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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 44 #70

Closed pyup-bot closed 3 years ago

pyup-bot commented 3 years ago

Update pydicom from 2.2.1 to 2.2.2.

Changelog ### 2.2.2 ``` Bug fixes and DICOM dictionary update to 2021d. ```
Links - PyPI: https://pypi.org/project/pydicom - Changelog: https://pyup.io/changelogs/pydicom/ - Repo: https://github.com/pydicom/pydicom/archive/master.zip

Update factory-boy from 3.2.0 to 3.2.1.

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

Links - PyPI: https://pypi.org/project/factory-boy - Changelog: https://pyup.io/changelogs/factory-boy/ - Repo: https://github.com/FactoryBoy/factory_boy

Update coverage from 5.5 to 6.1.1.

Changelog ### 6.1.1 ``` -------------------------- - Fix: The sticky header on the HTML report didn't work unless you had branch coverage enabled. This is now fixed: the sticky header works for everyone. (Do people still use coverage without branch measurement!? j/k) - Fix: When using explicitly declared namespace packages, the "already imported a file that will be measured" warning would be issued (`issue 888`_). This is now fixed. .. _issue 888: https://github.com/nedbat/coveragepy/issues/888 .. _changes_61: ``` ### 6.1 ``` ------------------------ - Deprecated: The ``annotate`` command and the ``Coverage.annotate`` function will be removed in a future version, unless people let me know that they are using it. Instead, the ``html`` command gives better-looking (and more accurate) output, and the ``report -m`` command will tell you line numbers of missing lines. Please get in touch if you have a reason to use ``annotate`` over those better options: nednedbatchelder.com. - Feature: Coverage now sets an environment variable, ``COVERAGE_RUN`` when running your code with the ``coverage run`` command. The value is not important, and may change in the future. Closes `issue 553`_. - Feature: The HTML report pages for Python source files now have a sticky header so the file name and controls are always visible. - Feature: The ``xml`` and ``json`` commands now describe what they wrote where. - Feature: The ``html``, ``combine``, ``xml``, and ``json`` commands all accept a ``-q/--quiet`` option to suppress the messages they write to stdout about what they are doing (`issue 1254`_). - Feature: The ``html`` command writes a ``.gitignore`` file into the HTML output directory, to prevent the report from being committed to git. If you want to commit it, you will need to delete that file. Closes `issue 1244`_. - Feature: Added support for PyPy 3.8. - Fix: More generated code is now excluded from measurement. Code such as `attrs`_ boilerplate, or doctest code, was being measured though the synthetic line numbers meant they were never reported. Once Cython was involved though, the generated .so files were parsed as Python, raising syntax errors, as reported in `issue 1160`_. This is now fixed. - Fix: When sorting human-readable names, numeric components are sorted correctly: file10.py will appear after file9.py. This applies to file names, module names, environment variables, and test contexts. - Performance: Branch coverage measurement is faster, though you might only notice on code that is executed many times, such as long-running loops. - Build: jQuery is no longer used or vendored (`issue 840`_ and `issue 1118`_). Huge thanks to Nils Kattenbeck (septatrix) for the conversion to vanilla JavaScript in `pull request 1248`_. .. _issue 553: https://github.com/nedbat/coveragepy/issues/553 .. _issue 840: https://github.com/nedbat/coveragepy/issues/840 .. _issue 1118: https://github.com/nedbat/coveragepy/issues/1118 .. _issue 1160: https://github.com/nedbat/coveragepy/issues/1160 .. _issue 1244: https://github.com/nedbat/coveragepy/issues/1244 .. _pull request 1248: https://github.com/nedbat/coveragepy/pull/1248 .. _issue 1254: https://github.com/nedbat/coveragepy/issues/1254 .. _attrs: https://www.attrs.org/ .. _changes_602: ``` ### 6.0.2 ``` -------------------------- - Namespace packages being measured weren't properly handled by the new code that ignores third-party packages. If the namespace package was installed, it was ignored as a third-party package. That problem (`issue 1231`_) is now fixed. - Packages named as "source packages" (with ``source``, or ``source_pkgs``, or pytest-cov's ``--cov``) might have been only partially measured. Their top-level statements could be marked as unexecuted, because they were imported by coverage.py before measurement began (`issue 1232`_). This is now fixed, but the package will be imported twice, once by coverage.py, then again by your test suite. This could cause problems if importing the package has side effects. - The :meth:`.CoverageData.contexts_by_lineno` method was documented to return a dict, but was returning a defaultdict. Now it returns a plain dict. It also no longer returns negative numbered keys. .. _issue 1231: https://github.com/nedbat/coveragepy/issues/1231 .. _issue 1232: https://github.com/nedbat/coveragepy/issues/1232 .. _changes_601: ``` ### 6.0.1 ``` -------------------------- - In 6.0, the coverage.py exceptions moved from coverage.misc to coverage.exceptions. These exceptions are not part of the public supported API, CoverageException is. But a number