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sjoerdk / idiscore

Deidentification of DICOM images using Attribute Confidentiality Profiles
GNU General Public License v3.0
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Scheduled weekly dependency update for week 11 #42

Closed pyup-bot closed 3 years ago

pyup-bot commented 3 years ago

Update sphinx from 3.4.3 to 3.5.2.

Changelog ### 3.5.2 ``` ===================================== Bugs fixed ---------- * 8943: i18n: Crashed by broken translation messages in ES, EL and HR * 8936: LaTeX: A custom LaTeX builder fails with unknown node error * 8952: Exceptions raised in a Directive cause parallel builds to hang ``` ### 3.5.1 ``` ===================================== Bugs fixed ---------- * 8883: autodoc: AttributeError is raised on assigning __annotations__ on read-only class * 8884: html: minified js stemmers not included in the distributed package * 8885: html: AttributeError is raised if CSS/JS files are installed via :confval:`html_context` * 8880: viewcode: ExtensionError is raised on incremental build after unparsable python module found ``` ### 3.5.0 ``` ===================================== Dependencies ------------ * LaTeX: ``multicol`` (it is anyhow a required part of the official latex2e base distribution) Incompatible changes -------------------- * Update Underscore.js to 1.12.0 * 6550: html: The config variable ``html_add_permalinks`` is replaced by :confval:`html_permalinks` and :confval:`html_permalinks_icon` Deprecated ---------- * pending_xref node for viewcode extension * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.anchors_ignore`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.auth`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.broken`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.good`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.redirected`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.rqueue`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.to_ignore`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.workers`` * ``sphinx.builders.linkcheck.CheckExternalLinksBuilder.wqueue`` * ``sphinx.builders.linkcheck.node_line_or_0()`` * ``sphinx.ext.autodoc.AttributeDocumenter.isinstanceattribute()`` * ``sphinx.ext.autodoc.directive.DocumenterBridge.reporter`` * ``sphinx.ext.autodoc.importer.get_module_members()`` * ``sphinx.ext.autosummary.generate._simple_info()`` * ``sphinx.ext.autosummary.generate._simple_warn()`` * ``sphinx.writers.html.HTMLTranslator.permalink_text`` * ``sphinx.writers.html5.HTML5Translator.permalink_text`` Features added -------------- * 8022: autodoc: autodata and autoattribute directives does not show right-hand value of the variable if docstring contains ``:meta hide-value:`` in info-field-list * 8514: autodoc: Default values of overloaded functions are taken from actual implementation if they're ellipsis * 8775: autodoc: Support type union operator (PEP-604) in Python 3.10 or above * 8297: autodoc: Allow to extend :confval:`autodoc_default_options` via directive options * 8619: html: kbd role generates customizable HTML tags for compound keys * 8634: html: Allow to change the order of JS/CSS via ``priority`` parameter for :meth:`Sphinx.add_js_file()` and :meth:`Sphinx.add_css_file()` * 6241: html: Allow to add JS/CSS files to the specific page when an extension calls ``app.add_js_file()`` or ``app.add_css_file()`` on :event:`html-page-context` event * 6550: html: Allow to use HTML permalink texts via :confval:`html_permalinks_icon` * 1638: html: Add permalink icons to glossary terms * 8868: html search: performance issue with massive lists * 8867: html search: Update JavaScript stemmer code to the latest version of Snowball (v2.1.0) * 8852: i18n: Allow to translate heading syntax in MyST-Parser * 8649: imgconverter: Skip availability check if builder supports the image type * 8573: napoleon: Allow to change the style of custom sections using :confval:`napoleon_custom_styles` * 8004: napoleon: Type definitions in Google style docstrings are rendered as references when :confval:`napoleon_preprocess_types` enabled * 6241: mathjax: Include mathjax.js only on the document using equations * 8775: py domain: Support type union operator (PEP-604) * 8651: std domain: cross-reference for a rubric having inline item is broken * 7642: std domain: Optimize case-insensitive match of term * 8681: viewcode: Support incremental build * 8132: Add :confval:`project_copyright` as an alias of :confval:`copyright` * 207: Now :confval:`highlight_language` supports multiple languages * 2030: :rst:dir:`code-block` and :rst:dir:`literalinclude` supports automatic dedent via no-argument ``:dedent:`` option * C++, also hyperlink operator overloads in expressions and alias declarations. * 8247: Allow production lists to refer to tokens from other production groups * 8813: Show what extension (or module) caused it on errors