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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 15 #91

Closed pyup-bot closed 2 years ago

pyup-bot commented 2 years ago

Update sphinx from 4.4.0 to 4.5.0.

Changelog ### 4.5.0 ``` ===================================== Incompatible changes -------------------- * 10112: extlinks: Disable hardcoded links detector by default * 9993, 10177: std domain: Disallow to refer an inline target via :rst:role:`ref` role Deprecated ---------- * ``sphinx.ext.napoleon.docstring.GoogleDocstring._qualify_name()`` Features added -------------- * 10260: Enable ``FORCE_COLOR`` and ``NO_COLOR`` for terminal colouring * 10234: autosummary: Add "autosummary" CSS class to summary tables * 10125: extlinks: Improve suggestion message for a reference having title * 10112: extlinks: Add :confval:`extlinks_detect_hardcoded_links` to enable hardcoded links detector feature * 9494, 9456: html search: Add a config variable :confval:`html_show_search_summary` to enable/disable the search summaries * 9337: HTML theme, add option ``enable_search_shortcuts`` that enables :kbd:'/' as a Quick search shortcut and :kbd:`Esc` shortcut that removes search highlighting. * 10107: i18n: Allow to suppress translation warnings by adding ``noqa`` comment to the tail of each translation message * 10252: C++, support attributes on classes, unions, and enums. * 10253: :rst:dir:`pep` role now generates URLs based on peps.python.org Bugs fixed ---------- * 9876: autodoc: Failed to document an imported class that is built from native binary module * 10133: autodoc: Crashed when mocked module is used for type annotation * 10146: autodoc: :confval:`autodoc_default_options` does not support ``no-value`` option * 9971: autodoc: TypeError is raised when the target object is annotated by unhashable object * 10205: extlinks: Failed to compile regexp on checking hardcoded links * 10277: html search: Could not search short words (ex. "use") * 9529: LaTeX: named auto numbered footnote (ex. ``[named]``) that is referred multiple times was rendered to a question mark * 9924: LaTeX: multi-line :rst:dir:`cpp:function` directive has big vertical spacing in Latexpdf * 10158: LaTeX: excessive whitespace since v4.4.0 for undocumented variables/structure members * 10175: LaTeX: named footnote reference is linked to an incorrect footnote if the name is also used in the different document * 10269: manpage: Failed to resolve the title of :ref: cross references * 10179: i18n: suppress "rST localization" warning * 10118: imgconverter: Unnecessary availablity check is called for remote URIs * 10181: napoleon: attributes are displayed like class attributes for google style docstrings when :confval:`napoleon_use_ivar` is enabled * 10122: sphinx-build: make.bat does not check the installation of sphinx-build command before showing help ```
Links - PyPI: https://pypi.org/project/sphinx - Changelog: https://pyup.io/changelogs/sphinx/ - Homepage: https://www.sphinx-doc.org/

Update pytest from 7.0.1 to 7.1.1.

