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robertopreste / HmtNote

Human mitochondrial variants annotation using HmtVar.
https://hmtnote.readthedocs.io
MIT License
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Update click to 8.1.4 #154

Closed pyup-bot closed 1 year ago

pyup-bot commented 1 year ago

This PR updates click from 7.0 to 8.1.4.

Changelog ### 8.1.4 ``` ------------- Released 2023-07-06 - Replace all ``typing.Dict`` occurrences to ``typing.MutableMapping`` for parameter hints. :issue:`2255` - Improve type hinting for decorators and give all generic types parameters. :issue:`2398` - Fix return value and type signature of `shell_completion.add_completion_class` function. :pr:`2421` - Bash version detection doesn't fail on Windows. :issue:`2461` - Completion works if there is a dot (``.``) in the program name. :issue:`2166` - Improve type annotations for pyright type checker. :issue:`2268` - Improve responsiveness of ``click.clear()``. :issue:`2284` - Improve command name detection when using Shiv or PEX. :issue:`2332` - Avoid showing empty lines if command help text is empty. :issue:`2368` - ZSH completion script works when loaded from ``fpath``. :issue:`2344`. - ``EOFError`` and ``KeyboardInterrupt`` tracebacks are not suppressed when ``standalone_mode`` is disabled. :issue:`2380` - ``group.command`` does not fail if the group was created with a custom ``command_class``. :issue:`2416` - ``multiple=True`` is allowed for flag options again and does not require setting ``default=()``. :issue:`2246, 2292, 2295` - Make the decorators returned by ``argument()`` and ``option()`` reusable when the ``cls`` parameter is used. :issue:`2294` - Don't fail when writing filenames to streams with strict errors. Replace invalid bytes with the replacement character (``�``). :issue:`2395` - Remove unnecessary attempt to detect MSYS2 environment. :issue:`2355` - Remove outdated and unnecessary detection of App Engine environment. :pr:`2554` - ``echo()`` does not fail when no streams are attached, such as with ``pythonw`` on Windows. :issue:`2415` - Argument with ``expose_value=False`` do not cause completion to fail. :issue:`2336` ``` ### 8.1.3 ``` ------------- Released 2022-04-28 - Use verbose form of ``typing.Callable`` for ``command`` and ``group``. :issue:`2255` - Show error when attempting to create an option with ``multiple=True, is_flag=True``. Use ``count`` instead. :issue:`2246` ``` ### 8.1.2 ``` ------------- Released 2022-03-31 - Fix error message for readable path check that was mixed up with the executable check. :pr:`2236` - Restore parameter order for ``Path``, placing the ``executable`` parameter at the end. It is recommended to use keyword arguments instead of positional arguments. :issue:`2235` ``` ### 8.1.1 ``` ------------- Released 2022-03-30 - Fix an issue with decorator typing that caused type checking to report that a command was not callable. :issue:`2227` ``` ### 8.1.0 ``` ------------- Released 2022-03-28 - Drop support for Python 3.6. :pr:`2129` - Remove previously deprecated code. :pr:`2130` - ``Group.resultcallback`` is renamed to ``result_callback``. - ``autocompletion`` parameter to ``Command`` is renamed to ``shell_complete``. - ``get_terminal_size`` is removed, use ``shutil.get_terminal_size`` instead. - ``get_os_args`` is removed, use ``sys.argv[1:]`` instead. - Rely on :pep:`538` and :pep:`540` to handle selecting UTF-8 encoding instead of ASCII. Click's locale encoding detection is removed. :issue:`2198` - Single options boolean flags with ``show_default=True`` only show the default if it is ``True``. :issue:`1971` - The ``command`` and ``group`` decorators can be applied with or without parentheses. :issue:`1359` - The ``Path`` type can check whether the target is executable. :issue:`1961` - ``Command.show_default`` overrides ``Context.show_default``, instead of the other way around. :issue:`1963` - Parameter decorators and ``group`` handles ``cls=None`` the same as not passing ``cls``. ``option`` handles ``help=None`` the same as not passing ``help``. :issue:`1959` - A flag option with ``required=True`` requires that the flag is passed instead of choosing the implicit default value. :issue:`1978` - Indentation in help text passed to ``Option`` and ``Command`` is cleaned the same as using the ``option`` and ``command`` decorators does. A command's ``epilog`` and ``short_help`` are also processed. :issue:`1985` - Store unprocessed ``Command.help``, ``epilog`` and ``short_help`` strings. Processing is only done when formatting help text for output. :issue:`2149` - Allow empty str input for ``prompt()`` when ``confirmation_prompt=True`` and ``default=""``. :issue:`2157` - Windows glob pattern expansion doesn't fail if a value is an invalid pattern. :issue:`2195` - It's possible to pass a list of ``params`` to ``command``. Any params defined with decorators are appended to the passed params. :issue:`2131`. - ``command`` decorator is annotated as returning the correct type if a ``cls`` argument is used. :issue:`2211` - A ``Group`` with ``invoke_without_command=True`` and ``chain=False`` will invoke its result callback with the group function's return value. :issue:`2124` - ``to_info_dict`` will not fail if a ``ParamType`` doesn't define a ``name``. :issue:`2168` - Shell completion prioritizes option values with option prefixes over new options. :issue:`2040` - Options that get an environment variable value using ``autoenvvar_prefix`` treat an empty value as ``None``, consistent with a direct ``envvar``. :issue:`2146` ``` ### 8.0.4 ``` ------------- Released 2022-02-18 - ``open_file`` recognizes ``Path("-")`` as a standard stream, the same as the string ``"-"``. :issue:`2106` - The ``option`` and ``argument`` decorators preserve the type annotation of the decorated function. :pr:`2155` - A callable default value can customize its help text by overriding ``__str__`` instead of always showing ``(dynamic)``. :issue:`2099` - Fix a typo in the Bash completion script that affected file and directory completion. If this script was generated by a previous version, it should be regenerated. :issue:`2163` - Fix typing for ``echo`` and ``secho`` file argument. :issue:`2174, 2185` ``` ### 8.0.3 ``` ------------- Released 2021-10-10 - Fix issue with ``Path(resolve_path=True)`` type creating invalid paths. :issue:`2088` - Importing ``readline`` does not cause the ``confirm()`` prompt to disappear when pressing backspace. :issue:`2092` - Any default values injected by ``invoke()`` are cast to the corresponding parameter's type. :issue:`2089, 2090` ``` ### 8.0.2 ``` ------------- Released 2021-10-08 - ``is_bool_flag`` is not set to ``True`` if ``is_flag`` is ``False``. :issue:`1925` - Bash version detection is locale independent. :issue:`1940` - Empty ``default`` value is not shown for ``multiple=True``. :issue:`1969` - Fix shell completion for arguments that start with a forward slash such as absolute file paths. :issue:`1929` - ``Path`` type with ``resolve_path=True`` resolves relative symlinks to be relative to the containing directory. :issue:`1921` - Completion does not skip Python's resource cleanup when exiting, avoiding some unexpected warning output. :issue:`1738, 2017` - Fix type annotation for ``type`` argument in ``prompt`` function. :issue:`2062` - Fix overline and italic styles, which were incorrectly added when adding underline. :pr:`2058` - An option with ``count=True`` will not show "[x>=0]" in help text. :issue:`2072` - Default values are not cast to the parameter type twice during processing. :issue:`2085` - Options with ``multiple`` and ``flag_value`` use the flag value instead of leaving an internal placeholder. :issue:`2001` ``` ### 8.0.1 ``` ------------- Released 2021-05-19 - Mark top-level names as exported so type checking understand imports in user projects. :issue:`1879` - Annotate ``Context.obj`` as ``Any`` so type checking allows all operations on the arbitrary object. :issue:`1885` - Fix some types that weren't available in Python 3.6.0. :issue:`1882` - Fix type checking for iterating over ``ProgressBar`` object. :issue:`1892` - The ``importlib_metadata`` backport package is installed on Python < 3.8. :issue:`1889` - Arguments with ``nargs=-1`` only use env var value if no command line values are given. :issue:`1903` - Flag options guess their type from ``flag_value`` if given, like regular options do from ``default``. :issue:`1886` - Added documentation that custom parameter types may be passed already valid values in addition to strings. :issue:`1898` - Resolving commands returns the name that was given, not ``command.name``, fixing