on event handler * 8213: C++: add ``maxdepth`` option to :rst:dir:`cpp:alias` to insert nested declarations. * C, add ``noroot`` option to :rst:dir:`c:alias` to render only nested declarations. * C++, add ``noroot`` option to :rst:dir:`cpp:alias` to render only nested declarations. Bugs fixed ---------- * 8727: apidoc: namespace module file is not generated if no submodules there * 741: autodoc: inherited-members doesn't work for instance attributes on super class * 8592: autodoc: ``:meta public:`` does not effect to variables * 8594: autodoc: empty __all__ attribute is ignored * 8315: autodoc: Failed to resolve struct.Struct type annotation * 8652: autodoc: All variable comments in the module are ignored if the module contains invalid type comments * 8693: autodoc: Default values for overloaded functions are rendered as string * 8134: autodoc: crashes when mocked decorator takes arguments * 8800: autodoc: Uninitialized attributes in superclass are recognized as undocumented * 8655: autodoc: Failed to generate document if target module contains an object that raises an exception on ``hasattr()`` * 8306: autosummary: mocked modules are documented as empty page when using :recursive: option * 8232: graphviz: Image node is not rendered if graph file is in subdirectory * 8618: html: kbd role produces incorrect HTML when compound-key separators (-, + or ^) are used as keystrokes * 8629: html: A type warning for html_use_opensearch is shown twice * 8714: html: kbd role with "Caps Lock" rendered incorrectly * 8123: html search: fix searching for terms containing + (Requires a custom search language that does not split on +) * 8665: html theme: Could not override globaltoc_maxdepth in theme.conf * 8446: html: consecutive spaces are displayed as single space * 8745: i18n: crashes with KeyError when translation message adds a new auto footnote reference * 4304: linkcheck: Fix race condition that could lead to checking the availability of the same URL twice * 8791: linkcheck: The docname for each hyperlink is not displayed * 7118: sphinx-quickstart: questionare got Mojibake if libreadline unavailable * 8094: texinfo: image files on the different directory with document are not copied * 8782: todo: Cross references in todolist get broken * 8720: viewcode: module pages are generated for epub on incremental build * 8704: viewcode: anchors are generated in incremental build after singlehtml * 8756: viewcode: highlighted code is generated even if not referenced * 8671: :confval:`highlight_options` is not working * 8341: C, fix intersphinx lookup types for names in declarations. * C, C++: in general fix intersphinx and role lookup types. * 8683: :confval:`html_last_updated_fmt` does not support UTC offset (%z) * 8683: :confval:`html_last_updated_fmt` generates wrong time zone for %Z * 1112: ``download`` role creates duplicated copies when relative path is specified * 2616 (fifth item): LaTeX: footnotes from captions are not clickable, and for manually numbered footnotes only first one with same number is an hyperlink * 7576: LaTeX with French babel and memoir crash: "Illegal parameter number in definition of ``\FNHprefntext``" * 8055: LaTeX (docs): A potential display bug with the LaTeX generation step in Sphinx (how to generate one-column index) * 8072: LaTeX: Directive :rst:dir:`hlist` not implemented in LaTeX * 8214: LaTeX: The :rst:role:`index` role and the glossary generate duplicate entries in the LaTeX index (if both used for same term) * 8735: LaTeX: wrong internal links in pdf to captioned code-blocks when :confval:`numfig` is not True * 8442: LaTeX: some indexed terms are ignored when using xelatex engine (or pdflatex and :confval:`latex_use_xindy` set to True) with memoir class * 8750: LaTeX: URLs as footnotes fail to show in PDF if originating from inside function type signatures * 8780: LaTeX: long words in narrow columns may not be hyphenated * 8788: LaTeX: ``\titleformat`` last argument in sphinx.sty should be bracketed, not braced (and is anyhow not needed) * 8849: LaTex: code-block printed out of margin (see the opt-in LaTeX syntax boolean :ref:`verbatimforcewraps <latexsphinxsetupforcewraps>` for use via the :ref:`'sphinxsetup' <latexsphinxsetup>` key of ``latex_elements``) * 8183: LaTeX: Remove substitution_reference nodes from doctree only on LaTeX builds * 8865: LaTeX: Restructure the index nodes inside title nodes only on LaTeX builds * 8796: LaTeX: potentially critical low level TeX coding mistake has gone unnoticed so far * C, :rst:dir:`c:alias` skip symbols without explicit declarations instead of crashing. * C, :rst:dir:`c:alias` give a warning when the root symbol is not declared. * C, ``expr`` role should start symbol lookup in the current scope. ```
Links - PyPI: https://pypi.org/project/sphinx - Changelog: https://pyup.io/changelogs/sphinx/ - Homepage: http://sphinx-doc.org/

Update sphinx-autobuild from 2020.9.1 to 2021.3.14.

