Skpkg migration

.clang-format

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+BasedOnStyle: Google
+
+IndentWidth: 2
+ContinuationIndentWidth: 2
+TabWidth: 2
+UseTab: Never
+
+ColumnLimit: 80
+
+SortIncludes: false

.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]
+
+# SCons compiles copies of the sources in build/coverage-<arch>/, map them back to src/
+fixes:
+  - "build/coverage-x86_64/::src/"

.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
+
+;; variable name for a pair type multiplicity in BaseDebyeSum.cpp
+multipl
+
+;; custom scattering factor label used in TestScatteringFactorTable.hpp
+ccustom

.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

.gitattributes

@@ -1,6 +1,4 @@
 /.gitattributes  export-ignore
 /.gitignore  export-ignore
-/.travis*  export-ignore
-/conda-recipe/  export-ignore
-/doc  export-ignore
+/docs  export-ignore
 gitarchive.cfg  export-subst

.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 GitHub and conda-forge release
+title: "Ready for <version-number> GitHub/conda-forge release"
+labels: "release"
+assignees: ""
+---
+
+### 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 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.
+- [ ] Grammar and writing quality are checked (no typos).
+- [ ] `FALLBACK_VERSION` in `site_scons/fallback_version.py` is updated to `<version-number>.post0`. Without this, the SCons build fails after tagging.
+- [ ] `scons test` passes locally with the latest conda-forge compilers and dependencies.
+- [ ] Dispatch matrix testing to test the release on all systems. If you do not have permission to run this workflow, tag the maintainer and say `@maintainer, please dispatch matrix testing workflow`. Matrix testing also runs automatically after a GitHub release is published, but it does not block the release, so check that it passes.
+
+Please tag the maintainer (e.g., @username) in the comment here when you are ready for the GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here:
+
+### GitHub full-release preparation checklist:
+
+- [ ] The rc GitHub release and its source tarball appear correctly on the releases page.
+- [ ] Docs are deployed successfully to `https://www.diffpy.org/libdiffpy`.
+- [ ] Successfully run all tests and do functional testing, e.g., with `diffpy.srreal` built against the rc.
+
+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 on GitHub, please check the following when creating a PR for conda-forge release.-->
+
+- [ ] Ensure that the full release has appeared on GitHub successfully.
+- [ ] `version` and `sha256` of the GitHub source tarball are updated in `meta.yaml` in the feedstock.
+- [ ] New package dependencies listed in `build.txt`, `conda.txt` and `tests.txt` are added to `meta.yaml` in the feedstock.
+- [ ] `license_file` in `meta.yaml` points to `LICENSE.rst` (renamed from `LICENSE.txt`).
+- [ ] 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: -->
+
+- [ ] Install the released package from conda-forge and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
+- [ ] Documentation (README, 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/actions/setup-tests/action.yml

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+name: Set up C++ tests
+
+runs:
+  using: composite
+  steps:
+    - name: Fetch upstream release tags
+      shell: bash
+      run: git fetch --tags https://github.com/diffpy/libdiffpy.git
+
+    - name: Check out CxxTest 4.4
+      uses: actions/checkout@v6
+      with:
+        repository: CxxTest/cxxtest
+        ref: 191adddb3876ab389c0c856e1c03874bf70f8ee4
+        path: build/cxxtest
+
+    - name: Prepare C++ test configuration
+      shell: python {0}
+      run: |
+        import runpy
+        runpy.run_path('.github/scripts/configure-tests.py')
+
+    - name: Create build environment
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        activate-environment: test
+        channels: conda-forge
+        conda-remove-defaults: "true"
+        auto-update-conda: false
+        auto-activate-base: false
+        python-version: "3.14"
+        environment-file: build/test-environment.yml
+        channel-priority: strict

