diff --git a/.buildinfo b/.buildinfo new file mode 100644 index 0000000..8b1dc70 --- /dev/null +++ b/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file records the configuration used when building these files. When it is not found, a full rebuild will be done. +config: b32e99c4f1f61d21170bff8851943f8f +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/.codecov.yml b/.codecov.yml deleted file mode 100644 index 4af5eb2..0000000 --- a/.codecov.yml +++ /dev/null @@ -1,14 +0,0 @@ -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] diff --git a/.codespell/ignore_lines.txt b/.codespell/ignore_lines.txt deleted file mode 100644 index 07fa7c8..0000000 --- a/.codespell/ignore_lines.txt +++ /dev/null @@ -1,2 +0,0 @@ -;; Please include filenames and explanations for each ignored line. -;; See https://docs.openverse.org/meta/codespell.html for docs. diff --git a/.codespell/ignore_words.txt b/.codespell/ignore_words.txt deleted file mode 100644 index 04b4fcf..0000000 --- a/.codespell/ignore_words.txt +++ /dev/null @@ -1,8 +0,0 @@ -;; 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 diff --git a/.flake8 b/.flake8 deleted file mode 100644 index 88077af..0000000 --- a/.flake8 +++ /dev/null @@ -1,13 +0,0 @@ -# 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 diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index b695799..0000000 --- a/.gitattributes +++ /dev/null @@ -1,3 +0,0 @@ -/.gitattributes export-ignore -/.gitignore export-ignore -gitarchive.cfg export-subst diff --git a/.github/ISSUE_TEMPLATE/bug_feature.md b/.github/ISSUE_TEMPLATE/bug_feature.md deleted file mode 100644 index b3454de..0000000 --- a/.github/ISSUE_TEMPLATE/bug_feature.md +++ /dev/null @@ -1,16 +0,0 @@ ---- -name: Bug Report or Feature Request -about: Report a bug or suggest a new feature! -title: "" -labels: "" -assignees: "" ---- - -### Problem - - - -### Proposed solution diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md b/.github/ISSUE_TEMPLATE/release_checklist.md deleted file mode 100644 index 56c5fca..0000000 --- a/.github/ISSUE_TEMPLATE/release_checklist.md +++ /dev/null @@ -1,47 +0,0 @@ ---- -name: Release -about: Checklist and communication channel for PyPI and GitHub release -title: "Ready for 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 ==??`) -- [ ] License information on PyPI is correct. -- [ ] Docs are deployed successfully to `https:///`. -- [ ] 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: - - - -- [ ] 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 - - - -- [ ] 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. diff --git a/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md b/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md deleted file mode 100644 index 1099d86..0000000 --- a/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md +++ /dev/null @@ -1,15 +0,0 @@ -### What problem does this PR address? - - - -### What should the reviewer(s) do? - - - - diff --git a/.github/workflows/build-and-publish-docs-on-dispatch.yml b/.github/workflows/build-and-publish-docs-on-dispatch.yml deleted file mode 100644 index 6a3cbff..0000000 --- a/.github/workflows/build-and-publish-docs-on-dispatch.yml +++ /dev/null @@ -1,18 +0,0 @@ -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: diffpy.distanceprinter - c_extension: false - headless: false - python_version: ${{ fromJSON(needs.get-python-version.outputs.latest_python_version) }} diff --git a/.github/workflows/build-wheel-release-upload.yml b/.github/workflows/build-wheel-release-upload.yml deleted file mode 100644 index ba0aa46..0000000 --- a/.github/workflows/build-wheel-release-upload.yml +++ /dev/null @@ -1,76 +0,0 @@ -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: - - "*" - -# ── Release modality ────────────────────────────────────────────────────────── -# Three options are provided below. Only ONE job should be active at a time. -# To switch: comment out the active job 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 wheel is 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. - # - # Choose this for open-source packages distributed via PyPI and/or - # conda-forge where broad public availability is the goal. - build-release: - uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0 - with: - project: diffpy.distanceprinter - c_extension: false - maintainer_github_username: sbillinge - secrets: - PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }} - PAT_TOKEN: ${{ secrets.PAT_TOKEN }} - - # 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.distanceprinter - # c_extension: false - # maintainer_github_username: sbillinge, bobleesj - # 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.distanceprinter - # maintainer_github_username: sbillinge, bobleesj - # secrets: - # PAT_TOKEN: ${{ secrets.PAT_TOKEN }} diff --git a/.github/workflows/check-news-item.yml b/.github/workflows/check-news-item.yml deleted file mode 100644 index d6cf892..0000000 --- a/.github/workflows/check-news-item.yml +++ /dev/null @@ -1,12 +0,0 @@ -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.distanceprinter diff --git a/.github/workflows/matrix-and-codecov.yml b/.github/workflows/matrix-and-codecov.yml deleted file mode 100644 index 3bb1452..0000000 --- a/.github/workflows/matrix-and-codecov.yml +++ /dev/null @@ -1,21 +0,0 @@ -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.distanceprinter - c_extension: false - headless: false - secrets: - CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/tests-on-pr.yml b/.github/workflows/tests-on-pr.yml deleted file mode 100644 index 4f1528b..0000000 --- a/.github/workflows/tests-on-pr.yml +++ /dev/null @@ -1,15 +0,0 @@ -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.distanceprinter - c_extension: false - headless: false - secrets: - CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} diff --git a/.gitignore b/.gitignore deleted file mode 100644 index 099e294..0000000 --- a/.gitignore +++ /dev/null @@ -1,93 +0,0 @@ -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] -*$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 diff --git a/.isort.cfg b/.isort.cfg deleted file mode 100644 index 86f162b..0000000 --- a/.isort.cfg +++ /dev/null @@ -1,5 +0,0 @@ -[settings] -# Keep import statement below line_length character limit -line_length = 79 -multi_line_output = 3 -include_trailing_comma = True diff --git a/docs/source/_static/.placeholder b/.nojekyll similarity index 100% rename from docs/source/_static/.placeholder rename to .nojekyll diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml deleted file mode 100644 index 4a95879..0000000 --- a/.pre-commit-config.yaml +++ /dev/null @@ -1,65 +0,0 @@ -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: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8 - hooks: - - id: prettier - additional_dependencies: - - "prettier@^3.2.4" - - repo: https://github.com/PyCQA/docformatter - rev: v1.7.8 - hooks: - - id: docformatter - additional_dependencies: [tomli] - args: [--in-place, --config, ./pyproject.toml] diff --git a/.readthedocs.yaml b/.readthedocs.yaml deleted file mode 100644 index aaa8889..0000000 --- a/.readthedocs.yaml +++ /dev/null @@ -1,13 +0,0 @@ -version: 2 - -build: - os: "ubuntu-22.04" - tools: - python: "latest" - -python: - install: - - requirements: requirements/docs.txt - -sphinx: - configuration: docs/source/conf.py diff --git a/AUTHORS.rst b/AUTHORS.rst deleted file mode 100644 index 68e8471..0000000 --- a/AUTHORS.rst +++ /dev/null @@ -1,10 +0,0 @@ -Authors -======= - -Xiaohao Yang and Billinge Group members - -Contributors ------------- - -For a list of contributors, visit -https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors diff --git a/CHANGELOG.rst b/CHANGELOG.rst deleted file mode 100644 index 6291829..0000000 --- a/CHANGELOG.rst +++ /dev/null @@ -1,37 +0,0 @@ -============= -Release notes -============= - -.. current developments - -1.1.0 -===== - -**Added:** - -* Added support for Python 3.14. - -**Removed:** - -* Removed support for Python 3.11. - - -1.0.2 -===== - - -1.0.1 -===== - -**Fixed:** - -* Fixed command line control usability - - -1.0.0 -===== - -**Changed:** - -* Updated from Python 2.6-2.7 to Python 3.11-3.13 -* Support ``scikit-package`` Level 5 standard (https://scikit-package.github.io/scikit-package/). diff --git a/CODE-OF-CONDUCT.rst b/CODE-OF-CONDUCT.rst deleted file mode 100644 index 25fafe2..0000000 --- a/CODE-OF-CONDUCT.rst +++ /dev/null @@ -1,133 +0,0 @@ -===================================== - Contributor Covenant Code of Conduct -===================================== - -Our Pledge ----------- - -We as members, contributors, and leaders pledge to make participation in our -community a harassment-free experience for everyone, regardless of age, body -size, visible or invisible disability, ethnicity, sex characteristics, gender -identity and expression, level of experience, education, socioeconomic status, -nationality, personal appearance, race, caste, color, religion, or sexual -identity and orientation. - -We pledge to act and interact in ways that contribute to an open, welcoming, -diverse, inclusive, and healthy community. - -Our Standards -------------- - -Examples of behavior that contributes to a positive environment for our -community include: - -* Demonstrating empathy and kindness toward other people -* Being respectful of differing opinions, viewpoints, and experiences -* Giving and gracefully accepting constructive feedback -* Accepting responsibility and apologizing to those affected by our mistakes, - and learning from the experience -* Focusing on what is best not just for us as individuals, but for the overall - community - -Examples of unacceptable behavior include: - -* The use of sexualized language or imagery, and sexual attention or advances of - any kind -* Trolling, insulting or derogatory comments, and personal or political attacks -* Public or private harassment -* Publishing others' private information, such as a physical or email address, - without their explicit permission -* Other conduct which could reasonably be considered inappropriate in a - professional setting - -Enforcement Responsibilities ----------------------------- - -Community leaders are responsible for clarifying and enforcing our standards of -acceptable behavior and will take appropriate and fair corrective action in -response to any behavior that they deem inappropriate, threatening, offensive, -or harmful. - -Community leaders have the right and responsibility to remove, edit, or reject -comments, commits, code, wiki edits, issues, and other contributions that are -not aligned to this Code of Conduct, and will communicate reasons for moderation -decisions when appropriate. - -Scope ------ - -This Code of Conduct applies within all community spaces, and also applies when -an individual is officially representing the community in public spaces. -Examples of representing our community include using an official email address, -posting via an official social media account, or acting as an appointed -representative at an online or offline event. - -Enforcement ------------ - -Instances of abusive, harassing, or otherwise unacceptable behavior may be -reported to the community leaders responsible for enforcement at -sbillinge@ucsb.edu. All complaints will be reviewed and investigated promptly and fairly. - -All community leaders are obligated to respect the privacy and security of the -reporter of any incident. - -Enforcement Guidelines ----------------------- - -Community leaders will follow these Community Impact Guidelines in determining -the consequences for any action they deem in violation of this Code of Conduct: - -1. Correction -**************** - -**Community Impact**: Use of inappropriate language or other behavior deemed -unprofessional or unwelcome in the community. - -**Consequence**: A private, written warning from community leaders, providing -clarity around the nature of the violation and an explanation of why the -behavior was inappropriate. A public apology may be requested. - -2. Warning -************* - -**Community Impact**: A violation through a single incident or series of -actions. - -**Consequence**: A warning with consequences for continued behavior. No -interaction with the people involved, including unsolicited interaction with -those enforcing the Code of Conduct, for a specified period of time. This -includes avoiding interactions in community spaces as well as external channels -like social media. Violating these terms may lead to a temporary or permanent -ban. - -3. Temporary Ban -****************** - -**Community Impact**: A serious violation of community standards, including -sustained inappropriate behavior. - -**Consequence**: A temporary ban from any sort of interaction or public -communication with the community for a specified period of time. No public or -private interaction with the people involved, including unsolicited interaction -with those enforcing the Code of Conduct, is allowed during this period. -Violating these terms may lead to a permanent ban. - -4. Permanent Ban -****************** - -**Community Impact**: Demonstrating a pattern of violation of community -standards, including sustained inappropriate behavior, harassment of an -individual, or aggression toward or disparagement of classes of individuals. - -**Consequence**: A permanent ban from any sort of public interaction within the -community. - -Attribution ------------ - -This Code of Conduct is adapted from the `Contributor Covenant `_. - -Community Impact Guidelines were inspired by `Mozilla's code of conduct enforcement ladder `_. - -For answers to common questions about this code of conduct, see the `FAQ `_. `Translations are available `_ diff --git a/INSTRUCTIONS.txt b/INSTRUCTIONS.txt deleted file mode 100644 index 848f5d5..0000000 --- a/INSTRUCTIONS.txt +++ /dev/null @@ -1,18 +0,0 @@ -Distance Printer, calculate the inter atomic distances. Part of xPDFsuite. - ------------------------------------------------------------------------- -1. License Notice - -Use of this software is permitted only under a separate, written -Use License granted by Columbia University. If you are unsure about -your license status, contact Prof. Simon Billinge at sb2896@columbia.edu -before installing. - -Use without a valid license is prohibited. ------------------------------------------------------------------------- -2. Installation - -This package is not designed to be installed standalone and is usually -installed as part of the xpdfsuite package. Please refer to the -INSTRUCTIONS.txt file and any other installation directions in the -diffpy.xpdfsuite software. diff --git a/LICENSE.rst b/LICENSE.rst deleted file mode 100644 index 1a60cc5..0000000 --- a/LICENSE.rst +++ /dev/null @@ -1,30 +0,0 @@ -BSD 3-Clause License - -Copyright (c) 2009-2025, The Trustees of Columbia University in the City of New York. -Copyright (c) 2026-present, The Contributors to the diffpy.distanceprinter project. -All rights reserved. - -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: - -1. Redistributions of source code must retain the above copyright notice, this - list of conditions and the following disclaimer. - -2. Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimer in the documentation - and/or other materials provided with the distribution. - -3. Neither the name of the copyright holder nor the names of its contributors - may be used to endorse or promote products derived from this software - without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE -FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index f1a78ee..0000000 --- a/MANIFEST.in +++ /dev/null @@ -1,12 +0,0 @@ -graft src -graft tests -graft requirements - -include AUTHORS.rst LICENSE*.rst README.rst - -# Exclude all bytecode files and __pycache__ directories -global-exclude *.py[cod] # Exclude all .pyc, .pyo, and .pyd files. -global-exclude .DS_Store # Exclude Mac filesystem artifacts. -global-exclude __pycache__ # Exclude Python cache directories. -global-exclude .git* # Exclude git files and directories. -global-exclude .idea # Exclude PyCharm project settings. diff --git a/README.rst b/README.rst deleted file mode 100644 index 9cd5a54..0000000 --- a/README.rst +++ /dev/null @@ -1,137 +0,0 @@ -|Icon| |title|_ -=============== - -.. |title| replace:: diffpy.distanceprinter -.. _title: https://diffpy.github.io/diffpy.distanceprinter - -.. |Icon| image:: https://avatars.githubusercontent.com/diffpy - :target: https://diffpy.github.io/diffpy.distanceprinter - :height: 100px - -|PyPI| |Forge| |PythonVersion| |PR| - -|CI| |Codecov| |Black| |Tracking| - -.. |Black| image:: https://img.shields.io/badge/code_style-black-black - :target: https://github.com/psf/black - -.. |CI| image:: https://github.com/diffpy/diffpy.distanceprinter/actions/workflows/matrix-and-codecov.yml/badge.svg - :target: https://github.com/diffpy/diffpy.distanceprinter/actions/workflows/matrix-and-codecov.yml - -.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.distanceprinter/branch/main/graph/badge.svg - :target: https://codecov.io/gh/diffpy/diffpy.distanceprinter - -.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.distanceprinter - :target: https://anaconda.org/conda-forge/diffpy.distanceprinter - -.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff - :target: https://github.com/diffpy/diffpy.distanceprinter/pulls - -.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.distanceprinter - :target: https://pypi.org/project/diffpy.distanceprinter/ - -.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.distanceprinter - :target: https://pypi.org/project/diffpy.distanceprinter/ - -.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue - :target: https://github.com/diffpy/diffpy.distanceprinter/issues - -Distance Printer, calculate the inter atomic distances. Part of xPDFsuite. - -For more information about the diffpy.distanceprinter library, please consult our `online documentation `_. - -Citation --------- - -If you use diffpy.distanceprinter in a scientific publication, we would like you to cite this package as - - Xiaohao Yang, Pavol Juhas, Christopher L. Farrow and Simon J. L. Billinge, xPDFsuite: an end-to-end - software solution for high throughput pair distribution function transformation, visualization and - analysis, arXiv 1402.3163 (2025) - -Installation ------------- - -The preferred method is to use `Miniconda Python -`_ -and install from the "conda-forge" channel of Conda packages. - -To add "conda-forge" to the conda channels, run the following in a terminal. :: - - conda config --add channels conda-forge - -We want to install our packages in a suitable conda environment. -The following creates and activates a new environment named ``diffpy.distanceprinter_env`` :: - - conda create -n diffpy.distanceprinter_env diffpy.distanceprinter - conda activate diffpy.distanceprinter_env - -The output should print the latest version displayed on the badges above. - -If the above does not work, you can use ``pip`` to download and install the latest release from -`Python Package Index `_. -To install using ``pip`` into your ``diffpy.distanceprinter_env`` environment, type :: - - pip install diffpy.distanceprinter - -If you prefer to install from sources, after installing the dependencies, obtain the source archive from -`GitHub `_. Once installed, ``cd`` into your ``diffpy.distanceprinter`` directory -and run the following :: - - pip install . - -This package also provides command-line utilities. To check the software has been installed correctly, type :: - - diffpy.distanceprinter --version - -You can also type the following command to verify the installation. :: - - python -c "import diffpy.distanceprinter; print(diffpy.distanceprinter.__version__)" - - -To view the basic usage and available commands, type :: - - diffpy.distanceprinter -h - -Getting Started ---------------- - -You may consult our `online documentation `_ for tutorials and API references. - -Support and Contribute ----------------------- - -If you see a bug or want to request a feature, please `report it as an issue `_ and/or `submit a fix as a PR `_. - -Feel free to fork the project and contribute. To install diffpy.distanceprinter -in a development mode, with its sources being directly used by Python -rather than copied to a package directory, use the following in the root -directory :: - - pip install -e . - -To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit -hooks. - -1. Install pre-commit in your working environment by running ``conda install pre-commit``. - -2. Initialize pre-commit (one time only) ``pre-commit install``. - -Thereafter your code will be linted by black and isort and checked against flake8 before you can commit. -If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should -pass after they are modified). If the flake8 test fails please see the error messages and fix them manually before -trying to commit again. - -Improvements and fixes are always appreciated. - -Before contributing, please read our `Code of Conduct `_. - -Contact -------- - -For more information on diffpy.distanceprinter please visit the project `web-page `_ or email the maintainers ``Simon Billinge(sbillinge@ucsb.edu)``. - -Acknowledgements ----------------- - -``diffpy.distanceprinter`` is built and maintained with `scikit-package `_. diff --git a/docs/source/api/diffpy.distanceprinter.rst b/_sources/api/diffpy.distanceprinter.rst.txt similarity index 100% rename from docs/source/api/diffpy.distanceprinter.rst rename to _sources/api/diffpy.distanceprinter.rst.txt diff --git a/docs/source/index.rst b/_sources/index.rst.txt similarity index 100% rename from docs/source/index.rst rename to _sources/index.rst.txt diff --git a/docs/source/license.rst b/_sources/license.rst.txt similarity index 100% rename from docs/source/license.rst rename to _sources/license.rst.txt diff --git a/docs/source/release.rst b/_sources/release.rst.txt similarity index 100% rename from docs/source/release.rst rename to _sources/release.rst.txt diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/_static/base-stemmer.js b/_static/base-stemmer.js new file mode 100644 index 0000000..e6fa0c4 --- /dev/null +++ b/_static/base-stemmer.js @@ -0,0 +1,476 @@ +// @ts-check + +/**@constructor*/ +BaseStemmer = function() { + /** @protected */ + this.current = ''; + this.cursor = 0; + this.limit = 0; + this.limit_backward = 0; + this.bra = 0; + this.ket = 0; + + /** + * @param {string} value + */ + this.setCurrent = function(value) { + this.current = value; + this.cursor = 0; + this.limit = this.current.length; + this.limit_backward = 0; + this.bra = this.cursor; + this.ket = this.limit; + }; + + /** + * @return {string} + */ + this.getCurrent = function() { + return this.current; + }; + + /** + * @param {BaseStemmer} other + */ + this.copy_from = function(other) { + /** @protected */ + this.current = other.current; + this.cursor = other.cursor; + this.limit = other.limit; + this.limit_backward = other.limit_backward; + this.bra = other.bra; + this.ket = other.ket; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.in_grouping = function(s, min, max) { + /** @protected */ + if (this.cursor >= this.limit) return false; + var ch = this.current.charCodeAt(this.cursor); + if (ch > max || ch < min) return false; + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) return