pymzml / pymzML

pymzML - an interface between Python and mzML Mass spectrometry Files
https://pymzml.readthedocs.io/en/latest/
MIT License
160 stars 91 forks source link

Update dependency sphinx to v3.2.1 #251

Closed renovate[bot] closed 3 years ago

renovate[bot] commented 3 years ago

This PR contains the following updates:

Package Update Change
sphinx (source) minor ==3.1.2 -> ==3.2.1

Release Notes

sphinx-doc/sphinx ### [`v3.2.1`](https://togithub.com/sphinx-doc/sphinx/blob/master/CHANGES#Release-321-released-Aug-14-2020) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v3.2.0...v3.2.1) ===================================== ## Features added - [#​8095](https://togithub.com/sphinx-doc/sphinx/issues/8095): napoleon: Add :confval:`napoleon_preprocess_types` to enable the type preprocessor for numpy style docstrings - [#​8114](https://togithub.com/sphinx-doc/sphinx/issues/8114): C and C++, parse function attributes after parameters and qualifiers. ## Bugs fixed - [#​8074](https://togithub.com/sphinx-doc/sphinx/issues/8074): napoleon: Crashes during processing C-ext module - [#​8088](https://togithub.com/sphinx-doc/sphinx/issues/8088): napoleon: "Inline literal start-string without end-string" warning in Numpy style Parameters section - [#​8084](https://togithub.com/sphinx-doc/sphinx/issues/8084): autodoc: KeyError is raised on documenting an attribute of the broken class - [#​8091](https://togithub.com/sphinx-doc/sphinx/issues/8091): autodoc: AttributeError is raised on documenting an attribute on Python 3.5.2 - [#​8099](https://togithub.com/sphinx-doc/sphinx/issues/8099): autodoc: NameError is raised when target code uses `TYPE_CHECKING` - C++, fix parsing of template template paramters, broken by the fix of [#​7944](https://togithub.com/sphinx-doc/sphinx/issues/7944) ### [`v3.2.0`](https://togithub.com/sphinx-doc/sphinx/blob/master/CHANGES#Release-320-released-Aug-08-2020) [Compare Source](https://togithub.com/sphinx-doc/sphinx/compare/v3.1.2...v3.2.0) ===================================== ## Deprecated - `sphinx.ext.autodoc.members_set_option()` - `sphinx.ext.autodoc.merge_special_members_option()` - `sphinx.writers.texinfo.TexinfoWriter.desc` - C, parsing of pre-v3 style type directives and roles, along with the options :confval:`c_allow_pre_v3` and :confval:`c_warn_on_allowed_pre_v3`. ## Features added - [#​2076](https://togithub.com/sphinx-doc/sphinx/issues/2076): autodoc: Allow overriding of exclude-members in skip-member function - [#​8034](https://togithub.com/sphinx-doc/sphinx/issues/8034): autodoc: `:private-member:` can take an explicit list of member names to be documented - [#​2024](https://togithub.com/sphinx-doc/sphinx/issues/2024): autosummary: Add :confval:`autosummary_filename_map` to avoid conflict of filenames between two object with different case - [#​8011](https://togithub.com/sphinx-doc/sphinx/issues/8011): autosummary: Support instance attributes as a target of autosummary directive - [#​7849](https://togithub.com/sphinx-doc/sphinx/issues/7849): html: Add :confval:`html_codeblock_linenos_style` to change the style of line numbers for code-blocks - [#​7853](https://togithub.com/sphinx-doc/sphinx/issues/7853): C and C++, support parameterized GNU style attributes. - [#​7888](https://togithub.com/sphinx-doc/sphinx/issues/7888): napoleon: Add aliases Warn and Raise. - [#​7690](https://togithub.com/sphinx-doc/sphinx/issues/7690): napoleon: parse type strings and make them hyperlinks as possible. The conversion rule can be updated via :confval:`napoleon_type_aliases` - [#​8049](https://togithub.com/sphinx-doc/sphinx/issues/8049): napoleon: Create a hyperlink for each the type of parameter when :confval:`napoleon_use_params` is False - C, added :rst:dir:`c:alias` directive for inserting copies of existing declarations. - [#​7745](https://togithub.com/sphinx-doc/sphinx/issues/7745): html: inventory is broken if the docname contains a space - [#​7991](https://togithub.com/sphinx-doc/sphinx/issues/7991): html