diffpy.srreal 1.4.0__tar.gz → 1.5.0__tar.gz

diffpy_srreal-1.5.0/.codecov.yml

@@ -0,0 +1,14 @@
+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]

diffpy_srreal-1.5.0/.codespell/ignore_lines.txt

@@ -0,0 +1,2 @@
+;; Please include filenames and explanations for each ignored line.
+;; See https://docs.openverse.org/meta/codespell.html for docs.

diffpy_srreal-1.5.0/.codespell/ignore_words.txt

@@ -0,0 +1,17 @@
+;; 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
+
+;; structure file format
+discus
+
+;; variable name within pdfbaseline module
+aline
+
+;; variable name within TestSFAverageObjCryst class
+fo

diffpy_srreal-1.5.0/.flake8

@@ -0,0 +1,13 @@
+# 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

diffpy_srreal-1.5.0/.github/ISSUE_TEMPLATE/bug_feature.md

@@ -0,0 +1,16 @@
+---
+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

diffpy_srreal-1.5.0/.github/ISSUE_TEMPLATE/release_checklist.md

@@ -0,0 +1,47 @@
+---
+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.

diffpy_srreal-1.5.0/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -0,0 +1,15 @@
+### 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).
+-->

diffpy_srreal-1.5.0/.github/workflows/build-and-publish-docs-on-dispatch.yml

@@ -0,0 +1,20 @@
+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:
+    needs: get-python-version
+    uses: scikit-package/release-scripts/.github/workflows/_release-docs.yml@v0
+    with:
+      project: diffpy.srreal
+      submodules: recursive
+      c_extension: true
+      headless: false
+      python_version: ${{ fromJSON(needs.get-python-version.outputs.latest_python_version) }}

diffpy_srreal-1.5.0/.github/workflows/build-wheel-release-upload.yml

@@ -0,0 +1,117 @@
+name: Build Wheel and Release
+
+# Trigger on tag push or manual dispatch.
+# Tag and release privilege are verified by the check-* jobs below.
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - "*"
+
+# ── Release modality ──────────────────────────────────────────────────────────
+# Three options are provided below. Only ONE option should be active at a time.
+# To switch: comment out the active jobs and uncomment your preferred option,
+# then commit the change to main before tagging a release.
+# ─────────────────────────────────────────────────────────────────────────────
+
+jobs:
+  # Option 1 (default): Release to GitHub, publish to PyPI, and deploy docs.
+  #
+  # The sdist and wheels are uploaded to PyPI so users can install with
+  # `pip install`. A GitHub release is created with the changelog as the
+  # release body, and the Sphinx documentation is rebuilt and deployed to
+  # GitHub Pages.
+  #
+  # The wheels come from build-wheels.yml rather than the shared
+  # scikit-package workflow: they link Boost and GSL statically, so they
+  # work without a conda environment.
+  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 }}
+
+  check-pypi-token-validity:
+    uses: scikit-package/release-scripts/.github/workflows/_check-pypi-token-validity.yml@v0
+    secrets:
+      PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+
+  get-python-version:
+    needs:
+      [check-tag-privilege, check-pat-token-validity, check-pypi-token-validity]
+    uses: scikit-package/release-scripts/.github/workflows/_get-python-version-latest.yml@v0
+
+  build-wheels:
+    needs:
+      [check-tag-privilege, check-pat-token-validity, check-pypi-token-validity]
+    uses: ./.github/workflows/build-wheels.yml
+
+  release-github:
+    needs: [build-wheels]
+    uses: scikit-package/release-scripts/.github/workflows/_release-github.yml@v0
+    secrets:
+      PAT_TOKEN: ${{ secrets.PAT_TOKEN }}
+
+  # Uploads every artifact of this run: the sdist and all wheels.
+  release-pypi:
+    needs: [release-github, get-python-version]
+    uses: scikit-package/release-scripts/.github/workflows/_release-pypi.yml@v0
+    with:
+      python_version: ${{ fromJSON(needs.get-python-version.outputs.latest_python_version) }}
+    secrets:
+      PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+
+  docs-release:
+    needs: [release-github, get-python-version]
+    uses: scikit-package/release-scripts/.github/workflows/_release-docs.yml@v0
+    with:
+      submodules: recursive
+      project: diffpy.srreal
+      c_extension: true
+      python_version: ${{ fromJSON(needs.get-python-version.outputs.latest_python_version) }}
+
+  # Option 2: Release to GitHub and deploy docs, without publishing to PyPI.
+  #
+  # A GitHub release is created and the Sphinx docs are deployed, but the
+  # wheel is not uploaded to PyPI. The source code remains publicly visible
+  # on GitHub and can be installed directly from there.
+  #
+  # Choose this when the package is public but you prefer to keep it off the
+  # default pip index — for example, if you distribute via conda-forge only,
+  # or if the package is not yet ready for a permanent PyPI presence.
+  #
+  # To use: comment out Option 1 above and uncomment the lines below.
+  # build-release-no-pypi:
+  #   uses: scikit-package/release-scripts/.github/workflows/_build-release-github-no-pypi.yml@v0
+  #   with:
+  #     project: diffpy.srreal
+  #     c_extension: true
+  #     maintainer_github_username: sbillinge
+  #   secrets:
+  #     PAT_TOKEN: ${{ secrets.PAT_TOKEN }}
+
+  # Option 3: Release to GitHub with wheel, license, and instructions bundled
+  # as a downloadable zip attached to the GitHub release asset.
+  #
+  # The wheel is built and packaged together with INSTRUCTIONS.txt and the
+  # LICENSE file into a zip that is attached directly to the GitHub release.
+  # Users with access to the (private) repo download the zip, follow the
+  # instructions inside, and install locally with pip. No PyPI or conda-forge
+  # upload occurs, and no docs are deployed.
+  #
+  # Choose this for private or restricted packages where distribution must be
+  # controlled: only users with repo access can download the release asset,
+  # making the GitHub release itself the distribution channel.
+  #
+  # To use: comment out Option 1 above and uncomment the lines below.
+  # build-release-private:
+  #   uses: scikit-package/release-scripts/.github/workflows/_build-release-github-private-pure.yml@v0
+  #   with:
+  #     project: diffpy.srreal
+  #     maintainer_github_username: sbillinge
+  #   secrets:
+  #     PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