Changelog ### 7.1.0 ``` ========================= Breaking Changes ---------------- - `8838 <https://github.com/pytest-dev/pytest/issues/8838>`_: As per our policy, the following features have been deprecated in the 6.X series and are now removed: * ``pytest._fillfuncargs`` function. * ``pytest_warning_captured`` hook - use ``pytest_warning_recorded`` instead. * ``-k -foobar`` syntax - use ``-k 'not foobar'`` instead. * ``-k foobar:`` syntax. * ``pytest.collect`` module - import from ``pytest`` directly. For more information consult `Deprecations and Removals <https://docs.pytest.org/en/latest/deprecations.html>`__ in the docs. - `9437 <https://github.com/pytest-dev/pytest/issues/9437>`_: Dropped support for Python 3.6, which reached `end-of-life <https://devguide.python.org/#status-of-python-branches>`__ at 2021-12-23. Improvements ------------ - `5192 <https://github.com/pytest-dev/pytest/issues/5192>`_: Fixed test output for some data types where ``-v`` would show less information. Also, when showing diffs for sequences, ``-q`` would produce full diffs instead of the expected diff. - `9362 <https://github.com/pytest-dev/pytest/issues/9362>`_: pytest now avoids specialized assert formatting when it is detected that the default ``__eq__`` is overridden in ``attrs`` or ``dataclasses``. - `9536 <https://github.com/pytest-dev/pytest/issues/9536>`_: When ``-vv`` is given on command line, show skipping and xfail reasons in full instead of truncating them to fit the terminal width. - `9644 <https://github.com/pytest-dev/pytest/issues/9644>`_: More information about the location of resources that led Python to raise :class:`ResourceWarning` can now be obtained by enabling :mod:`tracemalloc`. See :ref:`resource-warnings` for more information. - `9678 <https://github.com/pytest-dev/pytest/issues/9678>`_: More types are now accepted in the ``ids`` argument to ``pytest.mark.parametrize``. Previously only `str`, `float`, `int` and `bool` were accepted; now `bytes`, `complex`, `re.Pattern`, `Enum` and anything with a `__name__` are also accepted. - `9692 <https://github.com/pytest-dev/pytest/issues/9692>`_: :func:`pytest.approx` now raises a :class:`TypeError` when given an unordered sequence (such as :class:`set`). Note that this implies that custom classes which only implement ``__iter__`` and ``__len__`` are no longer supported as they don't guarantee order. Bug Fixes --------- - `8242 <https://github.com/pytest-dev/pytest/issues/8242>`_: The deprecation of raising :class:`unittest.SkipTest` to skip collection of tests during the pytest collection phase is reverted - this is now a supported feature again. - `9493 <https://github.com/pytest-dev/pytest/issues/9493>`_: Symbolic link components are no longer resolved in conftest paths. This means that if a conftest appears twice in collection tree, using symlinks, it will be executed twice. For example, given tests/real/conftest.py tests/real/test_it.py tests/link -> tests/real running ``pytest tests`` now imports the conftest twice, once as ``tests/real/conftest.py`` and once as ``tests/link/conftest.py``. This is a fix to match a similar change made to test collection itself in pytest 6.0 (see :pull:`6523` for details). - `9626 <https://github.com/pytest-dev/pytest/issues/9626>`_: Fixed count of selected tests on terminal collection summary when there were errors or skipped modules. If there were errors or skipped modules on collection, pytest would mistakenly subtract those from the selected count. - `9645 <https://github.com/pytest-dev/pytest/issues/9645>`_: Fixed regression where ``--import-mode=importlib`` used together with :envvar:`PYTHONPATH` or :confval:`pythonpath` would cause import errors in test suites. - `9708 <https://github.com/pytest-dev/pytest/issues/9708>`_: :fixture:`pytester` now requests a :fixture:`monkeypatch` fixture instead of creating one internally. This solves some issues with tests that involve pytest environment variables. - `9730 <https://github.com/pytest-dev/pytest/issues/9730>`_: Malformed ``pyproject.toml`` files now produce a clearer error message. ```
Links - PyPI: https://pypi.org/project/pytest - Changelog: https://pyup.io/changelogs/pytest/ - Homepage: https://docs.pytest.org/en/latest/

Update pydicom from 2.2.2 to 2.3.0.

Changelog ### 2.3.0 ``` A number of changes, enhancements and bug fixes. See the [release notes](https://pydicom.github.io/pydicom/stable/release_notes/index.html#version-2-3-0). ```
Links - PyPI: https://pypi.org/project/pydicom - Changelog: https://pyup.io/changelogs/pydicom/ - Repo: https://github.com/pydicom/pydicom/archive/master.zip

Update pip from 22.0.3 to 22.0.4.

Changelog ### 22.0.4 ``` =================== Deprecations and Removals ------------------------- - Drop the doctype check, that presented a warning for index pages that use non-compliant HTML 5. (`10903 <https://github.com/pypa/pip/issues/10903>`_) Vendored Libraries ------------------ - Downgrade distlib to 0.3.3. ```
Links - PyPI: https://pypi.org/project/pip - Changelog: https://pyup.io/changelogs/pip/ - Homepage: https://pip.pypa.io/

Update tox from 3.24.5 to 3.25.0.

