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 v6 #314

Closed renovate[bot] closed 1 year ago

renovate[bot] commented 1 year ago

Mend Renovate

This PR contains the following updates:

Package Change Age Adoption Passing Confidence
sphinx (changelog) ==5.0.2 -> ==6.1.3 age adoption passing confidence

Release Notes

sphinx-doc/sphinx ### [`v6.1.3`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-613-released-Jan-10-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v6.1.2...v6.1.3) \===================================== ## Bugs fixed - [#​11116](https://togithub.com/sphinx-doc/sphinx/issues/11116): Reverted to previous Sphinx 5 node copying method - [#​11117](https://togithub.com/sphinx-doc/sphinx/issues/11117): Reverted changes to parallel image processing from Sphinx 6.1.0 - [#​11119](https://togithub.com/sphinx-doc/sphinx/issues/11119): Supress `ValueError` in the `linkcheck` builder ### [`v6.1.2`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-612-released-Jan-07-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v6.1.1...v6.1.2) \===================================== ## Bugs fixed - [#​11101](https://togithub.com/sphinx-doc/sphinx/issues/11101): LaTeX: `div.topic_padding` key of sphinxsetup documented at 5.1.0 was implemented with name `topic_padding` - [#​11099](https://togithub.com/sphinx-doc/sphinx/issues/11099): LaTeX: `shadowrule` key of sphinxsetup causes PDF build to crash since Sphinx 5.1.0 - [#​11096](https://togithub.com/sphinx-doc/sphinx/issues/11096): LaTeX: `shadowsize` key of sphinxsetup causes PDF build to crash since Sphinx 5.1.0 - [#​11095](https://togithub.com/sphinx-doc/sphinx/issues/11095): LaTeX: shadow of :dudir:`topic` and contents\_ boxes not in page margin since Sphinx 5.1.0 .. \_contents: https://docutils.sourceforge.io/docs/ref/rst/directives.html#table-of-contents - [#​11100](https://togithub.com/sphinx-doc/sphinx/issues/11100): Fix copying images when running under parallel mode. ### [`v6.1.1`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-611-released-Jan-05-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v6.1.0...v6.1.1) \===================================== ## Bugs fixed - [#​11091](https://togithub.com/sphinx-doc/sphinx/issues/11091): Fix `util.nodes.apply_source_workaround` for `literal_block` nodes with no source information in the node or the node's parents. ### [`v6.1.0`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-610-released-Jan-05-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v6.0.1...v6.1.0) \===================================== ## Dependencies - Adopted the `Ruff`\_ code linter. .. \_Ruff: https://github.com/charliermarsh/ruff ## Incompatible changes - [#​10979](https://togithub.com/sphinx-doc/sphinx/issues/10979): gettext: Removed support for pluralisation in `get_translation`. This was unused and complicated other changes to `sphinx.locale`. ## Deprecated - `sphinx.util` functions: - Renamed `sphinx.util.typing.stringify()` to `sphinx.util.typing.stringify_annotation()` - Moved `sphinx.util.xmlname_checker()` to `sphinx.builders.epub3._XML_NAME_PATTERN` Moved to `sphinx.util.display`: - `sphinx.util.status_iterator` - `sphinx.util.display_chunk` - `sphinx.util.SkipProgressMessage` - `sphinx.util.progress_message` Moved to `sphinx.util.http_date`: - `sphinx.util.epoch_to_rfc1123` - `sphinx.util.rfc1123_to_epoch` Moved to `sphinx.util.exceptions`: - `sphinx.util.save_traceback` - `sphinx.util.format_exception_cut_frames` ## Features added - Cache doctrees in the build environment during the writing phase. - Make all writing phase tasks support parallel execution. - [#​11072](https://togithub.com/sphinx-doc/sphinx/issues/11072): Use PEP 604 (`X | Y`) display conventions for `typing.Optional` and `typing.Optional` types within the Python domain and autodoc. - [#​10700](https://togithub.com/sphinx-doc/sphinx/issues/10700): autodoc: Document `typing.NewType()` types as classes rather than 'data'. - Cache doctrees between the reading and writing phases. ## Bugs fixed - [#​10962](https://togithub.com/sphinx-doc/sphinx/issues/10962): HTML: Fix the multi-word key name lookup table. - Fixed support for Python 3.12 alpha 3 (changes in the `enum` module). - [#​11069](https://togithub.com/sphinx-doc/sphinx/issues/11069): HTML Theme: Removed outdated "shortcut" link relation keyword. - [#​10952](https://togithub.com/sphinx-doc/sphinx/issues/10952): Properly