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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 28 #56

Closed pyup-bot closed 3 years ago

pyup-bot commented 3 years ago

Update sphinx from 3.5.4 to 4.1.0.

Changelog ### 4.1.0 ``` ===================================== Dependencies ------------ * Support jinja2-3.0 Deprecated ---------- * The ``app`` argument of ``sphinx.environment.BuildEnvironment`` becomes required * ``sphinx.application.Sphinx.html_theme`` * ``sphinx.ext.autosummary._app`` * ``sphinx.util.docstrings.extract_metadata()`` Features added -------------- * 8107: autodoc: Add ``class-doc-from`` option to :rst:dir:`autoclass` directive to control the content of the specific class like :confval:`autoclass_content` * 8588: autodoc: :confval:`autodoc_type_aliases` now supports dotted name. It allows you to define an alias for a class with module name like ``foo.bar.BazClass`` * 9175: autodoc: Special member is not documented in the module * 9195: autodoc: The arguments of ``typing.Literal`` are wrongly rendered * 9185: autodoc: :confval:`autodoc_typehints` allows ``'both'`` setting to allow typehints to be included both in the signature and description * 4257: autodoc: Add :confval:`autodoc_class_signature` to separate the class entry and the definition of ``__init__()`` method * 8061, 9218: autodoc: Support variable comment for alias classes * 3014: autodoc: Add :event:`autodoc-process-bases` to modify the base classes of the class definitions * 9272: autodoc: Render enum values for the default argument value better * 9384: autodoc: ``autodoc_typehints='none'`` now erases typehints for variables, attributes and properties * 3257: autosummary: Support instance attributes for classes * 9358: html: Add "heading" role to the toctree items * 9225: html: Add span tag to the return typehint of method/function * 9129: html search: Show search summaries when html_copy_source = False * 9307: html search: Prevent corrections and completions in search field * 9120: html theme: Eliminate prompt characters of code-block from copyable text * 9176: i18n: Emit a debug message if message catalog file not found under :confval:`locale_dirs` * 9414: LaTeX: Add xeCJKVerbAddon to default fvset config for Chinese documents * 9016: linkcheck: Support checking anchors on github.com * 9016: linkcheck: Add a new event :event:`linkcheck-process-uri` to modify URIs before checking hyperlinks * 6525: linkcheck: Add :confval:`linkcheck_allowed_redirects` to mark hyperlinks that are redirected to expected URLs as "working" * 1874: py domain: Support union types using ``|`` in info-field-list * 9268: py domain: :confval:`python_use_unqualified_type_names` supports type field in info-field-list * 9097: Optimize the parallel build * 9131: Add :confval:`nitpick_ignore_regex` to ignore nitpicky warnings using regular expressions * 9174: Add ``Sphinx.set_html_assets_policy`` to tell extensions to include HTML assets in all the pages. Extensions can check this via ``Sphinx.registry.html_assets_policy`` * C++, add support for - ``inline`` variables, - ``consteval`` functions, - ``constinit`` variables, - ``char8_t``, - ``explicit(<constant expression>)`` specifier, - digit separators in literals, and - constraints in placeholder type specifiers, aka. adjective syntax (e.g., ``Sortable auto &v``). * C, add support for digit separators in literals. * 9166: LaTeX: support containers in LaTeX output Bugs fixed ---------- * 8872: autodoc: stacked singledispatches are wrongly rendered * 8597: autodoc: a docsting having metadata only should be treated as undocumented * 9185: autodoc: typehints for overloaded functions and methods are inaccurate * 9250: autodoc: The inherited method not having docstring is wrongly parsed * 9283: autodoc: autoattribute directive failed to generate document for an attribute not having any comment * 9364: autodoc: single element tuple on the default argument value is wrongly rendered * 9362: autodoc: AttributeError is raised on processing a subclass of Tuple[()] * 9404: autodoc: TypeError is raised on processing dict-like object (not a class) via autoclass directive * 9317: html: Pushing left key causes visiting the next page at the first page * 9381: html: URL for html_favicon and html_log does not work * 9270: html theme : pyramid theme generates incorrect logo links * 9217: manpage: The name of manpage directory that is generated by :confval:`man_make_section_directory` is not correct * 9350: manpage: Fix font isn't reset after keyword at the top of samp role * 9306: Linkcheck reports broken link when remote server closes the connection on HEAD request * 9280: py domain: "exceptions" module is not displayed * 9418: py domain: a Callable annotation with no parameters (e.g. ``Callable[[], None])`` will be rendered with a bracket