diffpy_srreal-1.5.0/.github/workflows/build-wheels.yml

@@ -0,0 +1,60 @@
+name: Build Wheels
+
+# Builds the sdist and self-contained wheels (Boost and GSL linked
+# statically, see [tool.cibuildwheel] in pyproject.toml). Called by the
+# release workflow; run it manually to check the wheels before tagging.
+on:
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  build-sdist:
+    name: Build sdist
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v6
+        with:
+          submodules: recursive
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.14"
+
+      - name: Build sdist
+        run: |
+          python -m pip install --upgrade build
+          python -m build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  build-wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+          - macos-15-intel
+          - macos-latest
+          - windows-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v6
+        with:
+          submodules: recursive
+          fetch-depth: 0
+
+      - name: Build and test wheels
+        uses: pypa/cibuildwheel@v4.3.5
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}
+          path: wheelhouse/*.whl

diffpy_srreal-1.5.0/.github/workflows/check-news-item.yml

@@ -0,0 +1,12 @@
+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: diffpy.srreal

diffpy_srreal-1.5.0/.github/workflows/matrix-and-codecov.yml

@@ -0,0 +1,22 @@
+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: diffpy.srreal
+      submodules: recursive
+      c_extension: true
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

diffpy_srreal-1.5.0/.github/workflows/tests-on-pr.yml

@@ -0,0 +1,16 @@
+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: diffpy.srreal
+      submodules: recursive
+      c_extension: true
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

diffpy_srreal-1.5.0/.gitignore

@@ -0,0 +1,93 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+_build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+venv/
+*.egg-info/
+.installed.cfg
+*.egg
+bin/
+temp/
+tags/
+errors.err
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+MANIFEST
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/build/
+docs/source/generated/
+
+# pytest
+.pytest_cache/
+
+# PyBuilder
+target/
+
+# Editor files
+# mac
+.DS_Store
+*~
+
+# vim
+*.swp
+*.swo
+
+# pycharm
+.idea/
+
+# VSCode
+.vscode/
+
+# Ipython Notebook
+.ipynb_checkpoints