false; + this.cursor++; + return true; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.go_in_grouping = function(s, min, max) { + /** @protected */ + while (this.cursor < this.limit) { + var ch = this.current.charCodeAt(this.cursor); + if (ch > max || ch < min) + return true; + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) + return true; + this.cursor++; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.in_grouping_b = function(s, min, max) { + /** @protected */ + if (this.cursor <= this.limit_backward) return false; + var ch = this.current.charCodeAt(this.cursor - 1); + if (ch > max || ch < min) return false; + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) return false; + this.cursor--; + return true; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.go_in_grouping_b = function(s, min, max) { + /** @protected */ + while (this.cursor > this.limit_backward) { + var ch = this.current.charCodeAt(this.cursor - 1); + if (ch > max || ch < min) return true; + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) return true; + this.cursor--; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.out_grouping = function(s, min, max) { + /** @protected */ + if (this.cursor >= this.limit) return false; + var ch = this.current.charCodeAt(this.cursor); + if (ch > max || ch < min) { + this.cursor++; + return true; + } + ch -= min; + if ((s[ch >>> 3] & (0X1 << (ch & 0x7))) == 0) { + this.cursor++; + return true; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.go_out_grouping = function(s, min, max) { + /** @protected */ + while (this.cursor < this.limit) { + var ch = this.current.charCodeAt(this.cursor); + if (ch <= max && ch >= min) { + ch -= min; + if ((s[ch >>> 3] & (0X1 << (ch & 0x7))) != 0) { + return true; + } + } + this.cursor++; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.out_grouping_b = function(s, min, max) { + /** @protected */ + if (this.cursor <= this.limit_backward) return false; + var ch = this.current.charCodeAt(this.cursor - 1); + if (ch > max || ch < min) { + this.cursor--; + return true; + } + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) { + this.cursor--; + return true; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.go_out_grouping_b = function(s, min, max) { + /** @protected */ + while (this.cursor > this.limit_backward) { + var ch = this.current.charCodeAt(this.cursor - 1); + if (ch <= max && ch >= min) { + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) != 0) { + return true; + } + } + this.cursor--; + } + return false; + }; + + /** + * @param {string} s + * @return {boolean} + */ + this.eq_s = function(s) + { + /** @protected */ + if (this.limit - this.cursor < s.length) return false; + if (this.current.slice(this.cursor, this.cursor + s.length) != s) + { + return false; + } + this.cursor += s.length; + return true; + }; + + /** + * @param {string} s + * @return {boolean} + */ + this.eq_s_b = function(s) + { + /** @protected */ + if (this.cursor - this.limit_backward < s.length) return false; + if (this.current.slice(this.cursor - s.length, this.cursor) != s) + { + return false; + } + this.cursor -= s.length; + return true; + }; + + /** + * @param {Among[]} v + * @return {number} + */ + this.find_among = function(v) + { + /** @protected */ + var i = 0; + var j = v.length; + + var c = this.cursor; + var l = this.limit; + + var common_i = 0; + var common_j = 0; + + var first_key_inspected = false; + + while (true) + { + var k = i + ((j - i) >>> 1); + var diff = 0; + var common = common_i < common_j ? common_i : common_j; // smaller + // w[0]: string, w[1]: substring_i, w[2]: result, w[3]: function (optional) + var w = v[k]; + var i2; + for (i2 = common; i2 < w[0].length; i2++) + { + if (c + common == l) + { + diff = -1; + break; + } + diff = this.current.charCodeAt(c + common) - w[0].charCodeAt(i2); + if (diff != 0) break; + common++; + } + if (diff < 0) + { + j = k; + common_j = common; + } + else + { + i = k; + common_i = common; + } + if (j - i <= 1) + { + if (i > 0) break; // v->s has been inspected + if (j == i) break; // only one item in v + + // - but now we need to go round once more to get + // v->s inspected. This looks messy, but is actually + // the optimal approach. + + if (first_key_inspected) break; + first_key_inspected = true; + } + } + do { + var w = v[i]; + if (common_i >= w[0].length) + { + this.cursor = c + w[0].length; + if (w.length < 4) return w[2]; + var res = w[3](this); + this.cursor = c + w[0].length; + if (res) return w[2]; + } + i = w[1]; + } while (i >= 0); + return 0; + }; + + // find_among_b is for backwards processing. Same comments apply + /** + * @param {Among[]} v + * @return {number} + */ + this.find_among_b = function(v) + { + /** @protected */ + var i = 0; + var j = v.length + + var c = this.cursor; + var lb = this.limit_backward; + + var common_i = 0; + var common_j = 0; + + var first_key_inspected = false; + + while (true) + { + var k = i + ((j - i) >> 1); + var diff = 0; + var common = common_i < common_j ? common_i : common_j; + var w = v[k]; + var i2; + for (i2 = w[0].length - 1 - common; i2 >= 0; i2--) + { + if (c - common == lb) + { + diff = -1; + break; + } + diff = this.current.charCodeAt(c - 1 - common) - w[0].charCodeAt(i2); + if (diff != 0) break; + common++; + } + if (diff < 0) + { + j = k; + common_j = common; + } + else + { + i = k; + common_i = common; + } + if (j - i <= 1) + { + if (i > 0) break; + if (j == i) break; + if (first_key_inspected) break; + first_key_inspected = true; + } + } + do { + var w = v[i]; + if (common_i >= w[0].length) + { + this.cursor = c - w[0].length; + if (w.length < 4) return w[2]; + var res = w[3](this); + this.cursor = c - w[0].length; + if (res) return w[2]; + } + i = w[1]; + } while (i >= 0); + return 0; + }; + + /* to replace chars between c_bra and c_ket in this.current by the + * chars in s. + */ + /** + * @param {number} c_bra + * @param {number} c_ket + * @param {string} s + * @return {number} + */ + this.replace_s = function(c_bra, c_ket, s) + { + /** @protected */ + var adjustment = s.length - (c_ket - c_bra); + this.current = this.current.slice(0, c_bra) + s + this.current.slice(c_ket); + this.limit += adjustment; + if (this.cursor >= c_ket) this.cursor += adjustment; + else if (this.cursor > c_bra) this.cursor = c_bra; + return adjustment; + }; + + /** + * @return {boolean} + */ + this.slice_check = function() + { + /** @protected */ + if (this.bra < 0 || + this.bra > this.ket || + this.ket > this.limit || + this.limit > this.current.length) + { + return false; + } + return true; + }; + + /** + * @param {number} c_bra + * @return {boolean} + */ + this.slice_from = function(s) + { + /** @protected */ + var result = false; + if (this.slice_check()) + { + this.replace_s(this.bra, this.ket, s); + result = true; + } + return result; + }; + + /** + * @return {boolean} + */ + this.slice_del = function() + { + /** @protected */ + return this.slice_from(""); + }; + + /** + * @param {number} c_bra + * @param {number} c_ket + * @param {string} s + */ + this.insert = function(c_bra, c_ket, s) + { + /** @protected */ + var adjustment = this.replace_s(c_bra, c_ket, s); + if (c_bra <= this.bra) this.bra += adjustment; + if (c_bra <= this.ket) this.ket += adjustment; + }; + + /** + * @return {string} + */ + this.slice_to = function() + { + /** @protected */ + var result = ''; + if (this.slice_check()) + { + result = this.current.slice(this.bra, this.ket); + } + return result; + }; + + /** + * @return {string} + */ + this.assign_to = function() + { + /** @protected */ + return this.current.slice(0, this.limit); + }; +}; diff --git a/_static/basic.css b/_static/basic.css new file mode 100644 index 0000000..4738b2e --- /dev/null +++ b/_static/basic.css @@ -0,0 +1,906 @@ +/* + * Sphinx stylesheet -- basic theme. + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; 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+ margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/_static/check-solid.svg b/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/_static/clipboard.min.js b/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/_static/copybutton.css b/_static/copybutton.css new file mode 100644 index 0000000..f1916ec --- /dev/null +++ b/_static/copybutton.css @@ -0,0 +1,94 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +/* Show the copybutton */ +.highlight:hover button.copybtn, button.copybtn.success { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/_static/copybutton.js b/_static/copybutton.js new file mode 100644 index 0000000..caa31c1 --- /dev/null +++ b/_static/copybutton.js @@ -0,0 +1,248 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copier dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for a moment, then changes it back +// We want the timeout of our `success` class to be a bit shorter than the +// tooltip and icon change, so that we can hide the icon before changing back. +var timeoutIcon = 2000; +var timeoutSuccessClass = 1500; + +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + // Remove success a little bit sooner than we change the tooltip + // So that we can use CSS to hide the copybutton first + setTimeout(() => el.classList.remove('success'), timeoutSuccessClass) + setTimeout(() => el.setAttribute('data-tooltip', oldText), timeoutIcon) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, timeoutIcon) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos'; + + let text = filterText(target, exclude); + return formatCopyText(text, '^\\$ ', true, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/_static/copybutton_funcs.js b/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/_static/css/badge_only.css b/_static/css/badge_only.css new file mode 100644 index 0000000..88ba55b --- /dev/null +++ b/_static/css/badge_only.css @@ -0,0 +1 @@ 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access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})`, + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); + }, + + /** + * Initialise the domain index toggle buttons + */ + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)), + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); + }, + + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS + && !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) + return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); + } + break; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); + } + break; + } + } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } + }); + }, +}; + +// quick alias for translations +const _ = Documentation.gettext; + +_ready(Documentation.init); diff --git a/_static/documentation_options.js b/_static/documentation_options.js new file mode 100644 index 0000000..ace8aca --- /dev/null +++ b/_static/documentation_options.js @@ -0,0 +1,13 @@ +const DOCUMENTATION_OPTIONS = { + VERSION: '1.1.0', + LANGUAGE: 'en', + COLLAPSE_INDEX: false, + BUILDER: 'html', + FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', + HAS_SOURCE: true, + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: true, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, +}; \ No newline at end of file diff --git a/_static/english-stemmer.js b/_static/english-stemmer.js new file mode 100644 index 0000000..056760e --- /dev/null +++ b/_static/english-stemmer.js @@ -0,0 +1,1066 @@ +// Generated from english.sbl by Snowball 3.0.1 - https://snowballstem.org/ + +/**@constructor*/ +var EnglishStemmer = function() { + var base = new BaseStemmer(); + + /** @const */ var a_0 = [ + ["arsen", -1, -1], + ["commun", -1, -1], + ["emerg", -1, -1], + ["gener", -1, -1], + ["later", -1, -1], + ["organ", -1, -1], + ["past", -1, -1], + ["univers", -1, -1] + ]; + + /** @const */ var a_1 = [ + ["'", -1, 1], + ["'s'", 0, 1], + ["'s", -1, 1] + ]; + + /** @const */ var a_2 = [ + ["ied", -1, 2], + ["s", -1, 3], + ["ies", 1, 2], + ["sses", 1, 1], + ["ss", 1, -1], + ["us", 1, -1] + ]; + + /** @const */ var a_3 = [ + ["succ", -1, 1], + ["proc", -1, 1], + ["exc", -1, 1] + ]; + + /** @const */ var a_4 = [ + ["even", -1, 2], + ["cann", -1, 2], + ["inn", -1, 2], + ["earr", -1, 2], + ["herr", -1, 2], + ["out", -1, 2], + ["y", -1, 1] + ]; + + /** @const */ var a_5 = [ + ["", -1, -1], + ["ed", 0, 2], + ["eed", 1, 1], + ["ing", 0, 3], + ["edly", 0, 2], + ["eedly", 4, 1], + ["ingly", 0, 2] + ]; + + /** @const */ var a_6 = [ + ["", -1, 3], + ["bb", 0, 2], + ["dd", 0, 2], + ["ff", 0, 2], + ["gg", 0, 2], + ["bl", 0, 1], + ["mm", 0, 2], + ["nn", 0, 2], + ["pp", 0, 2], + ["rr", 0, 2], + ["at", 0, 1], + ["tt", 0, 2], + ["iz", 0, 1] + ]; + + /** @const */ var a_7 = [ + ["anci", -1, 3], + ["enci", -1, 2], + ["ogi", -1, 14], + ["li", -1, 16], + ["bli", 3, 12], + ["abli", 4, 4], + ["alli", 3, 8], + ["fulli", 3, 9], + ["lessli", 3, 15], + ["ousli", 3, 10], + ["entli", 3, 5], + ["aliti", -1, 8], + ["biliti", -1, 12], + ["iviti", -1, 11], + ["tional", -1, 1], + ["ational", 14, 7], + ["alism", -1, 8], + ["ation", -1, 7], + ["ization", 17, 6], + ["izer", -1, 6], + ["ator", -1, 7], + ["iveness", -1, 11], + ["fulness", -1, 9], + ["ousness", -1, 10], + ["ogist", -1, 13] + ]; + + /** @const */ var a_8 = [ + ["icate", -1, 4], + ["ative", -1, 6], + ["alize", -1, 3], + ["iciti", -1, 4], + ["ical", -1, 4], + ["tional", -1, 1], + ["ational", 5, 2], + ["ful", -1, 5], + ["ness", -1, 5] + ]; + + /** @const */ var a_9 = [ + ["ic", -1, 1], + ["ance", -1, 1], + ["ence", -1, 1], + ["able", -1, 1], + ["ible", -1, 1], + ["ate", -1, 1], + ["ive", -1, 1], + ["ize", -1, 1], + ["iti", -1, 1], + ["al", -1, 1], + ["ism", -1, 1], + ["ion", -1, 2], + ["er", -1, 1], + ["ous", -1, 1], + ["ant", -1, 1], + ["ent", -1, 1], + ["ment", 15, 1], + ["ement", 16, 1] + ]; + + /** @const */ var a_10 = [ + ["e", -1, 1], + ["l", -1, 2] + ]; + + /** @const */ var a_11 = [ + ["andes", -1, -1], + ["atlas", -1, -1], + ["bias", -1, -1], + ["cosmos", -1, -1], + ["early", -1, 5], + ["gently", -1, 3], + ["howe", -1, -1], + ["idly", -1, 2], + ["news", -1, -1], + ["only", -1, 6], + ["singly", -1, 7], + ["skies", -1, 1], + ["sky", -1, -1], + ["ugly", -1, 4] + ]; + + /** @const */ var /** Array */ g_aeo = [17, 64]; + + /** @const */ var /** Array */ g_v = [17, 65, 16, 1]; + + /** @const */ var /** Array */ g_v_WXY = [1, 17, 65, 208, 1]; + + /** @const */ var /** Array */ g_valid_LI = [55, 141, 2]; + + var /** boolean */ B_Y_found = false; + var /** number */ I_p2 = 0; + var /** number */ I_p1 = 0; + + + /** @return {boolean} */ + function r_prelude() { + B_Y_found = false; + /** @const */ var /** number */ v_1 = base.cursor; + lab0: { + base.bra = base.cursor; + if (!(base.eq_s("'"))) + { + break lab0; + } + base.ket = base.cursor; + if (!base.slice_del()) + { + return false; + } + } + base.cursor = v_1; + /** @const */ var /** number */ v_2 = base.cursor; + lab1: { + base.bra = base.cursor; + if (!(base.eq_s("y"))) + { + break lab1; + } + base.ket = base.cursor; + if (!base.slice_from("Y")) + { + return false; + } + B_Y_found = true; + } + base.cursor = v_2; + /** @const */ var /** number */ v_3 = base.cursor; + lab2: { + while(true) + { + /** @const */ var /** number */ v_4 = base.cursor; + lab3: { + golab4: while(true) + { + /** @const */ var /** number */ v_5 = base.cursor; + lab5: { + if (!(base.in_grouping(g_v, 97, 121))) + { + break lab5; + } + base.bra = base.cursor; + if (!(base.eq_s("y"))) + { + break lab5; + } + base.ket = base.cursor; + base.cursor = v_5; + break golab4; + } + base.cursor = v_5; + if (base.cursor >= base.limit) + { + break lab3; + } + base.cursor++; + } + if (!base.slice_from("Y")) + { + return false; + } + B_Y_found = true; + continue; + } + base.cursor = v_4; + break; + } + } + base.cursor = v_3; + return true; + }; + + /** @return {boolean} */ + function r_mark_regions() { + I_p1 = base.limit; + I_p2 = base.limit; + /** @const */ var /** number */ v_1 = base.cursor; + lab0: { + lab1: { + /** @const */ var /** number */ v_2 = base.cursor; + lab2: { + if (base.find_among(a_0) == 0) + { + break lab2; + } + break lab1; + } + base.cursor = v_2; + if (!base.go_out_grouping(g_v, 97, 121)) + { + break lab0; + } + base.cursor++; + if (!base.go_in_grouping(g_v, 97, 121)) + { + break lab0; + } + base.cursor++; + } + I_p1 = base.cursor; + if (!base.go_out_grouping(g_v, 97, 121)) + { + break lab0; + } + base.cursor++; + if (!base.go_in_grouping(g_v, 97, 121)) + { + break lab0; + } + base.cursor++; + I_p2 = base.cursor; + } + base.cursor = v_1; + return true; + }; + + /** @return {boolean} */ + function r_shortv() { + lab0: { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab1: { + if (!(base.out_grouping_b(g_v_WXY, 89, 121))) + { + break lab1; + } + if (!(base.in_grouping_b(g_v, 97, 121))) + { + break lab1; + } + if (!(base.out_grouping_b(g_v, 97, 121))) + { + break lab1; + } + break lab0; + } + base.cursor = base.limit - v_1; + lab2: { + if (!(base.out_grouping_b(g_v, 97, 121))) + { + break lab2; + } + if (!(base.in_grouping_b(g_v, 97, 121))) + { + break lab2; + } + if (base.cursor > base.limit_backward) + { + break lab2; + } + break lab0; + } + base.cursor = base.limit - v_1; + if (!(base.eq_s_b("past"))) + { + return false; + } + } + return true; + }; + + /** @return {boolean} */ + function r_R1() { + return I_p1 <= base.cursor; + }; + + /** @return {boolean} */ + function r_R2() { + return I_p2 <= base.cursor; + }; + + /** @return {boolean} */ + function r_Step_1a() { + var /** number */ among_var; + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab0: { + base.ket = base.cursor; + if (base.find_among_b(a_1) == 0) + { + base.cursor = base.limit - v_1; + break lab0; + } + base.bra = base.cursor; + if (!base.slice_del()) + { + return false; + } + } + base.ket = base.cursor; + among_var = base.find_among_b(a_2); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + switch (among_var) { + case 1: + if (!base.slice_from("ss")) + { + return false; + } + break; + case 2: + lab1: { + /** @const */ var /** number */ v_2 = base.limit - base.cursor; + lab2: { + { + /** @const */ var /** number */ c1 = base.cursor - 2; + if (c1 < base.limit_backward) + { + break lab2; + } + base.cursor = c1; + } + if (!base.slice_from("i")) + { + return false; + } + break lab1; + } + base.cursor = base.limit - v_2; + if (!base.slice_from("ie")) + { + return false; + } + } + break; + case 3: + if (base.cursor <= base.limit_backward) + { + return false; + } + base.cursor--; + if (!base.go_out_grouping_b(g_v, 97, 121)) + { + return false; + } + base.cursor--; + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_1b() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_5); + base.bra = base.cursor; + lab0: { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab1: { + switch (among_var) { + case 1: + /** @const */ var /** number */ v_2 = base.limit - base.cursor; + lab2: { + lab3: { + /** @const */ var /** number */ v_3 = base.limit - base.cursor; + lab4: { + if (base.find_among_b(a_3) == 0) + { + break lab4; + } + if (base.cursor > base.limit_backward) + { + break lab4; + } + break lab3; + } + base.cursor = base.limit - v_3; + if (!r_R1()) + { + break lab2; + } + if (!base.slice_from("ee")) + { + return false; + } + } + } + base.cursor = base.limit - v_2; + break; + case 2: + break lab1; + case 3: + among_var = base.find_among_b(a_4); + if (among_var == 0) + { + break lab1; + } + switch (among_var) { + case 1: + /** @const */ var /** number */ v_4 = base.limit - base.cursor; + if (!(base.out_grouping_b(g_v, 97, 121))) + { + break lab1; + } + if (base.cursor > base.limit_backward) + { + break lab1; + } + base.cursor = base.limit - v_4; + base.bra = base.cursor; + if (!base.slice_from("ie")) + { + return false; + } + break; + case 2: + if (base.cursor > base.limit_backward) + { + break lab1; + } + break; + } + break; + } + break lab0; + } + base.cursor = base.limit - v_1; + /** @const */ var /** number */ v_5 = base.limit - base.cursor; + if (!base.go_out_grouping_b(g_v, 97, 121)) + { + return false; + } + base.cursor--; + base.cursor = base.limit - v_5; + if (!base.slice_del()) + { + return false; + } + base.ket = base.cursor; + base.bra = base.cursor; + /** @const */ var /** number */ v_6 = base.limit - base.cursor; + among_var = base.find_among_b(a_6); + switch (among_var) { + case 1: + if (!base.slice_from("e")) + { + return false; + } + return false; + case 2: + { + /** @const */ var /** number */ v_7 = base.limit - base.cursor; + lab5: { + if (!(base.in_grouping_b(g_aeo, 97, 111))) + { + break lab5; + } + if (base.cursor > base.limit_backward) + { + break lab5; + } + return false; + } + base.cursor = base.limit - v_7; + } + break; + case 3: + if (base.cursor != I_p1) + { + return false; + } + /** @const */ var /** number */ v_8 = base.limit - base.cursor; + if (!r_shortv()) + { + return false; + } + base.cursor = base.limit - v_8; + if (!base.slice_from("e")) + { + return false; + } + return false; + } + base.cursor = base.limit - v_6; + base.ket = base.cursor; + if (base.cursor <= base.limit_backward) + { + return false; + } + base.cursor--; + base.bra = base.cursor; + if (!base.slice_del()) + { + return false; + } + } + return true; + }; + + /** @return {boolean} */ + function r_Step_1c() { + base.ket = base.cursor; + lab0: { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab1: { + if (!(base.eq_s_b("y"))) + { + break lab1; + } + break lab0; + } + base.cursor = base.limit - v_1; + if (!(base.eq_s_b("Y"))) + { + return false; + } + } + base.bra = base.cursor; + if (!(base.out_grouping_b(g_v, 97, 121))) + { + return false; + } + lab2: { + if (base.cursor > base.limit_backward) + { + break lab2; + } + return false; + } + if (!base.slice_from("i")) + { + return false; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_2() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_7); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + if (!r_R1()) + { + return false; + } + switch (among_var) { + case 1: + if (!base.slice_from("tion")) + { + return false; + } + break; + case 2: + if (!base.slice_from("ence")) + { + return false; + } + break; + case 3: + if (!base.slice_from("ance")) + { + return false; + } + break; + case 4: + if (!base.slice_from("able")) + { + return false; + } + break; + case 5: + if (!base.slice_from("ent")) + { + return false; + } + break; + case 6: + if (!base.slice_from("ize")) + { + return false; + } + break; + case 7: + if (!base.slice_from("ate")) + { + return false; + } + break; + case 8: + if (!base.slice_from("al")) + { + return false; + } + break; + case 9: + if (!base.slice_from("ful")) + { + return false; + } + break; + case 10: + if (!base.slice_from("ous")) + { + return false; + } + break; + case 11: + if (!base.slice_from("ive")) + { + return false; + } + break; + case 12: + if (!base.slice_from("ble")) + { + return false; + } + break; + case 13: + if (!base.slice_from("og")) + { + return false; + } + break; + case 14: + if (!(base.eq_s_b("l"))) + { + return false; + } + if (!base.slice_from("og")) + { + return false; + } + break; + case 15: + if (!base.slice_from("less")) + { + return false; + } + break; + case 16: + if (!