skpkg: complete migration

.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.
+
+;; abbreviation for "materials" often used in a journal title
+mater
+
+;; Frobenius norm used in np.linalg.norm
+fro

.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,
+    docs/source/conf.py
+max-line-length = 79
+# 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 `tests.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.yml

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

.github/workflows/matrix-no-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-no-codecov-on-merge-to-main.yml@v0
+    with:
+      project: diffpy.distanceprinter
+      c_extension: false
+      headless: false