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Migration into main (#154)
* 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> * skpkg: add configuration files for pre-commit, readthedocs, codecov (#152) * skpkg: add config files for pre-commit * skpkg: add config files readthedocs, codecov, GitHub * style: remove stashed change indicators and modify code of conducts to pass pre-commit * skpkg: migrate documentation, README, and public static files (#153) * skpkg: migrate documentation * skpkg: add config files for authors, changelog, code of conduct, license * skpkg: add README.rst * skpkg: add news files * chore: add back necessary lines from the files * chore: fix files according to comments in the review --------- Co-authored-by: zmx27 <[email protected]> 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]

‎.codespell/ignore_words.txt

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;; abbreviation for "materials" often used in a journal title
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mater
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;; alternative use of socioeconomic
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socio-economic
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;; Frobenius norm used in np.linalg.norm
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fro

‎.flake8

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# As of now, flake8 does not natively support configuration via pyproject.toml
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# https://github.com/microsoft/vscode-flake8/issues/135
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[flake8]
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exclude =
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.git,

‎.github/ISSUE_TEMPLATE/release_checklist.md

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assignees: ""
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---
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### PyPI/GitHub release checklist:
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### PyPI/GitHub rc-release preparation checklist:
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- [ ] All PRs/issues attached to the release are merged.
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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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- [ ] Installation instructions in the README, documentation and on the website (e.g., diffpy.org) are updated.
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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 the website 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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- [ ] 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.
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Please mention @sbillinge here when you are ready for PyPI/GitHub release. Include any additional comments necessary, such as
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version information and details about the pre-release here:
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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:
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### conda-forge release checklist:
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### PyPI/GitHub full-release preparation checklist:
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<!-- After @sbillinge releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
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- [ ] Create a new conda environment and install the rc from PyPI (`pip install <package-name>==??`)
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- [ ] License information on PyPI is correct.
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- [ ] Docs are deployed successfully to `https://<github-username-or-orgname>/<package-name>`.
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- [ ] Successfully run all tests, tutorial examples or do functional testing.
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Please let the maintainer know that all checks are done and the package is ready for full release.
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### conda-forge release preparation checklist:
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<!-- After the maintainer releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
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- [ ] Ensure that the full release has appeared on PyPI successfully.
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- [ ] New package dependencies listed in `conda.txt` and `test.txt` are added to `meta.yaml` in the feedstock.
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- [ ] All relevant issues in the feedstock are addressed in the release PR.
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- [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions.
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- [ ] Tag the maintainer for conda-forge release.
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### Post-release checklist
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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/PULL_REQUEST_TEMPLATE/pull_request_template.md

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### What problem does this PR address?
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<!-- Provide a brief overview and link to the issue. Attach outputs, including screenshots (before/after), if helpful for the reviewer. -->
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### What should the reviewer(s) do?
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<!-- Merge the code, provide feedback, initiate a discussion, etc. -->
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<!--
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Use the following checklist items when applicable (select only what applies):
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- [ ] This PR introduces a public-facing change (e.g., figures, CLI input/output, API).
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- [ ] Documentation (e.g., tutorials, examples, README) has been updated.
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- [ ] A tracking issue or plan to update documentation exists.
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- [ ] This PR affects internal functionality only (no user-facing change).
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-->

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

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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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uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
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with:
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c_extension: false
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maintainer_GITHUB_username: sbillinge
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secrets:
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‎.github/workflows/check-news-item.yml

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

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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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‎.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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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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‎.gitignore

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_build/
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‎.isort.cfg

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[settings]
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# Keep import statement below line_length character limit
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line_length = 79
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‎.pre-commit-config.yaml

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default_language_version:
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python: python3
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ci:
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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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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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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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args: [--in-place, --config, ./pyproject.toml]

‎.readthedocs.yaml

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version: 2
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- requirements: requirements/docs.txt
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‎CHANGELOG.rst

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=============
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Release Notes
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Release notes
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=============
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‎CODE_OF_CONDUCT.rst

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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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identity and expression, level of experience, education, socio-economic status,
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identity and orientation.
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‎LICENSE.rst

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BSD 3-Clause License
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Copyright (c) 2023-2024, The Trustees of Columbia University
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in the City of New York.
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Copyright (c) 2023-2025, The Trustees of Columbia University in the City of New York.
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‎README.rst

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:target: https://diffpy.github.io/diffpy.snmf
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.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.snmf
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.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.snmf
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Contact
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For more information on diffpy.snmf please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at [email protected].
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For more information on diffpy.snmf please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon J.L. Billinge group at [email protected].
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Acknowledgements
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----------------
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``diffpy.snmf`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.

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