├── docs ├── .nojekyll ├── objects.inv ├── _static │ ├── file.png │ ├── minus.png │ ├── plus.png │ ├── documentation_options.js │ ├── sidebar.js │ ├── doctools.js │ ├── pygments.css │ ├── classic.css │ ├── language_data.js │ ├── sphinx_highlight.js │ ├── basic.css │ └── searchtools.js ├── .buildinfo ├── _sources │ └── index.rst.txt ├── _modules │ └── index.html ├── search.html ├── py-modindex.html ├── searchindex.js └── genindex.html ├── .tests ├── test_escaped.tre ├── test.nex.gz ├── test.nexml.gz ├── test.tre.gz ├── test.nexml ├── test.tre ├── test.nex └── tests.py ├── compile.sh ├── MANIFEST.in ├── treeswift ├── __init__.py └── Node.py ├── .travis.yml ├── docs_src ├── source │ ├── index.rst │ └── conf.py └── Makefile ├── setup.cfg ├── .github └── workflows │ └── treeswift_tests.yml ├── README.md ├── .gitignore ├── setup.py ├── CODE_OF_CONDUCT.md └── LICENSE /docs/.nojekyll: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.tests/test_escaped.tre: -------------------------------------------------------------------------------- 1 | [&R] ('https://youtube.com','&'); 2 | -------------------------------------------------------------------------------- /docs/objects.inv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/niemasd/TreeSwift/HEAD/docs/objects.inv -------------------------------------------------------------------------------- /.tests/test.nex.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/niemasd/TreeSwift/HEAD/.tests/test.nex.gz -------------------------------------------------------------------------------- /.tests/test.nexml.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/niemasd/TreeSwift/HEAD/.tests/test.nexml.gz -------------------------------------------------------------------------------- /.tests/test.tre.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/niemasd/TreeSwift/HEAD/.tests/test.tre.gz -------------------------------------------------------------------------------- /docs/_static/file.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/niemasd/TreeSwift/HEAD/docs/_static/file.png -------------------------------------------------------------------------------- /docs/_static/minus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/niemasd/TreeSwift/HEAD/docs/_static/minus.png -------------------------------------------------------------------------------- /docs/_static/plus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/niemasd/TreeSwift/HEAD/docs/_static/plus.png -------------------------------------------------------------------------------- /compile.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | rm -rf build dist treeswift.* 3 | python3 setup.py sdist 4 | python3 setup.py bdist_wheel --universal 5 | twine upload dist/* 6 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | # Include the README 2 | include *.md 3 | 4 | # Include the license file 5 | include LICENSE 6 | 7 | # Include the data files 8 | #recursive-include data * 9 | -------------------------------------------------------------------------------- /docs/.buildinfo: -------------------------------------------------------------------------------- 1 | # Sphinx build info version 1 2 | # This file records the configuration used when building these files. When it is not found, a full rebuild will be done. 3 | config: 7062db21fc60825e1e7ee52afe62bac4 4 | tags: 645f666f9bcd5a90fca523b33c5a78b7 5 | -------------------------------------------------------------------------------- /treeswift/__init__.py: -------------------------------------------------------------------------------- 1 | from treeswift.Tree import Tree,plot_ltt,read_tree,read_tree_dendropy,read_tree_newick,read_tree_nexml,read_tree_nexus 2 | from treeswift.Node import Node 3 | __all__ = ['Node','Tree','read_tree','read_tree_dendropy','read_tree_newick','read_tree_nexml','read_tree_nexus'] 4 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | # .travis.yml setup 2 | sudo: 3 | - enabled 4 | os: 5 | - linux 6 | dist: 7 | - trusty 8 | language: 9 | - python 10 | python: 11 | - "3.7" 12 | - "3.8" 13 | - "3.9" 14 | - "3.10" 15 | - "3.11" 16 | 17 | install: 18 | - pip install -e . 19 | 20 | # run tests 21 | script: 22 | - .travis_tests/tests.py 23 | -------------------------------------------------------------------------------- /docs/_static/documentation_options.js: -------------------------------------------------------------------------------- 1 | const DOCUMENTATION_OPTIONS = { 2 | VERSION: '', 3 | LANGUAGE: 'en', 4 | COLLAPSE_INDEX: false, 5 | BUILDER: 'html', 6 | FILE_SUFFIX: '.html', 7 | LINK_SUFFIX: '.html', 8 | HAS_SOURCE: true, 9 | SOURCELINK_SUFFIX: '.txt', 10 | NAVIGATION_WITH_KEYS: false, 11 | SHOW_SEARCH_SUMMARY: true, 12 | ENABLE_SEARCH_SHORTCUTS: true, 13 | }; -------------------------------------------------------------------------------- /docs_src/source/index.rst: -------------------------------------------------------------------------------- 1 | treeswift package 2 | ================= 3 | 4 | `TreeSwift `_ is a Python library for parsing, manipulating, and iterating over (rooted) tree structures. TreeSwift places an emphasis on speed. 5 | 6 | Module contents 7 | --------------- 8 | 9 | .. automodule:: treeswift 10 | :members: 11 | :undoc-members: 12 | :show-inheritance: 13 | -------------------------------------------------------------------------------- /docs/_sources/index.rst.txt: -------------------------------------------------------------------------------- 1 | treeswift package 2 | ================= 3 | 4 | `TreeSwift `_ is a Python library for parsing, manipulating, and iterating over (rooted) tree structures. TreeSwift places an emphasis on speed. 5 | 6 | Module contents 7 | --------------- 8 | 9 | .. automodule:: treeswift 10 | :members: 11 | :undoc-members: 12 | :show-inheritance: 13 | -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [metadata] 2 | # This includes the license file in the wheel. 3 | license_file = LICENSE 4 | 5 | [bdist_wheel] 6 | # This flag says to generate wheels that support both Python 2 and Python 7 | # 3. If your code will not run unchanged on both Python 2 and 3, you will 8 | # need to generate separate wheels for each Python version that you 9 | # support. Removing this line (or setting universal to 0) will prevent 10 | # bdist_wheel from trying to make a universal wheel. For more see: 11 | # https://packaging.python.org/tutorials/distributing-packages/#wheels 12 | universal=1 13 | -------------------------------------------------------------------------------- /docs_src/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | SHELL := /bin/bash 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | SPHINXPROJ = TreeSwift 8 | SOURCEDIR = source 9 | BUILDDIR = build 10 | DOCSDIR = ../docs 11 | 12 | # Put it first so that "make" without argument is like "make help". 13 | help: 14 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 15 | 16 | .PHONY: help Makefile 17 | 18 | # Catch-all target: route all unknown targets to Sphinx using the new 19 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 20 | %: Makefile 21 | $(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 22 | if [ "$(@)" == "clean" ]; then \ 23 | rm -rf "$(DOCSDIR)" "$(BUILDDIR)" ; \ 24 | fi 25 | if [ "$(@)" == "html" ]; then \ 26 | rm -rf "$(DOCSDIR)" && cp -R "$(BUILDDIR)/html" "$(DOCSDIR)" && rm -rf "$(BUILDDIR)" ; \ 27 | fi 28 | -------------------------------------------------------------------------------- /.github/workflows/treeswift_tests.yml: -------------------------------------------------------------------------------- 1 | name: TreeSwift Tests 2 | on: [push] 3 | 4 | jobs: 5 | treeswift_tests: 6 | runs-on: ubuntu-latest 7 | steps: 8 | - name: Set up Git repository 9 | uses: actions/checkout@v2 10 | - name: Run TreeSwift Tests 11 | run: | 12 | sudo apt-get update && sudo apt-get install -y python3 python3-pip && \ 13 | sudo -H pip3 install git+https://github.com/niemasd/TreeSwift.git && \ 14 | for f in .tests/*.tre* ; do echo "$f" | rev | cut -d'/' -f1 | rev && python3 -c "from treeswift import read_tree_newick; read_tree_newick('$f')" && echo "" || exit 1 ; done && \ 15 | for f in .tests/*.nex .tests/*.nex.* ; do echo "$f" | rev | cut -d'/' -f1 | rev && python3 -c "from treeswift import read_tree_nexus; read_tree_nexus('$f')" && echo "" || exit 1 ; done && \ 16 | for f in .tests/*.nexml* ; do echo "$f" | rev | cut -d'/' -f1 | rev && python3 -c "from treeswift import read_tree_nexml; read_tree_nexml('$f')" && echo "" || exit 1 ; done 17 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # TreeSwift 2 | TreeSwift is a pure Python library for parsing, manipulating, and iterating over (rooted) tree structures. TreeSwift places an emphasis on speed. 3 | 4 | We strongly recommend that you consider our new package, [CompactTree](https://github.com/niemasd/CompactTree) (a header-only C++ library that has a Python package wrapper with similar functionality as TreeSwift), though we will continue maintaining TreeSwift in parallel with CompactTree. 5 | 6 | ## Installation 7 | TreeSwift can be installed using `pip`: 8 | 9 | ```bash 10 | sudo pip install treeswift 11 | ``` 12 | 13 | If you are using a machine on which you lack administrative powers, TreeSwift can be installed locally using `pip`: 14 | 15 | ```bash 16 | pip install --user treeswift 17 | ``` 18 | 19 | ## Usage 20 | Typical usage should be as follows: 21 | 22 | 1. Import the `treeswift` package 23 | 2. Use `treeswift.read_tree_newick` to load your Newick tree 24 | 3. Use the various `Tree` class functions on the resulting object as you need 25 | 26 | ```python 27 | import treeswift 28 | tree = treeswift.read_tree_newick(my_newick_string) 29 | for node in tree.traverse_postorder(): 30 | print(node) 31 | ``` 32 | 33 | Full documentation can be found at [https://niema.net/TreeSwift](https://niema.net/TreeSwift), and more examples can be found in the [TreeSwift Wiki](https://github.com/niemasd/TreeSwift/wiki). 34 | 35 | ## Citing TreeSwift 36 | If you use TreeSwift in your work, please cite: 37 | 38 | > **Moshiri N** (2020). "TreeSwift: a massively scalable Python package for trees." *SoftwareX*. 11:100436. [doi:10.1016/j.softx.2020.100436](https://doi.org/10.1016/j.softx.2020.100436) 39 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # force keep 2 | !docs/ 3 | 4 | # tree files 5 | *.tre 6 | *.tree 7 | *.trees 8 | *.nex 9 | *.nexus 10 | *.nwk 11 | 12 | # Byte-compiled / optimized / DLL files 13 | __pycache__/ 14 | *.py[cod] 15 | *$py.class 16 | 17 | # C extensions 18 | *.so 19 | 20 | # Distribution / packaging 21 | .Python 22 | env/ 23 | build/ 24 | develop-eggs/ 25 | dist/ 26 | downloads/ 27 | eggs/ 28 | .eggs/ 29 | lib/ 30 | lib64/ 31 | parts/ 32 | sdist/ 33 | var/ 34 | wheels/ 35 | *.egg-info/ 36 | .installed.cfg 37 | *.egg 38 | 39 | # PyInstaller 40 | # Usually these files are written by a python script from a template 41 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 42 | *.manifest 43 | *.spec 44 | 45 | # Installer logs 46 | pip-log.txt 47 | pip-delete-this-directory.txt 48 | 49 | # Unit test / coverage reports 50 | htmlcov/ 51 | .tox/ 52 | .coverage 53 | .coverage.* 54 | .cache 55 | nosetests.xml 56 | coverage.xml 57 | *.cover 58 | .hypothesis/ 59 | 60 | # Translations 61 | *.mo 62 | *.pot 63 | 64 | # Django stuff: 65 | *.log 66 | local_settings.py 67 | 68 | # Flask stuff: 69 | instance/ 70 | .webassets-cache 71 | 72 | # Scrapy stuff: 73 | .scrapy 74 | 75 | # Sphinx documentation 76 | docs/_build/ 77 | 78 | # PyBuilder 79 | target/ 80 | 81 | # Jupyter Notebook 82 | .ipynb_checkpoints 83 | 84 | # pyenv 85 | .python-version 86 | 87 | # celery beat schedule file 88 | celerybeat-schedule 89 | 90 | # SageMath parsed files 91 | *.sage.py 92 | 93 | # dotenv 94 | .env 95 | 96 | # virtualenv 97 | .venv 98 | venv/ 99 | ENV/ 100 | 101 | # Spyder project settings 102 | .spyderproject 103 | .spyproject 104 | 105 | # Rope project settings 106 | .ropeproject 107 | 108 | # mkdocs documentation 109 | /site 110 | 111 | # mypy 112 | .mypy_cache/ 113 | -------------------------------------------------------------------------------- /.tests/test.nexml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | """A setuptools based setup module. 2 | 3 | See: 4 | https://packaging.python.org/en/latest/distributing.html 5 | https://github.com/pypa/sampleproject 6 | """ 7 | 8 | # Always prefer setuptools over distutils 9 | from setuptools import setup, find_packages 10 | # To use a consistent encoding 11 | from codecs import open 12 | from os import path 13 | 14 | here = path.abspath(path.dirname(__file__)) 15 | setup( 16 | name='treeswift', # Required 17 | version='1.1.45', # Required 18 | description='TreeSwift: Fast tree module for Python 2 and 3', # Required 19 | long_description='TreeSwift is a Python library for parsing, manipulating, and iterating over (rooted) tree structures. TreeSwift places an emphasis on speed.', # Optional 20 | long_description_content_type='text/plain', # Optional (see note above) 21 | url='https://github.com/niemasd/TreeSwift', # Optional 22 | author='Niema Moshiri', # Optional 23 | author_email='niemamoshiri@gmail.com', # Optional 24 | classifiers=[ # Optional 25 | # How mature is this project? Common values are 26 | # 3 - Alpha 27 | # 4 - Beta 28 | # 5 - Production/Stable 29 | 'Development Status :: 3 - Alpha', 30 | 31 | # Indicate who your project is intended for 32 | 'Intended Audience :: Developers', 33 | 'Topic :: Software Development :: Build Tools', 34 | 35 | # Pick your license as you wish 36 | 'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)', 37 | 38 | # Specify the Python versions you support here. In particular, ensure 39 | # that you indicate whether you support Python 2, Python 3 or both. 40 | 'Programming Language :: Python :: 3', 41 | 'Programming Language :: Python :: 3.7', 42 | 'Programming Language :: Python :: 3.8', 43 | 'Programming Language :: Python :: 3.9', 44 | 'Programming Language :: Python :: 3.10', 45 | 'Programming Language :: Python :: 3.11', 46 | ], 47 | keywords='tree phylogenetics fast', # Optional 48 | packages=find_packages(exclude=['contrib', 'docs', 'tests']), # Required 49 | extras_require={ # Optional 50 | 'dev': ['check-manifest'], 51 | }, 52 | project_urls={ # Optional 53 | 'Bug Reports': 'https://github.com/niemasd/TreeSwift/issues', 54 | 'Source': 'https://github.com/niemasd/TreeSwift', 55 | }, 56 | ) 57 | -------------------------------------------------------------------------------- /docs/_static/sidebar.js: -------------------------------------------------------------------------------- 1 | /* 2 | * This script makes the Sphinx sidebar collapsible. 3 | * 4 | * .sphinxsidebar contains .sphinxsidebarwrapper. This script adds 5 | * in .sphixsidebar, after .sphinxsidebarwrapper, the #sidebarbutton 6 | * used to collapse and expand the sidebar. 7 | * 8 | * When the sidebar is collapsed the .sphinxsidebarwrapper is hidden 9 | * and the width of the sidebar and the margin-left of the document 10 | * are decreased. When the sidebar is expanded the opposite happens. 11 | * This script saves a per-browser/per-session cookie used to 12 | * remember the position of the sidebar among the pages. 13 | * Once the browser is closed the cookie is deleted and the position 14 | * reset to the default (expanded). 15 | * 16 | */ 17 | 18 | const initialiseSidebar = () => { 19 | 20 | 21 | 22 | 23 | // global elements used by the functions. 24 | const bodyWrapper = document.getElementsByClassName("bodywrapper")[0] 25 | const sidebar = document.getElementsByClassName("sphinxsidebar")[0] 26 | const sidebarWrapper = document.getElementsByClassName('sphinxsidebarwrapper')[0] 27 | const sidebarButton = document.getElementById("sidebarbutton") 28 | const sidebarArrow = sidebarButton.querySelector('span') 29 | 30 | // for some reason, the document has no sidebar; do not run into errors 31 | if (typeof sidebar === "undefined") return; 32 | 33 | const flipArrow = element => element.innerText = (element.innerText === "»") ? "«" : "»" 34 | 35 | const collapse_sidebar = () => { 36 | bodyWrapper.style.marginLeft = ".8em"; 37 | sidebar.style.width = ".8em" 38 | sidebarWrapper.style.display = "none" 39 | flipArrow(sidebarArrow) 40 | sidebarButton.title = _('Expand sidebar') 41 | window.localStorage.setItem("sidebar", "collapsed") 42 | } 43 | 44 | const expand_sidebar = () => { 45 | bodyWrapper.style.marginLeft = "" 46 | sidebar.style.removeProperty("width") 47 | sidebarWrapper.style.display = "" 48 | flipArrow(sidebarArrow) 49 | sidebarButton.title = _('Collapse sidebar') 50 | window.localStorage.setItem("sidebar", "expanded") 51 | } 52 | 53 | sidebarButton.addEventListener("click", () => { 54 | (sidebarWrapper.style.display === "none") ? expand_sidebar() : collapse_sidebar() 55 | }) 56 | 57 | if (!window.localStorage.getItem("sidebar")) return 58 | const value = window.localStorage.getItem("sidebar") 59 | if (value === "collapsed") collapse_sidebar(); 60 | else if (value === "expanded") expand_sidebar(); 61 | } 62 | 63 | if (document.readyState !