terminate parallel processes on programme interuption. - [#​10988](https://togithub.com/sphinx-doc/sphinx/issues/10988): Speed up `TocTree.resolve()` through more efficient copying. - [#​6744](https://togithub.com/sphinx-doc/sphinx/issues/6744): LaTeX: support for seealso directive should be via an environment to allow styling. - [#​11074](https://togithub.com/sphinx-doc/sphinx/issues/11074): LaTeX: Can't change sphinxnote to use sphinxheavybox starting with 5.1.0 ### [`v6.0.1`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-601-released-Jan-05-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v6.0.0...v6.0.1) \===================================== ## Dependencies - Require Pygments 2.13 or later. ## Bugs fixed - [#​10944](https://togithub.com/sphinx-doc/sphinx/issues/10944): imgmath: Fix resolving image paths for files in nested folders. ### [`v6.0.0`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-600-released-Dec-29-2022) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v5.3.0...v6.0.0) \===================================== ## Dependencies - [#​10468](https://togithub.com/sphinx-doc/sphinx/issues/10468): Drop Python 3.6 support - [#​10470](https://togithub.com/sphinx-doc/sphinx/issues/10470): Drop Python 3.7, Docutils 0.14, Docutils 0.15, Docutils 0.16, and Docutils 0.17 support. Patch by Adam Turner ## Incompatible changes - [#​7405](https://togithub.com/sphinx-doc/sphinx/issues/7405): Removed the jQuery and underscore.js JavaScript frameworks. These frameworks are 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 to modern standards, or use the mitigation below. The first option is to use the sphinxcontrib.jquery\_ extension, which has been developed by the Sphinx team and contributors. To use this, add `sphinxcontrib.jquery` to the `extensions` list in `conf.py`, or call `app.setup_extension("sphinxcontrib.jquery")` if you develop a Sphinx theme or extension. The second option is to manually ensure that the frameworks are present. 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`: .. code-block:: html+jinja {%- block scripts %} {{ super() }} {%- endblock %} .. \_sphinxcontrib.jquery: https://github.com/sphinx-contrib/jquery/ Patch by Adam Turner. - [#​10471](https://togithub.com/sphinx-doc/sphinx/issues/10471), [#​10565](https://togithub.com/sphinx-doc/sphinx/issues/10565): Removed deprecated APIs scheduled for removal in Sphinx 6.0. See :ref:`dev-deprecated-apis` for details. Patch by Adam Turner. - [#​10901](https://togithub.com/sphinx-doc/sphinx/issues/10901): C Domain: Remove support for parsing pre-v3 style type directives and roles. Also remove associated configuration variables `c_allow_pre_v3` and `c_warn_on_allowed_pre_v3`. Patch by Adam Turner. ## Features added - [#​10924](https://togithub.com/sphinx-doc/sphinx/issues/10924): LaTeX: adopt better looking defaults for tables and code-blocks. See :confval:`latex_table_style` and the `pre_border-radius` and `pre_background-TeXcolor` :ref:`additionalcss` for the former defaults and how to re-enact them if desired. ## Bugs fixed - [#​10984](https://togithub.com/sphinx-doc/sphinx/issues/10984): LaTeX: Document :confval:`latex_additional_files` behavior for files with `.tex` extension. ### [`v5.3.0`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-530-released-Oct-16-2022) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v5.2.3...v5.3.0) \===================================== - [#​10759](https://togithub.com/sphinx-doc/sphinx/issues/10759): LaTeX: add :confval:`latex_table_style` and support the `'booktabs'`, `'borderless'`, and `'colorrows'` styles. (thanks to Stefan Wiehler for initial pull requests [#​6666](https://togithub.com/sphinx-doc/sphinx/issues/6666), [#​6671](https://togithub.com/sphinx-doc/sphinx/issues/6671)) - [#​10840](https://togithub.com/sphinx-doc/sphinx/issues/10840): One can cross-reference including an option value like `` :option:`--module=foobar```, ``:option:`--module[=foobar]``` or ``:option:`--module foobar\`\`\`. Patch by Martin Liska. - [#​10881](https://togithub.com/sphinx-doc/sphinx/issues/10881): autosectionlabel: Record the generated section label to the debug log. - [#​10268](https://togithub.com/sphinx-doc/sphinx/issues/10268): Correctly URI-escape image filenames. - [#​10887](https://togithub.com/sphinx-doc/sphinx/issues/10887): domains: Allow sections in all the content