of other third-party packages were importing the exceptions from coverage.misc, so they are now available from there again (`issue 1226`_). - Changed an internal detail of how tomli is imported, so that tomli can use coverage.py for their own test suite (`issue 1228`_). - Defend against an obscure possibility under code obfuscation, where a function can have an argument called "self", but no local named "self" (`pull request 1210`_). Thanks, Ben Carlsson. .. _pull request 1210: https://github.com/nedbat/coveragepy/pull/1210 .. _issue 1226: https://github.com/nedbat/coveragepy/issues/1226 .. _issue 1228: https://github.com/nedbat/coveragepy/issues/1228 .. _changes_60: ``` ### 6.0 ``` ------------------------ - The ``coverage html`` command now prints a message indicating where the HTML report was written. Fixes `issue 1195`_. - The ``coverage combine`` command now prints messages indicating each data file being combined. Fixes `issue 1105`_. - The HTML report now includes a sentence about skipped files due to ``skip_covered`` or ``skip_empty`` settings. Fixes `issue 1163`_. - Unrecognized options in the configuration file are no longer errors. They are now warnings, to ease the use of coverage across versions. Fixes `issue 1035`_. - Fix handling of exceptions through context managers in Python 3.10. A missing exception is no longer considered a missing branch from the with statement. Fixes `issue 1205`_. - Fix another rarer instance of "Error binding parameter 0 - probably unsupported type." (`issue 1010`_). - Creating a directory for the coverage data file now is safer against conflicts when two coverage runs happen simultaneously (`pull 1220`_). Thanks, Clément Pit-Claudel. .. _issue 1035: https://github.com/nedbat/coveragepy/issues/1035 .. _issue 1105: https://github.com/nedbat/coveragepy/issues/1105 .. _issue 1163: https://github.com/nedbat/coveragepy/issues/1163 .. _issue 1195: https://github.com/nedbat/coveragepy/issues/1195 .. _issue 1205: https://github.com/nedbat/coveragepy/issues/1205 .. _pull 1220: https://github.com/nedbat/coveragepy/pull/1220 .. _changes_60b1: ``` ### 6.0b1 ``` -------------------------- - Dropped support for Python 2.7, PyPy 2, and Python 3.5. - Added support for the Python 3.10 ``match/case`` syntax. - Data collection is now thread-safe. There may have been rare instances of exceptions raised in multi-threaded programs. - Plugins (like the `Django coverage plugin`_) were generating "Already imported a file that will be measured" warnings about Django itself. These have been fixed, closing `issue 1150`_. - Warnings generated by coverage.py are now real Python warnings. - Using ``--fail-under=100`` with coverage near 100% could result in the self-contradictory message :code:`total of 100 is less than fail-under=100`. This bug (`issue 1168`_) is now fixed. - The ``COVERAGE_DEBUG_FILE`` environment variable now accepts ``stdout`` and ``stderr`` to write to those destinations. - TOML parsing now uses the `tomli`_ library. - Some minor changes to usually invisible details of the HTML report: - Use a modern hash algorithm when fingerprinting, for high-security environments (`issue 1189`_). When generating the HTML report, we save the hash of the data, to avoid regenerating an unchanged HTML page. We used to use MD5 to generate the hash, and now use SHA-3-256. This was never a security concern, but security scanners would notice the MD5 algorithm and raise a false alarm. - Change how report file names are generated, to avoid leading underscores (`issue 1167`_), to avoid rare file name collisions (`issue 584`_), and to avoid file names becoming too long (`issue 580`_). .. _Django coverage plugin: https://pypi.org/project/django-coverage-plugin/ .. _issue 580: https://github.com/nedbat/coveragepy/issues/580 .. _issue 584: https://github.com/nedbat/coveragepy/issues/584 .. _issue 1150: https://github.com/nedbat/coveragepy/issues/1150 .. _issue 1167: https://github.com/nedbat/coveragepy/issues/1167 .. _issue 1168: https://github.com/nedbat/coveragepy/issues/1168 .. _issue 1189: https://github.com/nedbat/coveragepy/issues/1189 .. _tomli: https://pypi.org/project/tomli/ .. _changes_56b1: ``` ### 5.6b1 ``` -------------------------- Note: 5.6 final was never released. These changes are part of 6.0. - Third-party packages are now ignored in coverage reporting. This solves a few problems: - Coverage will no longer report about other people's code (`issue 876`_). This is true even when using ``--source=.`` with a venv in the current directory. - Coverage will no longer generate "Already imported a file that will be measured" warnings about coverage itself (`issue 905`_). - The HTML report uses j/k to move up and down among the highlighted chunks of code. They used to highlight the current chunk, but 5.0 broke that behavior. Now the highlighting is working again. - The JSON report now includes ``percent_covered_display``, a string with the total percentage, rounded to the same number of decimal places as the other reports' totals. .. _issue 876: https://github.com/nedbat/coveragepy/issues/876 .. _issue 905: https://github.com/nedbat/coveragepy/issues/905 .. _changes_55: ```
Links - PyPI: https://pypi.org/project/coverage - Changelog: https://pyup.io/changelogs/coverage/ - Repo: https://github.com/nedbat/coveragepy

