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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 43 #22

Closed pyup-bot closed 3 years ago

pyup-bot commented 3 years ago

Update sphinx from 3.1.2 to 3.2.1.

Changelog ### 3.2.1 ``` ===================================== Features added -------------- * 8095: napoleon: Add :confval:`napoleon_preprocess_types` to enable the type preprocessor for numpy style docstrings * 8114: C and C++, parse function attributes after parameters and qualifiers. Bugs fixed ---------- * 8074: napoleon: Crashes during processing C-ext module * 8088: napoleon: "Inline literal start-string without end-string" warning in Numpy style Parameters section * 8084: autodoc: KeyError is raised on documenting an attribute of the broken class * 8091: autodoc: AttributeError is raised on documenting an attribute on Python 3.5.2 * 8099: autodoc: NameError is raised when target code uses ``TYPE_CHECKING`` * C++, fix parsing of template template paramters, broken by the fix of 7944 ``` ### 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 sphinx-autobuild from 0.7.1 to 2020.9.1.

Changelog ### 2020.09.01 ``` ----------------------- * Adopt Calendar Versioning. * Modernize codebase and require Python 3.6+. * Directly depend on ``sphinx``. * Rewritten documentation. * Invoke sphinx via ``{sys.executable} -m sphinx`` instead of ``sphinx-build``. * Trim dependencies down to only ``livereload`` and ``sphinx``. * Drop custom adapter for ``watchdog``. * Drop ``--poll`` flag. * Drop single letter variants for flags that were specific to sphinx-autobuild. ```
Links - PyPI: https://pypi.org/project/sphinx-autobuild - Changelog: https://pyup.io/changelogs/sphinx-autobuild/ - Repo: https://github.com/GaretJax/sphinx_autobuild

Update sphinx_autodoc_typehints from 1.11.0 to 1.11.1.

Changelog ### 1.11.1 ``` ====== * Changed formatting of ``None`` to point to the Python stdlib docs (PR by Dominic Davis-Foster) * Updated special dataclass handling (PR by Lihu Ben-Ezri-Ravin) ```
Links - PyPI: https://pypi.org/project/sphinx-autodoc-typehints - Changelog: https://pyup.io/changelogs/sphinx-autodoc-typehints/

Update black from 19.10b0 to 20.8b1.

Changelog ### 20.8b1 ``` _Packaging_ - explicitly depend on Click 7.1.2 or newer as `Black` no longer works with versions older than 7.0 ``` ### 20.8b0 ``` _Black_ - re-implemented support for explicit trailing commas: now it works consistently within any bracket pair, including nested structures (1288 and duplicates) - `Black` now reindents docstrings when reindenting code around it (1053) - `Black` now shows colored diffs (1266) - `Black` is now packaged using 'py3' tagged wheels (1388) - `Black` now supports Python 3.8 code, e.g. star expressions in return statements (1121) - `Black` no longer normalizes capital R-string prefixes as those have a community-accepted meaning (1244) - `Black` now uses exit code 2 when specified configuration file doesn't exit (1361) - `Black` now works on AWS Lambda (1141) - added `--force-exclude` argument (1032) - removed deprecated `--py36` option (1236) - fixed `--diff` output when EOF is encountered (526) - fixed ` fmt: off` handling around decorators (560) - fixed unstable formatting with some ` type: ignore` comments (1113) - fixed invalid removal on organizing brackets followed by indexing (1575) - introduced `black-primer`, a CI tool that allows us to run regression tests against existing open source users of Black (1402) - introduced property-based fuzzing to our test suite based on Hypothesis and Hypothersmith (1566) - implemented experimental and disabled by default long string rewrapping (1132), hidden under a `--experimental-string-processing` flag while it's being worked on; this is an undocumented and unsupported feature, you lose Internet points for depending on it (1609) Vim plugin - prefer virtualenv packages over global packages (1383) ```
Links - PyPI: https://pypi.org/project/black - Changelog: https://pyup.io/changelogs/black/ - Repo: https://github.com/psf/black

Update bump2version from 1.0.0 to 1.0.1.

Changelog ### 1.0.1 ``` - Added: enable special characters in search/replace, thanks mckelvin - Added: allow globbing a pattern to match multiple files, thanks balrok - Added: way to only bump a specified file via --no-configured-files, thanks balrok - Fixed: dry-run now correctly outputs, thanks fmigneault - Housekeeping: documentation for lightweight tags improved, thanks GreatBahram - Housekeeping: added related tools document, thanks florisla - Fixed: no more falling back to default search, thanks florisla ```
Links - PyPI: https://pypi.org/project/bump2version - Changelog: https://pyup.io/changelogs/bump2version/ - Repo: https://github.com/c4urself/bump2version

Update pytest from 5.4.3 to 6.1.1.

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 factory-boy from 2.12 to 3.1.0.