(base.in_grouping_b(g_valid_LI, 99, 116))) + { + return false; + } + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_3() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_8); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + if (!r_R1()) + { + return false; + } + switch (among_var) { + case 1: + if (!base.slice_from("tion")) + { + return false; + } + break; + case 2: + if (!base.slice_from("ate")) + { + return false; + } + break; + case 3: + if (!base.slice_from("al")) + { + return false; + } + break; + case 4: + if (!base.slice_from("ic")) + { + return false; + } + break; + case 5: + if (!base.slice_del()) + { + return false; + } + break; + case 6: + if (!r_R2()) + { + return false; + } + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_4() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_9); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + if (!r_R2()) + { + return false; + } + switch (among_var) { + case 1: + if (!base.slice_del()) + { + return false; + } + break; + case 2: + lab0: { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab1: { + if (!(base.eq_s_b("s"))) + { + break lab1; + } + break lab0; + } + base.cursor = base.limit - v_1; + if (!(base.eq_s_b("t"))) + { + return false; + } + } + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_5() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_10); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + switch (among_var) { + case 1: + lab0: { + lab1: { + if (!r_R2()) + { + break lab1; + } + break lab0; + } + if (!r_R1()) + { + return false; + } + { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab2: { + if (!r_shortv()) + { + break lab2; + } + return false; + } + base.cursor = base.limit - v_1; + } + } + if (!base.slice_del()) + { + return false; + } + break; + case 2: + if (!r_R2()) + { + return false; + } + if (!(base.eq_s_b("l"))) + { + return false; + } + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_exception1() { + var /** number */ among_var; + base.bra = base.cursor; + among_var = base.find_among(a_11); + if (among_var == 0) + { + return false; + } + base.ket = base.cursor; + if (base.cursor < base.limit) + { + return false; + } + switch (among_var) { + case 1: + if (!base.slice_from("sky")) + { + return false; + } + break; + case 2: + if (!base.slice_from("idl")) + { + return false; + } + break; + case 3: + if (!base.slice_from("gentl")) + { + return false; + } + break; + case 4: + if (!base.slice_from("ugli")) + { + return false; + } + break; + case 5: + if (!base.slice_from("earli")) + { + return false; + } + break; + case 6: + if (!base.slice_from("onli")) + { + return false; + } + break; + case 7: + if (!base.slice_from("singl")) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_postlude() { + if (!B_Y_found) + { + return false; + } + while(true) + { + /** @const */ var /** number */ v_1 = base.cursor; + lab0: { + golab1: while(true) + { + /** @const */ var /** number */ v_2 = base.cursor; + lab2: { + base.bra = base.cursor; + if (!(base.eq_s("Y"))) + { + break lab2; + } + base.ket = base.cursor; + base.cursor = v_2; + break golab1; + } + base.cursor = v_2; + if (base.cursor >= base.limit) + { + break lab0; + } + base.cursor++; + } + if (!base.slice_from("y")) + { + return false; + } + continue; + } + base.cursor = v_1; + break; + } + return true; + }; + + this.stem = /** @return {boolean} */ function() { + lab0: { + /** @const */ var /** number */ v_1 = base.cursor; + lab1: { + if (!r_exception1()) + { + break lab1; + } + break lab0; + } + base.cursor = v_1; + lab2: { + { + /** @const */ var /** number */ v_2 = base.cursor; + lab3: { + { + /** @const */ var /** number */ c1 = base.cursor + 3; + if (c1 > base.limit) + { + break lab3; + } + base.cursor = c1; + } + break lab2; + } + base.cursor = v_2; + } + break lab0; + } + base.cursor = v_1; + r_prelude(); + r_mark_regions(); + base.limit_backward = base.cursor; base.cursor = base.limit; + /** @const */ var /** number */ v_3 = base.limit - base.cursor; + r_Step_1a(); + base.cursor = base.limit - v_3; + /** @const */ var /** number */ v_4 = base.limit - base.cursor; + r_Step_1b(); + base.cursor = base.limit - v_4; + /** @const */ var /** number */ v_5 = base.limit - base.cursor; + r_Step_1c(); + base.cursor = base.limit - v_5; + /** @const */ var /** number */ v_6 = base.limit - base.cursor; + r_Step_2(); + base.cursor = base.limit - v_6; + /** @const */ var /** number */ v_7 = base.limit - base.cursor; + r_Step_3(); + base.cursor = base.limit - v_7; + /** @const */ var /** number */ v_8 = base.limit - base.cursor; + r_Step_4(); + base.cursor = base.limit - v_8; + /** @const */ var /** number */ v_9 = base.limit - base.cursor; + r_Step_5(); + base.cursor = base.limit - v_9; + base.cursor = base.limit_backward; + /** @const */ var /** number */ v_10 = base.cursor; + r_postlude(); + base.cursor = v_10; + } + return true; + }; + + /**@return{string}*/ + this['stemWord'] = function(/**string*/word) { + base.setCurrent(word); + this.stem(); + return base.getCurrent(); + }; +}; diff --git a/_static/file.png b/_static/file.png new file mode 100644 index 0000000..a858a41 Binary files /dev/null and b/_static/file.png differ diff --git a/_static/fonts/Lato/lato-bold.eot b/_static/fonts/Lato/lato-bold.eot new file mode 100644 index 0000000..3361183 Binary files /dev/null and b/_static/fonts/Lato/lato-bold.eot differ diff --git a/_static/fonts/Lato/lato-bold.ttf 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query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +// Global search result kind enum, used by themes to style search results. +// prettier-ignore +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _escapeHTML = (text) => { + return text + .replaceAll("&", "&") + .replaceAll("<", "<") + .replaceAll(">", ">") + .replaceAll('"', """) + .replaceAll("'", "'"); +}; + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename, kind] = item; + + let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = _escapeHTML(title); + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + ` (${_escapeHTML(descr)})`; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) + // SPHINX_HIGHLIGHT_ENABLED is set in sphinx_highlight.js + highlightTerms.forEach((term) => + _highlightText(listItem, term, "highlighted"), + ); + } else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor), + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) + // SPHINX_HIGHLIGHT_ENABLED is set in sphinx_highlight.js + highlightTerms.forEach((term) => + _highlightText(listItem, term, "highlighted"), + ); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories.", + ); + else + Search.status.innerText = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, + ).replace("${resultCount}", resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5, + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => + query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter((term) => term); // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString( + htmlString, + "text/html", + ); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { + el.remove(); + }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector( + `[role="main"] ${anchor}`, + ); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.`, + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template.", + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.setAttribute("role", "list"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords set is from language_data.js + if (stopwords.has(queryTermLower) || queryTerm.match(/^\d+$/)) return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { + // SPHINX_HIGHLIGHT_ENABLED is set in sphinx_highlight.js + localStorage.setItem( + "sphinx_highlight_terms", + [...highlightTerms].join(" "), + ); + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: ( + query, + searchTerms, + excludedTerms, + highlightTerms, + objectTerms, + ) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if ( + title.toLowerCase().trim().includes(queryLower) + && queryLower.length >= title.length / 2 + ) { + for (const [file, id] of foundTitles) { + const score = Math.round( + (Scorer.title * queryLower.length) / title.length, + ); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + SearchResultKind.title, + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && queryLower.length >= entry.length / 2) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round((100 * queryLower.length) / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + SearchResultKind.index, + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)), + ); + + // lookup as search terms in fulltext + normalResults.push( + ...Search.performTermsSearch(searchTerms, excludedTerms), + ); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result + .slice(0, 4) + .concat([result[5]]) + .map((v) => String(v)) + .join(","); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [ + searchQuery, + searchTerms, + excludedTerms, + highlightTerms, + objectTerms, + ] = Search._parseQuery(query); + const results = Search._performSearch( + searchQuery, + searchTerms, + excludedTerms, + highlightTerms, + objectTerms, + ); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4]; + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + SearchResultKind.object, + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => objectSearchCallback(prefix, array)), + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + // find documents, if any, containing the query word in their text/title term indices + // use Object.hasOwnProperty to avoid mismatching against prototype properties + const arr = [ + { + files: terms.hasOwnProperty(word) ? terms[word] : undefined, + score: Scorer.term, + }, + { + files: titleTerms.hasOwnProperty(word) ? titleTerms[word] : undefined, + score: Scorer.title, + }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, new Map()); + const fileScores = scoreMap.get(file); + fileScores.set(word, record.score); + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2, + ).length; + if ( + wordList.length !== searchTerms.size + && wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file + || titleTerms[term] === file + || (terms[term] || []).includes(file) + || (titleTerms[term] || []).includes(file), + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file).get(w))); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + SearchResultKind.text, + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = + top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..a74e103 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,159 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true; + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 + && !parent.classList.contains(className) + && !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore(span, parent.insertBefore(rest, node.nextSibling)); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect", + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target), + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms"); + // Update history only if '?highlight' is present; otherwise it + // clears text fragments (not set in window.location by the browser) + if (url.searchParams.has("highlight")) { + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + } + + // get individual terms from highlight string + const terms = highlight + .toLowerCase() + .split(/\s+/) + .filter((x) => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '", + ), + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms"); + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) + return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) + return; + if ( + DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + && event.key === "Escape" + ) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/api/diffpy.distanceprinter.html b/api/diffpy.distanceprinter.html new file mode 100644 index 0000000..8f27038 --- /dev/null +++ b/api/diffpy.distanceprinter.html @@ -0,0 +1,133 @@ + + + + + + + + + diffpy.distanceprinter package — diffpy.distanceprinter 1.1.0 documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

