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chore: finalize pre-commit cleanup with spelling suppressions and formatting
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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_lines.txt

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;; Please include filenames and explanations for each ignored line.
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;; See https://docs.openverse.org/meta/codespell.html for docs.
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src/diffpy/structure/parsers/p_discus.py:.*DISCUS.* ;; DISCUS is a valid software/tool name
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src/diffpy/structure/parsers/p_discus.py:.*discus.* ;; Same reason as above, lowercase version
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src/diffpy/structure/parsers/p_pdb.py:.*CONECT.* ;; CONECT is a valid PDB record name
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src/diffpy/structure/parsers/p_xcfg.py:.*Te.* ;; Te is the chemical symbol for Tellurium
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src/diffpy/structure/parsers/p_xcfg.py:.*Nd.* ;; Nd is the chemical symbol for Neodymium
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src/diffpy/structure/parsers/p_xcfg.py:.*BU.* ;; BU is used in the file with intended meaning
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src/diffpy/structure/parsers/parser_index_mod.py:.*Discus.* ;; Capitalized variant
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src/diffpy/structure/parsers/parser_index_mod.py:.*discus.* ;; lowercase variant
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tests/test_loadstructure.py:.*discus.* ;; test file with valid usage
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tests/test_p_discus.py:.*discus.* ;; test file with valid usage

‎.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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- [ ] 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:

‎.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:

‎.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 = 115
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multi_line_output = 3
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include_trailing_comma = True

‎.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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name: Prevent Commit to Main Branch
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args: ["--branch", "main"]
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stages: [pre-commit]
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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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args:
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- "--ignore-words=.codespell/ignore_words.txt"
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- "--ignore-regex"
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- "(?i)\\b(discus|conect|te|nd|bu)\\b"
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exclude: .*/\.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]

‎CHANGELOG.rst

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**Fixed:**
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* Add getting started section and re-arrange install success check instructions
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* Added termial script for transtru app in pyproject.toml
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* Added terminal script for transtru app in pyproject.toml
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* Changed requires-python to align with classifiers
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‎README.rst

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Improvements and fixes are always appreciated.
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Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE-OF-CONDUCT.rst>`_.
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Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE-OF-CONDUCT.rst>`_.
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Acknowledgement
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---------------

‎devutils/sgtbx_extra_groups.py

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#!/usr/bin/env python
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"""Quick and extremely dirty script for generating code for SpaceGroup that
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are defined in cctbx, but not in mmLib. It was used to generate module
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"""Quick and extremely dirty script for generating code for SpaceGroup that are
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defined in cctbx, but not in mmLib. It was used to generate module
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sgtbxspacegroups.
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This is a utility script that should not be included with code distribution.
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This is a utility script that should not be included with code
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distribution.
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Not to be included with code distributions.
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"""

‎diffpy-structure/.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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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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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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hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage]

‎diffpy-structure/.codespell/ignore_lines.txt

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;; Please include filenames and explanations for each ignored line.
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;; See https://docs.openverse.org/meta/codespell.html for docs.

‎diffpy-structure/.codespell/ignore_words.txt

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;; Please include explanations for each ignored word (lowercase).
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;; See https://docs.openverse.org/meta/codespell.html for docs.
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;; abbreviation for "materials" often used in a journal title
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mater
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;; Frobenius norm used in np.linalg.norm
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fro

‎diffpy-structure/.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,
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__pycache__,
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build,
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dist,
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doc/source/conf.py
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max-line-length = 79
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# Ignore some style 'errors' produced while formatting by 'black'
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# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
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extend-ignore = E203

‎diffpy-structure/.github/ISSUE_TEMPLATE/bug_feature.md

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

‎diffpy-structure/.github/ISSUE_TEMPLATE/release_checklist.md

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---
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name: Release
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about: Checklist and communication channel for PyPI and GitHub release
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title: "Ready for <version-number> PyPI/GitHub release"
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labels: "release"
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assignees: ""
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---
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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 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 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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### PyPI/GitHub full-release preparation checklist:
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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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- [ ] 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.

‎diffpy-structure/.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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-->

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

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name: Release (GitHub/PyPI) and Deploy Docs
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on:
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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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jobs:
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release:
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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 }}

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

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name: Check for News
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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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jobs:
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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

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

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name: CI
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on:
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push:
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branches:
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- main
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release:
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types:
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- prereleased
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- published
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workflow_dispatch:
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jobs:
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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
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headless: false
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secrets:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

‎diffpy-structure/.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

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

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name: Tests on PR
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on:
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pull_request:
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workflow_dispatch:
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jobs:
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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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project: diffpy-structure
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c_extension: false
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headless: false
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secrets:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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