Changelog ### 3.1.0 ``` ------------------ *New:* - Allow all types of declarations in :class:`factory.Faker` calls - enables references to other faker-defined attributes. ``` ### 3.0.1 ``` ------------------ *Bugfix:* - :issue:`769`: Fix ``import factory; factory.django.DjangoModelFactory`` and similar calls. ``` ### 3.0.0 ``` ------------------ Breaking changes """""""""""""""" The following aliases were removed: +------------------------------------------------+---------------------------------------------------+ | Broken alias | New import | +================================================+===================================================+ | ``from factory import DjangoModelFactory`` | ``from factory.django import DjangoModelFactory`` | +------------------------------------------------+---------------------------------------------------+ | ``from factory import MogoFactory`` | ``from factory.mogo import MogoFactory`` | +------------------------------------------------+---------------------------------------------------+ | ``from factory.fuzzy import get_random_state`` | ``from factory.random import get_random_state`` | +------------------------------------------------+---------------------------------------------------+ | ``from factory.fuzzy import set_random_state`` | ``from factory.random import set_random_state`` | +------------------------------------------------+---------------------------------------------------+ | ``from factory.fuzzy import reseed_random`` | ``from factory.random import reseed_random`` | +------------------------------------------------+---------------------------------------------------+ *Removed:* - Drop support for Python 2 and 3.4. These versions `are not maintained anymore <https://devguide.python.org/devcycle/end-of-life-branches>`__. - Drop support for Django 2.0 and 2.1. These versions `are not maintained anymore <https://www.djangoproject.com/download/supported-versions>`__. - Remove deprecated ``force_flush`` from ``SQLAlchemyModelFactory`` options. Use ``sqlalchemy_session_persistence = "flush"`` instead. - Drop deprecated ``attributes()`` from :class:`~factory.Factory` subclasses; use ``factory.make_factory(dict, FactoryClass._meta.pre_declarations)`` instead. - Drop deprecated ``declarations()`` from :class:`~factory.Factory` subclasses; use ``FactoryClass._meta.pre_declarations`` instead. - Drop ``factory.compat`` module. *New:* - Add support for Python 3.8 - Add support for Django 2.2 and 3.0 - Report misconfiguration when a :py:class:`~factory.Factory` is used as the :py:attr:`~factory.Factory.model` for another :py:class:`~factory.Factory`. - Allow configuring the color palette of :py:class:`~factory.django.ImageField`. - :py:meth:`get_random_state()` now represents the state of Faker and ``factory_boy`` fuzzy attributes. - Add SQLAlchemy ``get_or_create`` support *Improvements:* - :issue:`561`: Display a developer-friendly error message when providing a model instead of a factory in a :class:`~factory.declarations.SubFactory` class. *Bugfix:* - Fix issue with SubFactory not preserving signal muting behaviour of the used factory, thanks `Patrick Stein <https://github.com/PFStein>`_. - Fix issue with overriding params in a Trait, thanks `Grégoire Rocher <https://github.com/cecedille1>`_. - :issue:`598`: Limit ``get_or_create`` behavior to fields specified in ``django_get_or_create``. - :issue:`606`: Re-raise :class:`~django.db.IntegrityError` when ``django_get_or_create`` with multiple fields fails to lookup model using user provided keyword arguments. - :issue:`630`: TypeError masked by __repr__ AttributeError when initializing ``Maybe`` with inconsistent phases. ```
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 5.2 to 5.3.

Changelog ### 5.3 ``` -------------------------- - The ``source`` setting has always been interpreted as either a file path or a module, depending on which existed. If both interpretations were valid, it was assumed to be a file path. The new ``source_pkgs`` setting can be used to name a package to disambiguate this case. Thanks, Thomas Grainger. Fixes `issue 268`_. - If a plugin was disabled due to an exception, we used to still try to record its information, causing an exception, as reported in `issue 1011`_. This is now fixed. .. _issue 268: https://github.com/nedbat/coveragepy/issues/268 .. _issue 1011: https://github.com/nedbat/coveragepy/issues/1011 .. _changes_521: ``` ### 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 flake8 from 3.8.3 to 3.8.4.

Changelog ### 3.8.4 ``` ------------------- You can view the `3.8.4 milestone`_ on GitLab for more details. Bugs Fixed ~~~~~~~~~~ - Fix multiprocessing errors on platforms without ``sem_open`` syscall. (See also `GitLab!448`_) - Fix skipping of physical checks on the last line of a file which does not end in a newline (See also `GitLab!451`_) .. all links .. _3.8.4 milestone: https://gitlab.com/pycqa/flake8/-/milestones/37 .. merge request links .. _GitLab!448: https://gitlab.com/pycqa/flake8/merge_requests/448 .. _GitLab!451: https://gitlab.com/pycqa/flake8/merge_requests/451 ```
Links - PyPI: https://pypi.org/project/flake8 - Changelog: https://pyup.io/changelogs/flake8/ - Repo: https://gitlab.com/pycqa/flake8

Update pip from 20.1.1 to 20.2.4.

