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SimonGreenhill / treemaker

A Python library for creating a Newick formatted tree from a set of classification strings
BSD 3-Clause "New" or "Revised" License
8 stars 2 forks source link

Update sphinx to 3.5.3 #52

Closed pyup-bot closed 3 years ago

pyup-bot commented 3 years ago

This PR updates sphinx from 3.3.1 to 3.5.3.

Changelog ### 3.5.3 ``` ===================================== Features added -------------- * 8959: using UNIX path separator in image directive confuses Sphinx on Windows ``` ### 3.5.2 ``` ===================================== Bugs fixed ---------- * 8943: i18n: Crashed by broken translation messages in ES, EL and HR * 8936: LaTeX: A custom LaTeX builder fails with unknown node error * 8952: Exceptions raised in a Directive cause parallel builds to hang ``` ### 3.5.1 ``` ===================================== Bugs fixed ---------- * 8883: autodoc: AttributeError is raised on assigning __annotations__ on read-only class * 8884: html: minified js stemmers not included in the distributed package * 8885: html: AttributeError is raised if CSS/JS files are installed via :confval:`html_context` * 8880: viewcode: ExtensionError is raised on incremental build after unparsable python module found ``` ### 3.5.0 ``` ===================================== Dependencies ------------ * LaTeX: ``multicol`` (it is anyhow a required part of the official latex2e base distribution) Incompatible changes -------------------- * Update Underscore.js to 1.12.0 * 6550: html: The config variable ``html_add_permalinks`` is replaced by :confval:`html_permalinks` and :confval:`html_permalinks_icon` Deprecated ---------- * pending_xref node for viewcode extension * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.anchors_ignore`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.auth`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.broken`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.good`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.redirected`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.rqueue`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.to_ignore`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.workers`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.wqueue`` * ``sphinx.builders.linkcheck.node_line_or_0()`` * ``sphinx.ext.autodoc.AttributeDocumenter.isinstanceattribute()`` * ``sphinx.ext.autodoc.directive.DocumenterBridge.reporter`` * ``sphinx.ext.autodoc.importer.get_module_members()`` * ``sphinx.ext.autosummary.generate._simple_info()`` * ``sphinx.ext.autosummary.generate._simple_warn()`` * ``sphinx.writers.html.HTMLTranslator.permalink_text`` * ``sphinx.writers.html5.HTML5Translator.permalink_text`` Features added -------------- * 8022: autodoc: autodata and autoattribute directives does not show right-hand value of the variable if docstring contains ``:meta hide-value:`` in info-field-list * 8514: autodoc: Default values of overloaded functions are taken from actual implementation if they're ellipsis * 8775: autodoc: Support type union operator (PEP-604) in Python 3.10 or above * 8297: autodoc: Allow to extend :confval:`autodoc_default_options` via directive options * 8619: html: kbd role generates customizable HTML tags for compound keys * 8634: html: Allow to change the order of JS/CSS via ``priority`` parameter for :meth:`Sphinx.add_js_file()` and :meth:`Sphinx.add_css_file()` * 6241: html: Allow to add JS/CSS files to the specific page when an extension calls ``app.add_js_file()`` or ``app.add_css_file()`` on :event:`html-page-context` event * 6550: html: Allow to use HTML permalink texts via :confval:`html_permalinks_icon` * 1638: html: Add permalink icons to glossary terms * 8868: html search: performance issue with massive lists * 8867: html search: Update JavaScript stemmer code to the latest version of Snowball (v2.1.0) * 8852: i18n: Allow to translate heading syntax in MyST-Parser * 8649: imgconverter: Skip availability check if builder supports the image type * 8573: napoleon: Allow to change the style of custom sections using :confval:`napoleon_custom_styles` * 8004: napoleon: Type definitions in Google style docstrings are rendered as references when :confval:`napoleon_preprocess_types` enabled * 6241: mathjax: Include mathjax.js only on the document using equations * 8775: py domain: Support type union operator (PEP-604) * 8651: std domain: cross-reference for a rubric having inline item is broken * 7642: std domain: Optimize case-insensitive match of term * 8681: viewcode: Support incremental build * 8132: Add :confval:`project_copyright` as an alias of :confval:`copyright` * 207: Now :confval:`highlight_language` supports multiple languages * 2030: :rst:dir:`code-block` and :rst:dir:`literalinclude` supports automatic dedent via no-argument ``:dedent:`` option * C++, also hyperlink operator overloads in expressions and alias declarations. * 8247: Allow production lists to refer to tokens from other production groups * 8813: Show what extension (or module) caused it on errors on event handler * 8213: C++: add ``maxdepth`` option to :rst:dir:`cpp:alias` to insert nested declarations. * C, add ``noroot`` option to :rst:dir:`c:alias` to render only nested declarations. * C++, add ``noroot`` option to :rst:dir:`cpp:alias` to