diffpy.distanceprinter package

+

Distance Printer, calculate the inter atomic distances.

+

Part of xPDFsuite.

+
+

Subpackages

+
+
+
+
+

Submodules

+
+
+

diffpy.distanceprinter.example_submodule module

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/cookiecutter.json b/cookiecutter.json deleted file mode 100644 index 9367ea9..0000000 --- a/cookiecutter.json +++ /dev/null @@ -1,18 +0,0 @@ -{ - "maintainer_name": "Simon Billinge", - "maintainer_email": "sb2896@columbia.edu", - "maintainer_github_username": "sbillinge", - "contributors": "Xiaohao Yang and Billinge Group members", - "license_holders": "The Trustees of Columbia University in the City of New York", - "project_name": "diffpy.distanceprinter", - "github_username_or_orgname": "diffpy", - "github_repo_name": "diffpy.distanceprinter", - "conda_pypi_package_dist_name": "diffpy.distanceprinter", - "package_dir_name": "diffpy.distanceprinter", - "project_short_description": "Distance Printer, calculate the inter atomic distances. Part of xPDFsuite.", - "project_keywords": "diffpy, pdf, data-interpretation", - "minimum_supported_python_version": "3.12", - "maximum_supported_python_version": "3.14", - "project_needs_c_code_compiled": "No", - "project_has_gui_tests": "No" -} diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index 9d60f49..0000000 --- a/docs/Makefile +++ /dev/null @@ -1,194 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -PAPER = -BUILDDIR = build -BASENAME = $(subst .,,$(subst $() $(),,diffpy.distanceprinter)) - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) -$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) -endif - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source -# the i18n builder cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source - -.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext - -help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " dirhtml to make HTML files named index.html in directories" - @echo " singlehtml to make a single large HTML file" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " qthelp to make HTML files and a qthelp project" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " latexpdf to make LaTeX files and run them through pdflatex" - @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" - @echo " text to make text files" - @echo " man to make manual pages" - @echo " texinfo to make Texinfo files" - @echo " info to make Texinfo files and run them through makeinfo" - @echo " gettext to make PO message catalogs" - @echo " changes to make an overview of all changed/added/deprecated items" - @echo " xml to make Docutils-native XML files" - @echo " pseudoxml to make pseudoxml-XML files for display purposes" - @echo " linkcheck to check all external links for integrity" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - -clean: - rm -rf $(BUILDDIR)/* - -html: - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." - -dirhtml: - $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." - -singlehtml: - $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml - @echo - @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." - -pickle: - $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle - @echo - @echo "Build finished; now you can process the pickle files." - -json: - $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json - @echo - @echo "Build finished; now you can process the JSON files." - -htmlhelp: - $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp - @echo - @echo "Build finished; now you can run HTML Help Workshop with the" \ - ".hhp project file in $(BUILDDIR)/htmlhelp." - -qthelp: - $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp - @echo - @echo "Build finished; now you can run "qcollectiongenerator" with the" \ - ".qhcp project file in $(BUILDDIR)/qthelp, like this:" - @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/$(BASENAME).qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/$(BASENAME).qhc" - -devhelp: - $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp - @echo - @echo "Build finished." - @echo "To view the help file:" - @echo "# mkdir -p $$HOME/.local/share/devhelp/$(BASENAME)" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/$(BASENAME)" - @echo "# devhelp" - -epub: - $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub - @echo - @echo "Build finished. The epub file is in $(BUILDDIR)/epub." - -latex: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo - @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." - @echo "Run \`make' in that directory to run these through (pdf)latex" \ - "(use \`make latexpdf' here to do that automatically)." - -latexpdf: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through pdflatex..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -latexpdfja: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through platex and dvipdfmx..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -text: - $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text - @echo - @echo "Build finished. The text files are in $(BUILDDIR)/text." - -man: - $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man - @echo - @echo "Build finished. The manual pages are in $(BUILDDIR)/man." - -texinfo: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo - @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." - @echo "Run \`make' in that directory to run these through makeinfo" \ - "(use \`make info' here to do that automatically)." - -info: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo "Running Texinfo files through makeinfo..." - make -C $(BUILDDIR)/texinfo info - @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." - -gettext: - $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale - @echo - @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." - -changes: - $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes - @echo - @echo "The overview file is in $(BUILDDIR)/changes." - -linkcheck: - $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck - @echo - @echo "Link check complete; look for any errors in the above output " \ - "or in $(BUILDDIR)/linkcheck/output.txt." - -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." - -# Manual publishing to the gh-pages branch - -GITREPOPATH = $(shell cd $(CURDIR) && git rev-parse --git-dir) -GITREMOTE = origin -GITREMOTEURL = $(shell git config --get remote.$(GITREMOTE).url) -GITLASTCOMMIT = $(shell git rev-parse --short HEAD) - -publish: - @test -d build/html || \ - ( echo >&2 "Run 'make html' first!"; false ) - git show-ref --verify --quiet refs/heads/gh-pages || \ - git branch --track gh-pages $(GITREMOTE)/gh-pages - test -d build/gh-pages || \ - git clone -s -b gh-pages $(GITREPOPATH) build/gh-pages - cd build/gh-pages && \ - git pull $(GITREMOTEURL) gh-pages - rsync -acv --delete --exclude=.git --exclude=.rsync-exclude \ - --exclude-from=build/gh-pages/.rsync-exclude \ - --link-dest=$(CURDIR)/build/html build/html/ build/gh-pages/ - cd build/gh-pages && \ - git add --all . && \ - git diff --cached --quiet || \ - git commit -m "Sync with the source at $(GITLASTCOMMIT)." - cd build/gh-pages && \ - git push origin gh-pages diff --git a/docs/make.bat b/docs/make.bat deleted file mode 100644 index ac53d5b..0000000 --- a/docs/make.bat +++ /dev/null @@ -1,36 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=source -set BUILDDIR=build -set SPHINXPROJ=PackagingScientificPython - -if "%1" == "" goto help - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ - exit /b 1 -) - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% - -:end -popd diff --git a/docs/source/conf.py b/docs/source/conf.py deleted file mode 100644 index bef4011..0000000 --- a/docs/source/conf.py +++ /dev/null @@ -1,322 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -# -# diffpy.distanceprinter documentation build configuration file, created by # noqa: E501 -# sphinx-quickstart on Thu Jan 30 15:49:41 2014. -# -# This file is execfile()d with the current directory set to its -# containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -import sys -import time -from importlib.metadata import version -from pathlib import Path - -# Attempt to import the version dynamically from GitHub tag. -try: - fullversion = version("diffpy.distanceprinter") -except Exception: - fullversion = "No version found. The correct version will appear in the released version." # noqa: E501 - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use Path().resolve() to make it absolute, like shown here. # noqa: E501 -# sys.path.insert(0, str(Path(".").resolve())) -sys.path.insert(0, str(Path("../..").resolve())) -sys.path.insert(0, str(Path("../../src").resolve())) - -# abbreviations -ab_authors = "Xiaohao Yang and Billinge Group members" - -# -- General configuration ------------------------------------------------ - -# If your documentation needs a minimal Sphinx version, state it here. -# needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = [ - "sphinx.ext.autodoc", - "sphinx.ext.napoleon", - "sphinx.ext.todo", - "sphinx.ext.viewcode", - "sphinx.ext.intersphinx", - "sphinx_rtd_theme", - "sphinx_copybutton", - "m2r2", -] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ["_templates"] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# -source_suffix = [".rst", ".md"] - -# The encoding of source files. -# source_encoding = 'utf-8-sig' - -# The master toctree document. -master_doc = "index" - -# General information about the project. -project = "diffpy.distanceprinter" -copyright = "%Y, The Trustees of Columbia University in the City of New York" - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. - -# The short X.Y version. -version = "".join(fullversion.split(".post")[:1]) -# The full version, including alpha/beta/rc tags. -release = fullversion - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# language = None - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -# today = '' -today = time.strftime("%B %d, %Y", time.localtime()) -year = today.split()[-1] -# Else, today_fmt is used as the format for a strftime call. -# today_fmt = '%B %d, %Y' -# substitute YEAR in the copyright string -copyright = copyright.replace("%Y", year) - -# For sphinx_copybutton extension. -# Do not copy "$" for shell commands in code-blocks. -copybutton_prompt_text = r"^\$ " -copybutton_prompt_is_regexp = True - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -exclude_patterns = ["build"] - -# The reST default role (used for this markup: `text`) to use for all -# documents. -# default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -# add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -# add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -# show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = "sphinx" - -# A list of ignored prefixes for module index sorting. -modindex_common_prefix = ["diffpy.distanceprinter"] - -# Display all warnings for missing links. -nitpicky = True - -# -- Options for HTML output ---------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -html_theme = "sphinx_rtd_theme" - -html_context = { - "display_github": True, - "github_user": "diffpy", - "github_repo": "diffpy.distanceprinter", - "github_version": "main", - "conf_py_path": "/docs/source/", -} - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# -html_theme_options = { - "navigation_with_keys": "true", -} - -# Add any paths that contain custom themes here, relative to this directory. -# html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -# html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -# html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -# html_logo = None - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -# html_favicon = None - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -# html_static_path = ['_static'] - -# Add any extra paths that contain custom files (such as robots.txt or -# .htaccess) here, relative to this directory. These files are copied -# directly to the root of the documentation. -# html_extra_path = [] - -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -# html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -# html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -# html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -# html_additional_pages = {} - -# If false, no module index is generated. -# html_domain_indices = True - -# If false, no index is generated. -# html_use_index = True - -# If true, the index is split into individual pages for each letter. -# html_split_index = False - -# If true, links to the reST sources are added to the pages. -# html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -# html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -# html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -# html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -# html_file_suffix = None - -# Output file base name for HTML help builder. -basename = "diffpy.distanceprinter".replace(" ", "").replace(".", "") -htmlhelp_basename = basename + "doc" - - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - # 'papersize': 'letterpaper', - # The font size ('10pt', '11pt' or '12pt'). - # 'pointsize': '10pt', - # Additional stuff for the LaTeX preamble. - # 'preamble': '', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - ( - "index", - "diffpy.distanceprinter.tex", - "diffpy.distanceprinter Documentation", - ab_authors, - "manual", - ), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -# latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -# latex_use_parts = False - -# If true, show page references after internal links. -# latex_show_pagerefs = False - -# If true, show URL addresses after external links. -# latex_show_urls = False - -# Documents to append as an appendix to all manuals. -# latex_appendices = [] - -# If false, no module index is generated. -# latex_domain_indices = True - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ( - "index", - "diffpy.distanceprinter", - "diffpy.distanceprinter Documentation", - ab_authors, - 1, - ) -] - -# If true, show URL addresses after external links. -# man_show_urls = False - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ( - "index", - "diffpy.distanceprinter", - "diffpy.distanceprinter Documentation", - ab_authors, - "diffpy.distanceprinter", - "One line description of project.", - "Miscellaneous", - ), -] - -# Documents to append as an appendix to all manuals. -# texinfo_appendices = [] - -# If false, no module index is generated. -# texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -# texinfo_show_urls = 'footnote' - -# If true, do not generate a @detailmenu in the "Top" node's menu. -# texinfo_no_detailmenu = False - - -# Example configuration for intersphinx: refer to the Python standard library. -# intersphinx_mapping = {'http://docs.python.org/': None} diff --git a/docs/source/img/.placeholder b/docs/source/img/.placeholder deleted file mode 100644 index e69de29..0000000 diff --git a/docs/source/snippets/.placeholder b/docs/source/snippets/.placeholder deleted file mode 100644 index e69de29..0000000 diff --git a/genindex.html b/genindex.html new file mode 100644 index 0000000..450b677 --- /dev/null +++ b/genindex.html @@ -0,0 +1,156 @@ + + + + + + + + Index — diffpy.distanceprinter 1.1.0 documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
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+ +
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+
+ + +