diffpy_srreal-1.5.0/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "extern/libdiffpy"]
+	path = extern/libdiffpy
+	url = https://github.com/diffpy/libdiffpy.git

diffpy_srreal-1.5.0/.isort.cfg

@@ -0,0 +1,5 @@
+[settings]
+# Keep import statement below line_length character limit
+line_length = 79
+multi_line_output = 3
+include_trailing_comma = True

diffpy_srreal-1.5.0/.pre-commit-config.yaml

@@ -0,0 +1,66 @@
+default_language_version:
+  python: python3
+ci:
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit hooks
+  autofix_prs: true
+  autoupdate_branch: "pre-commit-autoupdate"
+  autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate"
+  autoupdate_schedule: monthly
+  skip: [no-commit-to-branch]
+  submodules: false
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-added-large-files
+  - repo: https://github.com/psf/black
+    rev: 26.3.1
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.3.0
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pycqa/isort
+    rev: 9.0.0a3
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.9.1
+    hooks:
+      - id: nbstripout
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: no-commit-to-branch
+        name: Prevent Commit to Main Branch
+        args: ["--branch", "main"]
+        stages: [pre-commit]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.2
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+  # prettier - multi formatter for .json, .yml, and .md files
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - "prettier@^3.2.4"
+  # docformatter - PEP 257 compliant docstring formatter
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.8
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]

diffpy_srreal-1.5.0/.readthedocs.yaml

@@ -0,0 +1,13 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "latest"
+
+python:
+  install:
+    - requirements: requirements/docs.txt
+
+sphinx:
+  configuration: docs/source/conf.py

diffpy_srreal-1.5.0/CHANGELOG.rst

@@ -0,0 +1,65 @@
+=============
+Release notes
+=============
+
+.. current developments
+
+1.4.0
+=====
+
+**Added:**
+
+* Update linelength to sk-package standard of 79 characters.
+
+**Changed:**
+
+* Renamed CODE_OF_CONDUCTS.rst to CODE-OF-CONDUCTS.rst, doc folder to docs, and requirements/test.txt to requirements/tests.txt
+
+**Fixed:**
+
+* Configure ``black`` to have a linelength requirement of 79 characters.
+* Update requirements to use full release `libdiffpy` and remove wrong build dependencies.
+* Support ``scikit-package`` Level 5 standard (https://scikit-package.github.io/scikit-package/).
+
+
+
+Version 1.3.0  2019-03-13
+=========================
+
+Main differences from version 1.2.
+
+**Added:**
+
+* Support for Python 3.7, 3.6, 3.5 in addition to 2.7.
+* Validation of compiler options from `python-config`.
+* Make scons scripts compatible with Python 3 and Python 2.
+* `ConstantPeakWidth` attributes `uisowidth`, `bisowidth` to ease
+  PDF simulation with uniform isotropic atom displacements.
+
+**Changed:**
+
+* Require libdiffpy 1.4 or later.
+* Build Anaconda package with Anaconda C++ compiler.
+* Allow language standard c++11.
+* Pickle format for `PDFCalculator`, `DebyePDFCalculator`,
+  `OverlapCalculator`, `PeakWidthModel`, `PeakProfile`, `PDFEnvelope`,
+  `PDFBaseline`, and `ScatteringFactorTable` objects.
+
+**Deprecated:**
+
+* Variable `__gitsha__` in the `version` module renamed to `__git_commit__`.
+* `libdiffpy_version_info` attribute `git_sha` renamed to `git_commit`.
+
+**Removed**
+
+* Unused method `BVParam.__hash__`.
+* Disable pickling of `BasePairQuantity` as it is in effect abstract.
+* Pickling of Python-added attributes to exported C++ classes.
+* Function `get_libdiffpy_version_info` from the `version` module.
+
+**Fixed**
+
+* Return value conversion of `CrystalStructureAdapter` methods
+  `expandLatticeAtom` and `getEquivalentAtoms` methods.
+  Make them return a `list` of `Atom` objects.
+* Name suffix resolution of `boost_python` shared library.