== "loading") initialiseSidebar() 64 | else document.addEventListener("DOMContentLoaded", initialiseSidebar) -------------------------------------------------------------------------------- /.tests/test.tre: -------------------------------------------------------------------------------- 1 | ((((((L147:0.324701,(L175:0.162508,L176:0.162508)I148:0.162193)I29:1.62347,((L183:0.0724336,L184:0.0724336)I181:0.0359448,L182:0.108378)I30:1.83979)I19:0.271253,((L69:1.20308,(L143:0.331782,L144:0.331782)I70:0.871297)I27:0.75577,(L35:1.88978,(L57:1.42021,((L189:0.0395976,L190:0.0395976)I95:0.637178,(L139:0.36855,L140:0.36855)I96:0.308226)I58:0.743433)I36:0.469573)I28:0.0690669)I20:0.260577)I7:1.10718,(L9:3.25292,(((((L75:1.14979,(L89:0.744407,L90:0.744407)I76:0.405379)I33:0.74263,((L127:0.39989,L128:0.39989)I105:0.214571,L106:0.61446)I34:1.27796)I31:0.0278664,((((((L137:0.378239,L138:0.378239)I111:0.225106,L112:0.603346)I109:0.00133224,(L113:0.555049,L114:0.555049)I110:0.0496291)I71:0.549486,(L131:0.385135,(L169:0.207639,L170:0.207639)I132:0.177496)I72:0.769029)I55:0.266169,(((L167:0.216587,L168:0.216587)I63:1.01811,L64:1.23469)I59:0.134541,L60:1.36923)I56:0.0510984)I37:0.420969,((L195:0.0157525,L196:0.0157525)I119:0.4918,(L135:0.379121,L136:0.379121)I120:0.128432)I38:1.33375)I32:0.0789811)I17:0.412423,(((L49:1.56867,((L83:0.878255,(L149:0.31829,L150:0.31829)I84:0.559965)I51:0.608044,((L165:0.216912,L166:0.216912)I163:0.00113418,L164:0.218047)I52:1.26825)I50:0.082368)I39:0.177888,(((L121:0.501006,L122:0.501006)I87:0.332514,L88:0.83352)I43:0.875992,(L45:1.64687,(L197:0.0101516,L198:0.0101516)I46:1.63672)I44:0.0626436)I40:0.0370436)I23:0.327625,(((L191:0.0283096,L192:0.0283096)I157:0.244775,L158:0.273085)I47:1.34044,(((L155:0.280689,L156:0.280689)I99:0.355457,(L115:0.540277,(L129:0.398734,L130:0.398734)I116:0.141543)I100:0.0958687)I65:0.597191,((L117:0.508884,(L151:0.288475,L152:0.288475)I118:0.220409)I91:0.221151,L92:0.730035)I66:0.503301)I48:0.38019)I24:0.460654)I18:0.258526)I11:0.388327,((((L185:0.0553334,L186:0.0553334)I133:0.325215,L134:0.380548)I53:1.10324,((L179:0.127113,L180:0.127113)I73:1.02664,(L123:0.486099,((L171:0.19954,(L177:0.130493,L178:0.130493)I172:0.0690462)I153:0.0813941,L154:0.280934)I124:0.205165)I74:0.667651)I54:0.330035)I13:0.935043,(((L85:0.875518,L86:0.875518)I61:0.377524,(L107:0.611435,(L141:0.354415,(L173:0.180134,L174:0.180134)I142:0.174281)I108:0.25702)I62:0.641607)I25:0.713319,((L101:0.624081,(L187:0.0402426,L188:0.0402426)I102:0.583838)I41:1.11449,(L161:0.224613,L162:0.224613)I42:1.51396)I26:0.227792)I14:0.452467)I12:0.302205)I10:0.53189)I8:0.073686)I5:0.580838,((L21:2.13854,((L125:0.459897,L126:0.459897)I81:0.497392,L82:0.957289)I22:1.18125)I15:0.27409,L16:2.41263)I6:1.49482)I1:0.196532,(((L103:0.615274,(L193:0.0175106,L194:0.0175106)I104:0.597763)I77:0.441009,L78:1.05628)I3:2.99065,((L79:1.02514,((L145:0.329653,L146:0.329653)I93:0.369685,(L159:0.267641,L160:0.267641)I94:0.431698)I80:0.3258)I67:0.183439,(L97:0.649737,L98:0.649737)I68:0.558841)I4:2.83836)I2:0.0570458)I0:2.5469; 2 | -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- 1 | # Contributor Covenant Code of Conduct 2 | 3 | ## Our Pledge 4 | 5 | In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation. 6 | 7 | ## Our Standards 8 | 9 | Examples of behavior that contributes to creating a positive environment include: 10 | 11 | * Using welcoming and inclusive language 12 | * Being respectful of differing viewpoints and experiences 13 | * Gracefully accepting constructive criticism 14 | * Focusing on what is best for the community 15 | * Showing empathy towards other community members 16 | 17 | Examples of unacceptable behavior by participants include: 18 | 19 | * The use of sexualized language or imagery and unwelcome sexual attention or advances 20 | * Trolling, insulting/derogatory comments, and personal or political attacks 21 | * Public or private harassment 22 | * Publishing others' private information, such as a physical or electronic address, without explicit permission 23 | * Other conduct which could reasonably be considered inappropriate in a professional setting 24 | 25 | ## Our Responsibilities 26 | 27 | Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. 28 | 29 | Project maintainers 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, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. 30 | 31 | ## Scope 32 | 33 | This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. 34 | 35 | ## Enforcement 36 | 37 | Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at niemamoshiri@gmail.com. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. 38 | 39 | Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. 40 | 41 | ## Attribution 42 | 43 | This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version] 44 | 45 | [homepage]: http://contributor-covenant.org 46 | [version]: http://contributor-covenant.org/version/1/4/ 47 | -------------------------------------------------------------------------------- /docs/_modules/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | Overview: module code — TreeSwift documentation 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 31 | 32 |
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82 |
83 | 96 | 100 | 101 | -------------------------------------------------------------------------------- /docs/_static/doctools.js: -------------------------------------------------------------------------------- 1 | /* 2 | * Base JavaScript utilities for all Sphinx HTML documentation. 3 | */ 4 | "use strict"; 5 | 6 | const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ 7 | "TEXTAREA", 8 | "INPUT", 9 | "SELECT", 10 | "BUTTON", 11 | ]); 12 | 13 | const _ready = (callback) => { 14 | if (document.readyState !== "loading") { 15 | callback(); 16 | } else { 17 | document.addEventListener("DOMContentLoaded", callback); 18 | } 19 | }; 20 | 21 | /** 22 | * Small JavaScript module for the documentation. 23 | */ 24 | const Documentation = { 25 | init: () => { 26 | Documentation.initDomainIndexTable(); 27 | Documentation.initOnKeyListeners(); 28 | }, 29 | 30 | /** 31 | * i18n support 32 | */ 33 | TRANSLATIONS: {}, 34 | PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), 35 | LOCALE: "unknown", 36 | 37 | // gettext and ngettext don't access this so that the functions 38 | // can safely bound to a different name (_ = Documentation.gettext) 39 | gettext: (string) => { 40 | const translated = Documentation.TRANSLATIONS[string]; 41 | switch (typeof translated) { 42 | case "undefined": 43 | return string; // no translation 44 | case "string": 45 | return translated; // translation exists 46 | default: 47 | return translated[0]; // (singular, plural) translation tuple exists 48 | } 49 | }, 50 | 51 | ngettext: (singular, plural, n) => { 52 | const translated = Documentation.TRANSLATIONS[singular]; 53 | if (typeof translated !== "undefined") 54 | return translated[Documentation.PLURAL_EXPR(n)]; 55 | return n === 1 ? singular : plural; 56 | }, 57 | 58 | addTranslations: (catalog) => { 59 | Object.assign(Documentation.TRANSLATIONS, catalog.messages); 60 | Documentation.PLURAL_EXPR = new Function( 61 | "n", 62 | `return (${catalog.plural_expr})` 63 | ); 64 | Documentation.LOCALE = catalog.locale; 65 | }, 66 | 67 | /** 68 | * helper function to focus on search bar 69 | */ 70 | focusSearchBar: () => { 71 | document.querySelectorAll("input[name=q]")[0]?.focus(); 72 | }, 73 | 74 | /** 75 | * Initialise the domain index toggle buttons 76 | */ 77 | initDomainIndexTable: () => { 78 | const toggler = (el) => { 79 | const idNumber = el.id.substr(7); 80 | const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); 81 | if (el.src.substr(-9) === "minus.png") { 82 | el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; 83 | toggledRows.forEach((el) => (el.style.display = "none")); 84 | } else { 85 | el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; 86 | toggledRows.forEach((el) => (el.style.display = "")); 87 | } 88 | }; 89 | 90 | const togglerElements = document.querySelectorAll("img.toggler"); 91 | togglerElements.forEach((el) => 92 | el.addEventListener("click", (event) => toggler(event.currentTarget)) 93 | ); 94 | togglerElements.forEach((el) => (el.style.display = "")); 95 | if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); 96 | }, 97 | 98 | initOnKeyListeners: () => { 99 | // only install a listener if it is really needed 100 | if ( 101 | !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && 102 | !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS 103 | ) 104 | return; 105 | 106 | document.addEventListener("keydown", (event) => { 107 | // bail for input elements 108 | if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; 109 | // bail with special keys 110 | if (event.altKey || event.ctrlKey || event.metaKey) return; 111 | 112 | if (!event.shiftKey) { 113 | switch (event.key) { 114 | case "ArrowLeft": 115 | if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; 116 | 117 | const prevLink = document.querySelector('link[rel="prev"]'); 118 | if (prevLink && prevLink.href) { 119 | window.location.href = prevLink.href; 120 | event.preventDefault(); 121 | } 122 | break; 123 | case "ArrowRight": 124 | if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; 125 | 126 | const nextLink = document.querySelector('link[rel="next"]'); 127 | if (nextLink && nextLink.href) { 128 | window.location.href = nextLink.href; 129 | event.preventDefault(); 130 | } 131 | break; 132 | } 133 | } 134 | 135 | // some keyboard layouts may need Shift to get / 136 | switch (event.key) { 137 | case "/": 138 | if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; 139 | Documentation.focusSearchBar(); 140 | event.preventDefault(); 141 | } 142 | }); 143 | }, 144 | }; 145 | 146 | // quick alias for translations 147 | const _ = Documentation.gettext; 148 | 149 | _ready(Documentation.init); 150 | -------------------------------------------------------------------------------- /docs/_static/pygments.css: -------------------------------------------------------------------------------- 1 | pre { line-height: 125%; } 2 | td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } 3 | span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } 4 | td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } 5 | span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } 6 | .highlight .hll { background-color: #ffffcc } 7 | .highlight { background: #eeffcc; } 8 | .highlight .c { color: #408090; font-style: italic } /* Comment */ 9 | .highlight .err { border: 1px solid #FF0000 } /* Error */ 10 | .highlight .k { color: #007020; font-weight: bold } /* Keyword */ 11 | .highlight .o { color: #666666 } /* Operator */ 12 | .highlight .ch { color: #408090; font-style: italic } /* Comment.Hashbang */ 13 | .highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */ 14 | .highlight .cp { color: #007020 } /* Comment.Preproc */ 15 | .highlight .cpf { color: #408090; font-style: italic } /* Comment.PreprocFile */ 16 | .highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */ 17 | .highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */ 18 | .highlight .gd { color: #A00000 } /* Generic.Deleted */ 19 | .highlight .ge { font-style: italic } /* Generic.Emph */ 20 | .highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */ 21 | .highlight .gr { color: #FF0000 } /* Generic.Error */ 22 | .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */ 23 | .highlight .gi { color: #00A000 } /* Generic.Inserted */ 24 | .highlight .go { color: #333333 } /* Generic.Output */ 25 | .highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */ 26 | .highlight .gs { font-weight: bold } /* Generic.Strong */ 27 | .highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */ 28 | .highlight .gt { color: #0044DD } /* Generic.Traceback */ 29 | .highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */ 30 | .highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */ 31 | .highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */ 32 | .highlight .kp { color: #007020 } /* Keyword.Pseudo */ 33 | .highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */ 34 | .highlight .kt { color: #902000 } /* Keyword.Type */ 35 | .highlight .m { color: #208050 } /* Literal.Number */ 36 | .highlight .s { color: #4070a0 } /* Literal.String */ 37 | .highlight .na { color: #4070a0 } /* Name.Attribute */ 38 | .highlight .nb { color: #007020 } /* Name.Builtin */ 39 | .highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */ 40 | .highlight .no { color: #60add5 } /* Name.Constant */ 41 | .highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */ 42 | .highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */ 43 | .highlight .ne { color: #007020 } /* Name.Exception */ 44 | .highlight .nf { color: #06287e } /* Name.Function */ 45 | .highlight .nl { color: #002070; font-weight: bold } /* Name.Label */ 46 | .highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */ 47 | .highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */ 48 | .highlight .nv { color: #bb60d5 } /* Name.Variable */ 49 | .highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */ 50 | .highlight .w { color: #bbbbbb } /* Text.Whitespace */ 51 | .highlight .mb { color: #208050 } /* Literal.Number.Bin */ 52 | .highlight .mf { color: #208050 } /* Literal.Number.Float */ 53 | .highlight .mh { color: #208050 } /* Literal.Number.Hex */ 54 | .highlight .mi { color: #208050 } /* Literal.Number.Integer */ 55 | .highlight .mo { color: #208050 } /* Literal.Number.Oct */ 56 | .highlight .sa { color: #4070a0 } /* Literal.String.Affix */ 57 | .highlight .sb { color: #4070a0 } /* Literal.String.Backtick */ 58 | .highlight .sc { color: #4070a0 } /* Literal.String.Char */ 59 | .highlight .dl { color: #4070a0 } /* Literal.String.Delimiter */ 60 | .highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */ 61 | .highlight .s2 { color: #4070a0 } /* Literal.String.Double */ 62 | .highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */ 63 | .highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */ 64 | .highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */ 65 | .highlight .sx { color: #c65d09 } /* Literal.String.Other */ 66 | .highlight .sr { color: #235388 } /* Literal.String.Regex */ 67 | .highlight .s1 { color: #4070a0 } /* Literal.String.Single */ 68 | .highlight .ss { color: #517918 } /* Literal.String.Symbol */ 69 | .highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */ 70 | .highlight .fm { color: #06287e } /* Name.Function.Magic */ 71 | .highlight .vc { color: #bb60d5 } /* Name.Variable.Class */ 72 | .highlight .vg { color: #bb60d5 } /* Name.Variable.Global */ 73 | .highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */ 74 | .highlight .vm { color: #bb60d5 } /* Name.Variable.Magic */ 75 | .highlight .il { color: #208050 } /* Literal.Number.Integer.Long */ -------------------------------------------------------------------------------- /.tests/test.nex: -------------------------------------------------------------------------------- 1 | begin trees; 2 | translate 3 | 1 Ephedra, 4 | 2 Gnetum, 5 | 3 Welwitschia, 6 | 4 Ginkgo, 7 | 5 Pinus 8 | ; 9 | tree one = [&U] ((((((L147:0.324701,(L175:0.162508,L176:0.162508)I148:0.162193)I29:1.62347,((L183:0.0724336,L184:0.0724336)I181:0.0359448,L182:0.108378)I30:1.83979)I19:0.271253,((L69:1.20308,(L143:0.331782,L144:0.331782)I70:0.871297)I27:0.75577,(L35:1.88978,(L57:1.42021,((L189:0.0395976,L190:0.0395976)I95:0.637178,(L139:0.36855,L140:0.36855)I96:0.308226)I58:0.743433)I36:0.469573)I28:0.0690669)I20:0.260577)I7:1.10718,(L9:3.25292,(((((L75:1.14979,(L89:0.744407,L90:0.744407)I76:0.405379)I33:0.74263,((L127:0.39989,L128:0.39989)I105:0.214571,L106:0.61446)I34:1.27796)I31:0.0278664,((((((L137:0.378239,L138:0.378239)I111:0.225106,L112:0.603346)I109:0.00133224,(L113:0.555049,L114:0.555049)I110:0.0496291)I71:0.549486,(L131:0.385135,(L169:0.207639,L170:0.207639)I132:0.177496)I72:0.769029)I55:0.266169,(((L167:0.216587,L168:0.216587)I63:1.01811,L64:1.23469)I59:0.134541,L60:1.36923)I56:0.0510984)I37:0.420969,((L195:0.0157525,L196:0.0157525)I119:0.4918,(L135:0.379121,L136:0.379121)I120:0.128432)I38:1.33375)I32:0.0789811)I17:0.412423,(((L49:1.56867,((L83:0.878255,(L149:0.31829,L150:0.31829)I84:0.559965)I51:0.608044,((L165:0.216912,L166:0.216912)I163:0.00113418,L164:0.218047)I52:1.26825)I50:0.082368)I39:0.177888,(((L121:0.501006,L122:0.501006)I87:0.332514,L88:0.83352)I43:0.875992,(L45:1.64687,(L197:0.0101516,L198:0.0101516)I46:1.63672)I44:0.0626436)I40:0.0370436)I23:0.327625,(((L191:0.0283096,L192:0.0283096)I157:0.244775,L158:0.273085)I47:1.34044,(((L155:0.280689,L156:0.280689)I99:0.355457,(L115:0.540277,(L129:0.398734,L130:0.398734)I116:0.141543)I100:0.0958687)I65:0.597191,((L117:0.508884,(L151:0.288475,L152:0.288475)I118:0.220409)I91:0.221151,L92:0.730035)I66:0.503301)I48:0.38019)I24:0.460654)I18:0.258526)I11:0.388327,((((L185:0.0553334,L186:0.0553334)I133:0.325215,L134:0.380548)I53:1.10324,((L179:0.127113,L180:0.127113)I73:1.02664,(L123:0.486099,((L171:0.19954,(L177:0.130493,L178:0.130493)I172:0.0690462)I153:0.0813941,L154:0.280934)I124:0.205165)I74:0.667651)I54:0.330035)I13:0.935043,(((L85:0.875518,L86:0.875518)I61:0.377524,(L107:0.611435,(L141:0.354415,(L173:0.180134,L174:0.180134)I142:0.174281)I108:0.25702)I62:0.641607)I25:0.713319,((L101:0.624081,(L187:0.0402426,L188:0.0402426)I102:0.583838)I41:1.11449,(L161:0.224613,L162:0.224613)I42:1.51396)I26:0.227792)I14:0.452467)I12:0.302205)I10:0.53189)I8:0.073686)I5:0.580838,((L21:2.13854,((L125:0.459897,L126:0.459897)I81:0.497392,L82:0.957289)I22:1.18125)I15:0.27409,L16:2.41263)I6:1.49482)I1:0.196532,(((L103:0.615274,(L193:0.0175106,L194:0.0175106)I104:0.597763)I77:0.441009,L78:1.05628)I3:2.99065,((L79:1.02514,((L145:0.329653,L146:0.329653)I93:0.369685,(L159:0.267641,L160:0.267641)I94:0.431698)I80:0.3258)I67:0.183439,(L97:0.649737,L98:0.649737)I68:0.558841)I4:2.83836)I2:0.0570458)I0:2.5469; 