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Merge pull request #18 from diffpy/migration
Migration
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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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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]

‎.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.

‎.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

‎.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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docs/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

‎.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

‎.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 `tests.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.

‎.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.yml‎

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name: Build Wheels and Release
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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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- "*"
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env:
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PYTHON_VERSIONS: '["3.11","3.12","3.13"]'
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permissions:
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contents: write
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actions: read
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packages: write
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concurrency:
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group: build-wheels-${{ github.ref }}
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cancel-in-progress: true
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defaults:
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run:
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shell: bash {0}
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jobs:
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get-python-versions:
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runs-on: ubuntu-latest
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outputs:
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py_ver: ${{ steps.set.outputs.py_ver }}
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py_last: ${{ steps.set.outputs.py_last }}
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steps:
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- id: set
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run: |
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echo py_ver=$PYTHON_VERSIONS >> $GITHUB_OUTPUT
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echo "py_last=${{ fromJson(env.PYTHON_VERSIONS)[0] }}" >> $GITHUB_OUTPUT
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check-tag-on-main:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository with full history
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uses: actions/checkout@v4
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with:
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token: ${{ secrets.PAT_TOKEN }}
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fetch-depth: 0
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- name: Verify tag
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run: |
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git fetch origin main
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TAG_COMMIT=$(git rev-parse ${{ github.ref_name }})
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if git merge-base --is-ancestor "$TAG_COMMIT" origin/main; then
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echo "Tag ${{ github.ref_name }} ($TAG_COMMIT) is contained in main"
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else
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echo "::error::Tag ${{ github.ref_name }} ($TAG_COMMIT) is not found in main. Please release from the main branch."
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exit 1
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fi
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check-tag-privilege:
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# No third party actions used
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uses: scikit-package/release-scripts/.github/workflows/_check-tag-privilege.yml@v0
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with:
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maintainer_github_username: sbillinge
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build-sdist:
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needs: [check-tag-privilege, get-python-versions, check-tag-on-main]
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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# GitHub officially-maintained actions
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python
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# GitHub officially-maintained actions
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uses: actions/setup-python@v5
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with:
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python-version: ${{ needs.get-python-versions.outputs.py_last }}
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- name: Build docs and remove fonts that blow up the wheel size
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run: |
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python -m pip install Sphinx sphinx-rtd-theme sphinx-copybutton m2r
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cd docs
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make html
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cd build/html/_static/css/fonts
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find . -type f ! -name '*.ttf' -delete
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cd ../..
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rm -rf fonts
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cd ..
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rm -rf _sources
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cd ..
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rm -rf doctrees
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cd ../..
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- name: Make sdist
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run: |
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python -m pip install --upgrade pip build cython setuptools setuptools-git-versioning
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python -m build --sdist --no-isolation
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- name: Strip source codes
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run: |
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set -euo pipefail
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tar xf dist/diffpy_srxconfutils-*.tar.gz
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SRC_DIR=$(find . -maxdepth 1 -type d -name 'diffpy_srxconfutils-*' | head -n1)
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find "$SRC_DIR" -type f -name '*.c' -print0 \
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| xargs -0 perl -i.bak -0777 -pe 's{/\*.*?\*/}{}gs'
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find "$SRC_DIR" -type f -name '*.c.bak' -delete
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tar czf dist/"${SRC_DIR#./}".tar.gz "$SRC_DIR"
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rm -rf "$SRC_DIR"
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- name: Upload sdist
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# GitHub officially-maintained actions
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uses: actions/upload-artifact@v4
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with:
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name: sdist
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path: dist/
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retention-days: 1
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- name: Upload INSTRUCTIONS.txt
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uses: actions/upload-artifact@v4
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with:
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name: instructions
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path: INSTRUCTIONS.txt
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build-wheels:
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needs: [build-sdist, get-python-versions]
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name: Build wheels ${{ matrix.python }}-${{ matrix.buildplat }}
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runs-on: ${{ matrix.buildplat }}
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strategy:
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fail-fast: false
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matrix:
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buildplat:
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- ubuntu-latest
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- macos-14
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- windows-latest
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python: ${{ fromJSON(needs.get-python-versions.outputs.py_ver) }}
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steps:
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- name: Download sdist
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# GitHub officially-maintained actions
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uses: actions/download-artifact@v4
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with:
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name: sdist
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path: dist/
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python }}
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- name: Build wheels
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run: |
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# setuptools-git-versioning only look into .git and PKG-INFO in the top directory
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which python; python --version
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which pip; pip --version
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python -m pip install --upgrade pip build cython setuptools setuptools-git-versioning
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tar xf dist/diffpy_srxconfutils-*.tar.gz
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cd diffpy_srxconfutils-*
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python -m pip wheel . --no-deps --no-build-isolation --wheel-dir ./../dist
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- name: Upload wheels
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uses: actions/upload-artifact@v4
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with:
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name: wheels-${{ matrix.python }}-${{ matrix.buildplat }}
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path: dist/*.whl
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test-wheels:
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needs: [build-wheels, get-python-versions]
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name: Test wheels ${{ matrix.python }}-${{ matrix.buildplat }}
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runs-on: ${{ matrix.buildplat }}
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strategy:
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fail-fast: false
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matrix:
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buildplat:
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- ubuntu-latest
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- macos-14
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- windows-latest
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python: ${{ fromJson(needs.get-python-versions.outputs.py_ver) }}
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Download wheels
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uses: actions/download-artifact@v4
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with:
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name: wheels-${{ matrix.python }}-${{ matrix.buildplat }}
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path: dist/
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python }}
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- name: Install wheels
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run: |
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python -m pip install --upgrade pip pytest setuptools-git-versioning
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python -m pip install dist/*.whl
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- name: Assert no source files in installed package
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run: |
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# For debugging
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# touch $(python -c "import sysconfig, os; print(os.path.join(sysconfig.get_paths()['purelib'], 'diffpy/srxconfutils', 'fake.py'))")
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python - << 'EOF'
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import os, glob, sys, sysconfig
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sp = sysconfig.get_paths()['purelib']
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pkg = os.path.join(sp, 'diffpy', 'srxconfutils')
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patterns = [os.path.join(pkg, '*.py'),
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os.path.join(pkg, '*.c')]
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bad = []
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for p in patterns:
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bad.extend(glob.glob(p))
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if bad:
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print("Found leftover source files in installed package:")
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for f in bad:
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print(" -", f)
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sys.exit(1)
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print("No .py or .c files present in diffpy/srxconfutils/")
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EOF
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- name: Run tests
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run: python -m pytest
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release:
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needs: [test-wheels]
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uses: ./.github/workflows/release-github.yml
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secrets:
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PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

‎.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.srxconfutils

‎.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-no-codecov-on-merge-to-main.yml@v0
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with:
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project: diffpy.srxconfutils
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c_extension: false
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headless: false

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