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 v7 #331

Closed renovate[bot] closed 10 months ago

renovate[bot] commented 1 year ago

Mend Renovate

This PR contains the following updates:

Package Change Age Adoption Passing Confidence
sphinx (changelog) ==6.2.1 -> ==7.2.5 age adoption passing confidence

Release Notes

sphinx-doc/sphinx (sphinx) ### [`v7.2.5`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-725-released-Aug-30-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v7.2.4...v7.2.5) \===================================== ## Bugs fixed - [#​11645](https://togithub.com/sphinx-doc/sphinx/issues/11645): Fix a regression preventing autodoc from importing modules within packages that make use of `if typing.TYPE_CHECKING:` to guard circular imports needed by type checkers. Patch by Matt Wozniski. - [#​11634](https://togithub.com/sphinx-doc/sphinx/issues/11634): Fixed inheritance diagram relative link resolution for sibling files in a subdirectory. Patch by Albert Shih. - [#​11659](https://togithub.com/sphinx-doc/sphinx/issues/11659): Allow `?config=...` in :confval:`mathjax_path`. - [#​11654](https://togithub.com/sphinx-doc/sphinx/issues/11654): autodoc: Fail with a more descriptive error message when an object claims to be an instance of `type`, but is not a class. Patch by James Braza. - 11620: Cease emitting :event:`source-read` events for files read via the :dudir:`include` directive. - 11620: Add a new :event:`include-read` for observing and transforming the content of included files via the :dudir:`include` directive. - [#​11627](https://togithub.com/sphinx-doc/sphinx/issues/11627): Restore support for copyright lines of the form `YYYY` when `SOURCE_DATE_EPOCH` is set. ### [`v7.2.4`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-724-released-Aug-28-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v7.2.3...v7.2.4) \===================================== ## Bugs fixed - [#​11618](https://togithub.com/sphinx-doc/sphinx/issues/11618): Fix a regression in the MoveModuleTargets transform, introduced in [#​10478](https://togithub.com/sphinx-doc/sphinx/issues/10478) ([#​9662](https://togithub.com/sphinx-doc/sphinx/issues/9662)). - [#​11649](https://togithub.com/sphinx-doc/sphinx/issues/11649): linkcheck: Resolve hanging tests for timezones west of London and incorrect conversion from UTC to offsets from the UNIX epoch. Patch by Dmitry Shachnev and Adam Turner. ### [`v7.2.3`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-723-released-Aug-23-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v7.2.2...v7.2.3) \===================================== ## Dependencies - [#​11576](https://togithub.com/sphinx-doc/sphinx/issues/11576): Require sphinxcontrib-serializinghtml 1.1.9. ## Bugs fixed - Fix regression in `autodoc.Documenter.parse_name()`. - Fix regression in JSON serialisation. - [#​11543](https://togithub.com/sphinx-doc/sphinx/issues/11543): autodoc: Support positional-only parameters in `classmethod` methods when `autodoc_preserve_defaults` is `True`. - Restore support string methods on path objects. This is deprecated and will be removed in Sphinx 8. Use :py:func:`os.fspath` to convert :py:class:`~pathlib.Path` objects to strings, or :py:class:`~pathlib.Path`'s methods to work with path objects. ### [`v7.2.2`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-722-released-Aug-17-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v7.2.1...v7.2.2) \===================================== ## Bugs fixed - Fix the signature of the `StateMachine.insert_input()` patch, for when calling with keyword arguments. - Fixed membership testing (`in`) for the :py:class:`str` interface of the asset classes (`_CascadingStyleSheet` and `_JavaScript`), which several extensions relied upon. - Fixed a type error in `SingleFileHTMLBuilder._get_local_toctree`, `includehidden` may be passed as a string or a boolean. - Fix `:noindex:` for `PyModule` and `JSModule`. ### [`v7.2.1`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-721-released-Aug-17-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v7.2.0...v7.2.1) \===================================== ## Bugs fixed - Restored the the :py:class:`str` interface of the asset classes (`_CascadingStyleSheet` and `_JavaScript`), which several extensions relied upon. This will be removed in Sphinx 9. - Restored calls to `Builder.add_{css,js}_file()`, which several extensions relied upon. - Restored the private API `TocTree.get_toctree_ancestors()`, which several extensions relied upon. ### [`v7.2.0`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-720-released-Aug-17-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v7.1.2...v7.2.0) \===================================== ## Dependencies - [#​11511](https://togithub.com/sphinx-doc/sphinx/issues/11511): Drop Python 3.8 support. - [#​11576](https://togithub.com/sphinx-doc/sphinx/issues/11576): Require Pygments 2.14 or later. ## Deprecated - [#​11512](https://togithub.com/sphinx-doc/sphinx/issues/11512): Deprecate `sphinx.util.md5` and `sphinx.util.sha1`. Use `hashlib` instead. - [#​11526](https://togithub.com/sphinx-doc/sphinx/issues/11526): Deprecate `sphinx.testing.path`. Use `os.path` or `pathlib` instead. - [#​11528](https://togithub.com/sphinx-doc/sphinx/issues/11528): Deprecate `sphinx.util.split_index_msg` and `sphinx.util.split_into`. Use `sphinx.util.index_entries.split_index_msg` instead. - Deprecate `sphinx.builders.html.Stylesheet` and `sphinx.builders.html.Javascript`. Use `sphinx.application.Sphinx.add_css_file()` and `sphinx.application.Sphinx.add_js_file()` instead. - [#​11582](https://togithub.com/sphinx-doc/sphinx/issues/11582): Deprecate `sphinx.builders.html.StandaloneHTMLBuilder.css_files` and `sphinx.builders.html.StandaloneHTMLBuilder.script_files`. Use `sphinx.application.Sphinx.add_css_file()` and `sphinx.application.Sphinx.add_js_file()` instead. - [#​11459](https://togithub.com/sphinx-doc/sphinx/issues/11459): Deprecate `sphinx.ext.autodoc.preserve_defaults.get_function_def()`. Patch by Bénédikt Tran. ## Features added - [#​11526](https://togithub.com/sphinx-doc/sphinx/issues/11526): Support `os.PathLike` types and `pathlib.Path` objects in many more places. - [#​5474](https://togithub.com/sphinx-doc/sphinx/issues/5474): coverage: Print summary statistics tables. Patch by Jorge Leitao. - [#​6319](https://togithub.com/sphinx-doc/sphinx/issues/6319): viewcode: Add :confval:`viewcode_line_numbers` to control whether line numbers are added to rendered source code. Patch by Ben Krikler. - [#​9662](https://togithub.com/sphinx-doc/sphinx/issues/9662): Add the `:no-typesetting:` option to suppress textual output and only create a linkable anchor. Patch by Latosha Maltba. - [#​11221](https://togithub.com/sphinx-doc/sphinx/issues/11221): C++: Support domain objects in the table of contents. Patch by Rouslan Korneychuk. - [#​10938](https://togithub.com/sphinx-doc/sphinx/issues/10938): doctest: Add :confval:`doctest_show_successes` option. Patch by Trey Hunner. - [#​11533](https://togithub.com/sphinx-doc/sphinx/issues/11533): Add `:no-index:`, `:no-index-entry:`, and `:no-contents-entry:`. - [#​11572](https://togithub.com/sphinx-doc/sphinx/issues/11572): Improve `debug` logging of reasons why files are detected as out of date. Patch by Eric Larson. - [#​10678](https://togithub.com/sphinx-doc/sphinx/issues/10678): Emit :event:`source-read` events for files read via the :dudir:`include` directive. Patch by Halldor Fannar. - [#​11570](https://togithub.com/sphinx-doc/sphinx/issues/11570): Use short names when using :pep:`585` built-in generics. Patch by Riccardo Mori. - [#​11300](https://togithub.com/sphinx-doc/sphinx/issues/11300): Improve `SigElementFallbackTransform` fallback logic and signature text elements nodes. See :doc:`the documentation ` for more details. Patch by Bénédikt Tran. - Allow running Sphinx with `python -m sphinx build ...