sp2

.codecov.yml

@@ -10,7 +10,7 @@ coverage:
   status:
     patch:
       default:
-        target: '80'
+        target: "80"
         if_no_uploads: error
         if_not_found: success
         if_ci_failed: failure
@@ -21,11 +21,11 @@ coverage:
         if_no_uploads: error
         if_not_found: success
         if_ci_failed: failure
-        paths: '!*/tests/.*'
+        paths: "!*/tests/.*"
 
       tests:
         target: 97.9%
-        paths: '*/tests/.*'
+        paths: "*/tests/.*"
 
 flags:
   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 +1,8 @@
+;; 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
+
+;; Frobenius norm used in np.linalg.norm
+fro

.flake8

@@ -0,0 +1,13 @@
+# As of now, flake8 does not natively support configuration via pyproject.toml
+# https://github.com/microsoft/vscode-flake8/issues/135
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    doc/source/conf.py
+max-line-length = 79
+# Ignore some style 'errors' produced while formatting by 'black'
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
+extend-ignore = E203

.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 +1,46 @@
+---
+name: Release
+about: Checklist and communication channel for PyPI and GitHub release
+title: "Ready for <version-number> PyPI/GitHub release"
+labels: "release"
+assignees: ""
+---
+
+### 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 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 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://<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.
+- [ ] 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.

.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

@@ -0,0 +1,18 @@
+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: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
+    with:
+      project: diffpy.srfit
+      c_extension: false
+      maintainer_GITHUB_username: sbillinge
+    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:
+  check-news-item:
+    uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0
+    with:
+      project: diffpy.srfit

.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:
+  matrix-coverage:
+    uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+    with:
+      project: diffpy.srfit
+      c_extension: false
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.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.srfit
+      c_extension: false
+      headless: false

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

@@ -0,0 +1,15 @@
+name: Tests on PR
+
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  tests-on-pr:
+    uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0
+    with:
+      project: diffpy.srfit
+      c_extension: false
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -1,44 +1,93 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
 *.py[cod]
+*$py.class
 
 # C extensions
 *.so
 
-# Packages
-*.egg
-*.egg-info
-dist
-build
-eggs
-parts
-bin
-var
-sdist
-temp
-develop-eggs
+# Distribution / packaging
+.Python
+env/
+build/
+_build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+venv/
+*.egg-info/
 .installed.cfg
-lib
-lib64
-tags
+*.egg
+bin/
+temp/
+tags/
 errors.err
 
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
 # Installer logs
 pip-log.txt
+pip-delete-this-directory.txt
 MANIFEST
 
 # Unit test / coverage reports
+htmlcov/
+.tox/
 .coverage
-.tox
+.coverage.*
+.cache
 nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
 
 # Translations
 *.mo
+*.pot
 
 # Mr Developer
 .mr.developer.cfg
 .project
 .pydevproject
-.settings
 
-# version information
-setup.cfg
-/src/diffpy/*/version.cfg
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/build/
+docs/source/generated/
+
+# pytest
+.pytest_cache/
+
+# PyBuilder
+target/
+
+# Editor files
+# mac
+.DS_Store
+*~
+
+# vim
+*.swp
+*.swo
+
+# pycharm
+.idea/
+
+# VSCode
+.vscode/
+
+# Ipython Notebook
+.ipynb_checkpoints

.isort.cfg

@@ -0,0 +1,5 @@
+[settings]
+# Keep import statement below line_length character limit
+line_length = 79
+multi_line_output = 3
+include_trailing_comma = True

.pre-commit-config.yaml

@@ -0,0 +1,66 @@
+default_language_version:
+  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
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - 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:
+      - id: black
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: no-commit-to-branch
+        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
+  # 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]