10 | tree two = [&U] ((((((L147:0.324701,(L175:0.162508,L176:0.162508)I148:0.162193)I29:1.62347,((L183:0.0724336,L184:0.0724336)I181:0.0359448,L182:0.108378)I30:1.83979)I19:0.271253,((L69:1.20308,(L143:0.331782,L144:0.331782)I70:0.871297)I27:0.75577,(L35:1.88978,(L57:1.42021,((L189:0.0395976,L190:0.0395976)I95:0.637178,(L139:0.36855,L140:0.36855)I96:0.308226)I58:0.743433)I36:0.469573)I28:0.0690669)I20:0.260577)I7:1.10718,(L9:3.25292,(((((L75:1.14979,(L89:0.744407,L90:0.744407)I76:0.405379)I33:0.74263,((L127:0.39989,L128:0.39989)I105:0.214571,L106:0.61446)I34:1.27796)I31:0.0278664,((((((L137:0.378239,L138:0.378239)I111:0.225106,L112:0.603346)I109:0.00133224,(L113:0.555049,L114:0.555049)I110:0.0496291)I71:0.549486,(L131:0.385135,(L169:0.207639,L170:0.207639)I132:0.177496)I72:0.769029)I55:0.266169,(((L167:0.216587,L168:0.216587)I63:1.01811,L64:1.23469)I59:0.134541,L60:1.36923)I56:0.0510984)I37:0.420969,((L195:0.0157525,L196:0.0157525)I119:0.4918,(L135:0.379121,L136:0.379121)I120:0.128432)I38:1.33375)I32:0.0789811)I17:0.412423,(((L49:1.56867,((L83:0.878255,(L149:0.31829,L150:0.31829)I84:0.559965)I51:0.608044,((L165:0.216912,L166:0.216912)I163:0.00113418,L164:0.218047)I52:1.26825)I50:0.082368)I39:0.177888,(((L121:0.501006,L122:0.501006)I87:0.332514,L88:0.83352)I43:0.875992,(L45:1.64687,(L197:0.0101516,L198:0.0101516)I46:1.63672)I44:0.0626436)I40:0.0370436)I23:0.327625,(((L191:0.0283096,L192:0.0283096)I157:0.244775,L158:0.273085)I47:1.34044,(((L155:0.280689,L156:0.280689)I99:0.355457,(L115:0.540277,(L129:0.398734,L130:0.398734)I116:0.141543)I100:0.0958687)I65:0.597191,((L117:0.508884,(L151:0.288475,L152:0.288475)I118:0.220409)I91:0.221151,L92:0.730035)I66:0.503301)I48:0.38019)I24:0.460654)I18:0.258526)I11:0.388327,((((L185:0.0553334,L186:0.0553334)I133:0.325215,L134:0.380548)I53:1.10324,((L179:0.127113,L180:0.127113)I73:1.02664,(L123:0.486099,((L171:0.19954,(L177:0.130493,L178:0.130493)I172:0.0690462)I153:0.0813941,L154:0.280934)I124:0.205165)I74:0.667651)I54:0.330035)I13:0.935043,(((L85:0.875518,L86:0.875518)I61:0.377524,(L107:0.611435,(L141:0.354415,(L173:0.180134,L174:0.180134)I142:0.174281)I108:0.25702)I62:0.641607)I25:0.713319,((L101:0.624081,(L187:0.0402426,L188:0.0402426)I102:0.583838)I41:1.11449,(L161:0.224613,L162:0.224613)I42:1.51396)I26:0.227792)I14:0.452467)I12:0.302205)I10:0.53189)I8:0.073686)I5:0.580838,((L21:2.13854,((L125:0.459897,L126:0.459897)I81:0.497392,L82:0.957289)I22:1.18125)I15:0.27409,L16:2.41263)I6:1.49482)I1:0.196532,(((L103:0.615274,(L193:0.0175106,L194:0.0175106)I104:0.597763)I77:0.441009,L78:1.05628)I3:2.99065,((L79:1.02514,((L145:0.329653,L146:0.329653)I93:0.369685,(L159:0.267641,L160:0.267641)I94:0.431698)I80:0.3258)I67:0.183439,(L97:0.649737,L98:0.649737)I68:0.558841)I4:2.83836)I2:0.0570458)I0:2.5469; 11 | end; 12 | -------------------------------------------------------------------------------- /docs/_static/classic.css: -------------------------------------------------------------------------------- 1 | /* 2 | * Sphinx stylesheet -- classic theme. 3 | */ 4 | 5 | @import url("basic.css"); 6 | 7 | /* -- page layout ----------------------------------------------------------- */ 8 | 9 | html { 10 | /* CSS hack for macOS's scrollbar (see #1125) */ 11 | background-color: #FFFFFF; 12 | } 13 | 14 | body { 15 | font-family: sans-serif; 16 | font-size: 100%; 17 | background-color: #11303d; 18 | color: #000; 19 | margin: 0; 20 | padding: 0; 21 | } 22 | 23 | div.document { 24 | display: flex; 25 | background-color: #1c4e63; 26 | } 27 | 28 | div.documentwrapper { 29 | float: left; 30 | width: 100%; 31 | } 32 | 33 | div.bodywrapper { 34 | margin: 0 0 0 230px; 35 | } 36 | 37 | div.body { 38 | background-color: #ffffff; 39 | color: #000000; 40 | padding: 0 20px 30px 20px; 41 | } 42 | 43 | div.footer { 44 | color: #ffffff; 45 | width: 100%; 46 | padding: 9px 0 9px 0; 47 | text-align: center; 48 | font-size: 75%; 49 | } 50 | 51 | div.footer a { 52 | color: #ffffff; 53 | text-decoration: underline; 54 | } 55 | 56 | div.related { 57 | background-color: #133f52; 58 | line-height: 30px; 59 | color: #ffffff; 60 | } 61 | 62 | div.related a { 63 | color: #ffffff; 64 | } 65 | 66 | div.sphinxsidebar { 67 | } 68 | 69 | div.sphinxsidebar h3 { 70 | font-family: 'Trebuchet MS', sans-serif; 71 | color: #ffffff; 72 | font-size: 1.4em; 73 | font-weight: normal; 74 | margin: 0; 75 | padding: 0; 76 | } 77 | 78 | div.sphinxsidebar h3 a { 79 | color: #ffffff; 80 | } 81 | 82 | div.sphinxsidebar h4 { 83 | font-family: 'Trebuchet MS', sans-serif; 84 | color: #ffffff; 85 | font-size: 1.3em; 86 | font-weight: normal; 87 | margin: 5px 0 0 0; 88 | padding: 0; 89 | } 90 | 91 | div.sphinxsidebar p { 92 | color: #ffffff; 93 | } 94 | 95 | div.sphinxsidebar p.topless { 96 | margin: 5px 10px 10px 10px; 97 | } 98 | 99 | div.sphinxsidebar ul { 100 | margin: 10px; 101 | padding: 0; 102 | color: #ffffff; 103 | } 104 | 105 | div.sphinxsidebar a { 106 | color: #98dbcc; 107 | } 108 | 109 | div.sphinxsidebar input { 110 | border: 1px solid #98dbcc; 111 | font-family: sans-serif; 112 | font-size: 1em; 113 | } 114 | 115 | 116 | 117 | /* -- hyperlink styles ------------------------------------------------------ */ 118 | 119 | a { 120 | color: #355f7c; 121 | text-decoration: none; 122 | } 123 | 124 | a:visited { 125 | color: #551a8b; 126 | text-decoration: none; 127 | } 128 | 129 | a:hover { 130 | text-decoration: underline; 131 | } 132 | 133 | 134 | 135 | /* -- body styles ----------------------------------------------------------- */ 136 | 137 | div.body h1, 138 | div.body h2, 139 | div.body h3, 140 | div.body h4, 141 | div.body h5, 142 | div.body h6 { 143 | font-family: 'Trebuchet MS', sans-serif; 144 | background-color: #f2f2f2; 145 | font-weight: normal; 146 | color: #20435c; 147 | border-bottom: 1px solid #ccc; 148 | margin: 20px -20px 10px -20px; 149 | padding: 3px 0 3px 10px; 150 | } 151 | 152 | div.body h1 { margin-top: 0; font-size: 200%; } 153 | div.body h2 { font-size: 160%; } 154 | div.body h3 { font-size: 140%; } 155 | div.body h4 { font-size: 120%; } 156 | div.body h5 { font-size: 110%; } 157 | div.body h6 { font-size: 100%; } 158 | 159 | a.headerlink { 160 | color: #c60f0f; 161 | font-size: 0.8em; 162 | padding: 0 4px 0 4px; 163 | text-decoration: none; 164 | } 165 | 166 | a.headerlink:hover { 167 | background-color: #c60f0f; 168 | color: white; 169 | } 170 | 171 | div.body p, div.body dd, div.body li, div.body blockquote { 172 | text-align: justify; 173 | line-height: 130%; 174 | } 175 | 176 | div.admonition p.admonition-title + p { 177 | display: inline; 178 | } 179 | 180 | div.admonition p { 181 | margin-bottom: 5px; 182 | } 183 | 184 | div.admonition pre { 185 | margin-bottom: 5px; 186 | } 187 | 188 | div.admonition ul, div.admonition ol { 189 | margin-bottom: 5px; 190 | } 191 | 192 | div.note { 193 | background-color: #eee; 194 | border: 1px solid #ccc; 195 | } 196 | 197 | div.seealso { 198 | background-color: #ffc; 199 | border: 1px solid #ff6; 200 | } 201 | 202 | nav.contents, 203 | aside.topic, 204 | div.topic { 205 | background-color: #eee; 206 | } 207 | 208 | div.warning { 209 | background-color: #ffe4e4; 210 | border: 1px solid #f66; 211 | } 212 | 213 | p.admonition-title { 214 | display: inline; 215 | } 216 | 217 | p.admonition-title:after { 218 | content: ":"; 219 | } 220 | 221 | pre { 222 | padding: 5px; 223 | background-color: unset; 224 | color: unset; 225 | line-height: 120%; 226 | border: 1px solid #ac9; 227 | border-left: none; 228 | border-right: none; 229 | } 230 | 231 | code { 232 | background-color: #ecf0f3; 233 | padding: 0 1px 0 1px; 234 | font-size: 0.95em; 235 | } 236 | 237 | th, dl.field-list > dt { 238 | background-color: #ede; 239 | } 240 | 241 | .warning code { 242 | background: #efc2c2; 243 | } 244 | 245 | .note code { 246 | background: #d6d6d6; 247 | } 248 | 249 | .viewcode-back { 250 | font-family: sans-serif; 251 | } 252 | 253 | div.viewcode-block:target { 254 | background-color: #f4debf; 255 | border-top: 1px solid #ac9; 256 | border-bottom: 1px solid #ac9; 257 | } 258 | 259 | div.code-block-caption { 260 | color: #efefef; 261 | background-color: #1c4e63; 262 | } -------------------------------------------------------------------------------- /docs/_static/language_data.js: -------------------------------------------------------------------------------- 1 | /* 2 | * This script contains the language-specific data used by searchtools.js, 3 | * namely the list of stopwords, stemmer, scorer and splitter. 4 | */ 5 | 6 | var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; 7 | 8 | 9 | /* Non-minified version is copied as a separate JS file, if available */ 10 | 11 | /** 12 | * Porter Stemmer 13 | */ 14 | var Stemmer = function() { 15 | 16 | var step2list = { 17 | ational: 'ate', 18 | tional: 'tion', 19 | enci: 'ence', 20 | anci: 'ance', 21 | izer: 'ize', 22 | bli: 'ble', 23 | alli: 'al', 24 | entli: 'ent', 25 | eli: 'e', 26 | ousli: 'ous', 27 | ization: 'ize', 28 | ation: 'ate', 29 | ator: 'ate', 30 | alism: 'al', 31 | iveness: 'ive', 32 | fulness: 'ful', 33 | ousness: 'ous', 34 | aliti: 'al', 35 | iviti: 'ive', 36 | biliti: 'ble', 37 | logi: 'log' 38 | }; 39 | 40 | var step3list = { 41 | icate: 'ic', 42 | ative: '', 43 | alize: 'al', 44 | iciti: 'ic', 45 | ical: 'ic', 46 | ful: '', 47 | ness: '' 48 | }; 49 | 50 | var c = "[^aeiou]"; // consonant 51 | var v = "[aeiouy]"; // vowel 52 | var C = c + "[^aeiouy]*"; // consonant sequence 53 | var V = v + "[aeiou]*"; // vowel sequence 54 | 55 | var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 56 | var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 57 | var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 58 | var s_v = "^(" + C + ")?" + v; // vowel in stem 59 | 60 | this.stemWord = function (w) { 61 | var stem; 62 | var suffix; 63 | var firstch; 64 | var origword = w; 65 | 66 | if (w.length < 3) 67 | return w; 68 | 69 | var re; 70 | var re2; 71 | var re3; 72 | var re4; 73 | 74 | firstch = w.substr(0,1); 75 | if (firstch == "y") 76 | w = firstch.toUpperCase() + w.substr(1); 77 | 78 | // Step 1a 79 | re = /^(.+?)(ss|i)es$/; 80 | re2 = /^(.+?)([^s])s$/; 81 | 82 | if (re.test(w)) 83 | w = w.replace(re,"$1$2"); 84 | else if (re2.test(w)) 85 | w = w.replace(re2,"$1$2"); 86 | 87 | // Step 1b 88 | re = /^(.+?)eed$/; 89 | re2 = /^(.+?)(ed|ing)$/; 90 | if (re.test(w)) { 91 | var fp = re.exec(w); 92 | re = new RegExp(mgr0); 93 | if (re.test(fp[1])) { 94 | re = /.$/; 95 | w = w.replace(re,""); 96 | } 97 | } 98 | else if (re2.test(w)) { 99 | var fp = re2.exec(w); 100 | stem = fp[1]; 101 | re2 = new RegExp(s_v); 102 | if (re2.test(stem)) { 103 | w = stem; 104 | re2 = /(at|bl|iz)$/; 105 | re3 = new RegExp("([^aeiouylsz])\\1$"); 106 | re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); 107 | if (re2.test(w)) 108 | w = w + "e"; 109 | else if (re3.test(w)) { 110 | re = /.$/; 111 | w = w.replace(re,""); 112 | } 113 | else if (re4.test(w)) 114 | w = w + "e"; 115 | } 116 | } 117 | 118 | // Step 1c 119 | re = /^(.+?)y$/; 120 | if (re.test(w)) { 121 | var fp = re.exec(w); 122 | stem = fp[1]; 123 | re = new RegExp(s_v); 124 | if (re.test(stem)) 125 | w = stem + "i"; 126 | } 127 | 128 | // Step 2 129 | re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; 130 | if (re.test(w)) { 131 | var fp = re.exec(w); 132 | stem = fp[1]; 133 | suffix = fp[2]; 134 | re = new RegExp(mgr0); 135 | if (re.test(stem)) 136 | w = stem + step2list[suffix]; 137 | } 138 | 139 | // Step 3 140 | re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; 141 | if (re.test(w)) { 142 | var fp = re.exec(w); 143 | stem = fp[1]; 144 | suffix = fp[2]; 145 | re = new RegExp(mgr0); 146 | if (re.test(stem)) 147 | w = stem + step3list[suffix]; 148 | } 149 | 150 | // Step 4 151 | re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; 152 | re2 = /^(.+?)(s|t)(ion)$/; 153 | if (re.test(w)) { 154 | var fp = re.exec(w); 155 | stem = fp[1]; 156 | re = new RegExp(mgr1); 157 | if (re.test(stem)) 158 | w = stem; 159 | } 160 | else if (re2.test(w)) { 161 | var fp = re2.exec(w); 162 | stem = fp[1] + fp[2]; 163 | re2 = new RegExp(mgr1); 164 | if (re2.test(stem)) 165 | w = stem; 166 | } 167 | 168 | // Step 5 169 | re = /^(.+?)e$/; 170 | if (re.test(w)) { 171 | var fp = re.exec(w); 172 | stem = fp[1]; 173 | re = new RegExp(mgr1); 174 | re2 = new RegExp(meq1); 175 | re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); 176 | if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) 177 | w = stem; 178 | } 179 | re = /ll$/; 180 | re2 = new RegExp(mgr1); 181 | if (re.test(w) && re2.test(w)) { 182 | re = /.$/; 183 | w = w.replace(re,""); 184 | } 185 | 186 | // and turn initial Y back to y 187 | if (firstch == "y") 188 | w = firstch.toLowerCase() + w.substr(1); 189 | return w; 190 | } 191 | } 192 | 193 | -------------------------------------------------------------------------------- /docs/_static/sphinx_highlight.js: -------------------------------------------------------------------------------- 1 | /* Highlighting utilities for Sphinx HTML documentation. */ 2 | "use strict"; 3 | 4 | const SPHINX_HIGHLIGHT_ENABLED = true 5 | 6 | /** 7 | * highlight a given string on a node by wrapping it in 8 | * span elements with the given class name. 9 | */ 10 | const _highlight = (node, addItems, text, className) => { 11 | if (node.nodeType === Node.TEXT_NODE) { 12 | const val = node.nodeValue; 13 | const parent = node.parentNode; 14 | const pos = val.toLowerCase().indexOf(text); 15 | if ( 16 | pos >= 0 && 17 | !parent.classList.contains(className) && 18 | !parent.classList.contains("nohighlight") 19 | ) { 20 | let span; 21 | 22 | const closestNode = parent.closest("body, svg, foreignObject"); 23 | const isInSVG = closestNode && closestNode.matches("svg"); 24 | if (isInSVG) { 25 | span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); 26 | } else { 27 | span = document.createElement("span"); 28 | span.classList.add(className); 29 | } 30 | 31 | span.appendChild(document.createTextNode(val.substr(pos, text.length))); 32 | const rest = document.createTextNode(val.substr(pos + text.length)); 33 | parent.insertBefore( 34 | span, 35 | parent.insertBefore( 36 | rest, 37 | node.nextSibling 38 | ) 39 | ); 40 | node.nodeValue = val.substr(0, pos); 41 | /* There may be more occurrences of search term in this node. So call this 42 | * function recursively on the remaining fragment. 43 | */ 44 | _highlight(rest, addItems, text, className); 45 | 46 | if (isInSVG) { 47 | const rect = document.createElementNS( 48 | "http://www.w3.org/2000/svg", 49 | "rect" 50 | ); 51 | const bbox = parent.getBBox(); 52 | rect.x.baseVal.value = bbox.x; 53 | rect.y.baseVal.value = bbox.y; 54 | rect.width.baseVal.value = bbox.width; 55 | rect.height.baseVal.value = bbox.height; 56 | rect.setAttribute("class", className); 57 | addItems.push({ parent: parent, target: rect }); 58 | } 59 | } 60 | } else if (node.matches && !node.matches("button, select, textarea")) { 61 | node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); 62 | } 63 | }; 64 | const _highlightText = (thisNode, text, className) => { 65 | let addItems = []; 66 | _highlight(thisNode, addItems, text, className); 67 | addItems.forEach((obj) => 68 | obj.parent.insertAdjacentElement("beforebegin", obj.target) 69 | ); 70 | }; 71 | 72 | /** 73 | * Small JavaScript module for the documentation. 74 | */ 75 | const SphinxHighlight = { 76 | 77 | /** 78 | * highlight the search words provided in localstorage in the text 79 | */ 80 | highlightSearchWords: () => { 81 | if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight 82 | 83 | // get and clear terms from localstorage 84 | const url = new URL(window.location); 85 | const highlight = 86 | localStorage.getItem("sphinx_highlight_terms") 87 | || url.searchParams.get("highlight") 88 | || ""; 89 | localStorage.removeItem("sphinx_highlight_terms") 90 | url.searchParams.delete("highlight"); 91 | window.history.replaceState({}, "", url); 92 | 93 | // get individual terms from highlight string 94 | const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); 95 | if (terms.length === 0) return; // nothing to do 96 | 97 | // There should never be more than one element matching "div.body" 98 | const divBody = document.querySelectorAll("div.body"); 99 | const body = divBody.length ? divBody[0] : document.querySelector("body"); 100 | window.setTimeout(() => { 101 | terms.forEach((term) => _highlightText(body, term, "highlighted")); 102 | }, 10); 103 | 104 | const searchBox = document.getElementById("searchbox"); 105 | if (searchBox === null) return; 106 | searchBox.appendChild( 107 | document 108 | .createRange() 109 | .createContextualFragment( 110 | '