Index

+ +
+ D + | L + | M + | R + +
+

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  • + diffpy.distanceprinter + +
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+ + +
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+

© Copyright 2026, The Trustees of Columbia University in the City of New York.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..12c3ca2 --- /dev/null +++ b/index.html @@ -0,0 +1,168 @@ + + + + + + + + + diffpy.distanceprinter documentation — diffpy.distanceprinter 1.1.0 documentation + + + + + + + + + + + + + + + + + + + +
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+ +
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+ +
+

diffpy.distanceprinter documentation

+

diffpy.distanceprinter - Distance Printer, calculate the inter atomic distances. Part of xPDFsuite.

+
+
Software version 1.1.0
+
Last updated June 04, 2026.
+
+
+

Getting started

+

Welcome to the diffpy.distanceprinter documentation!

+

This package is not designed to be installed independently. To get started, please visit +https://www.diffpy.org/products/xPDFsuite.html for more information about the xpdfsuite package and +download the package together with diffpy.xpdfsuite.

+
+
+

Authors

+

diffpy.distanceprinter is developed by Xiaohao Yang and Billinge Group members. This project is maintained by Simon Billinge and Billinge Group members. For a detailed list of contributors see +https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors.

+
+
+

Installation

+

See the README +file included with the distribution.

+
+
+

Acknowledgements

+

diffpy.distanceprinter is built and maintained with scikit-package.

+
+
+

Table of contents

+ +
+
+

Indices

+ +
+
+ + +
+
+
+ +
+ +
+

© Copyright 2026, The Trustees of Columbia University in the City of New York.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/license.html b/license.html new file mode 100644 index 0000000..3d18c58 --- /dev/null +++ b/license.html @@ -0,0 +1,143 @@ + + + + + + + + + License — diffpy.distanceprinter 1.1.0 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
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+ +
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+
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+ +
+

License

+
+

OPEN SOURCE LICENSE AGREEMENT

+

BSD 3-Clause License

+

Copyright (c) 2009-2025, The Trustees of Columbia University in the City of New York. +Copyright (c) 2026-present, The Contributors to the diffpy.distanceprinter project. +All Rights Reserved.

+

Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met:

+
    +
  1. Redistributions of source code must retain the above copyright notice, this +list of conditions and the following disclaimer.

  2. +
  3. Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution.

  4. +
  5. Neither the name of the copyright holder nor the names of its +contributors may be used to endorse or promote products derived from +this software without specific prior written permission.

  6. +
+

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

+
+
+ + +
+
+
+ +
+ +
+

© Copyright 2026, The Trustees of Columbia University in the City of New York.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/news/TEMPLATE.rst b/news/TEMPLATE.rst deleted file mode 100644 index 790d30b..0000000 --- a/news/TEMPLATE.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000..06ff60f Binary files /dev/null and b/objects.inv differ diff --git a/py-modindex.html b/py-modindex.html new file mode 100644 index 0000000..7081b3a --- /dev/null +++ b/py-modindex.html @@ -0,0 +1,129 @@ + + + + + + + + Python Module Index — diffpy.distanceprinter 1.1.0 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
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  • + +
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  • +
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+
+
+ + +

Python Module Index

+ +
+ d +
+ + + + + + + + + + +
 
+ d
+ diffpy +
    + diffpy.distanceprinter +
+ + +
+
+
+ +
+ +
+

© Copyright 2026, The Trustees of Columbia University in the City of New York.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 6444a5f..0000000 --- a/pyproject.toml +++ /dev/null @@ -1,88 +0,0 @@ -[build-system] -requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0"] -build-backend = "setuptools.build_meta" - -[project] -name = "diffpy.distanceprinter" -dynamic=['version', 'dependencies'] -authors = [ - {name='Simon Billinge', email='sbillinge@ucsb.edu'}, -] -maintainers = [ - {name='Simon Billinge', email='sbillinge@ucsb.edu'}, -] -description = "Distance Printer, calculate the inter atomic distances. Part of xPDFsuite." -keywords = ['diffpy', 'pdf', 'data-interpretation'] -readme = "README.rst" -requires-python = ">=3.12, <3.15" -classifiers = [ - 'Development Status :: 5 - Production/Stable', - 'Environment :: Console', - 'Intended Audience :: Developers', - 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: BSD License', - 'Operating System :: MacOS :: MacOS X', - 'Operating System :: Microsoft :: Windows', - 'Operating System :: POSIX', - 'Operating System :: Unix', - 'Programming Language :: Python :: 3.12', - 'Programming Language :: Python :: 3.13', - 'Programming Language :: Python :: 3.14', - 'Topic :: Scientific/Engineering :: Physics', - 'Topic :: Scientific/Engineering :: Chemistry', -] - -[project.urls] -Homepage = "https://github.com/diffpy/diffpy.distanceprinter/" -Issues = "https://github.com/diffpy/diffpy.distanceprinter/issues/" - -[tool.setuptools-git-versioning] -enabled = true -template = "{tag}" -dev_template = "{tag}" -dirty_template = "{tag}" - -[tool.setuptools.packages.find] -where = ["src"] # list of folders that contain the packages (["."] by default) -include = ["*"] # package names should match these glob patterns (["*"] by default) -exclude = [] # exclude packages matching these glob patterns (empty by default) -namespaces = false # to disable scanning PEP 420 namespaces (true by default) - -[project.scripts] -distanceprinter = "diffpy.distanceprinter.distanceprinter:main" - -[tool.setuptools.dynamic] -dependencies = {file = ["requirements/pip.txt"]} - -[tool.codespell] -exclude-file = ".codespell/ignore_lines.txt" -ignore-words = ".codespell/ignore_words.txt" -skip = "*.cif,*.dat" - -[tool.docformatter] -recursive = true -wrap-summaries = 72 -wrap-descriptions = 72 - -[tool.black] -line-length = 79 -include = '\.pyi?$' -exclude = ''' -/( - \.git - | \.hg - | \.mypy_cache - | \.tox - | \.venv - | \.rst - | \.txt - | _build - | buck-out - | build - | dist - - # The following are specific to Black, you probably don't want those. - | blib2to3 - | tests/data -)/ -''' diff --git a/release.html b/release.html new file mode 100644 index 0000000..6fe98cb --- /dev/null +++ b/release.html @@ -0,0 +1,148 @@ + + + + + + + + + Release notes — diffpy.distanceprinter 1.1.0 documentation + + + + + + + + + + + + + + + + + + + + +
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+

Release notes

+
+

1.1.0

+

Added:

+
    +
  • Added support for Python 3.14.

  • +
+

Removed:

+
    +
  • Removed support for Python 3.11.