.github/scripts/configure-tests.py

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+"""Configure SCons, CxxTest and the conda environment for CI tests."""
+
+import json
+from pathlib import Path
+
+requirements = ["python"]
+for filename in ("build.txt", "conda.txt", "tests.txt"):
+    for line in (Path("requirements") / filename).read_text().splitlines():
+        spec = line.split("#", 1)[0].strip()
+        if spec and spec != "cxxtest":
+            requirements.append(spec)
+
+Path("build").mkdir(exist_ok=True)
+Path("build/test-environment.yml").write_text(
+    json.dumps(
+        {
+            "name": "test",
+            "channels": ["conda-forge"],
+            "dependencies": requirements,
+        },
+        indent=2,
+    )
+    + "\n"
+)
+
+Path("sconscript.local").write_text("""\
+Import('env')
+import os
+import sys
+
+prefix = os.environ['CONDA_PREFIX']
+cxxtest = Dir('#/build/cxxtest').abspath
+env.Replace(CXXTEST=os.path.join(cxxtest, 'bin', 'cxxtestgen'),
+            CXXTEST_INSTALL_DIR=cxxtest, CXXTEST_PYTHON=sys.executable)
+
+if env['PLATFORM'] == 'win32':
+    from SCons.Platform.win32 import exec_spawn
+
+    # The outer CI shell already activates conda and SCons configures MSVC.
+    # /D stops each compiler/test-generator child from repeating cmd AutoRun.
+    def spawn_without_autorun(sh, escape, cmd, args, child_env):
+        return exec_spawn([sh, '/D', '/C', escape(' '.join(args))], child_env)
+
+    env['SPAWN'] = spawn_without_autorun
+else:
+    env.Replace(CXX=os.environ.get('CXX', os.path.join(prefix, 'bin', 'c++')))
+    env.Prepend(CCFLAGS=['-isystem' + os.path.join(prefix, 'include')])
+    env.Append(LIBPATH=os.path.join(prefix, 'lib'))
+    env.Append(LINKFLAGS='-Wl,-rpath,' + os.path.join(prefix, 'lib'))
+    if env['PLATFORM'] == 'darwin':
+        sdk = os.environ.get('CONDA_BUILD_SYSROOT')
+        if sdk:
+            env.Append(CXXFLAGS=['-isysroot', sdk])
+            env.Append(LINKFLAGS=['-isysroot', sdk])
+""")

.github/workflows/build-and-publish-docs-on-dispatch.yml

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+name: Build and Publish Docs on Dispatch
+
+on:
+  workflow_dispatch:
+
+jobs:
+  get-python-version:
+    uses: scikit-package/release-scripts/.github/workflows/_get-python-version-latest.yml@v0
+    with:
+      python_version: 0
+
+  docs:
+    uses: scikit-package/release-scripts/.github/workflows/_release-docs.yml@v0
+    with:
+      project: libdiffpy
+      c_extension: true
+      headless: false
+      # true: install the project with `python -m pip install -e . --no-deps`.
+      # false: skip project installation; still install dependencies and build docs.
+      # libdiffpy is a C++ library and does not need a Python package installed for docs.
+      install_project: false
+      python_version: ${{ fromJSON(needs.get-python-version.outputs.latest_python_version) }}

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

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

.github/workflows/matrix-and-codecov.yml

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+name: Matrix and Codecov
+
+on:
+  push:
+    branches:
+      - main
+
+  workflow_call:
+    secrets:
+      CODECOV_TOKEN:
+        required: false
+  workflow_dispatch:
+
+concurrency:
+  group: matrix-${{ github.ref }}
+  cancel-in-progress: ${{ !startsWith(github.ref, 'refs/tags/') }}
+
+jobs:
+  matrix-coverage:
+    name: C++ tests (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 45
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest, macos-15-intel]
+        include:
+          - os: ubuntu-latest
+            shell: bash -l {0}
+            build: coverage
+            jobs: 4
+          - os: windows-latest
+            shell: cmd /C CALL {0}
+            build: fast
+            jobs: 4
+          - os: macos-latest
+            shell: bash -l {0}
+            build: fast
+            jobs: 2
+          - os: macos-15-intel
+            shell: bash -l {0}
+            build: fast
+            jobs: 4
+    defaults:
+      run:
+        shell: ${{ matrix.shell }}
+
+    steps:
+      - name: Check out libdiffpy
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Set up C++ tests
+        uses: ./.github/actions/setup-tests
+
+      - name: Build and run C++ tests
+        run: scons -j${{ matrix.jobs }} build=${{ matrix.build }} test
+
+      - name: Generate coverage report
+        if: runner.os == 'Linux'
+        run: >-
+          gcovr --gcov-executable "$CONDA_PREFIX/bin/gcov"
+          --root . --filter 'build/coverage-.*/diffpy/'
+          --xml coverage.xml
+
+      - name: Save coverage report
+        if: runner.os == 'Linux'
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report
+          path: coverage.xml
+          if-no-files-found: error
+
+      - name: Upload coverage to Codecov
+        # Fork push builds have no upstream Codecov token; keep their artifact.
+        if: runner.os == 'Linux' && github.repository == 'diffpy/libdiffpy'
+        uses: codecov/codecov-action@v5
+        with:
+          files: coverage.xml
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}