`. ## Bugs fixed - [#​11077](https://togithub.com/sphinx-doc/sphinx/issues/11077): graphviz: Fix relative links from within the graph. Patch by Ralf Grubenmann. - [#​11529](https://togithub.com/sphinx-doc/sphinx/issues/11529): Line Block in LaTeX builder outputs spurious empty token. Patch by Adrian Vollmer. - [#​11196](https://togithub.com/sphinx-doc/sphinx/issues/11196): autosummary: Summary line extraction failed with "e.g." - [#​10614](https://togithub.com/sphinx-doc/sphinx/issues/10614): Fixed a number of bugs in inheritance diagrams that resulted in missing or broken links. Patch by Albert Shih. - [#​9428](https://togithub.com/sphinx-doc/sphinx/issues/9428): Exclude substitution definitions when running the `gettext` builder. Patch by Alvin Wong. - [#​10795](https://togithub.com/sphinx-doc/sphinx/issues/10795): Raise a descriptive error if `graphviz_dot` is falsy. - [#​11546](https://togithub.com/sphinx-doc/sphinx/issues/11546): Translated nodes identical to their original text are now marked with the `translated=True` attribute. - [#​10049](https://togithub.com/sphinx-doc/sphinx/issues/10049): html: Change "Permalink" to "Link" for title text in link anchors. - [#​4225](https://togithub.com/sphinx-doc/sphinx/issues/4225): Relax Pygments parsing on lexing failures. - [#​11246](https://togithub.com/sphinx-doc/sphinx/issues/11246): Allow inline links in the first line of a docstring and one-line type comments `#: :meta ...:` when using :mod:`sphinx.ext.napoleon`. Patch by Bénédikt Tran. - [#​10930](https://togithub.com/sphinx-doc/sphinx/issues/10930): Highlight all search terms on the search results page. Patch by Dmitry Shachnev. - [#​11473](https://togithub.com/sphinx-doc/sphinx/issues/11473): Type annotations containing :py:data:`~typing.Literal` enumeration values now render correctly. Patch by Bénédikt Tran. - [#​11591](https://togithub.com/sphinx-doc/sphinx/issues/11591): Fix support for C coverage in `sphinx.ext.coverage` extension. Patch by Stephen Finucane. - [#​11594](https://togithub.com/sphinx-doc/sphinx/issues/11594): HTML Theme: Enhancements to horizontal scrolling on smaller devices in the `agogo` theme. Patch by Lukas Engelter. - [#​11459](https://togithub.com/sphinx-doc/sphinx/issues/11459): Fix support for async and lambda functions in `sphinx.ext.autodoc.preserve_defaults`. Patch by Bénédikt Tran. ## Testing - [#​11577](https://togithub.com/sphinx-doc/sphinx/issues/11577): pytest: Fail tests on "XPASS". - [#​11577](https://togithub.com/sphinx-doc/sphinx/issues/11577): pytest: Use "importlib" import mode. - [#​11577](https://togithub.com/sphinx-doc/sphinx/issues/11577): pytest: Set PYTHONWARNINGS=error. - [#​11577](https://togithub.com/sphinx-doc/sphinx/issues/11577): pytest: Set strict config and strict markers. ### [`v7.1.2`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-712-released-Aug-02-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v7.1.1...v7.1.2) \===================================== ## Bugs fixed - [#​11542](https://togithub.com/sphinx-doc/sphinx/issues/11542): linkcheck: Properly respect :confval:`linkcheck_anchors` and do not spuriously report failures to validate anchors. Patch by James Addison. ### [`v7.1.1`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-711-released-Jul-27-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v7.1.0...v7.1.1) \===================================== ## Bugs fixed - [#​11514](https://togithub.com/sphinx-doc/sphinx/issues/11514): Fix `SOURCE_DATE_EPOCH` in multi-line copyright footer. Patch by Bénédikt Tran. ### [`v7.1.0`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-710-released-Jul-24-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v7.0.1...v7.1.0) \===================================== ## Incompatible changes - Releases