search: Allow searching for numbers - [#​7902](https://togithub.com/sphinx-doc/sphinx/issues/7902): html theme: Add a new option :confval:`globaltoc_maxdepth` to control the behavior of globaltoc in sidebar - [#​7840](https://togithub.com/sphinx-doc/sphinx/issues/7840): i18n: Optimize the dependencies check on bootstrap - [#​7768](https://togithub.com/sphinx-doc/sphinx/issues/7768): i18n: :confval:`figure_language_filename` supports `docpath` token - [#​5208](https://togithub.com/sphinx-doc/sphinx/issues/5208): linkcheck: Support checks for local links - [#​5090](https://togithub.com/sphinx-doc/sphinx/issues/5090): setuptools: Link verbosity to distutils' -v and -q option - [#​6698](https://togithub.com/sphinx-doc/sphinx/issues/6698): doctest: Add `:trim-doctest-flags:` and `:no-trim-doctest-flags:` options to doctest, testcode and testoutput directives - [#​7052](https://togithub.com/sphinx-doc/sphinx/issues/7052): add `:noindexentry:` to the Python, C, C++, and Javascript domains. Update the documentation to better reflect the relationship between this option and the `:noindex:` option. - [#​7899](https://togithub.com/sphinx-doc/sphinx/issues/7899): C, add possibility of parsing of some pre-v3 style type directives and roles and try to convert them to equivalent v3 directives/roles. Set the new option :confval:`c_allow_pre_v3` to `True` to enable this. The warnings printed from this functionality can be suppressed by setting :confval:\`c_warn_on_allowed_pre_v3`to`True``. The functionality is immediately deprecated. - [#​7999](https://togithub.com/sphinx-doc/sphinx/issues/7999): C, add support for named variadic macro arguments. - [#​8071](https://togithub.com/sphinx-doc/sphinx/issues/8071): Allow to suppress "self referenced toctrees" warning ## Bugs fixed - [#​7886](https://togithub.com/sphinx-doc/sphinx/issues/7886): autodoc: TypeError is raised on mocking generic-typed classes - [#​7935](https://togithub.com/sphinx-doc/sphinx/issues/7935): autodoc: function signature is not shown when the function has a parameter having `inspect._empty` as its default value - [#​7901](https://togithub.com/sphinx-doc/sphinx/issues/7901): autodoc: type annotations for overloaded functions are not resolved - [#​904](https://togithub.com/sphinx-doc/sphinx/issues/904): autodoc: An instance attribute cause a crash of autofunction directive - [#​1362](https://togithub.com/sphinx-doc/sphinx/issues/1362): autodoc: `private-members` option does not work for class attributes - [#​7983](https://togithub.com/sphinx-doc/sphinx/issues/7983): autodoc: Generator type annotation is wrongly rendered in py36 - [#​8030](https://togithub.com/sphinx-doc/sphinx/issues/8030): autodoc: An uninitialized annotated instance variable is not documented when `:inherited-members:` option given - [#​8032](https://togithub.com/sphinx-doc/sphinx/issues/8032): autodoc: A type hint for the instance variable defined at parent class is not shown in the document of the derived class - [#​8041](https://togithub.com/sphinx-doc/sphinx/issues/8041): autodoc: An annotated instance variable on super class is not documented when derived class has other annotated instance variables - [#​7839](https://togithub.com/sphinx-doc/sphinx/issues/7839): autosummary: cannot handle umlauts in function names - [#​7865](https://togithub.com/sphinx-doc/sphinx/issues/7865): autosummary: Failed to extract summary line when abbreviations found - [#​7866](https://togithub.com/sphinx-doc/sphinx/issues/7866): autosummary: Failed to extract correct summary line when docstring contains a hyperlink target - [#​7469](https://togithub.com/sphinx-doc/sphinx/issues/7469): autosummary: "Module attributes" header is not translatable - [#​7940](https://togithub.com/sphinx-doc/sphinx/issues/7940): apidoc: An extra newline is generated at the end of the rst file if a module has submodules - [#​4258](https://togithub.com/sphinx-doc/sphinx/issues/4258): napoleon: decorated special methods are not shown - [#​7799](https://togithub.com/sphinx-doc/sphinx/issues/7799): napoleon: parameters are not escaped for combined params in numpydoc - [#​7780](https://togithub.com/sphinx-doc/sphinx/issues/7780): napoleon: multiple paramaters declaration in numpydoc was wrongly recognized when napoleon_use_params=True - [#​7715](https://togithub.com/sphinx-doc/sphinx/issues/7715): LaTeX: `numfig_secnum_depth > 1` leads to wrong figure links - [#​7846](https://togithub.com/sphinx-doc/sphinx/issues/7846): html theme: XML-invalid files were generated - [#​7894](https://togithub.com/sphinx-doc/sphinx/issues/7894): gettext: Wrong source info is shown when using rst_epilog - [#​7691](https://togithub.com/sphinx-doc/sphinx/issues/7691): linkcheck: HEAD requests are not used for checking - [#​4888](https://togithub.com/sphinx-doc/sphinx/issues/4888): i18n: Failed to add an explicit title to `:ref:` role on translation - [#​7928](https://togithub.com/sphinx-doc/sphinx/issues/7928): py domain: failed to resolve a type annotation for the attribute - [#​8008](https://togithub.com/sphinx-doc/sphinx/issues/8008): py domain: failed to parse a type annotation containing ellipsis - [#​7994](https://togithub.com/sphinx-doc/sphinx/issues/7994): std domain: option directive does not generate old node_id compatible with 2.x or older - [#​7968](https://togithub.com/sphinx-doc/sphinx/issues/7968): i18n: The content of `math` directive is interpreted as reST on translation - [#​7768](https://togithub.com/sphinx-doc/sphinx/issues/7768): i18n: The `root` element for :confval:`figure_language_filename` is not a path that user specifies in the document - [#​7993](https://togithub.com/sphinx-doc/sphinx/issues/7993): texinfo: TypeError is raised for nested object descriptions - [#​7993](https://togithub.com/sphinx-doc/sphinx/issues/7993): texinfo: a warning not supporting desc_signature_line node is shown - [#​7869](https://togithub.com/sphinx-doc/sphinx/issues/7869): :rst:role:`abbr` role without an explanation will show the explanation from the previous abbr role - [#​8048](https://togithub.com/sphinx-doc/sphinx/issues/8048): graphviz: graphviz.css was copied on building non-HTML document - C and C++, removed `noindex` directive option as it did nothing. - [#​7619](https://togithub.com/sphinx-doc/sphinx/issues/7619): Duplicated node IDs are generated if node has multiple IDs - [#​2050](https://togithub.com/sphinx-doc/sphinx/issues/2050): Symbols sections are appeared twice in the index page - [#​8017](https://togithub.com/sphinx-doc/sphinx/issues/8017): Fix circular import in sphinx.addnodes - [#​7986](https://togithub.com/sphinx-doc/sphinx/issues/7986): CSS: make "highlight" selector more robust - [#​7944](https://togithub.com/sphinx-doc/sphinx/issues/7944): C++, parse non-type template parameters starting with a dependent qualified name. - C, don't deepcopy the entire symbol table and make a mess every time an enumerator is handled.

Renovate configuration

:date: Schedule: "before 6am on the first day of the month" (UTC).

:vertical_traffic_light: Automerge: Disabled by config. Please merge this manually once you are satisfied.

:recycle: Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

:no_bell: Ignore: Close this PR and you won't be reminded about this update again.



This PR has been generated by WhiteSource Renovate. View repository job log here.

codecov[bot] commented 3 years ago

Codecov Report

Merging #251 into dev will not change coverage. The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##              dev     #251   +/-   ##
=======================================
  Coverage   84.18%   84.18%           
=======================================
  Files          32       32           
  Lines        3698     3698           
=======================================
  Hits         3113     3113           
  Misses        585      585           

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 349da4d...f838c7f. Read the comment docs.