missing (``Callable[], None]``) * 9319: quickstart: Make sphinx-quickstart exit when conf.py already exists * 9387: xml: XML Builder ignores custom visitors * 9224: ``:param:`` and ``:type:`` fields does not support a type containing whitespace (ex. ``Dict[str, str]``) * 8945: when transforming typed fields, call the specified role instead of making an single xref. For C and C++, use the ``expr`` role for typed fields. ``` ### 4.0.3 ``` ===================================== Features added -------------- * C, add C23 keywords ``_Decimal32``, ``_Decimal64``, and ``_Decimal128``. * 9354: C, add :confval:`c_extra_keywords` to allow user-defined keywords during parsing. * Revert the removal of ``sphinx.util:force_decode()`` to become some 3rd party extensions available again during 5.0 Bugs fixed ---------- * 9330: changeset domain: :rst:dir:`versionchanged` with contents being a list will cause error during pdf build * 9313: LaTeX: complex table with merged cells broken since 4.0 * 9305: LaTeX: backslash may cause Improper discretionary list pdf build error with Japanese engines * 9354: C, remove special macro names from the keyword list. See also :confval:`c_extra_keywords`. * 9322: KeyError is raised on PropagateDescDomain transform ``` ### 4.0.2 ``` ===================================== Dependencies ------------ * 9216: Support jinja2-3.0 Incompatible changes -------------------- * 9222: Update Underscore.js to 1.13.1 * 9217: manpage: Stop creating a section directory on build manpage by default (see :confval:`man_make_section_directory`) Bugs fixed ---------- * 9210: viewcode: crashed if non importable modules found on parallel build * 9240: Unknown node error for pending_xref_condition is raised if an extension that does not support the node installs a missing-reference handler ``` ### 4.0.1 ``` ===================================== Bugs fixed ---------- * 9189: autodoc: crashed when ValueError is raised on generating signature from a property of the class * 9188: autosummary: warning is emitted if list value is set to autosummary_generate * 8380: html search: tags for search result are broken * 9198: i18n: Babel emits errors when running compile_catalog * 9205: py domain: The :canonical: option causes "more than one target for cross-reference" warning * 9201: websupport: UndefinedError is raised: 'css_tag' is undefined ``` ### 4.0.0 ``` ===================================== Dependencies ------------ ``` ### 4.0.0b3 ``` * 9167: html: Failed to add CSS files to the specific page ``` ### 4.0.0b2 ``` * C, C++, fix ``KeyError`` when an ``alias`` directive is the first C/C++ directive in a file with another C/C++ directive later. ``` ### 4.0.0b1 ``` * 8917: autodoc: Raises a warning if function has wrong __globals__ value * 8415: autodoc: a TypeVar imported from other module is not resolved (in Python 3.7 or above) * 8992: autodoc: Failed to resolve types.TracebackType type annotation * 8905: html: html_add_permalinks=None and html_add_permalinks="" are ignored * 8380: html search: Paragraphs in search results are not identified as ``<p>`` * 8915: html theme: The translation of sphinx_rtd_theme does not work * 8342: Emit a warning if a unknown domain is given for directive or role (ex. ``:unknown:doc:``) * 7241: LaTeX: No wrapping for ``cpp:enumerator`` * 8711: LaTeX: backticks in code-blocks trigger latexpdf build warning (and font change) with late TeXLive 2019 * 8253: LaTeX: Figures with no size defined get overscaled (compared to images with size explicitly set in pixels) (fixed for ``'pdflatex'/'lualatex'`` only) * 8881: LaTeX: The depth of bookmarks panel in PDF is not enough for navigation * 8874: LaTeX: the fix to two minor Pygments LaTeXFormatter output issues ignore Pygments style * 8925: LaTeX: 3.5.0 ``verbatimmaxunderfull`` setting does not work as expected * 8980: LaTeX: missing line break in ``\pysigline`` * 8995: LaTeX: legacy ``\pysiglinewithargsret`` does not compute correctly available horizontal space and should use a ragged right style * 9009: LaTeX: "release" value with underscore leads to invalid LaTeX * 8911: C++: remove the longest matching prefix in :confval:`cpp_index_common_prefix` instead of the first that matches. * C, properly reject function declarations when a keyword is used as parameter name. * 8933: viewcode: Failed to create back-links on parallel build * 8960: C and C++, fix rendering of (member) function pointer types in function parameter lists. * C++, fix linking of names in array declarators, pointer to member (function) declarators, and in the argument to ``sizeof...``. * C, fix linking of names in array declarators. ``` ### 3.5.5 ``` ============================== ```
Links - PyPI: https://pypi.org/project/sphinx - Changelog: https://pyup.io/changelogs/sphinx/ - Homepage: https://sphinx-doc.org/