of all object description directives (e.g. :rst:dir:`py:function`). Patch by Adam Turner ### [`v5.2.3`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-523-released-Sep-30-2022) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v5.2.2...v5.2.3) \===================================== - [#​10878](https://togithub.com/sphinx-doc/sphinx/issues/10878): Fix base64 image embedding in `sphinx.ext.imgmath` - [#​10886](https://togithub.com/sphinx-doc/sphinx/issues/10886): Add `:nocontentsentry:` flag and global domain table of contents entry control option. Patch by Adam Turner ### [`v5.2.2`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-522-released-Sep-27-2022) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v5.2.1...v5.2.2) \===================================== - [#​10872](https://togithub.com/sphinx-doc/sphinx/issues/10872): Restore link targets for autodoc modules to the top of content. Patch by Dominic Davis-Foster. ### [`v5.2.1`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-521-released-Sep-25-2022) \===================================== ## Bugs fixed - [#​10861](https://togithub.com/sphinx-doc/sphinx/issues/10861): Always normalise the `pycon3` lexer to `pycon`. - Fix using `sphinx.ext.autosummary` with modules containing titles in the module-level docstring. ### [`v5.2.0.post0`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-520post0-released-Sep-24-2022) \=========================================== - Recreated source tarballs for Debian maintainers. ### [`v5.2.0`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-520post0-released-Sep-24-2022) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v5.1.1...v5.2.0) \=========================================== - Recreated source tarballs for Debian maintainers. ### [`v5.1.1`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-511-released-Jul-26-2022) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v5.1.0...v5.1.1) \===================================== ## Bugs fixed - [#​10701](https://togithub.com/sphinx-doc/sphinx/issues/10701): Fix ValueError in the new `deque` based `sphinx.ext.napolean` iterator implementation. - [#​10702](https://togithub.com/sphinx-doc/sphinx/issues/10702): Restore compatability with third-party builders. ### [`v5.1.0`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-510-released-Jul-24-2022) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v5.0.2...v5.1.0) \===================================== ## Dependencies - [#​10656](https://togithub.com/sphinx-doc/sphinx/issues/10656): Support `Docutils 0.19`\_. Patch by Adam Turner. .. \_Docutils 0.19: https://docutils.sourceforge.io/RELEASE-NOTES.html#release-0-19-2022-07-05 ## Deprecated - [#​10467](https://togithub.com/sphinx-doc/sphinx/issues/10467): Deprecated `sphinx.util.stemmer` in favour of `snowballstemmer`. Patch by Adam Turner. - [#​9856](https://togithub.com/sphinx-doc/sphinx/issues/9856): Deprecated `sphinx.ext.napoleon.iterators`. ## Features added - [#​10444](https://togithub.com/sphinx-doc/sphinx/issues/10444): html theme: Allow specifying multiple CSS files through the `stylesheet` setting in `theme.conf` or by setting `html_style` to an iterable of strings. - [#​10366](https://togithub.com/sphinx-doc/sphinx/issues/10366): std domain: Add support for emphasising placeholders in :rst:dir:`option` directives through a new :confval:`option_emphasise_placeholders` configuration option. - [#​10439](https://togithub.com/sphinx-doc/sphinx/issues/10439): std domain: Use the repr of some variables when displaying warnings, making whitespace issues easier to identify. - [#​10571](https://togithub.com/sphinx-doc/sphinx/issues/10571): quickstart: Reduce content in the generated `conf.py` file. Patch by Pradyun Gedam. - [#​10648](https://togithub.com/sphinx-doc/sphinx/issues/10648): LaTeX: CSS-named-alike additional :ref:`'sphinxsetup' ` keys allow to configure four separate border-widths, four paddings, four corner radii, a shadow (possibly inset), colours for border, background, shadow for each of the code-block, topic, attention, caution, danger, error and warning directives. - [#​10655](https://togithub.com/sphinx-doc/sphinx/issues/10655): LaTeX: Explain non-standard encoding in LatinRules.xdy - [#​10599](https://togithub.com/sphinx-doc/sphinx/issues/10599): HTML Theme: Wrap consecutive footnotes in an `

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