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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 27 #98

Closed pyup-bot closed 2 years ago

pyup-bot commented 2 years ago

Update sphinx from 4.5.0 to 5.0.2.

Changelog ### 5.0.2 ``` ===================================== Features added -------------- * 10523: HTML Theme: Expose the Docutils's version info tuple as a template variable, ``docutils_version_info``. Patch by Adam Turner. Bugs fixed ---------- * 10538: autodoc: Inherited class attribute having docstring is documented even if :confval:`autodoc_inherit_docstring` is disabled * 10509: autosummary: autosummary fails with a shared library * 10497: py domain: Failed to resolve strings in Literal. Patch by Adam Turner. * 10523: HTML Theme: Fix double brackets on citation references in Docutils 0.18+. Patch by Adam Turner. * 10534: Missing CSS for nav.contents in Docutils 0.18+. Patch by Adam Turner. ``` ### 5.0.1 ``` ===================================== Bugs fixed ---------- * 10498: gettext: TypeError is raised when sorting warning messages if a node has no line number. Patch by Adam Turner. * 10493: HTML Theme: :rst:dir:`topic` directive is rendered incorrectly with Docutils 0.18. Patch by Adam Turner. * 10495: IndexError is raised for a :rst:role:`kbd` role having a separator. Patch by Adam Turner. ``` ### 5.0.0 ``` * 9575: autodoc: The annotation of return value should not be shown when ``autodoc_typehints="description"`` * 9648: autodoc: ``*args`` and ``**kwargs`` entries are duplicated when ``autodoc_typehints="description"`` * 8180: autodoc: Docstring metadata ignored for attributes * 10443: epub: EPUB builder can't detect the mimetype of .webp file * 10104: gettext: Duplicated locations are shown if 3rd party extension does not provide correct information * 10456: py domain: ``:meta:`` fields are displayed if docstring contains two or more meta-field * 9096: sphinx-build: the value of progress bar for paralle build is wrong * 10110: sphinx-build: exit code is not changed when error is raised on builder-finished event ```
Links - PyPI: https://pypi.org/project/sphinx - Changelog: https://pyup.io/changelogs/sphinx/ - Homepage: https://www.sphinx-doc.org/

Update sphinx_autodoc_typehints from 1.18.1 to 1.18.3.

Changelog ### 1.18.3 ``` - Support and require `nptyping>=2.1.2` ``` ### 1.18.2 ``` - Support and require `nptyping>=2.1.1` ```
Links - PyPI: https://pypi.org/project/sphinx-autodoc-typehints - Changelog: https://pyup.io/changelogs/sphinx-autodoc-typehints/ - Repo: https://github.com/tox-dev/sphinx-autodoc-typehints/archive/main.zip

Update coverage from 6.3.2 to 6.4.1.

Changelog ### 6.4.1 ``` -------------------------- - Greatly improved performance on PyPy, and other environments that need the pure Python trace function. Thanks, Carl Friedrich Bolz-Tereick (`pull 1381`_ and `pull 1388`_). Slightly improved performance when using the C trace function, as most environments do. Closes `issue 1339`_. - The conditions for using tomllib from the standard library have been made more precise, so that 3.11 alphas will continue to work. Closes `issue 1390`_. .. _issue 1339: https://github.com/nedbat/coveragepy/issues/1339 .. _pull 1381: https://github.com/nedbat/coveragepy/pull/1381 .. _pull 1388: https://github.com/nedbat/coveragepy/pull/1388 .. _issue 1390: https://github.com/nedbat/coveragepy/issues/1390 .. _changes_64: ``` ### 6.4 ``` ------------------------ - A new setting, :ref:`config_run_sigterm`, controls whether a SIGTERM signal handler is used. In 6.3, the signal handler was always installed, to capture data at unusual process ends. Unfortunately, this introduced other problems (see `issue 1310`_). Now the signal handler is only used if you opt-in by setting ``[run] sigterm = true``. - Small changes to the HTML report: - Added links to next and previous file, and more keyboard shortcuts: ``[`` and ``]`` for next file and previous file; ``u`` for up to the index; and ``?`` to open/close the help panel. Thanks, `J. M. F. Tsang <pull 1364_>`_. - The timestamp and version are displayed at the top of the report. Thanks, `Ammar Askar <pull 1354_>`_. Closes `issue 1351`_. - A new debug option ``debug=sqldata`` adds more detail to ``debug=sql``, logging all the data being written to the database. - Previously, running ``coverage report`` (or any of the reporting commands) in an empty directory would create a .coverage data file. Now they do not, fixing `issue 1328`_. - On Python 3.11, the ``[toml]`` extra no longer installs tomli, instead using tomllib from the standard library. Thanks `Shantanu <pull 1359_>`_. - In-memory CoverageData objects now properly update(), closing `issue 1323`_. .. _issue 1310: https://github.com/nedbat/coveragepy/issues/1310 .. _issue 1323: https://github.com/nedbat/coveragepy/issues/1323 .. _issue 1328: https://github.com/nedbat/coveragepy/issues/1328 .. _issue 1351: https://github.com/nedbat/coveragepy/issues/1351 .. _pull 1354: https://github.com/nedbat/coveragepy/pull/1354 .. _pull 1359: https://github.com/nedbat/coveragepy/pull/1359 .. _pull 1364: https://github.com/nedbat/coveragepy/pull/1364 .. _changes_633: ``` ### 6.3.3 ``` -------------------------- - Fix: Coverage.py now builds successfully on CPython 3.11 (3.11.0b1) again. Closes `issue 1367`_. Some results for generators may have changed. .. _issue 1367: https://github.com/nedbat/coveragepy/issues/1367 .. _changes_632: ```
Links - PyPI: https://pypi.org/project/coverage - Changelog: https://pyup.io/changelogs/coverage/ - Repo: https://github.com/nedbat/coveragepy