Update pytest from 6.2.3 to 6.2.4.

Changelog ### 6.2.4 ``` ========================= Bug Fixes --------- - `8539 <https://github.com/pytest-dev/pytest/issues/8539>`_: Fixed assertion rewriting on Python 3.10. ```
Links - PyPI: https://pypi.org/project/pytest - Changelog: https://pyup.io/changelogs/pytest/ - Homepage: https://docs.pytest.org/en/latest/

Update pytest-runner from 5.3.0 to 5.3.1.

Changelog ### 5.3.1 ``` ====== * 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 flake8 from 3.9.1 to 3.9.2.

Changelog ### 3.9.2 ``` ------------------- You can view the `3.9.2 milestone`_ on GitHub for more details. Bugs Fixed ~~~~~~~~~~ - Fix error message for ``E111`` in ``pycodestyle`` (See also :pull:`1328`, :issue:`1327`). Deprecations ~~~~~~~~~~~~ - ``indent_size_str`` is deprecated, use ``str(indent_size)`` instead (See also :pull:`1328`, :issue:`1327`). .. all links .. _3.9.2 milestone: https://github.com/PyCQA/flake8/milestone/40 ```
Links - PyPI: https://pypi.org/project/flake8 - Changelog: https://pyup.io/changelogs/flake8/ - Repo: https://gitlab.com/pycqa/flake8

Update pip from 21.1.1 to 21.1.3.

Changelog ### 21.1.3 ``` =================== Bug Fixes --------- - Remove unused optional ``tornado`` import in vendored ``tenacity`` to prevent old versions of Tornado from breaking pip. (`10020 <https://github.com/pypa/pip/issues/10020>`_) - Require ``setup.cfg``-only projects to be built via PEP 517, by requiring an explicit dependency on setuptools declared in pyproject.toml. (`10031 <https://github.com/pypa/pip/issues/10031>`_) ``` ### 21.1.2 ``` =================== Bug Fixes --------- - New resolver: Correctly exclude an already installed package if its version is known to be incompatible to stop the dependency resolution process with a clear error message. (`9841 <https://github.com/pypa/pip/issues/9841>`_) - Allow ZIP to archive files with timestamps earlier than 1980. (`9910 <https://github.com/pypa/pip/issues/9910>`_) - Emit clearer error message when a project root does not contain either ``pyproject.toml``, ``setup.py`` or ``setup.cfg``. (`9944 <https://github.com/pypa/pip/issues/9944>`_) - Fix detection of existing standalone pip instance for PEP 517 builds. (`9953 <https://github.com/pypa/pip/issues/9953>`_) ```
Links - PyPI: https://pypi.org/project/pip - Changelog: https://pyup.io/changelogs/pip/ - Homepage: https://pip.pypa.io/

Update tox from 3.23.0 to 3.23.1.

