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zmx27pre-commit-ci[bot]
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skpkg: setup CI after migrating tests, src, requirements, and .github folder (#151)
* skpkg: migrate src folder * skpkg: migrate tests folder * skpkg: list dependencies in requirements folder * skpkg: add CI and issue/PR templates * skpkg: add pyproject.toml * skpkg: standardize files by removing examples and adding back necessary scripts * skpkg: modify copyright years and contributors in a missed file * style: changed line length to 115 and ran pre-commit again * fix: testing if adding .github/workflow will pass CI * [pre-commit.ci] auto fixes from pre-commit hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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‎.codecov.yml

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

‎.github/ISSUE_TEMPLATE/release_checklist.md

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- [ ] All the badges on the README are passing.
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- [ ] License information is verified as correct. If you are unsure, please comment below.
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- [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are
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missing), tutorials, and other human written text is up-to-date with any changes in the code.
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missing), tutorials, and other human written text is up-to-date with any changes in the code.
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- [ ] Installation instructions in the README, documentation and on the website (e.g., diffpy.org) are updated.
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- [ ] Successfully run any tutorial examples or do functional testing with the latest Python version.
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- [ ] Grammar and writing quality are checked (no typos).
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<!-- Before closing this issue, please complete the following: -->
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- [ ] Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
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- [ ] Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.
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- [ ] Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
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- [ ] Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.

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

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workflow_dispatch:
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push:
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tags:
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- '*' # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
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- "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
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jobs:
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release:
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uses: Billingegroup/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
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uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
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with:
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project: diffpy.snmf
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c_extension: false
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maintainer_GITHUB_username: sbillinge
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secrets:
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PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
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PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

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

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on:
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pull_request_target:
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branches:
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- main
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- main
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jobs:
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build:
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uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
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check-news-item:
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uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0
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with:
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project: diffpy.snmf

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

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

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

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

‎.github/workflows/tests-on-pr.yml

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name: Tests on PR
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on:
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push:
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branches:
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- main
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pull_request:
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workflow_dispatch:
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jobs:
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validate:
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uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
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tests-on-pr:
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uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0
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with:
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c_extension: false

‎.gitignore

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.Python
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env/
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build/
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_build/
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develop-eggs/
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dist/
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downloads/
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# Ipython Notebook
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.ipynb_checkpoints
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# version information
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setup.cfg
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/src/diffpy/*/version.cfg
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# Rever
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rever/

‎.pre-commit-config.yaml

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

‎pyproject.toml

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name = "diffpy.snmf"
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dynamic=['version', 'dependencies']
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authors = [
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{ name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
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{ name="Simon J.L. Billinge group", email="sb2896@columbia.edu" },
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]
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maintainers = [
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{ name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
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{ name="Simon J.L. Billinge group", email="sb2896@columbia.edu" },
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]
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description = "Python package implementing the stretched NMF algorithm."
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keywords = ['diffpy', 'PDF']
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readme = "README.rst"
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requires-python = ">=3.11, <3.14"
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classifiers = [
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'Development Status :: 4 - Beta',
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'Development Status :: 5 - Production/Stable',
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'Environment :: Console',
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'Intended Audience :: Developers',
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'Intended Audience :: Science/Research',

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