Changelog ### 3.25.0 ``` -------------------- Bugfixes ^^^^^^^^ - Fixed failing isolated_build because setuptools warning was captured in ``build_requires``. -- by :user:`zariiii9003` `2332 <https://github.com/tox-dev/tox/issues/2332>`_ - Avoid potential 30s delay caused by socket.getfqdn(). -- by :user:`ssbarnea` `2375 <https://github.com/tox-dev/tox/issues/2375>`_ Features ^^^^^^^^ - Ignore missing commands if they are prefixed by ``-`` -- by :user:`cdown`. `2315 <https://github.com/tox-dev/tox/issues/2315>`_ - Add default environment variables (such as http_proxy) regardless of their case to passenv on UNIX -- by :user:`poggenhans`. `2372 <https://github.com/tox-dev/tox/issues/2372>`_ - On Windows ``PROGRAMFILES``, ``PROGRAMFILES(X86)``, and ``PROGRAMDATA`` environment variables are now passed through, unmasking system values necessary to locate resources such as a C compiler. `2382 <https://github.com/tox-dev/tox/issues/2382>`_ Documentation ^^^^^^^^^^^^^ - Deleted the tox mailing list -- by :user:`jugmac00` `2364 <https://github.com/tox-dev/tox/issues/2364>`_ ```
Links - PyPI: https://pypi.org/project/tox - Changelog: https://pyup.io/changelogs/tox/ - Docs: https://tox.readthedocs.io

Update twine from 3.8.0 to 4.0.0.

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 2.1.6 to 2.1.7.

Changelog ### 2.1.7 ``` ~~~~~ 2022-03-25 • `full history <https://github.com/gorakhargosh/watchdog/compare/v2.1.6...v2.1.7>`__ - Eliminate timeout in waiting on event queue. (`861 <https://github.com/gorakhargosh/watchdog/pull/861>`_) - [inotify] Fix ``not`` equality implementation for ``InotifyEvent``. (`848 <https://github.com/gorakhargosh/watchdog/pull/848>`_) - [watchmedo] Fix calling commands from within a Python script. (`879 <https://github.com/gorakhargosh/watchdog/pull/879>`_) - [watchmedo] ``PyYAML`` is loaded only when strictly necessary. Simple usages of ``watchmedo`` are possible without the module being installed. (`847 <https://github.com/gorakhargosh/watchdog/pull/847>`_) - Thanks to our beloved contributors: sattlerc, JanzenLiu, 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 2.17.0 to 2.18.1.

Changelog ### 2.18.1 ``` =================== Fixes - Fix regression for `repo: local` hooks running `python<3.7` - 2324 PR by asottile. ``` ### 2.18.0 ``` =================== Features - Keep `GIT_HTTP_PROXY_AUTHMETHOD` in git environ. - 2272 PR by VincentBerthier. - 2271 issue by VincentBerthier. - Support both `cs` and `coursier` executables for coursier hooks. - 2293 PR by Holzhaus. - Include more information in errors for `language_version` / `additional_dependencies` for languages which do not support them. - 2315 PR by asottile. - Have autoupdate preferentially pick tags which look like versions when there are multiple equivalent tags. - 2312 PR by mblayman. - 2311 issue by mblayman. - Upgrade `ruby-build`. - 2319 PR by jalessio. - Add top level `default_install_hook_types` which will be installed when `--hook-types` is not specified in `pre-commit install`. - 2322 PR by asottile. Fixes - Fix typo in help message for `--from-ref` and `--to-ref`. - 2266 PR by leetrout. - Prioritize binary builds for R dependencies. - 2277 PR by lorenzwalthert. - Fix handling of git worktrees. - 2252 PR by daschuer. - Fix handling of `$R_HOME` for R hooks. - 2301 PR by jeff-m-sullivan. - 2300 issue by jeff-m-sullivan. - Fix a rare race condition in change stashing. - 2323 PR by asottile. - 2287 issue by ian-h-chamberlain. Updating - Remove python3.6 support. Note that pre-commit still supports running hooks written in older versions, but pre-commit itself requires python 3.7+. - 2215 PR by asottile. - pre-commit has migrated from the `master` branch to `main`. - 2302 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

Update beautifulsoup4 from 4.10.0 to 4.11.1.

