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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 32 #10

Closed pyup-bot closed 4 years ago

pyup-bot commented 4 years ago

Update sphinx from 3.1.2 to 3.2.0.

Changelog ### 3.2.0 ``` ===================================== 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: autodoc: Allow overriding of exclude-members in skip-member function * 8034: autodoc: ``:private-member:`` can take an explicit list of member names to be documented * 2024: autosummary: Add :confval:`autosummary_filename_map` to avoid conflict of filenames between two object with different case * 8011: autosummary: Support instance attributes as a target of autosummary directive * 7849: html: Add :confval:`html_codeblock_linenos_style` to change the style of line numbers for code-blocks * 7853: C and C++, support parameterized GNU style attributes. * 7888: napoleon: Add aliases Warn and Raise. * 7690: napoleon: parse type strings and make them hyperlinks as possible. The conversion rule can be updated via :confval:`napoleon_type_aliases` * 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: html: inventory is broken if the docname contains a space * 7991: html search: Allow searching for numbers * 7902: html theme: Add a new option :confval:`globaltoc_maxdepth` to control the behavior of globaltoc in sidebar * 7840: i18n: Optimize the dependencies check on bootstrap * 7768: i18n: :confval:`figure_language_filename` supports ``docpath`` token * 5208: linkcheck: Support checks for local links * 5090: setuptools: Link verbosity to distutils' -v and -q option * 6698: doctest: Add ``:trim-doctest-flags:`` and ``:no-trim-doctest-flags:`` options to doctest, testcode and testoutput directives * 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: 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: C, add support for named variadic macro arguments. * 8071: Allow to suppress "self referenced toctrees" warning Bugs fixed ---------- * 7886: autodoc: TypeError is raised on mocking generic-typed classes * 7935: autodoc: function signature is not shown when the function has a parameter having ``inspect._empty`` as its default value * 7901: autodoc: type annotations for overloaded functions are not resolved * 904: autodoc: An instance attribute cause a crash of autofunction directive * 1362: autodoc: ``private-members`` option does not work for class attributes * 7983: autodoc: Generator type annotation is wrongly rendered in py36 * 8030: autodoc: An uninitialized annotated instance variable is not documented when ``:inherited-members:`` option given * 8032: autodoc: A type hint for the instance variable defined at parent class is not shown in the document of the derived class * 8041: autodoc: An annotated instance variable on super class is not documented when derived class has other annotated instance variables * 7839: autosummary: cannot handle umlauts in function names * 7865: autosummary: Failed to extract summary line when abbreviations found * 7866: autosummary: Failed to extract correct summary line when docstring contains a hyperlink target * 7469: autosummary: "Module attributes" header is not translatable * 7940: apidoc: An extra newline is generated at the end of the rst file if a module has submodules * 4258: napoleon: decorated special methods are not shown * 7799: napoleon: parameters are not escaped for combined params in numpydoc * 7780: napoleon: multiple paramaters declaration in numpydoc was wrongly recognized when napoleon_use_params=True * 7715: LaTeX: ``numfig_secnum_depth > 1`` leads to wrong figure links * 7846: html theme: XML-invalid files were generated * 7894: gettext: Wrong source info is shown when using rst_epilog * 7691: linkcheck: HEAD requests are not used for checking * 4888: i18n: Failed to add an explicit title to ``:ref:`` role on translation * 7928: py domain: failed to resolve a type annotation for the attribute * 8008: py domain: failed to parse a type annotation containing ellipsis * 7994: std domain: option directive does not generate old node_id compatible with 2.x or older * 7968: i18n: The content of ``math`` directive is interpreted as reST on translation * 7768: i18n: The ``root`` element for :confval:`figure_language_filename` is not a path that user specifies in the document * 7993: texinfo: TypeError is raised for nested object descriptions * 7993: texinfo: a warning not supporting desc_signature_line node is shown * 7869: :rst:role:`abbr` role without an explanation will show the explanation from the previous abbr role * 8048: graphviz: graphviz.css was copied on building non-HTML document * C and C++, removed ``noindex`` directive option as it did nothing. * 7619: Duplicated node IDs are generated if node has multiple IDs * 2050: Symbols sections are appeared twice in the index page * 8017: Fix circular import in sphinx.addnodes * 7986: CSS: make "highlight" selector more robust * 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. ```
Links - PyPI: https://pypi.org/project/sphinx - Changelog: https://pyup.io/changelogs/sphinx/ - Homepage: http://sphinx-doc.org/

Update pytest from 5.4.3 to 6.0.1.

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

Links - PyPI: https://pypi.org/project/pytest - Homepage: https://docs.pytest.org/en/latest/

Update coverage from 5.2 to 5.2.1.