render only nested declarations. Bugs fixed ---------- * 8727: apidoc: namespace module file is not generated if no submodules there * 741: autodoc: inherited-members doesn't work for instance attributes on super class * 8592: autodoc: ``:meta public:`` does not effect to variables * 8594: autodoc: empty __all__ attribute is ignored * 8315: autodoc: Failed to resolve struct.Struct type annotation * 8652: autodoc: All variable comments in the module are ignored if the module contains invalid type comments * 8693: autodoc: Default values for overloaded functions are rendered as string * 8134: autodoc: crashes when mocked decorator takes arguments * 8800: autodoc: Uninitialized attributes in superclass are recognized as undocumented * 8655: autodoc: Failed to generate document if target module contains an object that raises an exception on ``hasattr()`` * 8306: autosummary: mocked modules are documented as empty page when using :recursive: option * 8232: graphviz: Image node is not rendered if graph file is in subdirectory * 8618: html: kbd role produces incorrect HTML when compound-key separators (-, + or ^) are used as keystrokes * 8629: html: A type warning for html_use_opensearch is shown twice * 8714: html: kbd role with "Caps Lock" rendered incorrectly * 8123: html search: fix searching for terms containing + (Requires a custom search language that does not split on +) * 8665: html theme: Could not override globaltoc_maxdepth in theme.conf * 8446: html: consecutive spaces are displayed as single space * 8745: i18n: crashes with KeyError when translation message adds a new auto footnote reference * 4304: linkcheck: Fix race condition that could lead to checking the availability of the same URL twice * 8791: linkcheck: The docname for each hyperlink is not displayed * 7118: sphinx-quickstart: questionare got Mojibake if libreadline unavailable * 8094: texinfo: image files on the different directory with document are not copied * 8782: todo: Cross references in todolist get broken * 8720: viewcode: module pages are generated for epub on incremental build * 8704: viewcode: anchors are generated in incremental build after singlehtml * 8756: viewcode: highlighted code is generated even if not referenced * 8671: :confval:`highlight_options` is not working * 8341: C, fix intersphinx lookup types for names in declarations. * C, C++: in general fix intersphinx and role lookup types. * 8683: :confval:`html_last_updated_fmt` does not support UTC offset (%z) * 8683: :confval:`html_last_updated_fmt` generates wrong time zone for %Z * 1112: ``download`` role creates duplicated copies when relative path is specified * 2616 (fifth item): LaTeX: footnotes from captions are not clickable, and for manually numbered footnotes only first one with same number is an hyperlink * 7576: LaTeX with French babel and memoir crash: "Illegal parameter number in definition of ``\FNHprefntext``" * 8055: LaTeX (docs): A potential display bug with the LaTeX generation step in Sphinx (how to generate one-column index) * 8072: LaTeX: Directive :rst:dir:`hlist` not implemented in LaTeX * 8214: LaTeX: The :rst:role:`index` role and the glossary generate duplicate entries in the LaTeX index (if both used for same term) * 8735: LaTeX: wrong internal links in pdf to captioned code-blocks when :confval:`numfig` is not True * 8442: LaTeX: some indexed terms are ignored when using xelatex engine (or pdflatex and :confval:`latex_use_xindy` set to True) with memoir class * 8750: LaTeX: URLs as footnotes fail to show in PDF if originating from inside function type signatures * 8780: LaTeX: long words in narrow columns may not be hyphenated * 8788: LaTeX: ``\titleformat`` last argument in sphinx.sty should be bracketed, not braced (and is anyhow not needed) * 8849: LaTex: code-block printed out of margin (see the opt-in LaTeX syntax boolean :ref:`verbatimforcewraps <latexsphinxsetupforcewraps>` for use via the :ref:`'sphinxsetup' <latexsphinxsetup>` key of ``latex_elements``) * 8183: LaTeX: Remove substitution_reference nodes from doctree only on LaTeX builds * 8865: LaTeX: Restructure the index nodes inside title nodes only on LaTeX builds * 8796: LaTeX: potentially critical low level TeX coding mistake has gone unnoticed so far * C, :rst:dir:`c:alias` skip symbols without explicit declarations instead of crashing. * C, :rst:dir:`c:alias` give a warning when the root symbol is not declared. * C, ``expr`` role should start symbol lookup in the current scope. ``` ### 3.4.3 ``` ===================================== Bugs fixed ---------- * 8655: autodoc: Failed to generate document if target module contains an object that raises an exception on ``hasattr()`` ``` ### 3.4.2 ``` ===================================== Bugs fixed ---------- * 8164: autodoc: Classes that inherit mocked class are not documented * 8602: autodoc: The ``autodoc-process-docstring`` event is emitted to the non-datadescriptors unexpectedly * 8616: autodoc: AttributeError is raised on non-class object is passed to autoclass directive ``` ### 3.4.1 ``` ===================================== Bugs fixed ---------- * 8559: autodoc: AttributeError is raised when using forward-reference type annotations * 8568: autodoc: TypeError is raised on checking slots attribute * 8567: autodoc: Instance attributes are incorrectly