Initial phase of scikit-package 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]
+
+# 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

.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
 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 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, tutorials, and other human-written text is up-to-date with any changes in the code.
+- [ ] All API references are included. To check this, run `conda install scikit-package` and then `package build api-doc`. Review any edits made by rerendering the docs locally.
+- [ ] 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.
+- [ ] Dispatch matrix testing to test the release on all Python versions and systems. If you do not have permission to run this workflow, tag the maintainer and say `@maintainer, please dispatch matrix testing workflow`.
+
+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-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
+      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:
+    branches:
+      - main  # GitHub does not evaluate expressions in trigger filters; edit this value if your base branch is not main
+
+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
+  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: libdiffpy
+      c_extension: true
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/release-github-on-tag.yml

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+name: Build Wheel and Release
+
+# Trigger on tag push or manual dispatch.
+# Tag and release privilege are verified inside the reusable workflow.
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - "*"
+
+jobs:
+  check-tag-privilege:
+    uses: scikit-package/release-scripts/.github/workflows/_check-tag-privilege.yml@v0
+    with:
+      maintainer_github_username: sbillinge
+
+  check-pat-token-validity:
+    uses: scikit-package/release-scripts/.github/workflows/_check-pat-token-validity.yml@v0
+    secrets:
+      PAT_TOKEN: ${{ secrets.PAT_TOKEN }}
+
+  release-github:
+    needs: [check-tag-privilege, check-pat-token-validity]
+    uses: scikit-package/release-scripts/.github/workflows/_release-github.yml@v0
+    secrets:
+      PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

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

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+name: Tests on PR
+
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  tests-on-pr:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Check out libdiffpy
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Initialize miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: test
+          channels: conda-forge
+          conda-remove-defaults: "true"
+          auto-update-conda: true
+          auto-activate-base: false
+
+      - name: Conda config
+        run: >-
+          conda config --set always_yes yes
+          --set changeps1 no
+
+      - name: Install requirements
+        run: >-
+          conda install
+          --file requirements/build.txt
+          --file requirements/conda.txt
+          --file requirements/tests.txt
+
+      - name: Configure SCons for the conda environment
+        run: |
+          cat > sconscript.local <<'EOF'
+          Import('env')
+          import os
+          prefix = os.environ['CONDA_PREFIX']
+          env.Replace(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'))
+          EOF
+
+      - name: Build and run C++ tests with coverage
+        run: |
+          "$CONDA_PREFIX/bin/c++" --version
+          scons build=coverage test
+
+      - name: Generate coverage report
+        run: >-
+          gcovr --gcov-executable "$CONDA_PREFIX/bin/gcov"
+          --root . --filter 'build/coverage-.*/diffpy/'
+          --xml coverage.xml
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          files: coverage.xml
+          verbose: true
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}