' + 111 | '' + 112 | _("Hide Search Matches") + 113 | "

" 114 | ) 115 | ); 116 | }, 117 | 118 | /** 119 | * helper function to hide the search marks again 120 | */ 121 | hideSearchWords: () => { 122 | document 123 | .querySelectorAll("#searchbox .highlight-link") 124 | .forEach((el) => el.remove()); 125 | document 126 | .querySelectorAll("span.highlighted") 127 | .forEach((el) => el.classList.remove("highlighted")); 128 | localStorage.removeItem("sphinx_highlight_terms") 129 | }, 130 | 131 | initEscapeListener: () => { 132 | // only install a listener if it is really needed 133 | if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; 134 | 135 | document.addEventListener("keydown", (event) => { 136 | // bail for input elements 137 | if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; 138 | // bail with special keys 139 | if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; 140 | if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { 141 | SphinxHighlight.hideSearchWords(); 142 | event.preventDefault(); 143 | } 144 | }); 145 | }, 146 | }; 147 | 148 | _ready(() => { 149 | /* Do not call highlightSearchWords() when we are on the search page. 150 | * It will highlight words from the *previous* search query. 151 | */ 152 | if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); 153 | SphinxHighlight.initEscapeListener(); 154 | }); 155 | -------------------------------------------------------------------------------- /docs_src/source/conf.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # 3 | # Configuration file for the Sphinx documentation builder. 4 | # 5 | # This file does only contain a selection of the most common options. For a 6 | # full list see the documentation: 7 | # http://www.sphinx-doc.org/en/master/config 8 | 9 | # -- Path setup -------------------------------------------------------------- 10 | 11 | # If extensions (or modules to document with autodoc) are in another directory, 12 | # add these directories to sys.path here. If the directory is relative to the 13 | # documentation root, use os.path.abspath to make it absolute, like shown here. 14 | # 15 | # import os 16 | # import sys 17 | # sys.path.insert(0, os.path.abspath('.')) 18 | 19 | 20 | # -- Project information ----------------------------------------------------- 21 | 22 | project = 'TreeSwift' 23 | copyright = '2018, Niema Moshiri' 24 | author = 'Niema Moshiri' 25 | 26 | # The short X.Y version 27 | version = '' 28 | # The full version, including alpha/beta/rc tags 29 | release = '' 30 | 31 | 32 | # -- General configuration --------------------------------------------------- 33 | 34 | # If your documentation needs a minimal Sphinx version, state it here. 35 | # 36 | # needs_sphinx = '1.0' 37 | 38 | # Add any Sphinx extension module names here, as strings. They can be 39 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 40 | # ones. 41 | extensions = [ 42 | 'sphinx.ext.autodoc', 43 | 'sphinx.ext.doctest', 44 | 'sphinx.ext.mathjax', 45 | 'sphinx.ext.viewcode', 46 | 'sphinx.ext.githubpages', 47 | ] 48 | 49 | # Add any paths that contain templates here, relative to this directory. 50 | templates_path = ['.templates'] 51 | 52 | # The suffix(es) of source filenames. 53 | # You can specify multiple suffix as a list of string: 54 | # 55 | # source_suffix = ['.rst', '.md'] 56 | source_suffix = '.rst' 57 | 58 | # The master toctree document. 59 | master_doc = 'index' 60 | 61 | # The language for content autogenerated by Sphinx. Refer to documentation 62 | # for a list of supported languages. 63 | # 64 | # This is also used if you do content translation via gettext catalogs. 65 | # Usually you set "language" from the command line for these cases. 66 | language = None 67 | 68 | # List of patterns, relative to source directory, that match files and 69 | # directories to ignore when looking for source files. 70 | # This pattern also affects html_static_path and html_extra_path . 71 | exclude_patterns = [] 72 | 73 | # The name of the Pygments (syntax highlighting) style to use. 74 | pygments_style = 'sphinx' 75 | 76 | 77 | # -- Options for HTML output ------------------------------------------------- 78 | 79 | # The theme to use for HTML and HTML Help pages. See the documentation for 80 | # a list of builtin themes. 81 | # 82 | html_theme = 'classic' 83 | 84 | # Theme options are theme-specific and customize the look and feel of a theme 85 | # further. For a list of options available for each theme, see the 86 | # documentation. 87 | # 88 | # html_theme_options = {} 89 | 90 | # Add any paths that contain custom static files (such as style sheets) here, 91 | # relative to this directory. They are copied after the builtin static files, 92 | # so a file named "default.css" will overwrite the builtin "default.css". 93 | html_static_path = ['.static'] 94 | 95 | # Custom sidebar templates, must be a dictionary that maps document names 96 | # to template names. 97 | # 98 | # The default sidebars (for documents that don't match any pattern) are 99 | # defined by theme itself. Builtin themes are using these templates by 100 | # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', 101 | # 'searchbox.html']``. 102 | # 103 | # html_sidebars = {} 104 | 105 | 106 | # -- Options for HTMLHelp output --------------------------------------------- 107 | 108 | # Output file base name for HTML help builder. 109 | htmlhelp_basename = 'TreeSwiftdoc' 110 | 111 | 112 | # -- Options for LaTeX output ------------------------------------------------ 113 | 114 | latex_elements = { 115 | # The paper size ('letterpaper' or 'a4paper'). 116 | # 117 | # 'papersize': 'letterpaper', 118 | 119 | # The font size ('10pt', '11pt' or '12pt'). 120 | # 121 | # 'pointsize': '10pt', 122 | 123 | # Additional stuff for the LaTeX preamble. 124 | # 125 | # 'preamble': '', 126 | 127 | # Latex figure (float) alignment 128 | # 129 | # 'figure_align': 'htbp', 130 | } 131 | 132 | # Grouping the document tree into LaTeX files. List of tuples 133 | # (source start file, target name, title, 134 | # author, documentclass [howto, manual, or own class]). 135 | latex_documents = [ 136 | (master_doc, 'TreeSwift.tex', 'TreeSwift Documentation', 137 | 'Niema Moshiri', 'manual'), 138 | ] 139 | 140 | 141 | # -- Options for manual page output ------------------------------------------ 142 | 143 | # One entry per manual page. List of tuples 144 | # (source start file, name, description, authors, manual section). 145 | man_pages = [ 146 | (master_doc, 'treeswift', 'TreeSwift Documentation', 147 | [author], 1) 148 | ] 149 | 150 | 151 | # -- Options for Texinfo output ---------------------------------------------- 152 | 153 | # Grouping the document tree into Texinfo files. List of tuples 154 | # (source start file, target name, title, author, 155 | # dir menu entry, description, category) 156 | texinfo_documents = [ 157 | (master_doc, 'TreeSwift', 'TreeSwift Documentation', 158 | author, 'TreeSwift', 'One line description of project.', 159 | 'Miscellaneous'), 160 | ] 161 | 162 | 163 | # -- Options for Epub output ------------------------------------------------- 164 | 165 | # Bibliographic Dublin Core info. 166 | epub_title = project 167 | epub_author = author 168 | epub_publisher = author 169 | epub_copyright = copyright 170 | 171 | # The unique identifier of the text. This can be a ISBN number 172 | # or the project homepage. 173 | # 174 | # epub_identifier = '' 175 | 176 | # A unique identification for the text. 177 | # 178 | # epub_uid = '' 179 | 180 | # A list of files that should not be packed into the epub file. 181 | epub_exclude_files = ['search.html'] 182 | 183 | 184 | # -- Extension configuration ------------------------------------------------- 185 | -------------------------------------------------------------------------------- /.tests/tests.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | from copy import copy 3 | from os.path import dirname, realpath 4 | from random import sample 5 | from treeswift import read_tree_newick, read_tree_nexml, read_tree_nexus 6 | PATH = dirname(realpath(__file__)) 7 | NEWICK_FILE = '%s/test.tre' % PATH 8 | NEWICK_GZIP = '%s/test.tre.gz' % PATH 9 | NEWICK_STR = open(NEWICK_FILE).read().strip() 10 | NEXUS_FILE = '%s/test.nex' % PATH 11 | NEXUS_GZIP = '%s/test.nex.gz' % PATH 12 | NEXUS_STR = open(NEXUS_FILE).read().strip() 13 | NEXML_FILE = '%s/test.nexml' % PATH 14 | NEXML_GZIP = '%s/test.nexml.gz' % PATH 15 | NEXML_STR = open(NEXML_FILE).read().strip() 16 | 17 | # tests 18 | def test_avg_branch_length(t): 19 | o = t.avg_branch_length() 20 | o = t.avg_branch_length(terminal=False) 21 | o = t.avg_branch_length(internal=False) 22 | def test_branch_lengths(t): 23 | o = t.branch_lengths() 24 | o = t.branch_lengths(terminal=False) 25 | o = t.branch_lengths(internal=False) 26 | def test_closest_leaf_to_root(t): 27 | l,d = t.closest_leaf_to_root() 28 | def test_coalescence_times(t): 29 | for d in t.coalescence_times(): 30 | pass 31 | for d in t.coalescence_times(backward=False): 32 | pass 33 | def test_coalescence_waiting_times(t): 34 | for l in t.coalescence_waiting_times(): 35 | pass 36 | for l in t.coalescence_waiting_times(backward=False): 37 | pass 38 | def test_collapse_short_branches(t): 39 | copy(t).collapse_short_branches(float('inf')) 40 | def test_contract_low_support(t): 41 | copy(t).contract_low_support(float('inf')) 42 | def test_copy(t): 43 | o = copy(t) 44 | def test_diameter(t): 45 | d = t.diameter() 46 | def test_distance_between(t): 47 | u,v = list(t.traverse_leaves())[:2] 48 | d = t.distance_between(u,v) 49 | def test_distance_matrix(t): 50 | m = t.distance_matrix() 51 | def test_distances_from_parent(t): 52 | for n,d in t.distances_from_parent(): 53 | pass 54 | for n,d in t.distances_from_parent(leaves=False): 55 | pass 56 | for n,d in t.distances_from_parent(internal=False): 57 | pass 58 | for n,d in t.distances_from_parent(unlabeled=True): 59 | pass 60 | for n,d in t.distances_from_parent(leaves=False, internal=False, unlabeled=True): 61 | pass 62 | def test_distances_from_root(t): 63 | for n,d in t.distances_from_root(): 64 | pass 65 | for n,d in t.distances_from_root(leaves=False): 66 | pass 67 | for n,d in t.distances_from_root(internal=False): 68 | pass 69 | for n,d in t.distances_from_root(unlabeled=True): 70 | pass 71 | for n,d in t.distances_from_root(leaves=False, internal=False, unlabeled=True): 72 | pass 73 | def test_edge_length_sum(t): 74 | o = t.edge_length_sum() 75 | o = t.edge_length_sum(terminal=False) 76 | o = t.edge_length_sum(internal=False) 77 | o = t.edge_length_sum(terminal=False, internal=False) 78 | def test_extract_tree_with(t): 79 | o = t.extract_tree_with(sample([str(l) for l in t.traverse_leaves()],10)) 80 | def test_extract_tree_without(t): 81 | o = t.extract_tree_without(sample([str(l) for l in t.traverse_leaves()],10)) 82 | def test_furthest_from_root(t): 83 | n,d = t.furthest_from_root() 84 | def test_gamma_statistic(t): 85 | g = t.gamma_statistic() 86 | def test_get_edge_length(t): 87 | for n in t.traverse_preorder(): 88 | l = n.get_edge_length() 89 | def test_get_label(t): 90 | for n in t.traverse_preorder(): 91 | l = n.get_label() 92 | def test_height(t): 93 | h = t.height() 94 | def test_indent(t): 95 | s = t.indent() 96 | def test_label_to_node(t): 97 | for l,n in t.label_to_node().items(): 98 | pass 99 | def test_labels(t): 100 | for l in t.labels(): 101 | pass 102 | for l in t.labels(leaves=False): 103 | pass 104 | for l in t.labels(internal=False): 105 | pass 106 | for l in t.labels(leaves=False,internal=False): 107 | pass 108 | def test_ladderize(t): 109 | t.ladderize() 110 | t.ladderize(ascending=False) 111 | def test_mrca(t): 112 | o = t.mrca(sample([str(l) for l in t.traverse_leaves()],10)) 113 | def test_mrca_matrix(t): 114 | m = t.mrca_matrix() 115 | def test_newick(t): 116 | s = t.newick(); s = str(t) 117 | def test_num_lineages_at(t): 118 | o = t.num_lineages_at(0) 119 | o = t.num_lineages_at(1) 120 | o = t.num_lineages_at(float('inf')) 121 | def test_num_nodes(t): 122 | o = t.num_nodes() 123 | o = t.num_nodes(leaves=False) 124 | o = t.num_nodes(internal=False) 125 | o = t.num_nodes(leaves=False,internal=False) 126 | def test_order(t): 127 | t.order('edge_length') 128 | t.order('edge_length_then_label') 129 | t.order('edge_length_then_label_then_num_descendants') 130 | t.order('edge_length_then_num_descendants') 131 | t.order('edge_length_then_num_descendants_then_label') 132 | t.order('label') 133 | t.order('label_then_edge_length') 134 | t.order('label_then_edge_length_then_num_descendants') 135 | t.order('label_then_num_descendants') 136 | t.order('label_then_num_descendants_then_edge_length') 137 | t.order('num_descendants') 138 | t.order('num_descendants_then_label') 139 | t.order('num_descendants_then_label_then_edge_length') 140 | t.order('num_descendants_then_edge_length') 141 | t.order('num_descendants_then_edge_length_then_label') 142 | def test_rename_nodes_condense(t): 143 | m = dict() 144 | for l in t.traverse_leaves(): 145 | m[str(l)] = 'NIEMA' 146 | t2 = copy(t) 147 | t2.rename_nodes(m) 148 | t2.condense() 149 | def test_resolve_polytomies(t): 150 | t2 = copy(t) 151 | t2.collapse_short_branches(float('inf')) 152 | t2.resolve_polytomies() 153 | def test_sackin(t): 154 | o = t.sackin() 155 | o = t.sackin(None) 156 | o = t.sackin('yule') 157 | o = t.sackin('pda') 158 | def test_scale_edges(t): 159 | copy(t).scale_edges(1.5) 160 | def test_set_edge_length(t): 161 | for n in copy(t).traverse_preorder(): 162 | n.set_edge_length(0) 163 | def test_set_label(t): 164 | for n in copy(t).traverse_preorder(): 165 | n.set_label('NIEMA') 166 | def test_traverse_inorder(t): 167 | for n in t.traverse_inorder(): 168 | pass 169 | def test_traverse_leaves(t): 170 | for l in t.traverse_leaves(): 171 | pass 172 | def test_traverse_levelorder(t): 173 | for n in t.traverse_levelorder(): 174 | pass 175 | def test_traverse_postorder(t): 176 | for n in t.traverse_postorder(): 177 | pass 178 | def test_traverse_preorder(t): 179 | for n in t.traverse_preorder(): 180 | pass 181 | def test_traverse_rootdistorder(t): 182 | for n in t.traverse_rootdistorder(ascending=True): 183 | pass 184 | for n in t.traverse_rootdistorder(ascending=False): 185 | pass 186 | def test_treeness(t): 187 | o = t.treeness() 188 | def test_write_tree_newick(t): 189 | t.write_tree_newick('test_write_tree_newick.tre') 190 | read_tree_newick('test_write_tree_newick.tre') 191 | t.write_tree_newick('test_write_tree_newick.tre.gz') 192 | read_tree_newick('test_write_tree_newick.tre.gz') 193 | 194 | # run tests 195 | if __name__ == "__main__": 196 | tests = [v for k,v in locals().items() if callable(v) and v.