Skpkg: update pyobjcryst

.codecov.yml

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+coverage:
+ status:
+ project: # more options at https://docs.codecov.com/docs/commit-status
+ default:
+ target: auto # use the coverage from the base commit, fail if coverage is lower
+ threshold: 0% # allow the coverage to drop by
+
+comment:
+ layout: " diff, flags, files"
+ behavior: default
+ require_changes: false
+ require_base: false # [true :: must have a base report to post]
+ require_head: false # [true :: must have a head report to post]
+ 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.
+;; 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).
+;; See https://docs.openverse.org/meta/codespell.html for docs.
+
+;; ORTHORHOMBIC
+ORTHOROMBIC
+
+;; src/pyobjcryst/tests/testmolecule.py
+;; variable name, abbreviation for "a bottom"
+abot
+
+;; src/extensions/diffractiondatasinglecrystal_ext.cpp:148
+;; abbreviation for "register"
+regist
+
+;; src/pyobjcryst/crystal.py:548
+;; alabelstyle parameter
+inFront

.flake8

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+# As of now, flake8 does not natively support configuration via pyproject.toml
+# https://github.com/microsoft/vscode-flake8/issues/135
+[flake8]
+exclude =
+ .git,
+ __pycache__,
+ build,
+ dist,
+ doc/source/conf.py
+# huge loops in crystal.py
+max-line-length = 99
+# Ignore some style 'errors' produced while formatting by 'black'
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
+extend-ignore = E203

.github/ISSUE_TEMPLATE/bug_feature.md

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

.github/ISSUE_TEMPLATE/release_checklist.md

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+---
+name: Release
+about: Checklist and communication channel for PyPI and GitHub release
+title: "Ready for <version-number> PyPI/GitHub release"
+labels: "release"
+assignees: ""
+---
+
+### PyPI/GitHub rc-release preparation checklist:
+
+- [ ] All PRs/issues attached to the release are merged.
+- [ ] All the badges on the README are passing.
+- [ ] License information is verified as correct. If you are unsure, please comment below.
+- [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are
+ missing), tutorials, and other human-written text is up-to-date with any changes in the code.
+- [ ] Installation instructions in the README, documentation, and the website are updated.
+- [ ] Successfully run any tutorial examples or do functional testing with the latest Python version.
+- [ ] Grammar and writing quality are checked (no typos).
+- [ ] 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.
+
+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:
+
+### PyPI/GitHub full-release preparation checklist:
+
+- [ ] Create a new conda environment and install the rc from PyPI (`pip install <package-name>==??`)
+- [ ] License information on PyPI is correct.
+- [ ] Docs are deployed successfully to `https://<github-username-or-orgname>/<package-name>`.
+- [ ] Successfully run all tests, tutorial examples or do functional testing.
+
+Please let the maintainer know that all checks are done and the package is ready for full release.
+
+### conda-forge release preparation checklist:
+
+<!-- After the maintainer releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
+
+- [ ] Ensure that the full release has appeared on PyPI successfully.
+- [ ] New package dependencies listed in `conda.txt` and `test.txt` are added to `meta.yaml` in the feedstock.
+- [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions.
+- [ ] Tag the maintainer for conda-forge release.
+
+### Post-release checklist
+
+<!-- Before closing this issue, please complete the following: -->
+
+- [ ] Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
+- [ ] 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?
+
+<!-- Provide a brief overview and link to the issue. Attach outputs, including screenshots (before/after), if helpful for the reviewer. -->
+
+### What should the reviewer(s) do?
+
+<!-- Merge the code, provide feedback, initiate a discussion, etc. -->
+
+<!--
+Use the following checklist items when applicable (select only what applies):
+- [ ] This PR introduces a public-facing change (e.g., figures, CLI input/output, API).
+ - [ ] Documentation (e.g., tutorials, examples, README) has been updated.
+ - [ ] A tracking issue or plan to update documentation exists.
+- [ ] This PR affects internal functionality only (no user-facing change).
+-->

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

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+name: Release (GitHub/PyPI) and Deploy Docs
+
+on:
+ workflow_dispatch:
+ push:
+ tags:
+ - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
+
+jobs:
+ release:
+ uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
+ with:
+ project: pyobjcryst
+ c_extension: true
+ maintainer_GITHUB_username: sbillinge
+ secrets:
+ PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+ PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

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

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+name: Check for News
+
+on:
+ pull_request_target:
+ branches:
+ - main
+
+jobs:
+ check-news-item:
+ uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0
+ with:
+ project: pyobjcryst

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

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+name: CI
+
+on:
+ push:
+ branches:
+ - main
+ release:
+ types:
+ - prereleased
+ - published
+ workflow_dispatch:
+
+jobs:
+ matrix-coverage:
+ uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+ with:
+ project: pyobjcryst
+ c_extension: true
+ headless: false
+ secrets:
+ CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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

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

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

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+name: Tests on PR
+
+on:
+ pull_request:
+ workflow_dispatch:
+
+jobs:
+ tests-on-pr:
+ uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0
+ with:
+ project: pyobjcryst
+ c_extension: true
+ headless: false
+ secrets:
+ CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}