  • +
+
+
+

1.0.2

+
+
+

1.0.1

+

Fixed:

+
    +
  • Fixed command line control usability

  • +
+
+
+

1.0.0

+

Changed:

+ +
+
+ + +
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+ +
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https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors -# -# See LICENSE.rst for license information. -# -############################################################################## diff --git a/src/diffpy/distanceprinter/__init__.py b/src/diffpy/distanceprinter/__init__.py deleted file mode 100644 index a61da5a..0000000 --- a/src/diffpy/distanceprinter/__init__.py +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env python -############################################################################## -# -# (c) 2013-2025 The Trustees of Columbia University in the City of New York. -# (c) 2026-present, The Contributors to the diffpy.distanceprinter project. -# All rights reserved. -# -# File coded by: Xiaohao Yang and Billinge Group members. -# -# See GitHub contributions for a more detailed list of contributors. -# https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors -# -# See LICENSE.rst for license information. -# -############################################################################## -"""Distance Printer, calculate the inter atomic distances. - -Part of xPDFsuite. -""" - -# package version -from diffpy.distanceprinter.version import __version__ # noqa - -# silence the pyflakes syntax checker -assert __version__ or True - -# End of file diff --git a/src/diffpy/distanceprinter/distanceprinter.py b/src/diffpy/distanceprinter/distanceprinter.py deleted file mode 100644 index 2466ea8..0000000 --- a/src/diffpy/distanceprinter/distanceprinter.py +++ /dev/null @@ -1,153 +0,0 @@ -#!/usr/bin/env python -############################################################################## -# -# (c) 2013-2025 The Trustees of Columbia University in the City of New York. -# (c) 2026-present, The Contributors to the diffpy.distanceprinter project. -# All rights reserved. -# -# File coded by: Xiaohao Yang and Billinge Group members -# -# See GitHub contributions for a more detailed list of contributors. -# https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors -# noqa: E501 -# -# See LICENSE.rst for license information. -# -############################################################################## - -import sys - -import numpy as np - -from diffpy.pdffit2 import PdfFit -from diffpy.structure import PDFFitStructure - - -def calDistance(strufile, atomi, atomj, lb, ub, complete): - - stru = PDFFitStructure(filename=strufile) - pdffit = PdfFit() - pdffit.add_structure(stru) - ele = stru.element - - rv = pdffit.bond_length_types(atomi, atomj, lb, ub) - dij = np.around(rv["dij"], 6) - ddij = np.around(rv["ddij"], 10) - rv["all0ddij"] = np.all(ddij == 0) - ij0 = rv["ij0"] - - chardtype = "S8" if complete else "S4" - dtypec = [ - ("distance", float), - ("dd", float), - ("i", chardtype), - ("j", chardtype), - ] - distlist = np.zeros(len(dij), dtype=dtypec) - - if not complete: - for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0): - if ij[0] > ij[1]: - distlist[i] = (dist, dd, ele[ij[1]], ele[ij[0]]) - else: - distlist[i] = (dist, dd, ele[ij[0]], ele[ij[1]]) - distlist = np.unique(distlist) - else: - for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0): - distlist[i] = ( - dist, - dd, - "%s.%i" % (ele[ij[0]], ij[0]), - "%s.%i" % (ele[ij[1]], ij[1]), - ) - - distlist.sort(order="distance") - rv["distlist"] = distlist - rv["atomi"] = atomi - rv["atomj"] = atomj - rv["lb"] = lb - rv["ub"] = ub - rv["complete"] = complete - rv["stru"] = stru - rv["strufile"] = strufile - return rv - - -def formatResults(stru, distlist, complete, all0ddij, **kw): - """Format the distlist to string.""" - lines = [] - # header - lines.append("# Structure file: %s" % kw["strufile"]) - lines.append("# ") - strustr = stru.__str__().splitlines() - lines.append("# " + strustr[0]) - for i in range(1, len(strustr)): - lines.append("# %2i " % (i - 1) + strustr[i]) - lines.append("# ") - lines.append( - "# Inter-atomic distance of (%s, %s) in (%2.2f, %2.2f) A" - % (kw["atomi"], kw["atomj"], kw["lb"], kw["ub"]) - ) - lines.append("") - - if complete: - for dist in distlist: - try: - lines.append( - "%s-%s:\t%2.6f" - % ( - dist[2].decode("utf-8"), - dist[3].decode("utf-8"), - dist[0], - ) - ) - except AttributeError: - lines.append("%s-%s:\t%2.6f" % (dist[2], dist[3], dist[0])) - else: - for dist in distlist: - try: - lines.append( - "%s-%s:\t%2.6f (%1.1e)" - % ( - dist[2].decode("utf-8"), - dist[3].decode("utf-8"), - dist[0], - dist[1], - ) - ) - except AttributeError: - lines.append( - "%s-%s:\t%2.6f (%1.1e)" - % (dist[2], dist[3], dist[0], dist[1]) - ) - rv = "\n".join(lines) - return rv - - -def writeToFile(filename, rv): - f = open(filename, "w", encoding="utf-8") - try: - rv = rv.decode("utf-8") - f.write(rv) - f.close() - except AttributeError: - # No need to decode in python 3 - f.write(rv) - f.close() - pass - - -def main(): - sysargv = sys.argv[1:] - strufile, atomi, atomj, lb, ub, complete, filename = sysargv - lb = float(lb) - ub = float(ub) - complete = "1" == complete - rv = calDistance(strufile, atomi, atomj, lb, ub, complete) - strv = formatResults(**rv) - writeToFile(filename, strv) - return - - -if __name__ == "__main__": - main() diff --git a/src/diffpy/distanceprinter/distanceprinter_app.py b/src/diffpy/distanceprinter/distanceprinter_app.py deleted file mode 100644 index daa0cb8..0000000 --- a/src/diffpy/distanceprinter/distanceprinter_app.py +++ /dev/null @@ -1,34 +0,0 @@ -import argparse - -from diffpy.distanceprinter.version import __version__ # noqa - - -def main(): - parser = argparse.ArgumentParser( - prog="diffpy.distanceprinter", - description=( - "Distance Printer, calculate the inter atomic distances. " - "Part of xPDFsuite.\n\n" - "For more information, visit: " - "https://github.com/diffpy/diffpy.distanceprinter/" - ), - formatter_class=argparse.RawDescriptionHelpFormatter, - ) - - parser.add_argument( - "--version", - action="store_true", - help="Show the program's version number and exit", - ) - - args = parser.parse_args() - - if args.version: - print(f"diffpy.distanceprinter {__version__}") - else: - # Default behavior when no arguments are given - parser.print_help() - - -if __name__ == "__main__": - main() diff --git a/src/diffpy/distanceprinter/version.py b/src/diffpy/distanceprinter/version.py deleted file mode 100644 index cb7f46a..0000000 --- a/src/diffpy/distanceprinter/version.py +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env python -############################################################################## -# -# (c) 2013-2025 The Trustees of Columbia University in the City of New York. -# (c) 2026-present, The Contributors to the diffpy.distanceprinter project. -# All rights reserved. -# -# File coded by: Xiaohao Yang and Billinge Group members. -# -# See GitHub contributions for a more detailed list of contributors. -# https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors # noqa: E501 -# -# See LICENSE.rst for license information. -# -############################################################################## -"""Definition of __version__.""" - -# We do not use the other three variables, but can be added back if needed. -# __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"] - -# obtain version information -from importlib.metadata import PackageNotFoundError, version - -try: - __version__ = version("diffpy.distanceprinter") -except PackageNotFoundError: - __version__ = "unknown" diff --git a/tests/conftest.py b/tests/conftest.py deleted file mode 100644 index e3b6313..0000000 --- a/tests/conftest.py +++ /dev/null @@ -1,19 +0,0 @@ -import json -from pathlib import Path - -import pytest - - -@pytest.fixture -def user_filesystem(tmp_path): - base_dir = Path(tmp_path) - home_dir = base_dir / "home_dir" - home_dir.mkdir(parents=True, exist_ok=True) - cwd_dir = base_dir / "cwd_dir" - cwd_dir.mkdir(parents=True, exist_ok=True) - - home_config_data = {"username": "home_username", "email": "home@email.com"} - with open(home_dir / "diffpyconfig.json", "w") as f: - json.dump(home_config_data, f) - - yield tmp_path diff --git a/tests/data/Ni-9008476.cif b/tests/data/Ni-9008476.cif deleted file mode 100644 index 12aeff6..0000000 --- a/tests/data/Ni-9008476.cif +++ /dev/null @@ -1,250 +0,0 @@ -#------------------------------------------------------------------------------ -#$Date: 2017-10-15 03:23:08 +0300 (Sun, 15 Oct 2017) $ -#$Revision: 202022 $ -#$URL: file:///home/coder/svn-repositories/cod/cif/9/00/84/9008476.cif $ -#------------------------------------------------------------------------------ -# -# This file is available in the Crystallography Open Database (COD), -# http://www.crystallography.net/. The original data for this entry -# were provided the American Mineralogist Crystal Structure Database, -# http://rruff.geo.arizona.edu/AMS/amcsd.php -# -# The file may be used within the scientific community so long as -# proper attribution is given to the journal article from which the -# data were obtained. -# -data_9008476 -loop_ -_publ_author_name -'Wyckoff, R. W. G.' -_publ_section_title -; - Second edition. 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9.967009 -Ni.3-Ni.3: 9.967009 -Ni.3-Ni.3: 9.967009 -Ni.3-Ni.3: 9.967009 -Ni.3-Ni.3: 9.967009 -Ni.3-Ni.3: 9.967009 -Ni.3-Ni.3: 9.967009 -Ni.3-Ni.3: 9.967009 -Ni.3-Ni.3: 9.967009 diff --git a/tests/test_distanceprinter.py b/tests/test_distanceprinter.py deleted file mode 100644 index f4c987a..0000000 --- a/tests/test_distanceprinter.py +++ /dev/null @@ -1,57 +0,0 @@ -import os -from io import open - -from diffpy.distanceprinter.distanceprinter import main - - -def test_distanceprinter(monkeypatch): - current_module_dir = os.path.dirname(__file__) - example_file_dir = os.path.join(current_module_dir, "data") - # must be cif, stru, or xyz file - strufile = os.path.join(example_file_dir, "Ni-9008476.cif") - # atoms typically pull from list of elements in output of PDFFitStructure. - # 'all' is always first option - atomi = "all" - atomj = "all" - # lb and ub are lower an upper bound of distance to list in angstroms - lb = 1 - ub = 10 - # 1 means keep duplicate atom pairs with same inter-atomic distance - # 0 means not to - comp = "1" - monkeypatch.setattr( - "sys.argv", - [ - "distanceprinter", - strufile, - atomi, - atomj, - lb, - ub, - comp, - "tests\\outputs\\actual.res", - ], - ) - cwd = os.getcwd() - main() - generated_file_path = os.path.join(cwd, "tests\\outputs\\actual.res") - f = open(generated_file_path, "r", encoding="utf-8") - rv0 = f.readlines() - rv0 = "".join(rv0) - resultstr = rv0 - output_file_dir = os.path.join(current_module_dir, "outputs") - example_output = os.path.join(output_file_dir, "expected.res") - f = open(example_output, "r", encoding="utf-8") - rv1 = f.readlines() - rv1 = "".join(rv1) - teststr = rv1 - - # Remove stru file path when comparing as it may differ between machines - resultstr = resultstr.split("\n", 2)[2] - teststr = teststr.split("\n", 2)[2] - - # Remove irrelevant whitespace when comparing - resultstr = "".join(resultstr.split()) - teststr = "".join(teststr.split()) - - assert resultstr == teststr diff --git a/tests/test_version.py b/tests/test_version.py deleted file mode 100644 index b8b38df..0000000 --- a/tests/test_version.py +++ /dev/null @@ -1,10 +0,0 @@ -"""Unit tests for __version__.py.""" - -import diffpy.distanceprinter # noqa - - -def test_package_version(): - """Ensure the package version is defined and not set to the initial - placeholder.""" - assert hasattr(diffpy.distanceprinter, "__version__") - assert diffpy.distanceprinter.__version__ != "0.0.0"