Update pip from 22.0.4 to 22.1.2.

Changelog ### 22.1.2 ``` =================== Bug Fixes --------- - Revert `10979 <https://github.com/pypa/pip/issues/10979>`_ since it introduced a regression in certain edge cases. (`#10979 <https://github.com/pypa/pip/issues/10979>`_) - Fix an incorrect assertion in the logging logic, that prevented the upgrade prompt from being presented. (`11136 <https://github.com/pypa/pip/issues/11136>`_) ``` ### 22.1.1 ``` =================== Bug Fixes --------- - Properly filter out optional dependencies (i.e. extras) when checking build environment distributions. (`11112 <https://github.com/pypa/pip/issues/11112>`_) - Change the build environment dependency checking to be opt-in. (`11116 <https://github.com/pypa/pip/issues/11116>`_) - Allow using a pre-release version to satisfy a build requirement. This helps manually populated build environments to more accurately detect build-time requirement conflicts. (`11123 <https://github.com/pypa/pip/issues/11123>`_) ``` ### 22.1 ``` ================= Process ------- - Enable the ``importlib.metadata`` metadata implementation by default on Python 3.11 (or later). The environment variable ``_PIP_USE_IMPORTLIB_METADATA`` can still be used to enable the implementation on 3.10 and earlier, or disable it on 3.11 (by setting it to ``0`` or ``false``). Bug Fixes --------- - Revert `9243 <https://github.com/pypa/pip/issues/9243>`_ since it introduced a regression in certain edge cases. (`#10962 <https://github.com/pypa/pip/issues/10962>`_) - Fix missing ``REQUESTED`` metadata when using URL constraints. (`11079 <https://github.com/pypa/pip/issues/11079>`_) - ``pip config`` now normalizes names by converting underscores into dashes. (`9330 <https://github.com/pypa/pip/issues/9330>`_) ``` ### 22.1b1 ``` =================== Process ------- - Start migration of distribution metadata implementation from ``pkg_resources`` to ``importlib.metadata``. The new implementation is currently not exposed in any user-facing way, but included in the code base for easier development. Deprecations and Removals ------------------------- - Drop ``--use-deprecated=out-of-tree-build``, according to deprecation message. (`11001 <https://github.com/pypa/pip/issues/11001>`_) Features -------- - Add option to install and uninstall commands to opt-out from running-as-root warning. (`10556 <https://github.com/pypa/pip/issues/10556>`_) - Include Project-URLs in ``pip show`` output. (`10799 <https://github.com/pypa/pip/issues/10799>`_) - Improve error message when ``pip config edit`` is provided an editor that doesn't exist. (`10812 <https://github.com/pypa/pip/issues/10812>`_) - Add a user interface for supplying config settings to build backends. (`11059 <https://github.com/pypa/pip/issues/11059>`_) - Add support for Powershell autocompletion. (`9024 <https://github.com/pypa/pip/issues/9024>`_) - Explains why specified version cannot be retrieved when *Requires-Python* is not satisfied. (`9615 <https://github.com/pypa/pip/issues/9615>`_) - Validate build dependencies when using ``--no-build-isolation``. (`9794 <https://github.com/pypa/pip/issues/9794>`_) Bug Fixes --------- - Fix conditional checks to prevent ``pip.exe`` from trying to modify itself, on Windows. (`10560 <https://github.com/pypa/pip/issues/10560>`_) - Fix uninstall