zheminzhou / SPARSE

Strain Prediction and Analysis with Representative SEquence
https://www.biorxiv.org/content/biorxiv/early/2017/11/07/215707.full.pdf
GNU General Public License v3.0
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Update docutils to 0.19 #441

Closed pyup-bot closed 1 year ago

pyup-bot commented 2 years ago

This PR updates docutils from 0.14 to 0.19.

Changelog ### 0.19 ``` ========================= ``` ### 0.19b1 ``` * Drop support for Python 2.7, 3.5, and 3.6. * Output changes: HTML5: Wrap groups of footnotes in an ``<aside>`` for easier styling. The CSS rule ``.footnote-list { display: contents; }`` can be used to restore the behaviour of custom CSS styles. * After package installation, the CLI commands ``python -m docutils`` and ``docutils`` start the `generic command line front end tool`__. __ docs/user/tools.htmlgeneric-command-line-front-end * Support parsing "Markdown" input with 3rd party parsers myst_, pycmark_, or recommonmark_. * The default values for the "pep-references", "rfc-base-url", and "python-home" `configuration settings`_ now use the "https:" scheme. The PEP-writer template's header is updated to fix links and resemble the header of official PEPs. * Various bugfixes and improvements (see HISTORY_). .. _myst: https://pypi.org/project/myst-docutils .. _pycmark: https://pypi.org/project/pycmark/ .. _recommonmark: https://pypi.org/project/recommonmark/ .. _configuration settings: docs/user/config.html ``` ### 0.18.1 ``` =========================== .. Note:: Docutils 0.18.x is the last version supporting Python 2.7, 3.5, and 3.6. * ``nodes.Node.traverse()`` returns a list again to restore backwards compatibility (fixes bug 431). Use ``nodes.Node.findall()`` to get an iterator. * re-add module ``parsers.rst.directives.html`` (stub, emits deprecation warning and loads "Meta" directive from ist new place at ``parsers.rst.directives.misc``.) * Small bugfixes (see HISTORY_). ``` ### 0.18 ``` ========================= * Output changes: Identifiers: - During `identifier normalization`_, leading number and hyphen characters are no longer stripped from a `reference name`_, if the id_prefix_ setting is non-empty. Example: with ``--id-prefix="DU-"``, a section with title "34. May" currently gets the identifier key ``DU-may`` and after the change the identifier key ``DU-34-may``. - The default value for the auto_id_prefix_ setting changed to ``%``: "use the tag name as prefix for auto-generated IDs". Set auto_id_prefix_ to ``id`` for unchanged auto-IDs. HTML5: - Use the semantic tag <aside> for footnote text and citations, topics (except abstract and toc), admonitions, and system messages. Use <nav> for the Table of Contents. - Make "auto" table column widths the default: Only specify column widths, if the `"widths" option`_ is set and not "auto". The table-style__ setting "colwidths-grid" restores the current default. .. _"widths" option: __ docs/ref/rst/directives.htmltable __ docs/user/config.htmltable-style - Items of a definition list with class argument "details" are converted to `details disclosure elements`_. Example:: ..class:: details Summary This additional information should be hidden. - Do not add "compound-first", "compound-middle", or "compound-last" to elements nested in a compound. Use child selector and ":first-child", ":last-child" pseudo classes instead. - Use class value "backrefs" instead of "fn-backref" for a span of back-references. - Write footnote brackets and field term colons to HTML, so that they are present also without CSS and when copying text. - Move space character between section number and heading into "sectnum" span. `math-output`_: html - Support more commands, fix mapping of commands to Unicode characters. - Scale variable sized operators and big delimiters with CSS. - Don't use <tt> element (deprecated in HTML5). - Use STIX fonts if available. LaTeX: `legacy_class_functions`_ setting default changed to "False", admonitions are now environments. * New standard Docutils doctree node: <meta__>. * New configuration settings: - [latex writers] legacy_column_widths_ and - [html5 writer] image_loading_. * Removed files: ``iepngfix.htc`` and ``blank.gif`` (IE 6 workaround for `s5_html`). * Removed sub-module: ``parsers.rst.directives.html`` (reversed in release 0.18.1). * Removed function: utils.unique_combinations() (obsoleted by itertools.combinations()). * Removed attributes: - ``HTMLTranslator.topic_classes``: check ``node.parent.classes`` instead. - ``nodes.Text.rawsource``: we store the null-escaped text in Text nodes since 0.16 so there is no additional information in the rawsource. * Major refactoring and fixes/additions in ``docutils/utils/math/math2html.py`` and ``docutils/utils/math/latex2mathml.py`` (mathematical notation in HTML, cf. `LaTeX syntax for mathematics`_). * nodes.Node.traverse() returns an iterator instead of a list (reversed in release 0.18.1). * Various bugfixes and improvements (see HISTORY_). Fix