__module__ == __name__] 197 | trees = [read_tree_newick(NEWICK_FILE), read_tree_newick(NEWICK_GZIP), read_tree_newick(NEWICK_STR)] 198 | for nex in [NEXUS_FILE, NEXUS_GZIP, NEXUS_STR]: 199 | trees += read_tree_nexus(nex).values() 200 | for t in trees: 201 | for test in tests: 202 | test(t) 203 | for nexml in [NEXML_FILE, NEXML_GZIP, NEXML_STR]: 204 | read_tree_nexml(nexml) 205 | -------------------------------------------------------------------------------- /treeswift/Node.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python 2 | from collections import deque 3 | from copy import copy 4 | UNSAFE_SYMBOLS = {';', '(', ')', ',', '[', ']', ':', "'"} 5 | INORDER_NONBINARY = "Can't do inorder traversal on non-binary tree" 6 | INVALID_NEWICK = "Tree not valid Newick tree" 7 | 8 | class Node: 9 | '''``Node`` class''' 10 | def __init__(self, label=None, edge_length=None): 11 | '''``Node`` constructor 12 | 13 | Args: 14 | ``label`` (``str``): Label of this ``Node`` 15 | 16 | ``edge_length`` (``float``): Length of the edge incident to this ``Node`` 17 | 18 | Returns: 19 | ``Node`` object 20 | ''' 21 | self.children = [] # list of child Node objects 22 | self.parent = None # parent Node object (None for root) 23 | self.label = label # label 24 | self.edge_length = edge_length # length of incident edge 25 | 26 | def __lt__(self, other): 27 | '''Less Than operator. Just compares labels''' 28 | if not isinstance(other,Node): 29 | raise TypeError(f"'<' not supported between instances of '{type(self).__name__}' and '{type(other).__name__}'") 30 | elif self.label is None and other.label is not None: 31 | return True 32 | elif other.label is None: 33 | return False 34 | try: 35 | return float(self.label) < float(other.label) 36 | except: 37 | return str(self.label) < str(other.label) 38 | 39 | def __str__(self): 40 | '''Represent ``Node`` as a string (currently returns ``Node`` label as a string) 41 | 42 | Returns: 43 | ``str``: string representation of this ``Node`` 44 | ''' 45 | if self.label is None: 46 | return '' 47 | else: 48 | return str(self.label) 49 | 50 | def __copy__(self): 51 | '''Copy this ``Node`` 52 | 53 | Returns: 54 | ``Node``: A copy of this ``Node`` 55 | ''' 56 | out = Node(label=copy(self.label), edge_length=copy(self.edge_length)) 57 | out.children = copy(self.children) 58 | out.parent = self.parent 59 | return out 60 | 61 | def add_child(self, child): 62 | '''Add child to ``Node`` object 63 | 64 | Args: 65 | ``child`` (``Node``): The child ``Node`` to be added 66 | ''' 67 | if not isinstance(child, Node): 68 | raise TypeError("child must be a Node") 69 | self.children.append(child); child.parent = self 70 | 71 | def child_nodes(self): 72 | '''Return a ``list`` containing this ``Node`` object's children 73 | 74 | Returns: 75 | ``list``: A ``list`` containing this ``Node`` object's children 76 | ''' 77 | return copy(self.children) 78 | 79 | def contract(self): 80 | '''Contract this ``Node`` by directly connecting its children to its parent''' 81 | if self.is_root(): 82 | return 83 | for c in self.children: 84 | if self.edge_length is not None and c.edge_length is not None: 85 | c.edge_length += self.edge_length 86 | self.parent.add_child(c) 87 | self.parent.remove_child(self) 88 | 89 | def get_edge_length(self): 90 | '''Return the length of the edge incident to this ``Node`` 91 | 92 | Returns: 93 | ``float``: The length of the edge incident to this ``Node`` 94 | ''' 95 | return self.edge_length 96 | 97 | def get_label(self): 98 | '''Return the label of this ``Node`` 99 | 100 | Returns: 101 | ``object``: The label of this ``Node`` 102 | ''' 103 | return self.label 104 | 105 | def get_parent(self): 106 | '''Return the parent of this ``Node`` 107 | 108 | Returns: 109 | ``Node``: The parent of this ``Node`` 110 | ''' 111 | return self.parent 112 | 113 | def is_leaf(self): 114 | '''Returns ``True`` if this is a leaf 115 | 116 | Returns: 117 | ``bool``: ``True`` if this is a leaf, otherwise ``False`` 118 | ''' 119 | return len(self.children) == 0 120 | 121 | def is_root(self): 122 | '''Returns ``True`` if this is the ``root`` 123 | 124 | Returns: 125 | ``bool``: ``True`` if this is the root, otherwise ``False`` 126 | ''' 127 | return self.parent is None 128 | 129 | def newick(self): 130 | '''Newick string conversion starting at this ``Node`` object 131 | 132 | Returns: 133 | ``str``: Newick string conversion starting at this ``Node`` object 134 | ''' 135 | for node in self.traverse_postorder(): 136 | # handle current node's label 137 | if node.label is None: 138 | str_label = '' 139 | else: 140 | str_label = str(node.label) 141 | for c in UNSAFE_SYMBOLS: 142 | if c in str_label: 143 | str_label = f"'{str_label}'"; break 144 | 145 | # leaf Newick representation is just its label 146 | if node.is_leaf(): 147 | node.string_rep = str_label 148 | 149 | # handle internal node Newick representation 150 | else: 151 | out = ['('] 152 | for c in node.children: 153 | out.append(c.string_rep) 154 | if hasattr(c, 'node_params'): 155 | out.append(f'[{str(c.node_params)}]') 156 | if c.edge_length is not None or hasattr(c, 'edge_params'): 157 | out.append(':') 158 | if hasattr(c, 'edge_params'): 159 | out.append(f'[{str(c.edge_params)}]') 160 | if isinstance(c.edge_length, float) and c.edge_length.is_integer(): 161 | out.append(str(int(c.edge_length))) 162 | elif c.edge_length is not None: 163 | out.append(str(c.edge_length)) 164 | out.append(',') 165 | del c.string_rep 166 | out.pop() # trailing comma 167 | out.append(')') 168 | if node.label is not None: 169 | out.append(str_label) 170 | node.string_rep = ''.join(out) 171 | out = self.string_rep; del self.string_rep 172 | return out 173 | 174 | def num_children(self): 175 | '''Returns the number of children of this ``Node`` 176 | 177 | Returns: 178 | ``int``: The number of children of this ``Node`` 179 | ''' 180 | return len(self.children) 181 | 182 | def num_nodes(self, leaves=True, internal=True): 183 | '''Compute the total number of selected nodes in the subtree rooted by this ``Node`` (including itself) 184 | 185 | Args: 186 | ``leaves`` (``bool``): ``True`` to include leaves, otherwise ``False`` 187 | 188 | ``internal`` (``bool``): ``True`` to include internal nodes, otherwise ``False`` 189 | 190 | Returns: 191 | ``int``: The total number of selected nodes in this ``Tree`` 192 | ''' 193 | if not isinstance(leaves, bool): 194 | raise TypeError("leaves must be a bool") 195 | if not isinstance(internal, bool): 196 | raise TypeError("internal must be a bool") 197 | return sum((leaves and node.is_leaf()) or (internal and not node.is_leaf()) for node in self.traverse_preorder()) 198 | 199 | def remove_child(self, child): 200 | '''Remove child from ``Node`` object 201 | 202 | Args: 203 | ``child`` (``Node``): The child to remove 204 | ''' 205 | if not isinstance(child, Node): 206 | raise TypeError("child must be a Node") 207 | try: 208 | self.children.remove(child); child.parent = None 209 | except: 210 | raise RuntimeError("Attempting to remove non-existent child") 211 | 212 | def resolve_polytomies(self): 213 | '''Arbitrarily resolve polytomies below this ``Node`` with 0-lengthed edges.''' 214 | q = deque(); q.append(self) 215 | while len(q) != 0: 216 | node = q.popleft() 217 | while len(node.children) > 2: 218 | c1 = node.children.pop(); c2 = node.children.pop() 219 | nn = Node(edge_length=0); node.add_child(nn) 220 | nn.add_child(c1); nn.add_child(c2) 221 | q.extend(node.children) 222 | 223 | def set_edge_length(self, length): 224 | '''Set the length of the edge incident to this ``Node`` 225 | 226 | Args: 227 | ``length``: The new length of the edge incident to this ``Node`` 228 | ''' 229 | try: 230 | self.edge_length = float(length) 231 | except: 232 | raise TypeError("length must be a float") 233 | 234 | def set_label(self, label): 235 | '''Set the label of this ``Node`` object 236 | 237 | Args: 238 | ``label``: The new label 239 | ''' 240 | self.label = label 241 | 242 | def set_parent(self, parent): 243 | '''Set the parent of this ``Node`` object. Use this carefully, otherwise you may damage the structure of this ``Tree`` object. 244 | 245 | Args: 246 | ``Node``: The new parent of this ``Node`` 247 | ''' 248 | if not isinstance(parent, Node): 249 | raise TypeError("parent must be a Node") 250 | self.parent = parent 251 | 252 | def traverse_ancestors(self, include_self=True): 253 | '''Traverse over the ancestors of this ``Node`` 254 | 255 | Args: 256 | ``include_self`` (``bool``): ``True`` to include self in the traversal, otherwise ``False`` 257 | ''' 258 | if not isinstance(include_self, bool): 259 | raise TypeError("include_self must be a bool") 260 | if include_self: 261 | c = self 262 | else: 263 | c = self.parent 264 | while c is not None: 265 | yield c; c = c.parent 266 | 267 | def traverse_bfs(self, include_self=True): 268 | '''Perform a Breadth-First Search (BFS) starting at this ``Node`` object'. Yields (``Node``, distance) tuples 269 | 270 | Args: 271 | ``include_self`` (``bool``): ``True`` to include self in the traversal, otherwise ``False`` 272 | ''' 273 | if not isinstance(include_self, bool): 274 | raise TypeError("include_self must be a bool") 275 | q = deque(); dist = {self: 0}; q.append((self,0)) 276 | while len(q) != 0: 277 | curr = q.popleft(); yield curr 278 | for c in curr[0].children: 279 | if c not in dist: 280 | if c.edge_length is None: 281 | el = 0 282 | else: 283 | el = c.edge_length 284 | dist[c] = dist[curr[0]] + el; q.append((c,dist[c])) 285 | if curr[0].parent is not None and curr[0].parent not in dist: 286 | if curr[0].edge_length is None: 287 | el = 0 288 | else: 289 | el = curr[0].edge_length 290 | dist[curr[0].parent] = dist[curr[0]] + el; q.append((curr[0].parent,dist[curr[0].parent])) 291 | 292 | def traverse_inorder(self, leaves=True, internal=True): 293 | '''Perform an inorder traversal starting at this ``Node`` object 294 | 295 | Args: 296 | ``leaves`` (``bool``): ``True`` to include leaves, otherwise ``False`` 297 | 298 | ``internal`` (``bool``): ``True`` to include internal nodes, otherwise ``False`` 299 | ''' 300 | c = self; s = deque(); done = False 301 | while not done: 302 | if c is None: 303 | if len(s) == 0: 304 | done = True 305 | else: 306 | c = s.pop() 307 | if (leaves and c.is_leaf()) or (internal and not c.is_leaf()): 308 | yield c 309 | if len(c.children) == 0: 310 | c = None 311 | elif len(c.children) == 2: 312 | c = c.children[1] 313 | else: 314 | raise RuntimeError(INORDER_NONBINARY) 315 | else: 316 | s.append(c) 317 | if len(c.children) == 0: 318 | c = None 319 | elif len(c.children) == 2: 320 | c = c.children[0] 321 | else: 322 | raise RuntimeError(INORDER_NONBINARY) 323 | 324 | def traverse_internal(self): 325 | '''Traverse over the internal nodes below (and including) this ``Node`` object''' 326 | yield from self.traverse_preorder(leaves=False) 327 | 328 | def traverse_leaves(self): 329 | '''Traverse over the leaves below this ``Node`` object''' 330 | yield from self.traverse_preorder(internal=False) 331 | 332 | def traverse_levelorder(self, leaves=True, internal=True): 333 | '''Perform a levelorder traversal starting at this ``Node`` object 334 | 335 | Args: 336 | ``leaves`` (``bool``): ``True`` to include leaves, otherwise ``False`` 337 | 338 | ``internal`` (``bool``): ``True`` to include internal nodes, otherwise ``False`` 339 | ''' 340 | q = deque(); q.append(self) 341 | while len(q) != 0: 342 | n = q.popleft() 343 | if (leaves and n.is_leaf()) or (internal and not n.is_leaf()): 344 | yield n 345 | q.extend(n.children) 346 | 347 | def traverse_postorder(self, leaves=True, internal=True): 348 | '''Perform a postorder traversal starting at this ``Node`` object 349 | 350 | Args: 351 | ``leaves`` (``bool``): ``True`` to include leaves, otherwise ``False`` 352 | 353 | ``internal`` (``bool``): ``True`` to include internal nodes, otherwise ``False`` 354 | ''' 355 | s1 = deque(); s2 = deque(); s1.append(self) 356 | while len(s1) != 0: 357 | n = s1.pop(); s2.append(n); s1.extend(n.children) 358 | while len(s2) != 0: 359 | n = s2.pop() 360 | if (leaves and n.is_leaf()) or (internal and not n.is_leaf()): 361 | yield n 362 | 363 | def traverse_preorder(self, leaves=True, internal=True): 364 | '''Perform a preorder traversal starting at this ``Node`` object 365 | 366 | Args: 367 | ``leaves`` (``bool``): ``True`` to include leaves, otherwise ``False`` 368 | 369 | ``internal`` (``bool``): ``True`` to include internal nodes, otherwise ``False`` 370 | ''' 371 | s = deque(); s.append(self) 372 | while len(s) != 0: 373 | n = s.pop() 374 | if (leaves and n.is_leaf()) or (internal and not n.is_leaf()): 375 | yield n 376 | s.extend(n.children) 377 | 378 | def traverse_rootdistorder(self, ascending=True, leaves=True, internal=True): 379 | '''Perform a traversal of the ``Node`` objects in the subtree rooted at this ``Node`` in either ascending (``ascending=True``) or descending (``ascending=False``) order of distance from this ``Node`` 380 | 381 | Args: 382 | ``ascending`` (``bool``): ``True`` to perform traversal in ascending distance from the root, otherwise ``False`` for descending 383 | 384 | ``leaves`` (``bool``): ``True`` to include leaves, otherwise ``False`` 385 | 386 | ``internal`` (``bool``): ``True`` to include internal nodes, otherwise ``False`` 387 | ''' 388 | if not isinstance(ascending, bool): 389 | raise TypeError("ascending must be a bool") 390 | nodes = []; dist_from_root = {} 391 | for node in self.traverse_preorder(): 392 | if node == self: 393 | d = 0 394 | else: 395 | d = dist_from_root[node.parent] 396 | if node.edge_length is not None: 397 | d += node.edge_length 398 | dist_from_root[node] = d 399 | if (leaves and node.is_leaf()) or (internal and not node.is_leaf()): 400 | nodes.append((d,node)) 401 | nodes.sort(reverse=(not ascending)) 402 | yield from nodes 403 | 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"traverse_ancestor": 0, "traverse_bf": 0, "traverse_inord": 0, "traverse_intern": 0, "traverse_leav": 0, "traverse_levelord": 0, "traverse_postord": 0, "traverse_preord": 0, "traverse_rootdistord": 0, "treat": 0, "tree": 0, "treemodel": 0, "treeness": 0, "trifurc": 0, "true": 0, "tupl": 0, "u": 0, "unifurc": 0, "unlabel": 0, "unweight": 0, "up": 0, "us": 0, "util": 0, "v": 0, "valu": 0, "vertic": 0, "wa": 0, "wait": 0, "weight": 0, "well": 0, "when": 0, "where": 0, "which": 0, "whose": 0, "without": 0, "write": 0, "write_tree_newick": 0, "write_tree_nexu": 0, "x": 0, "xlabel": 0, "xmax": 0, "xmin": 0, "yield": 0, "ylabel": 0, "ymax": 0, "ymin": 0, "you": 0, "yule": 0}, "titles": ["treeswift package"], "titleterms": {"content": 0, "modul": 0, "packag": 0, "treeswift": 0}}) -------------------------------------------------------------------------------- /docs/genindex.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | Index — TreeSwift documentation 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 31 | 32 |
33 |
34 |
35 |
36 | 37 | 38 |