The bot wasn't able to find a changelog for this release. Got an idea?

Links - PyPI: https://pypi.org/project/sphinx-autobuild - Changelog: https://pyup.io/changelogs/sphinx-autobuild/ - Repo: https://github.com/executablebooks/sphinx-autobuild

Update pytest-runner from 5.2 to 5.3.0.

Changelog ### 5.3.0 ``` ====== * Require Python 3.6 or later. * Refreshed package metadata. ```
Links - PyPI: https://pypi.org/project/pytest-runner - Changelog: https://pyup.io/changelogs/pytest-runner/ - Repo: https://github.com/pytest-dev/pytest-runner/

Update coverage from 5.4 to 5.5.

Changelog ### 5.5 ``` -------------------------- - ``coverage combine`` has a new option, ``--keep`` to keep the original data files after combining them. The default is still to delete the files after they have been combined. This was requested in `issue 1108`_ and implemented in `pull request 1110`_. Thanks, Éric Larivière. - When reporting missing branches in ``coverage report``, branches aren't reported that jump to missing lines. This adds to the long-standing behavior of not reporting branches from missing lines. Now branches are only reported if both the source and destination lines are executed. Closes both `issue 1065`_ and `issue 955`_. - Minor improvements to the HTML report: - The state of the line visibility selector buttons is saved in local storage so you don't have to fiddle with them so often, fixing `issue 1123`_. - It has a little more room for line numbers so that 4-digit numbers work well, fixing `issue 1124`_. - Improved the error message when combining line and branch data, so that users will be more likely to understand what's happening, closing `issue 803`_. .. _issue 803: https://github.com/nedbat/coveragepy/issues/803 .. _issue 955: https://github.com/nedbat/coveragepy/issues/955 .. _issue 1065: https://github.com/nedbat/coveragepy/issues/1065 .. _issue 1108: https://github.com/nedbat/coveragepy/issues/1108 .. _pull request 1110: https://github.com/nedbat/coveragepy/pull/1110 .. _issue 1123: https://github.com/nedbat/coveragepy/issues/1123 .. _issue 1124: https://github.com/nedbat/coveragepy/issues/1124 .. _changes_54: ```
Links - PyPI: https://pypi.org/project/coverage - Changelog: https://pyup.io/changelogs/coverage/ - Repo: https://github.com/nedbat/coveragepy

Update flake8 from 3.8.4 to 3.9.0.

Changelog ### 3.9.0 ``` ------------------- You can view the `3.9.0 milestone`_ on GitLab for more details. New Dependency Information ~~~~~~~~~~~~~~~~~~~~~~~~~~ - Pyflakes has been updated to >= 2.3.0, < 2.4.0 (See also `GitLab!466`_) - pycodestyle has been updated to >= 2.7.0, < 2.8.0 (See also `GitLab!467`_) Deprecations ~~~~~~~~~~~~ - Drop support for python 3.4 (See also `GitLab!457`_) Features ~~~~~~~~ - Add ``--no-show-source`` option to disable ``--show-source`` (See also `GitLab!441`_) Bugs Fixed ~~~~~~~~~~ - Fix handling of ``crlf`` line endings when linting stdin (See also `GitLab!461`_) .. all links .. _3.9.0 milestone: https://gitlab.com/pycqa/flake8/-/milestones/38 .. merge request links .. _GitLab!441: https://gitlab.com/pycqa/flake8/-/merge_requests/441 .. _GitLab!457: https://gitlab.com/pycqa/flake8/-/merge_requests/457 .. _GitLab!461: https://gitlab.com/pycqa/flake8/-/merge_requests/461 .. _GitLab!466: https://gitlab.com/pycqa/flake8/-/merge_requests/466 .. _GitLab!467: https://gitlab.com/pycqa/flake8/-/merge_requests/467 ```
Links - PyPI: https://pypi.org/project/flake8 - Changelog: https://pyup.io/changelogs/flake8/ - Repo: https://gitlab.com/pycqa/flake8

Update tox from 3.21.4 to 3.23.0.

