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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 29 #100

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 6.4.2.

Changelog ### 6.4.2 ``` -------------------------- - Updated for a small change in Python 3.11.0 beta 4: modules now start with a line with line number 0, which is ignored. This line cannnot be executed, so coverage totals were thrown off. This line is now ignored by coverage.py, but this also means that truly empty modules (like ``__init__.py``) have no lines in them, rather than one phantom line. Fixes `issue 1419`_. - Internal debugging data added to sys.modules is now an actual module, to avoid confusing code that examines everything in sys.modules. Thanks, Yilei Yang (`pull 1399`_). .. _pull 1399: https://github.com/nedbat/coveragepy/pull/1399 .. _issue 1419: https://github.com/nedbat/coveragepy/issues/1419 .. _changes_6-4-1: ``` ### 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 2.20.0.

Changelog ### 2.20.0 ``` =================== Features - Expose `source` and `object-name` (positional args) of `prepare-commit-msg` hook as `PRE_COMMIT_COMIT_MSG_SOURCE` and `PRE_COMMIT_COMMIT_OBJECT_NAME`. - 2407 PR by M-Whitaker. - 2406 issue by M-Whitaker. Fixes - Fix `language: ruby` installs when `--user-install` is set in gemrc. - 2394 PR by narpfel. - 2393 issue by narpfel. - Adjust pty setup for solaris. - 2390 PR by gaige. - 2389 issue by gaige. - Remove unused `--config` option from `gc`, `sample-config`, `validate-config`, `validate-manifest` sub-commands. - 2429 PR by asottile. ``` ### 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 #101