Index

39 | 40 |
41 | A 42 | | B 43 | | C 44 | | D 45 | | E 46 | | F 47 | | G 48 | | H 49 | | I 50 | | L 51 | | M 52 | | N 53 | | O 54 | | R 55 | | S 56 | | T 57 | | W 58 | 59 |
60 |

A

61 | 62 | 66 | 70 |
71 | 72 |

B

73 | 74 | 78 |
79 | 80 |

C

81 | 82 | 92 | 104 |
105 | 106 |

D

107 | 108 | 118 | 128 |
129 | 130 |

E

131 | 132 | 138 | 146 |
147 | 148 |

F

149 | 150 | 154 | 158 |
159 | 160 |

G

161 | 162 | 168 | 174 |
175 | 176 |

H

177 | 178 | 182 |
183 | 184 |

I

185 | 186 | 190 | 196 |
197 | 198 |

L

199 | 200 | 206 | 214 |
215 | 216 |

M

217 | 218 | 227 | 233 |
    219 |
  • 220 | module 221 | 222 |
    • 226 |
234 | 235 |

N

236 | 237 | 249 | 261 |
262 | 263 |

O

264 | 265 | 269 |
270 | 271 |

R

272 | 273 | 285 | 299 |
300 | 301 |

S

302 | 303 | 311 | 319 |
320 | 321 |

T

322 | 323 | 353 | 384 |
385 | 386 |

W

387 | 388 | 392 | 396 |
397 | 398 | 399 | 400 |
401 |
402 |
403 |
404 | 418 |
419 |
420 | 433 | 437 | 438 | -------------------------------------------------------------------------------- /docs/_static/basic.css: -------------------------------------------------------------------------------- 1 | /* 2 | * Sphinx stylesheet -- basic theme. 3 | */ 4 | 5 | /* -- main layout ----------------------------------------------------------- */ 6 | 7 | div.clearer { 8 | clear: both; 9 | } 10 | 11 | div.section::after { 12 | display: block; 13 | content: ''; 14 | clear: left; 15 | } 16 | 17 | /* -- relbar ---------------------------------------------------------------- */ 18 | 19 | div.related { 20 | width: 100%; 21 | font-size: 90%; 22 | } 23 | 24 | div.related h3 { 25 | display: none; 26 | } 27 | 28 | div.related ul { 29 | margin: 0; 30 | padding: 0 0 0 10px; 31 | list-style: none; 32 | } 33 | 34 | div.related li { 35 | display: inline; 36 | } 37 | 38 | div.related li.right { 39 | float: right; 40 | margin-right: 5px; 41 | } 42 | 43 | /* -- sidebar --------------------------------------------------------------- */ 44 | 45 | div.sphinxsidebarwrapper { 46 | padding: 10px 5px 0 10px; 47 | } 48 | 49 | div.sphinxsidebar { 50 | float: left; 51 | width: 230px; 52 | margin-left: -100%; 53 | font-size: 90%; 54 | word-wrap: break-word; 55 | overflow-wrap : break-word; 56 | } 57 | 58 | div.sphinxsidebar ul { 59 | list-style: none; 60 | } 61 | 62 | div.sphinxsidebar ul ul, 63 | div.sphinxsidebar ul.want-points { 64 | margin-left: 20px; 65 | list-style: square; 66 | } 67 | 68 | div.sphinxsidebar ul ul { 69 | margin-top: 0; 70 | margin-bottom: 0; 71 | } 72 | 73 | div.sphinxsidebar form { 74 | margin-top: 10px; 75 | } 76 | 77 | div.sphinxsidebar input { 78 | border: 1px solid #98dbcc; 79 | font-family: sans-serif; 80 | font-size: 1em; 81 | } 82 | 83 | div.sphinxsidebar #searchbox form.search { 84 | overflow: hidden; 85 | } 86 | 87 | div.sphinxsidebar #searchbox input[type="text"] { 88 | float: left; 89 | width: 80%; 90 | padding: 0.25em; 91 | box-sizing: border-box; 92 | } 93 | 94 | div.sphinxsidebar #searchbox input[type="submit"] { 95 | float: left; 96 | width: 20%; 97 | border-left: none; 98 | padding: 0.25em; 99 | box-sizing: border-box; 100 | } 101 | 102 | 103 | img { 104 | border: 0; 105 | max-width: 100%; 106 | } 107 | 108 | /* -- search page ----------------------------------------------------------- */ 109 | 110 | ul.search { 111 | margin-top: 10px; 112 | } 113 | 114 | ul.search li { 115 | padding: 5px 0; 116 | } 117 | 118 | ul.search li a { 119 | font-weight: bold; 120 | } 121 | 122 | ul.search li p.context { 123 | color: #888; 124 | margin: 2px 0 0 30px; 125 | text-align: left; 126 | } 127 | 128 | ul.keywordmatches li.goodmatch a { 129 | font-weight: bold; 130 | } 131 | 132 | /* -- index page ------------------------------------------------------------ */ 133 | 134 | table.contentstable { 135 | width: 90%; 136 | margin-left: auto; 137 | margin-right: auto; 138 | } 139 | 140 | table.contentstable p.biglink { 141 | line-height: 150%; 142 | } 143 | 144 | a.biglink { 145 | font-size: 1.3em; 146 | } 147 | 148 | span.linkdescr { 149 | font-style: italic; 150 | padding-top: 5px; 151 | font-size: 90%; 152 | } 153 | 154 | /* -- general index --------------------------------------------------------- */ 155 | 156 | table.indextable { 157 | width: 100%; 158 | } 159 | 160 | table.indextable td { 161 | text-align: left; 162 | vertical-align: top; 163 | } 164 | 165 | table.indextable ul { 166 | margin-top: 0; 167 | margin-bottom: 0; 168 | list-style-type: none; 169 | } 170 | 171 | table.indextable > tbody > tr > td > ul { 172 | padding-left: 0em; 173 | } 174 | 175 | table.indextable tr.pcap { 176 | height: 10px; 177 | } 178 | 179 | table.indextable tr.cap { 180 | margin-top: 10px; 181 | background-color: #f2f2f2; 182 | } 183 | 184 | img.toggler { 185 | margin-right: 3px; 186 | margin-top: 3px; 187 | cursor: pointer; 188 | } 189 | 190 | div.modindex-jumpbox { 191 | border-top: 1px solid #ddd; 192 | border-bottom: 1px solid #ddd; 193 | margin: 1em 0 1em 0; 194 | padding: 0.4em; 195 | } 196 | 197 | div.genindex-jumpbox { 198 | border-top: 1px solid #ddd; 199 | border-bottom: 1px solid #ddd; 200 | margin: 1em 0 1em 0; 201 | padding: 0.4em; 202 | } 203 | 204 | /* -- domain module index --------------------------------------------------- */ 205 | 206 | table.modindextable td { 207 | padding: 2px; 208 | border-collapse: collapse; 209 | } 210 | 211 | /* -- general body styles --------------------------------------------------- */ 212 | 213 | div.body { 214 | min-width: 360px; 215 | max-width: 800px; 216 | } 217 | 218 | div.body p, div.body dd, div.body li, div.body blockquote { 219 | -moz-hyphens: auto; 220 | -ms-hyphens: auto; 221 | -webkit-hyphens: auto; 222 | hyphens: auto; 223 | } 224 | 225 | a.headerlink { 226 | visibility: hidden; 227 | } 228 | 229 | a:visited { 230 | color: #551A8B; 231 | } 232 | 233 | h1:hover > a.headerlink, 234 | h2:hover > a.headerlink, 235 | h3:hover > a.headerlink, 236 | h4:hover > a.headerlink, 237 | h5:hover > a.headerlink, 238 | h6:hover > a.headerlink, 239 | dt:hover > a.headerlink, 240 | caption:hover > a.headerlink, 241 | p.caption:hover > a.headerlink, 242 | div.code-block-caption:hover > a.headerlink { 243 | visibility: visible; 244 | } 245 | 246 | div.body p.caption { 247 | text-align: inherit; 248 | } 249 | 250 | div.body td { 251 | text-align: left; 252 | } 253 | 254 | .first { 255 | margin-top: 0 !important; 256 | } 257 | 258 | p.rubric { 259 | margin-top: 30px; 260 | font-weight: bold; 261 | } 262 | 263 | img.align-left, figure.align-left, .figure.align-left, object.align-left { 264 | clear: left; 265 | float: left; 266 | margin-right: 1em; 267 | } 268 | 269 | img.align-right, figure.align-right, .figure.align-right, object.align-right { 270 | clear: right; 271 | float: right; 272 | margin-left: 1em; 273 | } 274 | 275 | img.align-center, figure.align-center, .figure.align-center, object.align-center { 276 | display: block; 277 | margin-left: auto; 278 | margin-right: auto; 279 | } 280 | 281 | img.align-default, figure.align-default, .figure.align-default { 282 | display: block; 283 | margin-left: auto; 284 | margin-right: auto; 285 | } 286 | 287 | .align-left { 288 | text-align: left; 289 | } 290 | 291 | .align-center { 292 | text-align: center; 293 | } 294 | 295 | .align-default { 296 | text-align: center; 297 | } 298 | 299 | .align-right { 300 | text-align: right; 301 | } 302 | 303 | /* -- sidebars -------------------------------------------------------------- */ 304 | 305 | div.sidebar, 306 | aside.sidebar { 307 | margin: 0 0 0.5em 1em; 308 | border: 1px solid #ddb; 309 | padding: 7px; 310 | background-color: #ffe; 311 | width: 40%; 312 | float: right; 313 | clear: right; 314 | overflow-x: auto; 315 | } 316 | 317 | p.sidebar-title { 318 | font-weight: bold; 319 | } 320 | 321 | nav.contents, 322 | aside.topic, 323 | div.admonition, div.topic, blockquote { 324 | clear: left; 325 | } 326 | 327 | /* -- topics ---------------------------------------------------------------- */ 328 | 329 | nav.contents, 330 | aside.topic, 331 | div.topic { 332 | border: 1px solid #ccc; 333 | padding: 7px; 334 | margin: 10px 0 10px 0; 335 | } 336 | 337 | p.topic-title { 338 | font-size: 1.1em; 339 | font-weight: bold; 340 | margin-top: 10px; 341 | } 342 | 343 | /* -- admonitions ----------------------------------------------------------- */ 344 | 345 | div.admonition { 346 | margin-top: 10px; 347 | margin-bottom: 10px; 348 | padding: 7px; 349 | } 350 | 351 | div.admonition dt { 352 | font-weight: bold; 353 | } 354 | 355 | p.admonition-title { 356 | margin: 0px 10px 5px 0px; 357 | font-weight: bold; 358 | } 359 | 360 | div.body p.centered { 361 | text-align: center; 362 | margin-top: 25px; 363 | } 364 | 365 | /* -- content of sidebars/topics/admonitions -------------------------------- */ 366 | 367 | div.sidebar > :last-child, 368 | aside.sidebar > :last-child, 369 | nav.contents > :last-child, 370 | aside.topic > :last-child, 371 | div.topic > :last-child, 372 | div.admonition > :last-child { 373 | margin-bottom: 0; 374 | } 375 | 376 | div.sidebar::after, 377 | aside.sidebar::after, 378 | nav.contents::after, 379 | aside.topic::after, 380 | div.topic::after, 381 | div.admonition::after, 382 | blockquote::after { 383 | display: block; 384 | content: ''; 385 | clear: both; 386 | } 387 | 388 | /* -- tables ---------------------------------------------------------------- */ 389 | 390 | table.docutils { 391 | margin-top: 10px; 392 | margin-bottom: 10px; 393 | border: 0; 394 | border-collapse: collapse; 395 | } 396 | 397 | table.align-center { 398 | margin-left: auto; 399 | margin-right: auto; 400 | } 401 | 402 | table.align-default { 403 | margin-left: auto; 404 | margin-right: auto; 405 | } 406 | 407 | table caption span.caption-number { 408 | font-style: italic; 409 | } 410 | 411 | table caption span.caption-text { 412 | } 413 | 414 | table.docutils td, table.docutils th { 415 | padding: 1px 8px 1px 5px; 416 | border-top: 0; 417 | border-left: 0; 418 | border-right: 0; 419 | border-bottom: 1px solid #aaa; 420 | } 421 | 422 | th { 423 | text-align: left; 424 | padding-right: 5px; 425 | } 426 | 427 | table.citation { 428 | border-left: solid 1px gray; 429 | margin-left: 1px; 430 | } 431 | 432 | table.citation td { 433 | border-bottom: none; 434 | } 435 | 436 | th > :first-child, 437 | td > :first-child { 438 | margin-top: 0px; 439 | } 440 | 441 | th > :last-child, 442 | td > :last-child { 443 | margin-bottom: 0px; 444 | } 445 | 446 | /* -- figures --------------------------------------------------------------- */ 447 | 448 | div.figure, figure { 449 | margin: 0.5em; 450 | padding: 0.5em; 451 | } 452 | 453 | div.figure p.caption, figcaption { 454 | padding: 0.3em; 455 | } 456 | 457 | div.figure p.caption span.caption-number, 458 | figcaption span.caption-number { 459 | font-style: italic; 460 | } 461 | 462 | div.figure p.caption span.caption-text, 463 | figcaption span.caption-text { 464 | } 465 | 466 | /* -- field list styles ----------------------------------------------------- */ 467 | 468 | table.field-list td, table.field-list th { 469 | border: 0 !important; 470 | } 471 | 472 | .field-list ul { 473 | margin: 0; 474 | padding-left: 1em; 475 | } 476 | 477 | .field-list p { 478 | margin: 0; 479 | } 480 | 481 | .field-name { 482 | -moz-hyphens: manual; 483 | -ms-hyphens: manual; 484 | -webkit-hyphens: manual; 485 | hyphens: manual; 486 | } 487 | 488 | /* -- hlist styles ---------------------------------------------------------- */ 489 | 490 | table.hlist { 491 | margin: 1em 0; 492 | } 493 | 494 | table.hlist td { 495 | vertical-align: top; 496 | } 497 | 498 | /* -- object description styles --------------------------------------------- */ 499 | 500 | .sig { 501 | font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; 502 | } 503 | 504 | .sig-name, code.descname { 505 | background-color: transparent; 506 | font-weight: bold; 507 | } 508 | 509 | .sig-name { 510 | font-size: 1.1em; 511 | } 512 | 513 | code.descname { 514 | font-size: 1.2em; 515 | } 516 | 517 | .sig-prename, code.descclassname { 518 | background-color: transparent; 519 | } 520 | 521 | .optional { 522 | font-size: 1.3em; 523 | } 524 | 525 | .sig-paren { 526 | font-size: larger; 527 | } 528 | 529 | .sig-param.n { 530 | font-style: italic; 531 | } 532 | 533 | /* C++ specific styling */ 534 | 535 | .sig-inline.c-texpr, 536 | .sig-inline.cpp-texpr { 537 | font-family: unset; 538 | } 539 | 540 | .sig.c .k, .sig.c .kt, 541 | .sig.cpp .k, .sig.cpp .kt { 542 | color: #0033B3; 543 | } 544 | 545 | .sig.c .m, 546 | .sig.cpp .m { 547 | color: #1750EB; 548 | } 549 | 550 | .sig.c .s, .sig.c .sc, 551 | .sig.cpp .s, .sig.cpp .sc { 552 | color: #067D17; 553 | } 554 | 555 | 556 | /* -- other body styles ----------------------------------------------------- */ 557 | 558 | ol.arabic { 559 | list-style: decimal; 560 | } 561 | 562 | ol.loweralpha { 563 | list-style: lower-alpha; 564 | } 565 | 566 | ol.upperalpha { 567 | list-style: upper-alpha; 568 | } 569 | 570 | ol.lowerroman { 571 | list-style: lower-roman; 572 | } 573 | 574 | ol.upperroman { 575 | list-style: upper-roman; 576 | } 577 | 578 | :not(li) > ol > li:first-child > :first-child, 579 | :not(li) > ul > li:first-child > :first-child { 580 | margin-top: 0px; 581 | } 582 | 583 | :not(li) > ol > li:last-child > :last-child, 584 | :not(li) > ul > li:last-child > :last-child { 585 | margin-bottom: 0px; 586 | } 587 | 588 | ol.simple ol p, 589 | ol.simple ul p, 590 | ul.simple ol p, 591 | ul.simple ul p { 592 | margin-top: 0; 593 | } 594 | 595 | ol.simple > li:not(:first-child) > p, 596 | ul.simple > li:not(:first-child) > p { 597 | margin-top: 0; 598 | } 599 | 600 | ol.simple p, 601 | ul.simple p { 602 | margin-bottom: 0; 603 | } 604 | 605 | aside.footnote > span, 606 | div.citation > span { 607 | float: left; 608 | } 609 | aside.footnote > span:last-of-type, 610 | div.citation > span:last-of-type { 611 | padding-right: 0.5em; 612 | } 613 | aside.footnote > p { 614 | margin-left: 2em; 615 | } 616 | div.citation > p { 617 | margin-left: 4em; 618 | } 619 | aside.footnote > p:last-of-type, 620 | div.citation > p:last-of-type { 621 | margin-bottom: 0em; 622 | } 623 | aside.footnote > p:last-of-type:after, 624 | div.citation > p:last-of-type:after { 625 | content: ""; 626 | clear: both; 627 | } 628 | 629 | dl.field-list { 630 | display: grid; 631 | grid-template-columns: fit-content(30%) auto; 632 | } 633 | 634 | dl.field-list > dt { 635 | font-weight: bold; 636 | word-break: break-word; 637 | padding-left: 0.5em; 638 | padding-right: 5px; 639 | } 640 | 641 | dl.field-list > dd { 642 | padding-left: 0.5em; 643 | margin-top: 0em; 644 | margin-left: 0em; 645 | margin-bottom: 0em; 646 | } 647 | 648 | dl { 649 | margin-bottom: 15px; 650 | } 651 | 652 | dd > :first-child { 653 | margin-top: 0px; 654 | } 655 | 656 | dd ul, dd table { 657 | margin-bottom: 10px; 658 | } 659 | 660 | dd { 661 | margin-top: 3px; 662 | margin-bottom: 10px; 663 | margin-left: 30px; 664 | } 665 | 666 | .sig dd { 667 | margin-top: 0px; 668 | margin-bottom: 0px; 669 | } 670 | 671 | .sig dl { 672 | margin-top: 0px; 673 | margin-bottom: 0px; 674 | } 675 | 676 | dl > dd:last-child, 677 | dl > dd:last-child > :last-child { 678 | margin-bottom: 0; 