Update flake8 from 3.9.2 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/flake8 - Changelog: https://pyup.io/changelogs/flake8/ - Repo: https://github.com/pycqa/flake8

Update pip from 21.2.4 to 21.3.1.

Changelog ### 21.3.1 ``` =================== Bug Fixes --------- - Always refuse installing or building projects that have no ``pyproject.toml`` nor ``setup.py``. (`10531 <https://github.com/pypa/pip/issues/10531>`_) - Tweak running-as-root detection, to check ``os.getuid`` if it exists, on Unix-y and non-Linux/non-MacOS machines. (`10565 <https://github.com/pypa/pip/issues/10565>`_) - When installing projects with a ``pyproject.toml`` in editable mode, and the build backend does not support :pep:`660`, prepare metadata using ``prepare_metadata_for_build_wheel`` instead of ``setup.py egg_info``. Also, refuse installing projects that only have a ``setup.cfg`` and no ``setup.py`` nor ``pyproject.toml``. These restore the pre-21.3 behaviour. (`10573 <https://github.com/pypa/pip/issues/10573>`_) - Restore compatibility of where configuration files are loaded from on MacOS (back to ``Library/Application Support/pip``, instead of ``Preferences/pip``). (`10585 <https://github.com/pypa/pip/issues/10585>`_) Vendored Libraries ------------------ - Upgrade pep517 to 0.12.0 ``` ### 21.3 ``` ================= Deprecations and Removals ------------------------- - Improve deprecation warning regarding the copying of source trees when installing from a local directory. (`10128 <https://github.com/pypa/pip/issues/10128>`_) - Suppress location mismatch warnings when pip is invoked from a Python source tree, so ``ensurepip`` does not emit warnings on CPython ``make install``. (`10270 <https://github.com/pypa/pip/issues/10270>`_) - On Python 3.10 or later, the installation scheme backend has been changed to use ``sysconfig``. This is to anticipate the deprecation of ``distutils`` in Python 3.10, and its scheduled removal in 3.12. For compatibility considerations, pip installations running on Python 3.9 or lower will continue to use ``distutils``. (`10358 <https://github.com/pypa/pip/issues/10358>`_) - Remove the ``--build-dir`` option and aliases, one last time. (`10485 <https://github.com/pypa/pip/issues/10485>`_) - In-tree builds are now the default. ``--use-feature=in-tree-build`` is now ignored. ``--use-deprecated=out-of-tree-build`` may be used temporarily to ease the transition. (`10495 <https://github.com/pypa/pip/issues/10495>`_) - Un-deprecate source distribution re-installation behaviour. (`8711 <https://github.com/pypa/pip/issues/8711>`_) Features -------- - Replace vendored appdirs with platformdirs. (`10202 <https://github.com/pypa/pip/issues/10202>`_) - Support `PEP 610 <https://www.python.org/dev/peps/pep-0610/>`_ to detect editable installs in ``pip freeze`` and ``pip list``. The ``pip list`` column output has a new ``Editable project location`` column, and the JSON output has a new ``editable_project_location`` field. (`10249 <https://github.com/pypa/pip/issues/10249>`_) - ``pip freeze`` will now always fallback to reporting the editable project location when it encounters a VCS error while analyzing an editable requirement. Before, it sometimes reported the requirement as non-editable. (`10410 <https://github.com/pypa/pip/issues/10410>`_) - ``pip show`` now sorts ``Requires`` and ``Required-By`` alphabetically. (`10422 <https://github.com/pypa/pip/issues/10422>`_) - Do not raise error when there are no files to remove with ``pip cache purge/remove``. Instead log a warning and continue (to log that we removed 0 files). (`10459 <https://github.com/pypa/pip/issues/10459>`_) - When backtracking during dependency resolution, prefer the dependencies which are