Changelog ### 5.2.1 ``` ---------------------------- - The dark mode HTML report still used light colors for the context listing, making them unreadable (`issue 1009`_). This is now fixed. - The time stamp on the HTML report now includes the time zone. Thanks, Xie Yanbo (`pull request 960`_). .. _pull request 960: https://github.com/nedbat/coveragepy/pull/960 .. _issue 1009: https://github.com/nedbat/coveragepy/issues/1009 .. _changes_52: ```
Links - PyPI: https://pypi.org/project/coverage - Changelog: https://pyup.io/changelogs/coverage/ - Repo: https://github.com/nedbat/coveragepy

Update pip from 20.1.1 to 20.2.1.

Changelog ### 20.2.1 ``` =================== Features -------- - Ignore require-virtualenv in ``pip list`` (`8603 <https://github.com/pypa/pip/issues/8603>`_) Bug Fixes --------- - Correctly find already-installed distributions with dot (``.``) in the name and uninstall them when needed. (`8645 <https://github.com/pypa/pip/issues/8645>`_) - Trace a better error message on installation failure due to invalid ``.data`` files in wheels. (`8654 <https://github.com/pypa/pip/issues/8654>`_) - Fix SVN version detection for alternative SVN distributions. (`8665 <https://github.com/pypa/pip/issues/8665>`_) - New resolver: Correctly include the base package when specified with extras in ``--no-deps`` mode. (`8677 <https://github.com/pypa/pip/issues/8677>`_) - Use UTF-8 to handle ZIP archive entries on Python 2 according to PEP 427, so non-ASCII paths can be resolved as expected. (`8684 <https://github.com/pypa/pip/issues/8684>`_) Improved Documentation ---------------------- - Add details on old resolver deprecation and removal to migration documentation. (`8371 <https://github.com/pypa/pip/issues/8371>`_) - Fix feature flag name in docs. (`8660 <https://github.com/pypa/pip/issues/8660>`_) ``` ### 20.2 ``` ================= Deprecations and Removals ------------------------- - Deprecate setup.py-based builds that do not generate an ``.egg-info`` directory. (`6998 <https://github.com/pypa/pip/issues/6998>`_, `8617 <https://github.com/pypa/pip/issues/8617>`_) - Disallow passing install-location-related arguments in ``--install-options``. (`7309 <https://github.com/pypa/pip/issues/7309>`_) - Add deprecation warning for invalid requirements format "base>=1.0[extra]" (`8288 <https://github.com/pypa/pip/issues/8288>`_) - Deprecate legacy setup.py install when building a wheel failed for source distributions without pyproject.toml (`8368 <https://github.com/pypa/pip/issues/8368>`_) - Deprecate -b/--build/--build-dir/--build-directory. Its current behaviour is confusing and breaks in case different versions of the same distribution need to be built during the resolution process. Using the TMPDIR/TEMP/TMP environment variable, possibly combined with --no-clean covers known use cases. (`8372 <https://github.com/pypa/pip/issues/8372>`_) - Remove undocumented and deprecated option ``--always-unzip`` (`8408 <https://github.com/pypa/pip/issues/8408>`_) Features -------- - Log debugging information about pip, in ``pip install --verbose``. (`3166 <https://github.com/pypa/pip/issues/3166>`_) - Refine error messages to avoid showing Python tracebacks when an HTTP error occurs. (`5380 <https://github.com/pypa/pip/issues/5380>`_) - Install wheel files directly instead of extracting them to a temp directory. (`6030 <https://github.com/pypa/pip/issues/6030>`_) - Add a beta version of pip's next-generation dependency resolver. Move pip's new resolver into beta, remove the ``--unstable-feature=resolver`` flag, and enable the ``--use-feature=2020-resolver`` flag. The new resolver is significantly stricter and more consistent when it receives incompatible instructions, and reduces support for certain kinds of :ref:`Constraints Files`, so some workarounds and workflows may break. More details about how to test and migrate, and how to report issues, at :ref:`Resolver changes 2020` . Maintainers are preparing to ``` ### 20.2b1 ``` =================== Bug Fixes --------- - Correctly treat wheels containing non-ASCII file contents so they can be installed on Windows. (`5712 <https://github.com/pypa/pip/issues/5712>`_) - Prompt the user for password if the keyring backend doesn't return one (`7998 <https://github.com/pypa/pip/issues/7998>`_) Improved Documentation ---------------------- - Add GitHub issue template for reporting when the dependency resolver fails (`8207 <https://github.com/pypa/pip/issues/8207>`_) ```
Links - PyPI: https://pypi.org/project/pip - Changelog: https://pyup.io/changelogs/pip/ - Homepage: https://pip.pypa.io/

Update tox from 3.16.1 to 3.19.0.

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

Links - PyPI: https://pypi.org/project/tox - Docs: http://tox.readthedocs.org
codecov-commenter commented 4 years ago

Codecov Report

Merging #10 into master will not change coverage. The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##           master      #10   +/-   ##
=======================================
  Coverage   90.98%   90.98%           
=======================================
  Files          17       17           
  Lines         832      832           
=======================================
  Hits          757      757           
  Misses         75       75

Continue to review full report at Codecov.

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pyup-bot commented 4 years ago

Closing this in favor of #11