editable from Windows junction link. (`10696 <https://github.com/pypa/pip/issues/10696>`_) - Fallback to pyproject.toml-based builds if ``setup.py`` is present in a project, but ``setuptools`` cannot be imported. (`10717 <https://github.com/pypa/pip/issues/10717>`_) - When checking for conflicts in the build environment, correctly skip requirements containing markers that do not match the current environment. (`10883 <https://github.com/pypa/pip/issues/10883>`_) - Disable brotli import in vendored urllib3 so brotli could be uninstalled/upgraded by pip. (`10950 <https://github.com/pypa/pip/issues/10950>`_) - Prioritize URL credentials over netrc. (`10979 <https://github.com/pypa/pip/issues/10979>`_) - Filter available distributions using hash declarations from constraints files. (`9243 <https://github.com/pypa/pip/issues/9243>`_) - Fix an error when trying to uninstall packages installed as editable from a network drive. (`9452 <https://github.com/pypa/pip/issues/9452>`_) - Fix pip install issues using a proxy due to an inconsistency in how Requests is currently handling variable precedence in session. (`9691 <https://github.com/pypa/pip/issues/9691>`_) Vendored Libraries ------------------ - Upgrade CacheControl to 0.12.11 - Upgrade distro to 1.7.0 - Upgrade platformdirs to 2.5.2 - Remove ``progress`` from vendored dependencies. - Upgrade ``pyparsing`` to 3.0.8 for startup performance improvements. - Upgrade rich to 12.2.0 - Upgrade tomli to 2.0.1 - Upgrade typing_extensions to 4.2.0 Improved Documentation ---------------------- - Add more dedicated topic and reference pages to the documentation. (`10899 <https://github.com/pypa/pip/issues/10899>`_) - Capitalise Y as the default for "Proceed (y/n)?" when uninstalling. (`10936 <https://github.com/pypa/pip/issues/10936>`_) - Add ``scheme://`` requirement to ``--proxy`` option's description (`10951 <https://github.com/pypa/pip/issues/10951>`_) - The wheel command now references the build interface section instead of stating the legacy setuptools behavior as the default. (`10972 <https://github.com/pypa/pip/issues/10972>`_) - Improved usefulness of ``pip config --help`` output. (`11074 <https://github.com/pypa/pip/issues/11074>`_) ```
Links - PyPI: https://pypi.org/project/pip - Changelog: https://pyup.io/changelogs/pip/ - Homepage: https://pip.pypa.io/

Update tox from 3.25.0 to 3.25.1.

Changelog ### 3.25.1 ``` -------------------- Bugfixes ^^^^^^^^ - ``sitepackages = true`` will add user's site-package to the python path on Windows as expected -- by :user:`niander` `2402 <https://github.com/tox-dev/tox/issues/2402>`_ - Avoid importing ``pipes`` on Python 3.3+ to avoid ``DeprecationWarning`` on Python 3.11 -- by :user:`adamchainz` `2417 <https://github.com/tox-dev/tox/issues/2417>`_ - Fix ``isolated_build`` when the build process produces stderr at exit. `2449 <https://github.com/tox-dev/tox/issues/2449>`_ Documentation ^^^^^^^^^^^^^ - Explain advantages of ``PIP_CONSTRAINT`` environment variable over ``--constraint`` argument. `2423 <https://github.com/tox-dev/tox/issues/2423>`_ ```
Links - PyPI: https://pypi.org/project/tox - Changelog: https://pyup.io/changelogs/tox/ - Docs: https://tox.readthedocs.io

Update twine from 4.0.0 to 4.0.1.

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 2.1.7 to 2.1.9.

