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Merge pull request #139 from TingwenZhang/level-5-2
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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
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;; "discus" is the name of a software package
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discus
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DISCUS
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;; chemical elements
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Te
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Nd
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;; /src/diffpy/structure/parsers/p_pdb.py:100
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;; pdb identifier
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CONECT
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;; /src/diffpy/structure/parsers/p_xcfg.py:452
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;; used in a function
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BU

‎.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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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.structure
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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.structure

‎.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.structure
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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.structure
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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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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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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/

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