Changelog ### 3.22.0 ``` -------------------- Features ^^^^^^^^ - The value of the :conf:`requires` configuration option is now exposed via the :class:`tox.config.Config` object - by :user:`hroncok` `1918 <https://github.com/tox-dev/tox/issues/1918>`_ ```
Links - PyPI: https://pypi.org/project/tox - Changelog: https://pyup.io/changelogs/tox/ - Docs: http://tox.readthedocs.org

Update twine from 3.3.0 to 3.4.0.

The bot wasn't able to find a changelog for this release. Got an idea?

Links - PyPI: https://pypi.org/project/twine - Docs: https://twine.readthedocs.io/

Update watchdog from 1.0.2 to 2.0.2.

Changelog ### 2.0.2 ``` ~~~~~ 2021-02-22 • `full history <https://github.com/gorakhargosh/watchdog/compare/v2.0.1...v2.0.2>`__ - [mac] Add missing exception objects (`766 <https://github.com/gorakhargosh/watchdog/pull/766>`_) - Thanks to our beloved contributors: CCP-Aporia, BoboTiG ``` ### 2.0.1 ``` ~~~~~ 2021-02-17 • `full history <https://github.com/gorakhargosh/watchdog/compare/v2.0.0...v2.0.1>`__ - [mac] Fix a segmentation fault when dealing with unicode paths (`763 <https://github.com/gorakhargosh/watchdog/pull/763>`_) - Moved the CI from Travis-CI to GitHub Actions (`764 <https://github.com/gorakhargosh/watchdog/pull/764>`_) - Thanks to our beloved contributors: SamSchott, BoboTiG ``` ### 2.0.0 ``` ~~~~~ 2021-02-11 • `full history <https://github.com/gorakhargosh/watchdog/compare/v1.0.2...v2.0.0>`__ - Avoid deprecated ``PyEval_InitThreads`` on Python 3.7+ (`746 <https://github.com/gorakhargosh/watchdog/pull/746>`_) - [inotify] Add support for ``IN_CLOSE_WRITE`` events. A ``FileCloseEvent`` event will be fired. Note that ``IN_CLOSE_NOWRITE`` events are not handled to prevent much noise. (`184 <https://github.com/gorakhargosh/watchdog/pull/184>`_, `#245 <https://github.com/gorakhargosh/watchdog/pull/245>`_, `#280 <https://github.com/gorakhargosh/watchdog/pull/280>`_, `#313 <https://github.com/gorakhargosh/watchdog/pull/313>`_, `#690 <https://github.com/gorakhargosh/watchdog/pull/690>`_) - [inotify] Allow to stop the emitter multiple times (`760 <https://github.com/gorakhargosh/watchdog/pull/760>`_) - [mac] Support coalesced filesystem events (`734 <https://github.com/gorakhargosh/watchdog/pull/734>`_) - [mac] Drop support for macOS 10.12 and earlier (`750 <https://github.com/gorakhargosh/watchdog/pull/750>`_) - [mac] Fix an issue when renaming an item changes only the casing (`750 <https://github.com/gorakhargosh/watchdog/pull/750>`_) - Thanks to our beloved contributors: bstaletic, lukassup, ysard, SamSchott, CCP-Aporia, BoboTiG ```
Links - PyPI: https://pypi.org/project/watchdog - Changelog: https://pyup.io/changelogs/watchdog/ - Repo: http://github.com/gorakhargosh/watchdog - Docs: https://pythonhosted.org/watchdog/

Update pre-commit from 2.10.1 to 2.11.1.

Changelog ### 2.11.1 ``` =================== Fixes - Fix r hooks when hook repo is a package - 1831 PR by lorenzwalthert. ``` ### 2.11.0 ``` =================== Features - Improve warning for mutable ref. - 1809 PR by JamMarHer. - Add support for `post-merge` hook. - 1800 PR by psacawa. - 1762 issue by psacawa. - Add `r` as a supported hook language. - 1799 PR by lorenzwalthert. Fixes - Fix `pre-commit install` on `subst` / network drives on windows. - 1814 PR by asottile. - 1802 issue by goroderickgo. - Fix installation of `local` golang repositories for go 1.16. - 1818 PR by rafikdraoui. - 1815 issue by rafikdraoui. ```
Links - PyPI: https://pypi.org/project/pre-commit - Changelog: https://pyup.io/changelogs/pre-commit/ - Repo: https://github.com/pre-commit/pre-commit
pyup-bot commented 3 years ago

Closing this in favor of #43