involved in the most recent conflict. This can significantly reduce the amount of backtracking required. (`10479 <https://github.com/pypa/pip/issues/10479>`_) - Cache requirement objects, to improve performance reducing reparses of requirement strings. (`10550 <https://github.com/pypa/pip/issues/10550>`_) - Support editable installs for projects that have a ``pyproject.toml`` and use a build backend that supports :pep:`660`. (`8212 <https://github.com/pypa/pip/issues/8212>`_) - When a revision is specified in a Git URL, use git's partial clone feature to speed up source retrieval. (`9086 <https://github.com/pypa/pip/issues/9086>`_) - Add a ``--debug`` flag, to enable a mode that doesn't log errors and propagates them to the top level instead. This is primarily to aid with debugging pip's crashes. (`9349 <https://github.com/pypa/pip/issues/9349>`_) - If a host is explicitly specified as trusted by the user (via the --trusted-host option), cache HTTP responses from it in addition to HTTPS ones. (`9498 <https://github.com/pypa/pip/issues/9498>`_) Bug Fixes --------- - Present a better error message, when a ``file:`` URL is not found. (`10263 <https://github.com/pypa/pip/issues/10263>`_) - Fix the auth credential cache to allow for the case in which the index url contains the username, but the password comes from an external source, such as keyring. (`10269 <https://github.com/pypa/pip/issues/10269>`_) - Fix double unescape of HTML ``data-requires-python`` and ``data-yanked`` attributes. (`10378 <https://github.com/pypa/pip/issues/10378>`_) - New resolver: Fixes depth ordering of packages during resolution, e.g. a dependency 2 levels deep will be ordered before a dependency 3 levels deep. (`10482 <https://github.com/pypa/pip/issues/10482>`_) - Correctly indent metadata preparation messages in pip output. (`10524 <https://github.com/pypa/pip/issues/10524>`_) Vendored Libraries ------------------ - Remove appdirs as a vendored dependency. - Upgrade distlib to 0.3.3 - Upgrade distro to 1.6.0 - Patch pkg_resources to use platformdirs rather than appdirs. - Add platformdirs as a vendored dependency. - Upgrade progress to 1.6 - Upgrade resolvelib to 0.8.0 - Upgrade urllib3 to 1.26.7 Improved Documentation ---------------------- - Update links of setuptools as setuptools moved these documents. The Simple Repository link now points to PyPUG as that is the canonical place of packaging specification, and setuptools's ``easy_install`` is deprecated. (`10430 <https://github.com/pypa/pip/issues/10430>`_) - Create a "Build System Interface" reference section, for documenting how pip interacts with build systems. (`10497 <https://github.com/pypa/pip/issues/10497>`_) ```
Links - PyPI: https://pypi.org/project/pip - Changelog: https://pyup.io/changelogs/pip/ - Homepage: https://pip.pypa.io/

Update watchdog from 2.1.5 to 2.1.6.

Changelog ### 2.1.6 ``` ~~~~~ 2021-10-01 • `full history <https://github.com/gorakhargosh/watchdog/compare/v2.1.5...v2.1.6>`__ - [bsd] Fixed returned paths in ``kqueue.py`` and restored the overall results of the test suite. (`842 <https://github.com/gorakhargosh/watchdog/pull/842>`_) - [bsd] Updated FreeBSD CI support .(`841 <https://github.com/gorakhargosh/watchdog/pull/841>`_) - [watchmedo] Removed the ``argh`` dependency in favor of the builtin ``argparse`` module. (`836 <https://github.com/gorakhargosh/watchdog/pull/836>`_) - [watchmedo] Removed unexistant ``WindowsApiAsyncObserver`` references and ``--debug-force-winapi-async`` arguments. - [watchmedo] Improved the help output. - Thanks to our beloved contributors: knobix, AndreaRe9, 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/
pyup-bot commented 3 years ago

Closing this in favor of #71