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 v3.1.2 #245

Closed renovate[bot] closed 3 years ago

renovate[bot] commented 4 years ago

This PR contains the following updates:

Package Update Change
sphinx (source) minor ==3.0.3 -> ==3.1.2

Release Notes

sphinx-doc/sphinx ### [`v3.1.2`](https://togithub.com/sphinx-doc/sphinx/blob/master/CHANGES#Release-312-released-Jul-05-2020) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v3.1.1...v3.1.2) ===================================== ## Incompatible changes - [#​7650](https://togithub.com/sphinx-doc/sphinx/issues/7650): autodoc: the signature of base function will be shown for decorated functions, not a signature of decorator ## Bugs fixed - [#​7844](https://togithub.com/sphinx-doc/sphinx/issues/7844): autodoc: Failed to detect module when relative module name given - [#​7856](https://togithub.com/sphinx-doc/sphinx/issues/7856): autodoc: AttributeError is raised when non-class object is given to the autoclass directive - [#​7850](https://togithub.com/sphinx-doc/sphinx/issues/7850): autodoc: KeyError is raised for invalid mark up when autodoc_typehints is 'description' - [#​7812](https://togithub.com/sphinx-doc/sphinx/issues/7812): autodoc: crashed if the target name matches to both an attribute and module that are same name - [#​7650](https://togithub.com/sphinx-doc/sphinx/issues/7650): autodoc: function signature becomes `(*args, **kwargs)` if the function is decorated by generic decorator - [#​7812](https://togithub.com/sphinx-doc/sphinx/issues/7812): autosummary: generates broken stub files if the target code contains an attribute and module that are same name - [#​7806](https://togithub.com/sphinx-doc/sphinx/issues/7806): viewcode: Failed to resolve viewcode references on 3rd party builders - [#​7838](https://togithub.com/sphinx-doc/sphinx/issues/7838): html theme: List items have extra vertical space - [#​7878](https://togithub.com/sphinx-doc/sphinx/issues/7878): html theme: Undesired interaction between "overflow" and "float" ### [`v3.1.1`](https://togithub.com/sphinx-doc/sphinx/blob/master/CHANGES#Release-311-released-Jun-14-2020) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v3.1.0...v3.1.1) ===================================== ## Incompatible changes - [#​7808](https://togithub.com/sphinx-doc/sphinx/issues/7808): napoleon: a type for attribute are represented as typed field ## Features added - [#​7807](https://togithub.com/sphinx-doc/sphinx/issues/7807): autodoc: Show detailed warning when type_comment is mismatched with its signature ## Bugs fixed - [#​7808](https://togithub.com/sphinx-doc/sphinx/issues/7808): autodoc: Warnings raised on variable and attribute type annotations - [#​7802](https://togithub.com/sphinx-doc/sphinx/issues/7802): autodoc: EOFError is raised on parallel build - [#​7821](https://togithub.com/sphinx-doc/sphinx/issues/7821): autodoc: TypeError is raised for overloaded C-ext function - [#​7805](https://togithub.com/sphinx-doc/sphinx/issues/7805): autodoc: an object which descriptors returns is unexpectedly documented - [#​7807](https://togithub.com/sphinx-doc/sphinx/issues/7807): autodoc: wrong signature is shown for the function using contextmanager - [#​7812](https://togithub.com/sphinx-doc/sphinx/issues/7812): autosummary: generates broken stub files if the target code contains an attribute and module that are same name - [#​7808](https://togithub.com/sphinx-doc/sphinx/issues/7808): napoleon: Warnings raised on variable and attribute type annotations - [#​7811](https://togithub.com/sphinx-doc/sphinx/issues/7811): sphinx.util.inspect causes circular import problem ### [`v3.1.0`](https://togithub.com/sphinx-doc/sphinx/blob/master/CHANGES#Release-310-released-Jun-08-2020) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v3.0.4...v3.1.0) ===================================== ## Dependencies - [#​7746](https://togithub.com/sphinx-doc/sphinx/issues/7746): mathjax: Update to 2.7.5 ## Incompatible changes - [#​7477](https://togithub.com/sphinx-doc/sphinx/issues/7477): imgconverter: Invoke "magick convert" command by default on Windows ## Deprecated - The first argument for sphinx.ext.autosummary.generate.AutosummaryRenderer has been changed to Sphinx object - `sphinx.ext.autosummary.generate.AutosummaryRenderer` takes an object type as an argument - The `ignore` argument of `sphinx.ext.autodoc.Documenter.get_doc()` - The `template_dir` argument of `sphinx.ext.autosummary.generate. AutosummaryRenderer` - The `module` argument of `sphinx.ext.autosummary.generate. find_autosummary_in_docstring()` - The `builder` argument of `sphinx.ext.autosummary.generate. generate_autosummary_docs()` - The `template_dir` argument of `sphinx.ext.autosummary.generate. generate_autosummary_docs()` - The `ignore` argument of `sphinx.util.docstring.prepare_docstring()` - `sphinx.ext.autosummary.generate.AutosummaryRenderer.exists()` - `sphinx.util.rpartition()` ## Features added - LaTeX: Make the `toplevel_sectioning` setting optional in LaTeX theme - LaTeX: Allow to override papersize and pointsize from LaTeX themes - LaTeX: Add :confval:`latex_theme_options` to override theme options - [#​7410](https://togithub.com/sphinx-doc/sphinx/issues/7410): Allow to suppress "circular toctree references detected" warnings using :confval:`suppress_warnings` - C, added scope control directives, :rst:dir:`c:namespace`, :rst:dir:`c:namespace-push`, and :rst:dir:`c:namespace-pop`. - [#​2044](https://togithub.com/sphinx-doc/sphinx/issues/2044): autodoc: Suppress default value for instance attributes - [#​7473](https://togithub.com/sphinx-doc/sphinx/issues/7473): autodoc: consider a member public if docstring contains `:meta public:` in info-field-list - [#​7487](https://togithub.com/sphinx-doc/sphinx/issues/7487): autodoc: Allow to generate docs for singledispatch functions by py:autofunction - [#​7143](https://togithub.com/sphinx-doc/sphinx/issues/7143): autodoc: Support final classes and methods - [#​7384](https://togithub.com/sphinx-doc/sphinx/issues/7384): autodoc: Support signatures defined by `__new__()`, metaclasses and builtin base classes - [#​2106](https://togithub.com/sphinx-doc/sphinx/issues/2106): autodoc: Support multiple signatures on docstring - [#​4422](https://togithub.com/sphinx-doc/sphinx/issues/4422): autodoc: Support GenericAlias in Python 3.7 or above - [#​3610](https://togithub.com/sphinx-doc/sphinx/issues/3610): autodoc: Support overloaded functions - [#​7722](https://togithub.com/sphinx-doc/sphinx/issues/7722): autodoc: Support TypeVar - [#​7466](https://togithub.com/sphinx-doc/sphinx/issues/7466): autosummary: headings in generated documents are not translated - [#​7490](https://togithub.com/sphinx-doc/sphinx/issues/7490): autosummary: Add `:caption:` option to autosummary directive to set a caption to the toctree - [#​7469](https://togithub.com/sphinx-doc/sphinx/issues/7469): autosummary: Support module attributes - [#​248](https://togithub.com/sphinx-doc/sphinx/issues/248), [#​6040](https://togithub.com/sphinx-doc/sphinx/issues/6040): autosummary: Add `:recursive:` option to autosummary directive to generate stub files recursively - [#​4030](https://togithub.com/sphinx-doc/sphinx/issues/4030): autosummary: Add :confval:`autosummary_context` to add template variables for custom templates - [#​7530](https://togithub.com/sphinx-doc/sphinx/issues/7530): html: Support nested elements - [#​7481](https://togithub.com/sphinx-doc/sphinx/issues/7481): html theme: Add right margin to footnote/citation labels - [#​7482](https://togithub.com/sphinx-doc/sphinx/issues/7482), [#​7717](https://togithub.com/sphinx-doc/sphinx/issues/7717): html theme: CSS spacing for code blocks with captions and line numbers - [#​7443](https://togithub.com/sphinx-doc/sphinx/issues/7443): html theme: Add new options :confval:`globaltoc_collapse` and :confval:`globaltoc_includehidden` to control the behavior of globaltoc in sidebar - [#​7484](https://togithub.com/sphinx-doc/sphinx/issues/7484): html theme: Avoid clashes between sidebar and other blocks - [#​7476](https://togithub.com/sphinx-doc/sphinx/issues/7476): html theme: Relbar breadcrumb should contain current page - [#​7506](https://togithub.com/sphinx-doc/sphinx/issues/7506): html theme: A canonical URL is not escaped - [#​7533](https://togithub.com/sphinx-doc/sphinx/issues/7533): html theme: Avoid whitespace at the beginning of genindex.html - [#​7541](https://togithub.com/sphinx-doc/sphinx/issues/7541): html theme: Add a "clearer" at the end of the "body" - [#​7542](https://togithub.com/sphinx-doc/sphinx/issues/7542): html theme: Make admonition/topic/sidebar scrollable - [#​7543](https://togithub.com/sphinx-doc/sphinx/issues/7543): html theme: Add top and bottom margins to tables - [#​7695](https://togithub.com/sphinx-doc/sphinx/issues/7695): html theme: Add viewport meta tag for basic theme - [#​7721](https://togithub.com/sphinx-doc/sphinx/issues/7721): html theme: classic: default codetextcolor/codebgcolor doesn't override Pygments - C and C++: allow semicolon in the end of declarations. - C++, parse parameterized noexcept specifiers. - [#​7294](https://togithub.com/sphinx-doc/sphinx/issues/7294): C++, parse expressions with user-defined literals. - C++, parse trailing return types. - [#​7143](https://togithub.com/sphinx-doc/sphinx/issues/7143): py domain: Add `:final:` option to :rst:dir:`py:class:`, :rst:dir:`py:exception:` and :rst:dir:`py:method:` directives - [#​7596](https://togithub.com/sphinx-doc/sphinx/issues/7596): py domain: Change a type annotation for variables to a hyperlink - [#​7770](https://togithub.com/sphinx-doc/sphinx/issues/7770): std domain: :rst:dir:`option` directive support arguments in the form of `foo[=bar]` - [#​7582](https://togithub.com/sphinx-doc/sphinx/issues/7582): napoleon: a type for attribute are represented like type annotation - [#​7734](https://togithub.com/sphinx-doc/sphinx/issues/7734): napoleon: overescaped trailing underscore on attribute - [#​7247](https://togithub.com/sphinx-doc/sphinx/issues/7247): linkcheck: Add :confval:`linkcheck_request_headers` to send custom HTTP headers for specific host - [#​7792](https://togithub.com/sphinx-doc/sphinx/issues/7792): setuptools: Support `--verbosity` option - [#​7683](https://togithub.com/sphinx-doc/sphinx/issues/7683): Add `allowed_exceptions` parameter to `Sphinx.emit()` to allow handlers to raise specified exceptions - [#​7295](https://togithub.com/sphinx-doc/sphinx/issues/7295): C++, parse (trailing) requires clauses. ## Bugs fixed - [#​6703](https://togithub.com/sphinx-doc/sphinx/issues/6703): autodoc: incremental build does not work for imported objects - [#​7564](https://togithub.com/sphinx-doc/sphinx/issues/7564): autodoc: annotations not to be shown for descriptors - [#​6588](https://togithub.com/sphinx-doc/sphinx/issues/6588): autodoc: Decorated inherited method has no documentation - [#​7469](https://togithub.com/sphinx-doc/sphinx/issues/7469): autodoc: The change of autodoc-process-docstring for variables is cached unexpectedly - [#​7559](https://togithub.com/sphinx-doc/sphinx/issues/7559): autodoc: misdetects a sync function is async - [#​6857](https://togithub.com/sphinx-doc/sphinx/issues/6857): autodoc: failed to detect a classmethod on Enum class - [#​7562](https://togithub.com/sphinx-doc/sphinx/issues/7562): autodoc: a typehint contains spaces is wrongly rendered under autodoc_typehints='description' mode - [#​7551](https://togithub.com/sphinx-doc/sphinx/issues/7551): autodoc: failed to import nested class - [#​7362](https://togithub.com/sphinx-doc/sphinx/issues/7362): autodoc: does not render correct signatures for built-in functions - [#​7654](https://togithub.com/sphinx-doc/sphinx/issues/7654): autodoc: `Optional[Union[foo, bar]]` is presented as `Union[foo, bar, None]` - [#​7629](https://togithub.com/sphinx-doc/sphinx/issues/7629): autodoc: autofunction emits an unfriendly warning if an invalid object specified - [#​7650](https://togithub.com/sphinx-doc/sphinx/issues/7650): autodoc: undecorated signature is shown for decorated functions - [#​7676](https://togithub.com/sphinx-doc/sphinx/issues/7676): autodoc: typo in the default value of autodoc_member_order - [#​7676](https://togithub.com/sphinx-doc/sphinx/issues/7676): autodoc: wrong value for :member-order: option is ignored silently - [#​7676](https://togithub.com/sphinx-doc/sphinx/issues/7676): autodoc: member-order="bysource" does not work for C module - [#​3673](https://togithub.com/sphinx-doc/sphinx/issues/3673): autodoc: member-order="bysource" does not work for a module having **all** - [#​7668](https://togithub.com/sphinx-doc/sphinx/issues/7668): autodoc: wrong retann value is passed to a handler of autodoc-proccess-signature - [#​7711](https://togithub.com/sphinx-doc/sphinx/issues/7711): autodoc: fails with ValueError when processing numpy objects - [#​7791](https://togithub.com/sphinx-doc/sphinx/issues/7791): autodoc: TypeError is raised on documenting singledispatch function - [#​7551](https://togithub.com/sphinx-doc/sphinx/issues/7551): autosummary: a nested class is indexed as non-nested class - [#​7661](https://togithub.com/sphinx-doc/sphinx/issues/7661): autosummary: autosummary directive emits warnings twices if failed to import the target module - [#​7685](https://togithub.com/sphinx-doc/sphinx/issues/7685): autosummary: The template variable "members" contains imported members even if :confval:`autossummary_imported_members` is False - [#​7671](https://togithub.com/sphinx-doc/sphinx/issues/7671): autosummary: The location of import failure warning is missing - [#​7535](https://togithub.com/sphinx-doc/sphinx/issues/7535): sphinx-autogen: crashes when custom template uses inheritance - [#​7536](https://togithub.com/sphinx-doc/sphinx/issues/7536): sphinx-autogen: crashes when template uses i18n feature - [#​7781](https://togithub.com/sphinx-doc/sphinx/issues/7781): sphinx-build: Wrong error message when outdir is not directory - [#​7653](https://togithub.com/sphinx-doc/sphinx/issues/7653): sphinx-quickstart: Fix multiple directory creation for nested relpath - [#​2785](https://togithub.com/sphinx-doc/sphinx/issues/2785): html: Bad alignment of equation links - [#​7718](https://togithub.com/sphinx-doc/sphinx/issues/7718): html theme: some themes does not respect background color of Pygments style (agogo, haiku, nature, pyramid, scrolls, sphinxdoc and traditional) - [#​7544](https://togithub.com/sphinx-doc/sphinx/issues/7544): html theme: inconsistent padding in admonitions - [#​7581](https://togithub.com/sphinx-doc/sphinx/issues/7581): napoleon: bad parsing of inline code in attribute docstrings - [#​7628](https://togithub.com/sphinx-doc/sphinx/issues/7628): imgconverter: runs imagemagick once unnecessary for builders not supporting images - [#​7610](https://togithub.com/sphinx-doc/sphinx/issues/7610): incorrectly renders consecutive backslashes for docutils-0.16 - [#​7646](https://togithub.com/sphinx-doc/sphinx/issues/7646): handle errors on event handlers - [#​4187](https://togithub.com/sphinx-doc/sphinx/issues/4187): LaTeX: EN DASH disappears from PDF bookmarks in Japanese documents - [#​7701](https://togithub.com/sphinx-doc/sphinx/issues/7701): LaTeX: Anonymous indirect hyperlink target causes duplicated labels - [#​7723](https://togithub.com/sphinx-doc/sphinx/issues/7723): LaTeX: pdflatex crashed when URL contains a single quote - [#​7756](https://togithub.com/sphinx-doc/sphinx/issues/7756): py domain: The default value for positional only argument is not shown - [#​7760](https://togithub.com/sphinx-doc/sphinx/issues/7760): coverage: Add :confval:`coverage_show_missing_items` to show coverage result to console - C++, fix rendering and xrefs in nested names explicitly starting in global scope, e.g., `::A::B`. - C, fix rendering and xrefs in nested names explicitly starting in global scope, e.g., `.A.B`. - [#​7763](https://togithub.com/sphinx-doc/sphinx/issues/7763): C and C++, don't crash during display stringification of unary expressions and fold expressions. ### [`v3.0.4`](https://togithub.com/sphinx-doc/sphinx/blob/master/CHANGES#Release-304-released-May-27-2020) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v3.0.3...v3.0.4) ===================================== ## Bugs fixed - [#​7567](https://togithub.com/sphinx-doc/sphinx/issues/7567): autodoc: parametrized types are shown twice for generic types - [#​7637](https://togithub.com/sphinx-doc/sphinx/issues/7637): autodoc: system defined TypeVars are shown in Python 3.9 - [#​7696](https://togithub.com/sphinx-doc/sphinx/issues/7696): html: Updated jQuery version from 3.4.1 to 3.5.1 for security reasons - [#​7611](https://togithub.com/sphinx-doc/sphinx/issues/7611): md5 fails when OpenSSL FIPS is enabled - [#​7626](https://togithub.com/sphinx-doc/sphinx/issues/7626): release package does not contain `CODE_OF_CONDUCT`

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codecov[bot] commented 4 years ago

Codecov Report

Merging #245 into dev will not change coverage. The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##              dev     #245   +/-   ##
=======================================
  Coverage   84.17%   84.17%           
=======================================
  Files          32       32           
  Lines        3703     3703           
=======================================
  Hits         3117     3117           
  Misses        586      586           

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