an unintended change to help text and ``default_map`` lookups. When using patterns like ``AliasedGroup``, override ``resolve_command`` to change the name that is returned if needed. :issue:`1895` - If a default value is invalid, it does not prevent showing help text. :issue:`1889` - Pass ``windows_expand_args=False`` when calling the main command to disable pattern expansion on Windows. There is no way to escape patterns in CMD, so if the program needs to pass them on as-is then expansion must be disabled. :issue:`1901` ``` ### 8.0.0 ``` ------------- Released 2021-05-11 - Drop support for Python 2 and 3.5. - Colorama is always installed on Windows in order to provide style and color support. :pr:`1784` - Adds a repr to Command, showing the command name for friendlier debugging. :issue:`1267`, :pr:`1295` - Add support for distinguishing the source of a command line parameter. :issue:`1264`, :pr:`1329` - Add an optional parameter to ``ProgressBar.update`` to set the ``current_item``. :issue:`1226`, :pr:`1332` - ``version_option`` uses ``importlib.metadata`` (or the ``importlib_metadata`` backport) instead of ``pkg_resources``. The version is detected based on the package name, not the entry point name. The Python package name must match the installed package name, or be passed with ``package_name=``. :issue:`1582` - If validation fails for a prompt with ``hide_input=True``, the value is not shown in the error message. :issue:`1460` - An ``IntRange`` or ``FloatRange`` option shows the accepted range in its help text. :issue:`1525`, :pr:`1303` - ``IntRange`` and ``FloatRange`` bounds can be open (``<``) instead of closed (``<=``) by setting ``min_open`` and ``max_open``. Error messages have changed to reflect this. :issue:`1100` - An option defined with duplicate flag names (``"--foo/--foo"``) raises a ``ValueError``. :issue:`1465` - ``echo()`` will not fail when using pytest's ``capsys`` fixture on Windows. :issue:`1590` - Resolving commands returns the canonical command name instead of the matched name. This makes behavior such as help text and ``Context.invoked_subcommand`` consistent when using patterns like ``AliasedGroup``. :issue:`1422` - The ``BOOL`` type accepts the values "on" and "off". :issue:`1629` - A ``Group`` with ``invoke_without_command=True`` will always invoke its result callback. :issue:`1178` - ``nargs == -1`` and ``nargs > 1`` is parsed and validated for values from environment variables and defaults. :issue:`729` - Detect the program name when executing a module or package with ``python -m name``. :issue:`1603` - Include required parent arguments in help synopsis of subcommands. :issue:`1475` - Help for boolean flags with ``show_default=True`` shows the flag name instead of ``True`` or ``False``. :issue:`1538` - Non-string objects passed to ``style()`` and ``secho()`` will be converted to string. :pr:`1146` - ``edit(require_save=True)`` will detect saves for editors that exit very fast on filesystems with 1 second resolution. :pr:`1050` - New class attributes make it easier to use custom core objects throughout an entire application. :pr:`938` - ``Command.context_class`` controls the context created when running the command. - ``Context.invoke`` creates new contexts of the same type, so a custom type will persist to invoked subcommands. - ``Context.formatter_class`` controls the formatter used to generate help and usage. - ``Group.command_class`` changes the default type for subcommands with ``group.command()``. - ``Group.group_class`` changes the default type for subgroups with ``group.group()``. Setting it to ``type`` will create subgroups of the same type as the group itself. - Core objects use ``super()`` consistently for better support of subclassing. - Use ``Context.with_resource()`` to manage resources that would normally be used in a ``with`` statement, allowing them to be used across subcommands and callbacks, then cleaned up when the context ends. :pr:`1191` - The result object returned by the test runner's ``invoke()`` method has a ``return_value`` attribute with the value returned by the invoked command. :pr:`1312` - Required arguments with the ``Choice`` type show the choices in curly braces to indicate that one is required (``{a|b|c}``). :issue:`1272` - If only a name is passed to ``option()``, Click