are no longer signed, given the `change in PyPI policy`\_. .. \_change in PyPI policy: https://blog.pypi.org/posts/2023-05-23-removing-pgp/ ## Deprecated - [#​11412](https://togithub.com/sphinx-doc/sphinx/issues/11412): Emit warnings on using a deprecated Python-specific index entry type (namely, `module`, `keyword`, `operator`, `object`, `exception`, `statement`, and `builtin`) in the :rst:dir:`index` directive, and set the removal version to Sphinx 9. Patch by Adam Turner. ## Features added - [#​11415](https://togithub.com/sphinx-doc/sphinx/issues/11415): Add a checksum to JavaScript and CSS asset URIs included within generated HTML, using the CRC32 algorithm. - :meth:`~sphinx.application.Sphinx.require_sphinx` now allows the version requirement to be specified as `(major, minor)`. - [#​11011](https://togithub.com/sphinx-doc/sphinx/issues/11011): Allow configuring a line-length limit for object signatures, via :confval:`maximum_signature_line_length` and the domain-specific variants. If the length of the signature (in characters) is greater than the configured limit, each parameter in the signature will be split to its own logical line. This behaviour may also be controlled by options on object description directives, for example :rst:dir:`py:function:single-line-parameter-list`. Patch by Thomas Louf, Adam Turner, and Jean-François B. - [#​10983](https://togithub.com/sphinx-doc/sphinx/issues/10983): Support for multiline copyright statements in the footer block. Patch by Stefanie Molin - `sphinx.util.display.status_iterator` now clears the current line with ANSI control codes, rather than overprinting with space characters. - [#​11431](https://togithub.com/sphinx-doc/sphinx/issues/11431): linkcheck: Treat SSL failures as broken links. Patch by James Addison. - [#​11157](https://togithub.com/sphinx-doc/sphinx/issues/11157): Keep the `translated` attribute on translated nodes. - [#​11451](https://togithub.com/sphinx-doc/sphinx/issues/11451): Improve the traceback displayed when using :option:`sphinx-build -T` in parallel builds. Patch by Bénédikt Tran - [#​11324](https://togithub.com/sphinx-doc/sphinx/issues/11324): linkcheck: Use session-basd HTTP requests. - [#​11438](https://togithub.com/sphinx-doc/sphinx/issues/11438): Add support for the :rst:dir:`py:class` and :rst:dir:`py:function` directives for PEP 695 (generic classes and functions declarations) and PEP 696 (default type parameters). Multi-line support ([#​11011](https://togithub.com/sphinx-doc/sphinx/issues/11011)) is enabled for type parameters list and can be locally controlled on object description directives, e.g., :rst:dir:`py:function:single-line-type-parameter-list`. Patch by Bénédikt Tran. - [#​11484](https://togithub.com/sphinx-doc/sphinx/issues/11484): linkcheck: Allow HTML anchors to be ignored on a per-URL basis via :confval:`linkcheck_anchors_ignore_for_url` while still checking the validity of the page itself. Patch by Bénédikt Tran - [#​1246](https://togithub.com/sphinx-doc/sphinx/issues/1246): Add translation progress statistics and inspection support, via a new substitution (`|translation progress|`) and a new configuration variable (:confval:`translation_progress_classes`). These enable determining the percentage of translated elements within a document, and the remaining translated and untranslated elements. ## Bugs fixed - Restored the `footnote-reference` class that has been removed in the latest (unreleased) version of Docutils. - [#​11486](https://togithub.com/sphinx-doc/sphinx/issues/11486): Use :rfc:`8081` font file MIME types in the EPUB builder. Using the correct MIME type will prevent warnings from `epubcheck` and will generate a valid EPUB. - [#​11435](https://togithub.com/sphinx-doc/sphinx/issues/11435): Use microsecond-resolution timestamps for outdated file detection in `BuildEnvironment.get_outdated_files`. - [#​11437](https://togithub.com/sphinx-doc/sphinx/issues/11437): Top-level headings starting with a reStructuredText role now render properly when :confval:`rst_prolog` is set. Previously, a file starting with the below would have improperly rendered due to where the prologue text was inserted into the document. .. code:: rst # :mod:`lobster` -- The lobster module ... Patch by Bénédikt Tran. - [#​11337](https://togithub.com/sphinx-doc/sphinx/issues/11337): Fix a `MemoryError` in `sphinx.ext.intersphinx` when using `None` or `typing.