added to Parent class * 8566: autodoc: The ``autodoc-process-docstring`` event is emitted to the alias classes unexpectedly * 8583: autodoc: Unnecessary object comparision via ``__eq__`` method * 8565: linkcheck: Fix PriorityQueue crash when link tuples are not comparable ``` ### 3.4.0 ``` ===================================== Incompatible changes -------------------- * 8105: autodoc: the signature of class constructor will be shown for decorated classes, not a signature of decorator Deprecated ---------- * The ``follow_wrapped`` argument of ``sphinx.util.inspect.signature()`` * The ``no_docstring`` argument of ``sphinx.ext.autodoc.Documenter.add_content()`` * ``sphinx.ext.autodoc.Documenter.get_object_members()`` * ``sphinx.ext.autodoc.DataDeclarationDocumenter`` * ``sphinx.ext.autodoc.GenericAliasDocumenter`` * ``sphinx.ext.autodoc.InstanceAttributeDocumenter`` * ``sphinx.ext.autodoc.SlotsAttributeDocumenter`` * ``sphinx.ext.autodoc.TypeVarDocumenter`` * ``sphinx.ext.autodoc.importer._getannotations()`` * ``sphinx.ext.autodoc.importer._getmro()`` * ``sphinx.pycode.ModuleAnalyzer.parse()`` * ``sphinx.util.osutil.movefile()`` * ``sphinx.util.requests.is_ssl_error()`` Features added -------------- * 8119: autodoc: Allow to determine whether a member not included in ``__all__`` attribute of the module should be documented or not via :event:`autodoc-skip-member` event * 8219: autodoc: Parameters for generic class are not shown when super class is a generic class and show-inheritance option is given (in Python 3.7 or above) * autodoc: Add ``Documenter.config`` as a shortcut to access the config object * autodoc: Add Optional[t] to annotation of function and method if a default value equal to None is set. * 8209: autodoc: Add ``:no-value:`` option to :rst:dir:`autoattribute` and :rst:dir:`autodata` directive to suppress the default value of the variable * 8460: autodoc: Support custom types defined by typing.NewType * 8285: napoleon: Add :confval:`napoleon_attr_annotations` to merge type hints on source code automatically if any type is specified in docstring * 8236: napoleon: Support numpydoc's "Receives" section * 6914: Add a new event :event:`warn-missing-reference` to custom warning messages when failed to resolve a cross-reference * 6914: Emit a detailed warning when failed to resolve a ``:ref:`` reference * 6629: linkcheck: The builder now handles rate limits. See :confval:`linkcheck_retry_on_rate_limit` for details. Bugs fixed ---------- * 7613: autodoc: autodoc does not respect __signature__ of the class * 4606: autodoc: the location of the warning is incorrect for inherited method * 8105: autodoc: the signature of class constructor is incorrect if the class is decorated * 8434: autodoc: :confval:`autodoc_type_aliases` does not effect to variables and attributes * 8443: autodoc: autodata directive can't create document for PEP-526 based type annotated variables * 8443: autodoc: autoattribute directive can't create document for PEP-526 based uninitalized variables * 8480: autodoc: autoattribute could not create document for __slots__ attributes * 8503: autodoc: autoattribute could not create document for a GenericAlias as class attributes correctly * 8534: autodoc: autoattribute could not create document for a commented attribute in alias class * 8452: autodoc: autodoc_type_aliases doesn't work when autodoc_typehints is set to "description" * 8541: autodoc: autodoc_type_aliases doesn't work for the type annotation to instance attributes * 8460: autodoc: autodata and autoattribute directives do not display type information of TypeVars * 8493: autodoc: references to builtins not working in class aliases * 8522: autodoc: ``__bool__`` method could be called * 8067: autodoc: A typehint for the instance variable having type_comment on super class is not displayed * 8545: autodoc: a __slots__ attribute is not documented even having docstring * 741: autodoc: inherited-members doesn't work for instance attributes on super class * 8477: autosummary: non utf-8 reST files are generated when template contains multibyte characters * 8501: autosummary: summary extraction splits text after "el at." unexpectedly * 8524: html: Wrong url_root has been generated on a document named "index" * 8419: html search: Do not load ``language_data.js`` in non-search pages * 8549: i18n: ``-D gettext_compact=0`` is no longer working * 8454: graphviz: The layout option for graph and digraph directives don't work * 8131: linkcheck: Use GET when HEAD requests cause Too Many Redirects, to accommodate infinite redirect loops on HEAD * 8437: Makefile: ``make clean`` with empty BUILDDIR is dangerous * 8365: py domain: ``:type:`` and ``:rtype:`` gives false ambiguous class lookup warnings * 8352: std domain: Failed to parse an option that starts with bracket * 8519: LaTeX: Prevent page brake in the middle of a seealso * 8520: C, fix copying of AliasNode. ```
Links - PyPI: https://pypi.org/project/sphinx - Changelog: https://pyup.io/changelogs/sphinx/ - Homepage: http://sphinx-doc.org/
coveralls commented 3 years ago

Coverage Status

Coverage remained the same at 100.0% when pulling 8bbd2e90f37b5416e173abb152aefaa82d909dc2 on pyup-update-sphinx-3.3.1-to-3.5.3 into 4a6f22400561b21667ec34f34d8bda8636700fb6 on master.

pyup-bot commented 3 years ago

Closing this in favor of #53