.nmf_mapping
+      c_extension: false
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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

@@ -0,0 +1,16 @@
+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
+    with:
+      project: diffpy.nmf_mapping
+      c_extension: false
+      headless: false

.pre-commit-config.yaml

@@ -16,7 +16,10 @@ repos:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-        exclude: '\.(rst|txt)$'
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-added-large-files
   - repo: https://github.com/psf/black
     rev: 24.4.2
     hooks:
@@ -41,3 +44,9 @@ repos:
         name: Prevent Commit to Main Branch
         args: ["--branch", "main"]
         stages: [pre-commit]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    - id: codespell
+      additional_dependencies:
+        - tomli

AUTHORS.rst

@@ -1,7 +1,9 @@
 Authors
 =======
 
-Billinge Group and community contibutors.
+Simon J. L. Billinge
+Zachary A. Thatcher
+Billinge Group and community contributors.
 
 Contributors
 ------------

MANIFEST.in

@@ -1,14 +1,12 @@
-include AUTHORS.rst
-include LICENSE
-include README.rst
-include requirements.txt
-
-recursive-exclude * __pycache__
-recursive-exclude * *.py[co]
-
-recursive-include docs *.rst conf.py Makefile make.bat
-
-include diffpy.nmf_mapping/version.py
-
-# If including data files in the package, add them like:
-# include path/to/data_file
+graft src
+graft tests
+graft requirements
+
+include AUTHORS.rst LICENSE*.rst README.rst
+
+# Exclude all bytecode files and __pycache__ directories
+global-exclude *.py[cod]  # Exclude all .pyc, .pyo, and .pyd files.
+global-exclude .DS_Store  # Exclude Mac filesystem artifacts.
+global-exclude __pycache__  # Exclude Python cache directories.
+global-exclude .git*  # Exclude git files and directories.
+global-exclude .idea  # Exclude PyCharm project settings.