pymzml / pymzML

pymzML - an interface between Python and mzML Mass spectrometry Files
https://pymzml.readthedocs.io/en/latest/
MIT License
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Update dependency sphinx to v5 #298

Closed renovate[bot] closed 2 years ago

renovate[bot] commented 2 years ago

Mend Renovate

This PR contains the following updates:

Package Change Age Adoption Passing Confidence
sphinx (source) ==4.5.0 -> ==5.0.2 age adoption passing confidence

Release Notes

sphinx-doc/sphinx ### [`v5.0.2`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-502-released-Jun-17-2022) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v5.0.1...v5.0.2) \===================================== ## Features added - [#​10523](https://togithub.com/sphinx-doc/sphinx/issues/10523): HTML Theme: Expose the Docutils's version info tuple as a template variable, `docutils_version_info`. Patch by Adam Turner. ## Bugs fixed - [#​10538](https://togithub.com/sphinx-doc/sphinx/issues/10538): autodoc: Inherited class attribute having docstring is documented even if :confval:`autodoc_inherit_docstring` is disabled - [#​10509](https://togithub.com/sphinx-doc/sphinx/issues/10509): autosummary: autosummary fails with a shared library - [#​10497](https://togithub.com/sphinx-doc/sphinx/issues/10497): py domain: Failed to resolve strings in Literal. Patch by Adam Turner. - [#​10523](https://togithub.com/sphinx-doc/sphinx/issues/10523): HTML Theme: Fix double brackets on citation references in Docutils 0.18+. Patch by Adam Turner. - [#​10534](https://togithub.com/sphinx-doc/sphinx/issues/10534): Missing CSS for nav.contents in Docutils 0.18+. Patch by Adam Turner. ### [`v5.0.1`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-501-released-Jun-03-2022) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v5.0.0...v5.0.1) \===================================== ## Bugs fixed - [#​10498](https://togithub.com/sphinx-doc/sphinx/issues/10498): gettext: TypeError is raised when sorting warning messages if a node has no line number. Patch by Adam Turner. - [#​10493](https://togithub.com/sphinx-doc/sphinx/issues/10493): HTML Theme: :rst:dir:`topic` directive is rendered incorrectly with Docutils 0.18. Patch by Adam Turner. - [#​10495](https://togithub.com/sphinx-doc/sphinx/issues/10495): IndexError is raised for a :rst:role:`kbd` role having a separator. Patch by Adam Turner. ### [`v5.0.0`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-500-released-May-30-2022) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v4.5.0...v5.0.0) \===================================== ## Dependencies 5.0.0 b1 - [#​10164](https://togithub.com/sphinx-doc/sphinx/issues/10164): Support `Docutils 0.18`\_. Patch by Adam Turner. .. \_Docutils 0.18: https://docutils.sourceforge.io/RELEASE-NOTES.html#release-0-18-2021-10-26 ## Incompatible changes 5.0.0 b1 - [#​10031](https://togithub.com/sphinx-doc/sphinx/issues/10031): autosummary: `sphinx.ext.autosummary.import_by_name()` now raises `ImportExceptionGroup` instead of `ImportError` when it failed to import target object. Please handle the exception if your extension uses the function to import Python object. As a workaround, you can disable the behavior via `grouped_exception=False` keyword argument until v7.0. - [#​9962](https://togithub.com/sphinx-doc/sphinx/issues/9962): texinfo: Customizing styles of emphasized text via `@definfoenclose` command was not supported because the command was deprecated since texinfo 6.8 - [#​2068](https://togithub.com/sphinx-doc/sphinx/issues/2068): :confval:`intersphinx_disabled_reftypes` has changed default value from an empty list to `['std:doc']` as avoid too surprising silent intersphinx resolutions. To migrate: either add an explicit inventory name to the references intersphinx should resolve, or