Changelog ### 20.2.4 ``` =================== Deprecations and Removals ------------------------- - Document that certain removals can be fast tracked. (`8417 <https://github.com/pypa/pip/issues/8417>`_) - Document that Python versions are generally supported until PyPI usage falls below 5%. (`8927 <https://github.com/pypa/pip/issues/8927>`_) Features -------- - New resolver: Avoid accessing indexes when the installed candidate is preferred and considered good enough. (`8023 <https://github.com/pypa/pip/issues/8023>`_) - Improve error message friendliness when an environment has packages with corrupted metadata. (`8676 <https://github.com/pypa/pip/issues/8676>`_) - Cache package listings on index packages so they are guarenteed to stay stable during a pip command session. This also improves performance when a index page is accessed multiple times during the command session. (`8905 <https://github.com/pypa/pip/issues/8905>`_) - New resolver: Tweak resolution logic to improve user experience when user-supplied requirements conflict. (`8924 <https://github.com/pypa/pip/issues/8924>`_) Bug Fixes --------- - New resolver: Correctly respect ``Requires-Python`` metadata to reject incompatible packages in ``--no-deps`` mode. (`8758 <https://github.com/pypa/pip/issues/8758>`_) - New resolver: Pick up hash declarations in constraints files and use them to filter available distributions. (`8792 <https://github.com/pypa/pip/issues/8792>`_) - New resolver: If a package appears multiple times in user specification with different ``--hash`` options, only hashes that present in all specifications should be allowed. (`8839 <https://github.com/pypa/pip/issues/8839>`_) Improved Documentation ---------------------- - Add ux documentation (`8807 <https://github.com/pypa/pip/issues/8807>`_) ``` ### 20.2.3 ``` =================== Deprecations and Removals ------------------------- - Deprecate support for Python 3.5 (`8181 <https://github.com/pypa/pip/issues/8181>`_) Features -------- - Make the ``setup.py install`` deprecation warning less noisy. We warn only when ``setup.py install`` succeeded and ``setup.py bdist_wheel`` failed, as situations where both fails are most probably irrelevant to this deprecation. (`8752 <https://github.com/pypa/pip/issues/8752>`_) ``` ### 20.2.2 ``` =================== Bug Fixes --------- - Only attempt to use the keyring once and if it fails, don't try again. This prevents spamming users with several keyring unlock prompts when they cannot unlock or don't want to do so. (`8090 <https://github.com/pypa/pip/issues/8090>`_) - Fix regression that distributions in system site-packages are not correctly found when a virtual environment is configured with ``system-site-packages`` on. (`8695 <https://github.com/pypa/pip/issues/8695>`_) - Disable caching for range requests, which causes corrupted wheels when pip tries to obtain metadata using the feature ``fast-deps``. (`8701 <https://github.com/pypa/pip/issues/8701>`_, `8716 <https://github.com/pypa/pip/issues/8716>`_) - Always use UTF-8 to read ``pyvenv.cfg`` to match the built-in ``venv``. (`8717 <https://github.com/pypa/pip/issues/8717>`_) - 2020 Resolver: Correctly handle marker evaluation in constraints and exclude them if their markers do not match the current environment. (`8724 <https://github.com/pypa/pip/issues/8724>`_) ``` ### 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 3.20.1.

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

Update pre-commit from 2.6.0 to 2.7.1.

Changelog ### 2.7.1 ``` ================== Fixes - Improve performance of docker hooks by removing slow `ps` call - 1572 PR by rkm. - 1569 issue by asottile. - Fix un-`healthy()` invalidation followed by install being reported as un-`healthy()`. - 1576 PR by asottile. - 1575 issue by jab. - Fix rare file race condition on windows with `os.replace()` - 1577 PR by asottile. ``` ### 2.7.0 ``` ================== Features - Produce error message if an environment is immediately unhealthy - 1535 PR by asottile. - Add --no-allow-missing-config option to init-templatedir - 1539 PR by singergr. - Add warning for old list-style configuration - 1544 PR by asottile. - Allow pre-commit to succeed on a readonly store. - 1570 PR by asottile. - 1536 issue by asottile. Fixes - Fix error messaging when the store directory is readonly - 1546 PR by asottile. - 1536 issue by asottile. - Improve `diff` performance with many hooks - 1566 PR by jhenkens. - 1564 issue by jhenkens. ```
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 4.9.1 to 4.9.3.

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

Links - PyPI: https://pypi.org/project/beautifulsoup4 - Homepage: http://www.crummy.com/software/BeautifulSoup/bs4/
pyup-bot commented 3 years ago

Closing this in favor of #23