Changelog ### 2.1.9 ``` ~~~~~ 2022-06-10 • `full history <https://github.com/gorakhargosh/watchdog/compare/v2.1.8...v2.1.9>`__ - [fsevents] Fix flakey test to assert that there are no errors when stopping the emitter. - [inotify] Suppress occasional ``OSError: [Errno 9] Bad file descriptor`` at shutdown. (`805 <https://github.com/gorakhargosh/watchdog/issues/805>`__) - [watchmedo] Make ``auto-restart`` restart the sub-process if it terminates. (`896 <https://github.com/gorakhargosh/watchdog/pull/896>`__) - [watchmedo] Avoid zombie sub-processes when running ``shell-command`` without ``--wait``. (`405 <https://github.com/gorakhargosh/watchdog/issues/405>`__) - Thanks to our beloved contributors: samschott, taleinat, altendky, BoboTiG ``` ### 2.1.8 ``` ~~~~~ 2022-05-15 • `full history <https://github.com/gorakhargosh/watchdog/compare/v2.1.7...v2.1.8>`__ - Fix adding failed emitters on observer schedule. (`872 <https://github.com/gorakhargosh/watchdog/issues/872>`__) - [inotify] Fix hang when unscheduling watch on a path in an unmounted filesystem. (`869 <https://github.com/gorakhargosh/watchdog/pull/869>`__) - [watchmedo] Fix broken parsing of ``--kill-after`` argument for the ``auto-restart`` command. (`870 <https://github.com/gorakhargosh/watchdog/issues/870>`__) - [watchmedo] Fix broken parsing of boolean arguments. (`887 <https://github.com/gorakhargosh/watchdog/issues/887>`__) - [watchmedo] Fix broken parsing of commands from ``auto-restart``, and ``shell-command``. (`888 <https://github.com/gorakhargosh/watchdog/issues/888>`__) - [watchmedo] Support setting verbosity level via ``-q/--quiet`` and ``-v/--verbose`` arguments. (`889 <https://github.com/gorakhargosh/watchdog/pull/889>`__) - Thanks to our beloved contributors: taleinat, kianmeng, palfrey, IlayRosenberg, 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 2.18.1 to 2.19.0.

Changelog ### 2.19.0 ``` =================== Features - Allow multiple outputs from `language: dotnet` hooks. - 2332 PR by WallucePinkham. - Add more information to `healthy()` failure. - 2348 PR by asottile. - Upgrade ruby-build. - 2342 PR by jalessio. - Add `pre-commit validate-config` / `pre-commit validate-manifest` and deprecate `pre-commit-validate-config` and `pre-commit-validate-manifest`. - 2362 PR by asottile. Fixes - Fix `pre-push` when pushed ref contains spaces. - 2345 PR by wwade. - 2344 issue by wwade. Updating - Change `pre-commit-validate-config` / `pre-commit-validate-manifest` to `pre-commit validate-config` / `pre-commit validate-manifest`. - 2362 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 requests from 2.27.1 to 2.28.1.

Changelog ### 2.28.1 ``` ------------------- **Improvements** - Speed optimization in `iter_content` with transition to `yield from`. (6170) **Dependencies** - Added support for chardet 5.0.0 (6179) - Added support for charset-normalizer 2.1.0 (6169) ``` ### 2.28.0 ``` ------------------- **Deprecations** - ⚠️ Requests has officially dropped support for Python 2.7. ⚠️ (6091) - Requests has officially dropped support for Python 3.6 (including pypy3.6). (6091) **Improvements** - Wrap JSON parsing issues in Request's JSONDecodeError for payloads without an encoding to make `json()` API consistent. (6097) - Parse header components consistently, raising an InvalidHeader error in all invalid cases. (6154) - Added provisional 3.11 support with current beta build. (6155) - Requests got a makeover and we decided to paint it black. (6095) **Bugfixes** - Fixed bug where setting `CURL_CA_BUNDLE` to an empty string would disable cert verification. All Requests 2.x versions before 2.28.0 are affected. (6074) - Fixed urllib3 exception leak, wrapping `urllib3.exceptions.SSLError` with `requests.exceptions.SSLError` for `content` and `iter_content`. (6057) - Fixed issue where invalid Windows registry entires caused proxy resolution to raise an exception rather than ignoring the entry. (6149) - Fixed issue where entire payload could be included in the error message for JSONDecodeError. (6036) ```
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 #99