*` as inline type references. Patch by Bénédikt Tran (picnixz) ## Testing - [#​11345](https://togithub.com/sphinx-doc/sphinx/issues/11345): Always delete `docutils.conf` in test directories when running `SphinxTestApp.cleanup()`. ### [`v7.0.1`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-701-released-May-12-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v7.0.0...v7.0.1) \===================================== ## Dependencies - [#​11411](https://togithub.com/sphinx-doc/sphinx/issues/11411): Support `Docutils 0.20`\_. Patch by Adam Turner. .. \_Docutils 0.20: https://docutils.sourceforge.io/RELEASE-NOTES.html#release-0-20-2023-05-04 ## Bugs fixed - [#​11418](https://togithub.com/sphinx-doc/sphinx/issues/11418): Clean up remaining references to `sphinx.setup_command` following the removal of support for setuptools. Patch by Willem Mulder. ### [`v7.0.0`](https://togithub.com/sphinx-doc/sphinx/blob/HEAD/CHANGES#Release-700-released-Apr-29-2023) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v6.2.1...v7.0.0) \===================================== ## Incompatible changes - [#​11359](https://togithub.com/sphinx-doc/sphinx/issues/11359): Remove long-deprecated aliases for `MecabSplitter` and `DefaultSplitter` in `sphinx.search.ja`. - [#​11360](https://togithub.com/sphinx-doc/sphinx/issues/11360): Remove deprecated `make_old_id` functions in domain object description classes. - [#​11363](https://togithub.com/sphinx-doc/sphinx/issues/11363): Remove the Setuptools integration (`build_sphinx` hook in `setup.py`). - [#​11364](https://togithub.com/sphinx-doc/sphinx/issues/11364): Remove deprecated `sphinx.ext.napoleon.iterators` module. - [#​11365](https://togithub.com/sphinx-doc/sphinx/issues/11365): Remove support for the `jsdump` format in `sphinx.search`. - [#​11366](https://togithub.com/sphinx-doc/sphinx/issues/11366): Make `locale` a required argument to `sphinx.util.i18n.format_date()`. - [#​11370](https://togithub.com/sphinx-doc/sphinx/issues/11370): Remove deprecated `sphinx.util.stemmer` module. - [#​11371](https://togithub.com/sphinx-doc/sphinx/issues/11371): Remove deprecated `sphinx.pycode.ast.parse()` function. - [#​11372](https://togithub.com/sphinx-doc/sphinx/issues/11372): Remove deprecated `sphinx.io.read_doc()` function. - [#​11373](https://togithub.com/sphinx-doc/sphinx/issues/11373): Removed deprecated `sphinx.util.get_matching_files()` function. - [#​11378](https://togithub.com/sphinx-doc/sphinx/issues/11378): Remove deprecated `sphinx.util.docutils.is_html5_writer_available()` function. - [#​11379](https://togithub.com/sphinx-doc/sphinx/issues/11379): Make the `env` argument to `Builder` subclasses required. - [#​11380](https://togithub.com/sphinx-doc/sphinx/issues/11380): autosummary: Always emit grouped import exceptions. - [#​11381](https://togithub.com/sphinx-doc/sphinx/issues/11381): Remove deprecated `style` key for HTML templates. - [#​11382](https://togithub.com/sphinx-doc/sphinx/issues/11382): Remove deprecated `sphinx.writers.latex.LaTeXTranslator.docclasses` attribute. - [#​11383](https://togithub.com/sphinx-doc/sphinx/issues/11383): Remove deprecated `sphinx.builders.html.html5_ready` and `sphinx.builders.html.HTMLTranslator` attributes. - [#​11385](https://togithub.com/sphinx-doc/sphinx/issues/11385): Remove support for HTML 4 output.

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