Changelog ### 4.11.0 ``` * Ported unit tests to use pytest. * Added special string classes, RubyParenthesisString and RubyTextString, to make it possible to treat ruby text specially in get_text() calls. [bug=1941980] * It's now possible to customize the way output is indented by providing a value for the 'indent' argument to the Formatter constructor. The 'indent' argument works very similarly to the argument of the same name in the Python standard library's json.dump() function. [bug=1955497] * If the charset-normalizer Python module (https://pypi.org/project/charset-normalizer/) is installed, Beautiful Soup will use it to detect the character sets of incoming documents. This is also the module used by newer versions of the Requests library. For the sake of backwards compatibility, chardet and cchardet both take precedence if installed. [bug=1955346] * Added a workaround for an lxml bug (https://bugs.launchpad.net/lxml/+bug/1948551) that causes problems when parsing a Unicode string beginning with BYTE ORDER MARK. [bug=1947768] * Issue a warning when an HTML parser is used to parse a document that looks like XML but not XHTML. [bug=1939121] * Do a better job of keeping track of namespaces as an XML document is parsed, so that CSS selectors that use namespaces will do the right thing more often. [bug=1946243] * Some time ago, the misleadingly named "text" argument to find-type methods was renamed to the more accurate "string." But this supposed "renaming" didn't make it into important places like the method signatures or the docstrings. That's corrected in this version. "text" still works, but will give a DeprecationWarning. [bug=1947038] * Fixed a crash when pickling a BeautifulSoup object that has no tree builder. [bug=1934003] * Fixed a crash when overriding multi_valued_attributes and using the html5lib parser. [bug=1948488] * Standardized the wording of the MarkupResemblesLocatorWarning warnings to omit untrusted input and make the warnings less judgmental about what you ought to be doing. [bug=1955450] * Removed support for the iconv_codec library, which doesn't seem to exist anymore and was never put up on PyPI. (The closest replacement on PyPI, iconv_codecs, is GPL-licensed, so we can't use it--it's also quite old.) ```
Links - PyPI: https://pypi.org/project/beautifulsoup4 - Changelog: https://pyup.io/changelogs/beautifulsoup4/ - Homepage: https://www.crummy.com/software/BeautifulSoup/bs4/

Update requests from 2.26.0 to 2.27.1.

Changelog ### 2.27.1 ``` ------------------- **Bugfixes** - Fixed parsing issue that resulted in the `auth` component being dropped from proxy URLs. (6028) ``` ### 2.27.0 ``` ------------------- **Improvements** - Officially added support for Python 3.10. (5928) - Added a `requests.exceptions.JSONDecodeError` to unify JSON exceptions between Python 2 and 3. This gets raised in the `response.json()` method, and is backwards compatible as it inherits from previously thrown exceptions. Can be caught from `requests.exceptions.RequestException` as well. (5856) - Improved error text for misnamed `InvalidSchema` and `MissingSchema` exceptions. This is a temporary fix until exceptions can be renamed (Schema->Scheme). (6017) - Improved proxy parsing for proxy URLs missing a scheme. This will address recent changes to `urlparse` in Python 3.9+. (5917) **Bugfixes** - Fixed defect in `extract_zipped_paths` which could result in an infinite loop for some paths. (5851) - Fixed handling for `AttributeError` when calculating length of files obtained by `Tarfile.extractfile()`. (5239) - Fixed urllib3 exception leak, wrapping `urllib3.exceptions.InvalidHeader` with `requests.exceptions.InvalidHeader`. (5914) - Fixed bug where two Host headers were sent for chunked requests. (5391) - Fixed regression in Requests 2.26.0 where `Proxy-Authorization` was incorrectly stripped from all requests sent with `Session.send`. (5924) - Fixed performance regression in 2.26.0 for hosts with a large number of proxies available in the environment. (5924) - Fixed idna exception leak, wrapping `UnicodeError` with `requests.exceptions.InvalidURL` for URLs with a leading dot (.) in the domain. (5414) **Deprecations** - Requests support for Python 2.7 and 3.6 will be ending in 2022. While we don't have exact dates, Requests 2.27.x is likely to be the last release series providing support. ```
Links - PyPI: https://pypi.org/project/requests - Changelog: https://pyup.io/changelogs/requests/ - Docs: https://requests.readthedocs.io
pyup-bot commented 2 years ago

Closing this in favor of #92