679 | } 680 | 681 | dt:target, span.highlighted { 682 | background-color: #fbe54e; 683 | } 684 | 685 | rect.highlighted { 686 | fill: #fbe54e; 687 | } 688 | 689 | dl.glossary dt { 690 | font-weight: bold; 691 | font-size: 1.1em; 692 | } 693 | 694 | .versionmodified { 695 | font-style: italic; 696 | } 697 | 698 | .system-message { 699 | background-color: #fda; 700 | padding: 5px; 701 | border: 3px solid red; 702 | } 703 | 704 | .footnote:target { 705 | background-color: #ffa; 706 | } 707 | 708 | .line-block { 709 | display: block; 710 | margin-top: 1em; 711 | margin-bottom: 1em; 712 | } 713 | 714 | .line-block .line-block { 715 | margin-top: 0; 716 | margin-bottom: 0; 717 | margin-left: 1.5em; 718 | } 719 | 720 | .guilabel, .menuselection { 721 | font-family: sans-serif; 722 | } 723 | 724 | .accelerator { 725 | text-decoration: underline; 726 | } 727 | 728 | .classifier { 729 | font-style: oblique; 730 | } 731 | 732 | .classifier:before { 733 | font-style: normal; 734 | margin: 0 0.5em; 735 | content: ":"; 736 | display: inline-block; 737 | } 738 | 739 | abbr, acronym { 740 | border-bottom: dotted 1px; 741 | cursor: help; 742 | } 743 | 744 | .translated { 745 | background-color: rgba(207, 255, 207, 0.2) 746 | } 747 | 748 | .untranslated { 749 | background-color: rgba(255, 207, 207, 0.2) 750 | } 751 | 752 | /* -- code displays --------------------------------------------------------- */ 753 | 754 | pre { 755 | overflow: auto; 756 | overflow-y: hidden; /* fixes display issues on Chrome browsers */ 757 | } 758 | 759 | pre, div[class*="highlight-"] { 760 | clear: both; 761 | } 762 | 763 | span.pre { 764 | -moz-hyphens: none; 765 | -ms-hyphens: none; 766 | -webkit-hyphens: none; 767 | hyphens: none; 768 | white-space: nowrap; 769 | } 770 | 771 | div[class*="highlight-"] { 772 | margin: 1em 0; 773 | } 774 | 775 | td.linenos pre { 776 | border: 0; 777 | background-color: transparent; 778 | color: #aaa; 779 | } 780 | 781 | table.highlighttable { 782 | display: block; 783 | } 784 | 785 | table.highlighttable tbody { 786 | display: block; 787 | } 788 | 789 | table.highlighttable tr { 790 | display: flex; 791 | } 792 | 793 | table.highlighttable td { 794 | margin: 0; 795 | padding: 0; 796 | } 797 | 798 | table.highlighttable td.linenos { 799 | padding-right: 0.5em; 800 | } 801 | 802 | table.highlighttable td.code { 803 | flex: 1; 804 | overflow: hidden; 805 | } 806 | 807 | .highlight .hll { 808 | display: block; 809 | } 810 | 811 | div.highlight pre, 812 | table.highlighttable pre { 813 | margin: 0; 814 | } 815 | 816 | div.code-block-caption + div { 817 | margin-top: 0; 818 | } 819 | 820 | div.code-block-caption { 821 | margin-top: 1em; 822 | padding: 2px 5px; 823 | font-size: small; 824 | } 825 | 826 | div.code-block-caption code { 827 | background-color: transparent; 828 | } 829 | 830 | table.highlighttable td.linenos, 831 | span.linenos, 832 | div.highlight span.gp { /* gp: Generic.Prompt */ 833 | user-select: none; 834 | -webkit-user-select: text; /* Safari fallback only */ 835 | -webkit-user-select: none; /* Chrome/Safari */ 836 | -moz-user-select: none; /* Firefox */ 837 | -ms-user-select: none; /* IE10+ */ 838 | } 839 | 840 | div.code-block-caption span.caption-number { 841 | padding: 0.1em 0.3em; 842 | font-style: italic; 843 | } 844 | 845 | div.code-block-caption span.caption-text { 846 | } 847 | 848 | div.literal-block-wrapper { 849 | margin: 1em 0; 850 | } 851 | 852 | code.xref, a code { 853 | background-color: transparent; 854 | font-weight: bold; 855 | } 856 | 857 | h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { 858 | background-color: transparent; 859 | } 860 | 861 | .viewcode-link { 862 | float: right; 863 | } 864 | 865 | .viewcode-back { 866 | float: right; 867 | font-family: sans-serif; 868 | } 869 | 870 | div.viewcode-block:target { 871 | margin: -1px -10px; 872 | padding: 0 10px; 873 | } 874 | 875 | /* -- math display ---------------------------------------------------------- */ 876 | 877 | img.math { 878 | vertical-align: middle; 879 | } 880 | 881 | div.body div.math p { 882 | text-align: center; 883 | } 884 | 885 | span.eqno { 886 | float: right; 887 | } 888 | 889 | span.eqno a.headerlink { 890 | position: absolute; 891 | z-index: 1; 892 | } 893 | 894 | div.math:hover a.headerlink { 895 | visibility: visible; 896 | } 897 | 898 | /* -- printout stylesheet --------------------------------------------------- */ 899 | 900 | @media print { 901 | div.document, 902 | div.documentwrapper, 903 | div.bodywrapper { 904 | margin: 0 !important; 905 | width: 100%; 906 | } 907 | 908 | div.sphinxsidebar, 909 | div.related, 910 | div.footer, 911 | #top-link { 912 | display: none; 913 | } 914 | } -------------------------------------------------------------------------------- /docs/_static/searchtools.js: -------------------------------------------------------------------------------- 1 | /* 2 | * Sphinx JavaScript utilities for the full-text search. 3 | */ 4 | "use strict"; 5 | 6 | /** 7 | * Simple result scoring code. 8 | */ 9 | if (typeof Scorer === "undefined") { 10 | var Scorer = { 11 | // Implement the following function to further tweak the score for each result 12 | // The function takes a result array [docname, title, anchor, descr, score, filename] 13 | // and returns the new score. 14 | /* 15 | score: result => { 16 | const [docname, title, anchor, descr, score, filename, kind] = result 17 | return score 18 | }, 19 | */ 20 | 21 | // query matches the full name of an object 22 | objNameMatch: 11, 23 | // or matches in the last dotted part of the object name 24 | objPartialMatch: 6, 25 | // Additive scores depending on the priority of the object 26 | objPrio: { 27 | 0: 15, // used to be importantResults 28 | 1: 5, // used to be objectResults 29 | 2: -5, // used to be unimportantResults 30 | }, 31 | // Used when the priority is not in the mapping. 32 | objPrioDefault: 0, 33 | 34 | // query found in title 35 | title: 15, 36 | partialTitle: 7, 37 | // query found in terms 38 | term: 5, 39 | partialTerm: 2, 40 | }; 41 | } 42 | 43 | // Global search result kind enum, used by themes to style search results. 44 | class SearchResultKind { 45 | static get index() { return "index"; } 46 | static get object() { return "object"; } 47 | static get text() { return "text"; } 48 | static get title() { return "title"; } 49 | } 50 | 51 | const _removeChildren = (element) => { 52 | while (element && element.lastChild) element.removeChild(element.lastChild); 53 | }; 54 | 55 | /** 56 | * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping 57 | */ 58 | const _escapeRegExp = (string) => 59 | string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string 60 | 61 | const _displayItem = (item, searchTerms, highlightTerms) => { 62 | const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; 63 | const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; 64 | const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; 65 | const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; 66 | const contentRoot = document.documentElement.dataset.content_root; 67 | 68 | const [docName, title, anchor, descr, score, _filename, kind] = item; 69 | 70 | let listItem = document.createElement("li"); 71 | // Add a class representing the item's type: 72 | // can be used by a theme's CSS selector for styling 73 | // See SearchResultKind for the class names. 74 | listItem.classList.add(`kind-${kind}`); 75 | let requestUrl; 76 | let linkUrl; 77 | if (docBuilder === "dirhtml") { 78 | // dirhtml builder 79 | let dirname = docName + "/"; 80 | if (dirname.match(/\/index\/$/)) 81 | dirname = dirname.substring(0, dirname.length - 6); 82 | else if (dirname === "index/") dirname = ""; 83 | requestUrl = contentRoot + dirname; 84 | linkUrl = requestUrl; 85 | } else { 86 | // normal html builders 87 | requestUrl = contentRoot + docName + docFileSuffix; 88 | linkUrl = docName + docLinkSuffix; 89 | } 90 | let linkEl = listItem.appendChild(document.createElement("a")); 91 | linkEl.href = linkUrl + anchor; 92 | linkEl.dataset.score = score; 93 | linkEl.innerHTML = title; 94 | if (descr) { 95 | listItem.appendChild(document.createElement("span")).innerHTML = 96 | " (" + descr + ")"; 97 | // highlight search terms in the description 98 | if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js 99 | highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); 100 | } 101 | else if (showSearchSummary) 102 | fetch(requestUrl) 103 | .then((responseData) => responseData.text()) 104 | .then((data) => { 105 | if (data) 106 | listItem.appendChild( 107 | Search.makeSearchSummary(data, searchTerms, anchor) 108 | ); 109 | // highlight search terms in the summary 110 | if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js 111 | highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); 112 | }); 113 | Search.output.appendChild(listItem); 114 | }; 115 | const _finishSearch = (resultCount) => { 116 | Search.stopPulse(); 117 | Search.title.innerText = _("Search Results"); 118 | if (!resultCount) 119 | Search.status.innerText = Documentation.gettext( 120 | "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." 121 | ); 122 | else 123 | Search.status.innerText = Documentation.ngettext( 124 | "Search finished, found one page matching the search query.", 125 | "Search finished, found ${resultCount} pages matching the search query.", 126 | resultCount, 127 | ).replace('${resultCount}', resultCount); 128 | }; 129 | const _displayNextItem = ( 130 | results, 131 | resultCount, 132 | searchTerms, 133 | highlightTerms, 134 | ) => { 135 | // results left, load the summary and display it 136 | // this is intended to be dynamic (don't sub resultsCount) 137 | if (results.length) { 138 | _displayItem(results.pop(), searchTerms, highlightTerms); 139 | setTimeout( 140 | () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), 141 | 5 142 | ); 143 | } 144 | // search finished, update title and status message 145 | else _finishSearch(resultCount); 146 | }; 147 | // Helper function used by query() to order search results. 148 | // Each input is an array of [docname, title, anchor, descr, score, filename, kind]. 149 | // Order the results by score (in opposite order of appearance, since the 150 | // `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. 151 | const _orderResultsByScoreThenName = (a, b) => { 152 | const leftScore = a[4]; 153 | const rightScore = b[4]; 154 | if (leftScore === rightScore) { 155 | // same score: sort alphabetically 156 | const leftTitle = a[1].toLowerCase(); 157 | const rightTitle = b[1].toLowerCase(); 158 | if (leftTitle === rightTitle) return 0; 159 | return leftTitle > rightTitle ? -1 : 1; // inverted is intentional 160 | } 161 | return leftScore > rightScore ? 1 : -1; 162 | }; 163 | 164 | /** 165 | * Default splitQuery function. Can be overridden in ``sphinx.search`` with a 166 | * custom function per language. 167 | * 168 | * The regular expression works by splitting the string on consecutive characters 169 | * that are not Unicode letters, numbers, underscores, or emoji characters. 170 | * This is the same as ``\W+`` in Python, preserving the surrogate pair area. 171 | */ 172 | if (typeof splitQuery === "undefined") { 173 | var splitQuery = (query) => query 174 | .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) 175 | .filter(term => term) // remove remaining empty strings 176 | } 177 | 178 | /** 179 | * Search Module 180 | */ 181 | const Search = { 182 | _index: null, 183 | _queued_query: null, 184 | _pulse_status: -1, 185 | 186 | htmlToText: (htmlString, anchor) => { 187 | const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); 188 | for (const removalQuery of [".headerlink", "script", "style"]) { 189 | htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); 190 | } 191 | if (anchor) { 192 | const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); 193 | if (anchorContent) return anchorContent.textContent; 194 | 195 | console.warn( 196 | `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` 197 | ); 198 | } 199 | 200 | // if anchor not specified or not found, fall back to main content 201 | const docContent = htmlElement.querySelector('[role="main"]'); 202 | if (docContent) return docContent.textContent; 203 | 204 | console.warn( 205 | "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." 206 | ); 207 | return ""; 208 | }, 209 | 210 | init: () => { 211 | const query = new URLSearchParams(window.location.search).get("q"); 212 | document 213 | .querySelectorAll('input[name="q"]') 214 | .forEach((el) => (el.value = query)); 215 | if (query) Search.performSearch(query); 216 | }, 217 | 218 | loadIndex: (url) => 219 | (document.body.appendChild(document.createElement("script")).src = url), 220 | 221 | setIndex: (index) => { 222 | Search._index = index; 223 | if (Search._queued_query !== null) { 224 | const query = Search._queued_query; 225 | Search._queued_query = null; 226 | Search.query(query); 227 | } 228 | }, 229 | 230 | hasIndex: () => Search._index !== null, 231 | 232 | deferQuery: (query) => (Search._queued_query = query), 233 | 234 | stopPulse: () => (Search._pulse_status = -1), 235 | 236 | startPulse: () => { 237 | if (Search._pulse_status >= 0) return; 238 | 239 | const pulse = () => { 240 | Search._pulse_status = (Search._pulse_status + 1) % 4; 241 | Search.dots.innerText = ".".repeat(Search._pulse_status); 242 | if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); 243 | }; 244 | pulse(); 245 | }, 246 | 247 | /** 248 | * perform a search for something (or wait until index is loaded) 249 | */ 250 | performSearch: (query) => { 251 | // create the required interface elements 252 | const searchText = document.createElement("h2"); 253 | searchText.textContent = _("Searching"); 254 | const searchSummary = document.createElement("p"); 255 | searchSummary.classList.add("search-summary"); 256 | searchSummary.innerText = ""; 257 | const searchList = document.createElement("ul"); 258 | searchList.setAttribute("role", "list"); 259 | searchList.classList.add("search"); 260 | 261 | const out = document.getElementById("search-results"); 262 | Search.title = out.appendChild(searchText); 263 | Search.dots = Search.title.appendChild(document.createElement("span")); 264 | Search.status = out.appendChild(searchSummary); 265 | Search.output = out.appendChild(searchList); 266 | 267 | const searchProgress = document.getElementById("search-progress"); 268 | // Some themes don't use the search progress node 269 | if (searchProgress) { 270 | searchProgress.innerText = _("Preparing search..."); 271 | } 272 | Search.startPulse(); 273 | 274 | // index already loaded, the browser was quick! 275 | if (Search.hasIndex()) Search.query(query); 276 | else Search.deferQuery(query); 277 | }, 278 | 279 | _parseQuery: (query) => { 280 | // stem the search terms and add them to the correct list 281 | const stemmer = new Stemmer(); 282 | const searchTerms = new Set(); 283 | const excludedTerms = new Set(); 284 | const highlightTerms = new Set(); 285 | const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); 286 | splitQuery(query.trim()).forEach((queryTerm) => { 287 | const queryTermLower = queryTerm.toLowerCase(); 288 | 289 | // maybe skip this "word" 290 | // stopwords array is from language_data.js 291 | if ( 292 | stopwords.indexOf(queryTermLower) !