explicitly set the value of this configuration variable to an empty list. - [#​10197](https://togithub.com/sphinx-doc/sphinx/issues/10197): html theme: Reduce `body_min_width` setting in basic theme to 360px - [#​9999](https://togithub.com/sphinx-doc/sphinx/issues/9999): LaTeX: separate terms from their definitions by a CR (refs: [#​9985](https://togithub.com/sphinx-doc/sphinx/issues/9985)) - [#​10062](https://togithub.com/sphinx-doc/sphinx/issues/10062): Change the default language to `'en'` if any language is not set in `conf.py` 5.0.0 final - [#​10474](https://togithub.com/sphinx-doc/sphinx/issues/10474): :confval:`language` does not accept `None` as it value. The default value of `language` becomes to `'en'` now. Patch by Adam Turner and Takeshi KOMIYA. ## Deprecated 5.0.0 b1 - [#​10028](https://togithub.com/sphinx-doc/sphinx/issues/10028): jQuery and underscore.js will no longer be automatically injected into themes from Sphinx 6.0. If you develop a theme or extension that uses the `jQuery`, `$`, or `$u` global objects, you need to update your JavaScript or use the mitigation below. To re-add jQuery and underscore.js, you will need to copy `jquery.js` and `underscore.js` from `the Sphinx repository`\_ to your `static` directory, and add the following to your `layout.html`: .. \_the Sphinx repository: https://github.com/sphinx-doc/sphinx/tree/v4.3.2/sphinx/themes/basic/static .. code-block:: html+jinja {%- block scripts %} {{ super() }} {%- endblock %} Patch by Adam Turner. - setuptools integration. The `build_sphinx` sub-command for setup.py is marked as deprecated to follow the policy of setuptools team. - The `locale` argument of `sphinx.util.i18n:babel_format_date()` becomes required - The `language` argument of `sphinx.util.i18n:format_date()` becomes required - `sphinx.builders.html.html5_ready` - `sphinx.io.read_doc()` - `sphinx.util.docutils.__version_info__` - `sphinx.util.docutils.is_html5_writer_available()` - `sphinx.writers.latex.LaTeXWriter.docclasses` ## Features added 5.0.0 b1 - [#​9075](https://togithub.com/sphinx-doc/sphinx/issues/9075): autodoc: The default value of :confval:`autodoc_typehints_format` is changed to `'smart'`. It will suppress the leading module names of typehints (ex. `io.StringIO` -> `StringIO`). - [#​8417](https://togithub.com/sphinx-doc/sphinx/issues/8417): autodoc: `:inherited-members:` option now takes multiple classes. It allows to suppress inherited members of several classes on the module at once by specifying the option to :rst:dir:`automodule` directive - [#​9792](https://togithub.com/sphinx-doc/sphinx/issues/9792): autodoc: Add new option for `autodoc_typehints_description_target` to include undocumented return values but not undocumented parameters. - [#​10285](https://togithub.com/sphinx-doc/sphinx/issues/10285): autodoc: singledispatch functions having typehints are not documented - autodoc: :confval:`autodoc_typehints_format` now also applies to attributes, data, properties, and type variable bounds. - [#​10258](https://togithub.com/sphinx-doc/sphinx/issues/10258): autosummary: Recognize a documented attribute of a module as non-imported - [#​10028](https://togithub.com/sphinx-doc/sphinx/issues/10028): Removed internal usages of JavaScript frameworks (jQuery and underscore.js) and modernised `doctools.js` and `searchtools.js` to EMCAScript 2018. Patch by Adam Turner. - [#​10302](https://togithub.com/sphinx-doc/sphinx/issues/10302): C++, add support for conditional expressions (`?:`). - [#​5157](https://togithub.com/sphinx-doc/sphinx/issues/5157), [#​10251](https://togithub.com/sphinx-doc/sphinx/issues/10251): Inline code is able to be highlighted via :rst:dir:`role` directive - [#​10337](https://togithub.com/sphinx-doc/sphinx/issues/10337): Make sphinx-build faster by caching Publisher