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

Links - PyPI: https://pypi.org/project/tox - Changelog: https://pyup.io/changelogs/tox/ - Docs: http://tox.readthedocs.org

Update watchdog from 2.0.3 to 2.1.3.

Changelog ### 2.1.3 ``` ~~~~~ 2021-06-26 • `full history <https://github.com/gorakhargosh/watchdog/compare/v2.1.2...v2.1.3>`__ - Publish macOS ``arm64`` and ``universal2`` wheels. (`740 <https://github.com/gorakhargosh/watchdog/pull/740>`_) - Thanks to our beloved contributors: kainjow, BoboTiG ``` ### 2.1.2 ``` ~~~~~ 2021-05-19 • `full history <https://github.com/gorakhargosh/watchdog/compare/v2.1.1...v2.1.2>`__ - [mac] Fix relative path handling for non-recursive watch. (`797 <https://github.com/gorakhargosh/watchdog/pull/797>`_) - [windows] On PyPy, events happening right after ``start()`` were missed. Add a workaround for that. (`796 <https://github.com/gorakhargosh/watchdog/pull/796>`_) - Thanks to our beloved contributors: oprypin, CCP-Aporia, BoboTiG ``` ### 2.1.1 ``` ~~~~~ 2021-05-10 • `full history <https://github.com/gorakhargosh/watchdog/compare/v2.1.0...v2.1.1>`__ - [mac] Fix callback exceptions when the watcher is deleted but still receiving events (`786 <https://github.com/gorakhargosh/watchdog/pull/786>`_) - Thanks to our beloved contributors: rom1win, BoboTiG, CCP-Aporia ``` ### 2.1.0 ``` ~~~~~ 2021-05-04 • `full history <https://github.com/gorakhargosh/watchdog/compare/v2.0.3...v2.1.0>`__ - [inotify] Simplify ``libc`` loading (`776 <https://github.com/gorakhargosh/watchdog/pull/776>`_) - [mac] Add support for non-recursive watches in ``FSEventsEmitter`` (`779 <https://github.com/gorakhargosh/watchdog/pull/779>`_) - [watchmedo] Add support for ``--debug-force-*`` arguments to ``tricks`` (`781 <https://github.com/gorakhargosh/watchdog/pull/781>`_) - Thanks to our beloved contributors: CCP-Aporia, aodj, UnitedMarsupials, BoboTiG ```
Links - PyPI: https://pypi.org/project/watchdog - Changelog: https://pyup.io/changelogs/watchdog/ - Repo: https://github.com/gorakhargosh/watchdog - Docs: https://pythonhosted.org/watchdog/

Update pre-commit from 2.12.1 to 2.13.0.

Changelog ### 2.13.0 ``` =================== Features - Setting `SKIP=...` skips installation as well. - 1875 PR by asottile. - pre-commit-ci/issues53 issue by TylerYep. - Attempt to mount from host with docker-in-docker. - 1888 PR by okainov. - 1387 issue by okainov. - Enable `repo: local` for `r` hooks. - 1878 PR by lorenzwalthert. - Upgrade `ruby-build` and `rbenv`. - 1913 PR by jalessio. Fixes - Better detect `r` packages. - 1898 PR by lorenzwalthert. - Avoid warnings with mismatched `renv` versions. - 1841 PR by lorenzwalthert. - Reproducibly produce ruby tar resources. - 1915 PR by asottile. ```
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 #57