== -1 || 293 | queryTerm.match(/^\d+$/) 294 | ) 295 | return; 296 | 297 | // stem the word 298 | let word = stemmer.stemWord(queryTermLower); 299 | // select the correct list 300 | if (word[0] === "-") excludedTerms.add(word.substr(1)); 301 | else { 302 | searchTerms.add(word); 303 | highlightTerms.add(queryTermLower); 304 | } 305 | }); 306 | 307 | if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js 308 | localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) 309 | } 310 | 311 | // console.debug("SEARCH: searching for:"); 312 | // console.info("required: ", [...searchTerms]); 313 | // console.info("excluded: ", [...excludedTerms]); 314 | 315 | return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; 316 | }, 317 | 318 | /** 319 | * execute search (requires search index to be loaded) 320 | */ 321 | _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { 322 | const filenames = Search._index.filenames; 323 | const docNames = Search._index.docnames; 324 | const titles = Search._index.titles; 325 | const allTitles = Search._index.alltitles; 326 | const indexEntries = Search._index.indexentries; 327 | 328 | // Collect multiple result groups to be sorted separately and then ordered. 329 | // Each is an array of [docname, title, anchor, descr, score, filename, kind]. 330 | const normalResults = []; 331 | const nonMainIndexResults = []; 332 | 333 | _removeChildren(document.getElementById("search-progress")); 334 | 335 | const queryLower = query.toLowerCase().trim(); 336 | for (const [title, foundTitles] of Object.entries(allTitles)) { 337 | if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { 338 | for (const [file, id] of foundTitles) { 339 | const score = Math.round(Scorer.title * queryLower.length / title.length); 340 | const boost = titles[file] === title ? 1 : 0; // add a boost for document titles 341 | normalResults.push([ 342 | docNames[file], 343 | titles[file] !== title ? `${titles[file]} > ${title}` : title, 344 | id !== null ? "#" + id : "", 345 | null, 346 | score + boost, 347 | filenames[file], 348 | SearchResultKind.title, 349 | ]); 350 | } 351 | } 352 | } 353 | 354 | // search for explicit entries in index directives 355 | for (const [entry, foundEntries] of Object.entries(indexEntries)) { 356 | if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { 357 | for (const [file, id, isMain] of foundEntries) { 358 | const score = Math.round(100 * queryLower.length / entry.length); 359 | const result = [ 360 | docNames[file], 361 | titles[file], 362 | id ? "#" + id : "", 363 | null, 364 | score, 365 | filenames[file], 366 | SearchResultKind.index, 367 | ]; 368 | if (isMain) { 369 | normalResults.push(result); 370 | } else { 371 | nonMainIndexResults.push(result); 372 | } 373 | } 374 | } 375 | } 376 | 377 | // lookup as object 378 | objectTerms.forEach((term) => 379 | normalResults.push(...Search.performObjectSearch(term, objectTerms)) 380 | ); 381 | 382 | // lookup as search terms in fulltext 383 | normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); 384 | 385 | // let the scorer override scores with a custom scoring function 386 | if (Scorer.score) { 387 | normalResults.forEach((item) => (item[4] = Scorer.score(item))); 388 | nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); 389 | } 390 | 391 | // Sort each group of results by score and then alphabetically by name. 392 | normalResults.sort(_orderResultsByScoreThenName); 393 | nonMainIndexResults.sort(_orderResultsByScoreThenName); 394 | 395 | // Combine the result groups in (reverse) order. 396 | // Non-main index entries are typically arbitrary cross-references, 397 | // so display them after other results. 398 | let results = [...nonMainIndexResults, ...normalResults]; 399 | 400 | // remove duplicate search results 401 | // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept 402 | let seen = new Set(); 403 | results = results.reverse().reduce((acc, result) => { 404 | let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); 405 | if (!seen.has(resultStr)) { 406 | acc.push(result); 407 | seen.add(resultStr); 408 | } 409 | return acc; 410 | }, []); 411 | 412 | return results.reverse(); 413 | }, 414 | 415 | query: (query) => { 416 | const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); 417 | const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); 418 | 419 | // for debugging 420 | //Search.lastresults = results.slice(); // a copy 421 | // console.info("search results:", Search.lastresults); 422 | 423 | // print the results 424 | _displayNextItem(results, results.length, searchTerms, highlightTerms); 425 | }, 426 | 427 | /** 428 | * search for object names 429 | */ 430 | performObjectSearch: (object, objectTerms) => { 431 | const filenames = Search._index.filenames; 432 | const docNames = Search._index.docnames; 433 | const objects = Search._index.objects; 434 | const objNames = Search._index.objnames; 435 | const titles = Search._index.titles; 436 | 437 | const results = []; 438 | 439 | const objectSearchCallback = (prefix, match) => { 440 | const name = match[4] 441 | const fullname = (prefix ? prefix + "." : "") + name; 442 | const fullnameLower = fullname.toLowerCase(); 443 | if (fullnameLower.indexOf(object) < 0) return; 444 | 445 | let score = 0; 446 | const parts = fullnameLower.split("."); 447 | 448 | // check for different match types: exact matches of full name or 449 | // "last name" (i.e. last dotted part) 450 | if (fullnameLower === object || parts.slice(-1)[0] === object) 451 | score += Scorer.objNameMatch; 452 | else if (parts.slice(-1)[0].indexOf(object) > -1) 453 | score += Scorer.objPartialMatch; // matches in last name 454 | 455 | const objName = objNames[match[1]][2]; 456 | const title = titles[match[0]]; 457 | 458 | // If more than one term searched for, we require other words to be 459 | // found in the name/title/description 460 | const otherTerms = new Set(objectTerms); 461 | otherTerms.delete(object); 462 | if (otherTerms.size > 0) { 463 | const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); 464 | if ( 465 | [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) 466 | ) 467 | return; 468 | } 469 | 470 | let anchor = match[3]; 471 | if (anchor === "") anchor = fullname; 472 | else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; 473 | 474 | const descr = objName + _(", in ") + title; 475 | 476 | // add custom score for some objects according to scorer 477 | if (Scorer.objPrio.hasOwnProperty(match[2])) 478 | score += Scorer.objPrio[match[2]]; 479 | else score += Scorer.objPrioDefault; 480 | 481 | results.push([ 482 | docNames[match[0]], 483 | fullname, 484 | "#" + anchor, 485 | descr, 486 | score, 487 | filenames[match[0]], 488 | SearchResultKind.object, 489 | ]); 490 | }; 491 | Object.keys(objects).forEach((prefix) => 492 | objects[prefix].forEach((array) => 493 | objectSearchCallback(prefix, array) 494 | ) 495 | ); 496 | return results; 497 | }, 498 | 499 | /** 500 | * search for full-text terms in the index 501 | */ 502 | performTermsSearch: (searchTerms, excludedTerms) => { 503 | // prepare search 504 | const terms = Search._index.terms; 505 | const titleTerms = Search._index.titleterms; 506 | const filenames = Search._index.filenames; 507 | const docNames = Search._index.docnames; 508 | const titles = Search._index.titles; 509 | 510 | const scoreMap = new Map(); 511 | const fileMap = new Map(); 512 | 513 | // perform the search on the required terms 514 | searchTerms.forEach((word) => { 515 | const files = []; 516 | const arr = [ 517 | { files: terms[word], score: Scorer.term }, 518 | { files: titleTerms[word], score: Scorer.title }, 519 | ]; 520 | // add support for partial matches 521 | if (word.length > 2) { 522 | const escapedWord = _escapeRegExp(word); 523 | if (!terms.hasOwnProperty(word)) { 524 | Object.keys(terms).forEach((term) => { 525 | if (term.match(escapedWord)) 526 | arr.push({ files: terms[term], score: Scorer.partialTerm }); 527 | }); 528 | } 529 | if (!titleTerms.hasOwnProperty(word)) { 530 | Object.keys(titleTerms).forEach((term) => { 531 | if (term.match(escapedWord)) 532 | arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); 533 | }); 534 | } 535 | } 536 | 537 | // no match but word was a required one 538 | if (arr.every((record) => record.files === undefined)) return; 539 | 540 | // found search word in contents 541 | arr.forEach((record) => { 542 | if (record.files === undefined) return; 543 | 544 | let recordFiles = record.files; 545 | if (recordFiles.length === undefined) recordFiles = [recordFiles]; 546 | files.push(...recordFiles); 547 | 548 | // set score for the word in each file 549 | recordFiles.forEach((file) => { 550 | if (!scoreMap.has(file)) scoreMap.set(file, {}); 551 | scoreMap.get(file)[word] = record.score; 552 | }); 553 | }); 554 | 555 | // create the mapping 556 | files.forEach((file) => { 557 | if (!fileMap.has(file)) fileMap.set(file, [word]); 558 | else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); 559 | }); 560 | }); 561 | 562 | // now check if the files don't contain excluded terms 563 | const results = []; 564 | for (const [file, wordList] of fileMap) { 565 | // check if all requirements are matched 566 | 567 | // as search terms with length < 3 are discarded 568 | const filteredTermCount = [...searchTerms].filter( 569 | (term) => term.length > 2 570 | ).length; 571 | if ( 572 | wordList.length !== searchTerms.size && 573 | wordList.length !== filteredTermCount 574 | ) 575 | continue; 576 | 577 | // ensure that none of the excluded terms is in the search result 578 | if ( 579 | [...excludedTerms].some( 580 | (term) => 581 | terms[term] === file || 582 | titleTerms[term] === file || 583 | (terms[term] || []).includes(file) || 584 | (titleTerms[term] || []).includes(file) 585 | ) 586 | ) 587 | break; 588 | 589 | // select one (max) score for the file. 590 | const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); 591 | // add result to the result list 592 | results.push([ 593 | docNames[file], 594 | titles[file], 595 | "", 596 | null, 597 | score, 598 | filenames[file], 599 | SearchResultKind.text, 600 | ]); 601 | } 602 | return results; 603 | }, 604 | 605 | /** 606 | * helper function to return a node containing the 607 | * search summary for a given text. keywords is a list 608 | * of stemmed words. 609 | */ 610 | makeSearchSummary: (htmlText, keywords, anchor) => { 611 | const text = Search.htmlToText(htmlText, anchor); 612 | if (text === "") return null; 613 | 614 | const textLower = text.toLowerCase(); 615 | const actualStartPosition = [...keywords] 616 | .map((k) => textLower.indexOf(k.toLowerCase())) 617 | .filter((i) => i > -1) 618 | .slice(-1)[0]; 619 | const startWithContext = Math.max(actualStartPosition - 120, 0); 620 | 621 | const top = startWithContext === 0 ? "" : "..."; 622 | const tail = startWithContext + 240 < text.length ? "..." : ""; 623 | 624 | let summary = document.createElement("p"); 625 | summary.classList.add("context"); 626 | summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; 627 | 628 | return summary; 629 | }, 630 | }; 631 | 632 | _ready(Search.init); 633 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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No Surrender of Others' Freedom. 541 | 542 | If conditions are imposed on you (whether by court order, agreement or 543 | otherwise) that contradict the conditions of this License, they do not 544 | excuse you from the conditions of this License. If you cannot convey a 545 | covered work so as to satisfy simultaneously your obligations under this 546 | License and any other pertinent obligations, then as a consequence you may 547 | not convey it at all. For example, if you agree to terms that obligate you 548 | to collect a royalty for further conveying from those to whom you convey 549 | the Program, the only way you could satisfy both those terms and this 550 | License would be to refrain entirely from conveying the Program. 551 | 552 | 13. Use with the GNU Affero General Public License. 553 | 554 | Notwithstanding any other provision of this License, you have 555 | permission to link or combine any covered work with a work licensed 556 | under version 3 of the GNU Affero General Public License into a single 557 | combined work, and to convey the resulting work. The terms of this 558 | License will continue to apply to the part which is the covered work, 559 | but the special requirements of the GNU Affero General Public License, 560 | section 13, concerning interaction through a network will apply to the 561 | combination as such. 562 | 563 | 14. Revised Versions of this License. 564 | 565 | The Free Software Foundation may publish revised and/or new versions of 566 | the GNU General Public License from time to time. Such new versions will 567 | be similar in spirit to the present version, but may differ in detail to 568 | address new problems or concerns. 569 | 570 | Each version is given a distinguishing version number. If the 571 | Program specifies that a certain numbered version of the GNU General 572 | Public License "or any later version" applies to it, you have the 573 | option of following the terms and conditions either of that numbered 574 | version or of any later version published by the Free Software 575 | Foundation. If the Program does not specify a version number of the 576 | GNU General Public License, you may choose any version ever published 577 | by the Free Software Foundation. 578 | 579 | If the Program specifies that a proxy can decide which future 580 | versions of the GNU General Public License can be used, that proxy's 581 | public statement of acceptance of a version permanently authorizes you 582 | to choose that version for the Program. 583 | 584 | Later license versions may give you additional or different 585 | permissions. However, no additional obligations are imposed on any 586 | author or copyright holder as a result of your choosing to follow a 587 | later version. 588 | 589 | 15. Disclaimer of Warranty. 590 | 591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 592 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT 593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY 594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, 595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 596 | PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM 597 | IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF 598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 599 | 600 | 16. Limitation of Liability. 601 | 602 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS 604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY 605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE 606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF 607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD 608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), 609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF 610 | SUCH DAMAGES. 611 | 612 | 17. Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | --------------------------------------------------------------------------------