spelling errors in documentation and docstrings. Thanks to Dimitri Papadopoulos. __ docs/ref/doctree.htmlmeta .. _identifier normalization: docs/ref/rst/directives.htmlidentifier-normalization .. _id_prefix: docs/user/config.htmlid-prefix .. _auto_id_prefix: docs/user/config.htmlauto-id-prefix .. _details disclosure elements: https://www.w3.org/TR/html52/interactive-elements.html#the-details-element .. _LaTeX syntax for mathematics: docs/ref/rst/mathematics.html .. _legacy_column_widths: docs/user/config.htmllegacy-column-widths ``` ### 0.17.1 ``` =========================== * Bug fixes (for details see the Docutils `HISTORY`_). ``` ### 0.17 ``` ========================= * Numerous bug fixes and improvements (for details see the Docutils `HISTORY`_). * Installing with ``setup.py`` now requires setuptools_. Alternatively, install with pip_. * The generic command line front end tool docutils-cli.py_ allows the free selection of reader, parser, and writer components. * Support Arabic language. * New, **experimental** wrapper to integrate the `recommonmark`__ Markdown parser for use with Docutils. Currently only tested with recommonmark version 0.4.0. __ https://pypi.org/project/recommonmark/ * HTML5 writer: - New option embed_images_. - Use semantic tags (for details see the Docutils `HISTORY`_). - Change the `initial_header_level`_ setting's default to "2", as browsers use the `same style for <h1> and <h2> when nested in a section`__. - New optional style ``responsive.css``, adapts to different screen sizes. - Move non-essential styling from ``minimal.css`` to ``plain.css`` rsp. ``responsive.css``. - Show code line numbers as pseudo-elements so they are skipped when copying the code block from the page. .. _initial_header_level: docs/user/config.htmlinitial-header-level __ https://stackoverflow.com/questions/39547412/same-font-size-for-h1-and-h2-in-article .. _embed_images: docs/user/config.htmlembed-images * LaTeX writer: - New configuration setting `legacy_class_functions`_. - The special value "auto" for the `graphicx_option`_ setting is no longer supported (it never worked for xetex/luatex). - `Styling commands`__ using the legacy ``\docutilsrole`` prefix are now ignored. Use ``\DUrole``. __ docs/user/latex.htmlclasses - Most helper commands and element definitions are now defined in the LaTeX package `docutils.sty`_ and only inserted in the document preamble if the stylesheet__ setting does not lists "docutils". __ docs/user/config.htmlstylesheet-latex-writers - Remove legacy LaTeX stylesheet ``docutils-05-compat.sty``. .. _setuptools: https://pypi.org/project/setuptools/ .. _pip: https://pypi.org/project/pip/ .. _docutils-cli.py: docs/user/tools.htmldocutils-cli-py .. _legacy_class_functions: docs/user/config.htmllegacy-class-functions .. _graphicx_option: docs/user/config.htmlgraphicx-option .. _docutils.sty: https://ctan.org/pkg/docutils ``` ### 0.16 ``` ========================= .. Note:: Docutils 0.15.x is the last version supporting Python 2.6, 3.3 and 3.4. Docutils 0.16.x supports Python 2.7 and Python >= 3.5 natively, without the use of the ``2to3`` tool. * reStructuredText: - Keep `backslash escapes`__ in the document tree. This allows, e.g., escaping of author-separators in `bibliographic fields`__. __ https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html#escaping-mechanism __ docs/ref/rst/restructuredtext.htmlbibliographic-fields * LaTeX writer: - Informal titles of type "rubric" default to bold-italic and left aligned. - Deprecate ``\docutilsrole`` prefix for styling commands: use ``\DUrole`` instead. - Fix topic subtitle. - Add "latex writers" to the `config_section_dependencies`. - Ignore classes for `rubric` elements (class wrapper interferes with LaTeX formatting). * tools/buildhtml.py - New option ``--html-writer`` allows to select "html" (default), "html4" or "html5" (deprecated in favour of the `"writer" option`_ in release 0.18). .. _"writer" option: docs/user/config.htmlwriter-buildhtml-application * docutils/io.py - Remove the `handle_io_errors` argument from io.FileInput/Output. * docutils/nodes.py - If `auto_id_prefix`_ ends with "%", this is replaced with the tag name. .. _auto_id_prefix: docs/user/config.htmlauto-id-prefix * Various bugfixes and improvements (see HISTORY_). ``` ### 0.15 ``` ========================= .. Note:: Docutils 0.14.x is the last version supporting Python 2.4, 2.5, 3.1, and 3.2. Docutils 0.15.x is compatible with Python versions 2.6, 2.7 and 3.3 to 3.5 (cf. `Python 3 compatibility`_). * reStructuredText: - Allow embedded colons in field list field names (before, tokens like ``:this:example:`` were considered ordinary text). - Fixed a bug with the "trim" options of the "unicode" directive. * languages: Added Korean localisation (ko). ```
Links - PyPI: https://pypi.org/project/docutils - Changelog: https://pyup.io/changelogs/docutils/ - Homepage: https://docutils.sourceforge.io/
pyup-bot commented 1 year ago

Closing this in favor of #527