object during build. Patch by Adam Turner. ## Bugs fixed 5.0.0 b1 - [#​10200](https://togithub.com/sphinx-doc/sphinx/issues/10200): apidoc: Duplicated submodules are shown for modules having both .pyx and .so files. Patch by Adam Turner and Takeshi KOMIYA. - [#​10279](https://togithub.com/sphinx-doc/sphinx/issues/10279): autodoc: Default values for keyword only arguments in overloaded functions are rendered as a string literal - [#​10280](https://togithub.com/sphinx-doc/sphinx/issues/10280): autodoc: :confval:`autodoc_docstring_signature` unexpectedly generates return value typehint for constructors if docstring has multiple signatures - [#​10266](https://togithub.com/sphinx-doc/sphinx/issues/10266): autodoc: :confval:`autodoc_preserve_defaults` does not work for mixture of keyword only arguments with/without defaults - [#​10310](https://togithub.com/sphinx-doc/sphinx/issues/10310): autodoc: class methods are not documented when decorated with mocked function - [#​10305](https://togithub.com/sphinx-doc/sphinx/issues/10305): autodoc: Failed to extract optional forward-ref'ed typehints correctly via :confval:`autodoc_type_aliases` - [#​10421](https://togithub.com/sphinx-doc/sphinx/issues/10421): autodoc: :confval:`autodoc_preserve_defaults` doesn't work on class methods - [#​10214](https://togithub.com/sphinx-doc/sphinx/issues/10214): html: invalid language tag was generated if :confval:`language` contains a country code (ex. zh_CN) - [#​9974](https://togithub.com/sphinx-doc/sphinx/issues/9974): html: Updated jQuery version from 3.5.1 to 3.6.0 - [#​10236](https://togithub.com/sphinx-doc/sphinx/issues/10236): html search: objects are duplicated in search result - [#​9962](https://togithub.com/sphinx-doc/sphinx/issues/9962): texinfo: Deprecation message for `@definfoenclose` command on bulding texinfo document - [#​10000](https://togithub.com/sphinx-doc/sphinx/issues/10000): LaTeX: glossary terms with common definition are rendered with too much vertical whitespace - [#​10188](https://togithub.com/sphinx-doc/sphinx/issues/10188): LaTeX: alternating multiply referred footnotes produce a `?` in pdf output - [#​10363](https://togithub.com/sphinx-doc/sphinx/issues/10363): LaTeX: make `'howto'` title page rule use `\linewidth` for compatibility with usage of a `twocolumn` class option - [#​10318](https://togithub.com/sphinx-doc/sphinx/issues/10318): `:prepend:` option of :rst:dir:`literalinclude` directive does not work with `:dedent:` option 5.0.0 final - [#​9575](https://togithub.com/sphinx-doc/sphinx/issues/9575): autodoc: The annotation of return value should not be shown when `autodoc_typehints="description"` - [#​9648](https://togithub.com/sphinx-doc/sphinx/issues/9648): autodoc: `*args` and `**kwargs` entries are duplicated when `autodoc_typehints="description"` - [#​8180](https://togithub.com/sphinx-doc/sphinx/issues/8180): autodoc: Docstring metadata ignored for attributes - [#​10443](https://togithub.com/sphinx-doc/sphinx/issues/10443): epub: EPUB builder can't detect the mimetype of .webp file - [#​10104](https://togithub.com/sphinx-doc/sphinx/issues/10104): gettext: Duplicated locations are shown if 3rd party extension does not provide correct information - [#​10456](https://togithub.com/sphinx-doc/sphinx/issues/10456): py domain: `:meta:` fields are displayed if docstring contains two or more meta-field - [#​9096](https://togithub.com/sphinx-doc/sphinx/issues/9096): sphinx-build: the value of progress bar for paralle build is wrong - [#​10110](https://togithub.com/sphinx-doc/sphinx/issues/10110): sphinx-build: exit code is not changed when error is raised on builder-finished event

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Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

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