suggests renaming it to ``--name``. :pr:`1355` - A context's ``show_default`` parameter defaults to the value from the parent context. :issue:`1565` - ``click.style()`` can output 256 and RGB color codes. Most modern terminals support these codes. :pr:`1429` - When using ``CliRunner.invoke()``, the replaced ``stdin`` file has ``name`` and ``mode`` attributes. This lets ``File`` options with the ``-`` value match non-testing behavior. :issue:`1064` - When creating a ``Group``, allow passing a list of commands instead of a dict. :issue:`1339` - When a long option name isn't valid, use ``difflib`` to make better suggestions for possible corrections. :issue:`1446` - Core objects have a ``to_info_dict()`` method. This gathers information about the object's structure that could be useful for a tool generating user-facing documentation. To get the structure of an entire CLI, use ``Context(cli).to_info_dict()``. :issue:`461` - Redesign the shell completion system. :issue:`1484`, :pr:`1622` - Support Bash >= 4.4, Zsh, and Fish, with the ability for extensions to add support for other shells. - Allow commands, groups, parameters, and types to override their completions suggestions. - Groups complete the names commands were registered with, which can differ from the name they were created with. - The ``autocompletion`` parameter for options and arguments is renamed to ``shell_complete``. The function must take ``ctx, param, incomplete``, must do matching rather than return all values, and must return a list of strings or a list of ``CompletionItem``. The old name and behavior is deprecated and will be removed in 8.1. - The env var values used to start completion have changed order. The shell now comes first, such as ``{shell}_source`` rather than ``source_{shell}``, and is always required. - Completion correctly parses command line strings with incomplete quoting or escape sequences. :issue:`1708` - Extra context settings (``obj=...``, etc.) are passed on to the completion system. :issue:`942` - Include ``--help`` option in completion. :pr:`1504` - ``ParameterSource`` is an ``enum.Enum`` subclass. :issue:`1530` - Boolean and UUID types strip surrounding space before converting. :issue:`1605` - Adjusted error message from parameter type validation to be more consistent. Quotes are used to distinguish the invalid value. :issue:`1605` - The default value for a parameter with ``nargs`` > 1 and ``multiple=True`` must be a list of tuples. :issue:`1649` - When getting the value for a parameter, the default is tried in the same section as other sources to ensure consistent processing. :issue:`1649` - All parameter types accept a value that is already the correct type. :issue:`1649` - For shell completion, an argument is considered incomplete if its value did not come from the command line args. :issue:`1649` - Added ``ParameterSource.PROMPT`` to track parameter values that were prompted for. :issue:`1649` - Options with ``nargs`` > 1 no longer raise an error if a default is not given. Parameters with ``nargs`` > 1 default to ``None``, and parameters with ``multiple=True`` or ``nargs=-1`` default to an empty tuple. :issue:`472` - Handle empty env vars as though the option were not passed. This extends the change introduced in 7.1 to be consistent in more cases. :issue:`1285` - ``Parameter.get_default()`` checks ``Context.default_map`` to handle overrides consistently in help text, ``invoke()``, and prompts. :issue:`1548` - Add ``prompt_required`` param to ``Option``. When set to ``False``, the user will only be prompted for an input if no value was passed. :issue:`736` - Providing the value to an option can be made optional through ``is_flag=False``, and the value can instead be prompted for or passed in as a default value. :issue:`549, 736, 764, 921, 1015, 1618` - Fix formatting when ``Command.options_metavar`` is empty. :pr:`1551` - Revert adding space between option help text that wraps. :issue:`1831` - The default value passed to ``prompt`` will be cast to the correct type like an input value would be. :pr:`1517` - Automatically generated short help messages will stop at the first ending of a phrase or double linebreak. :issue:`1082` - Skip progress bar render steps for efficiency with very fast iterators by setting ``update_min_steps``. :issue:`676` - Respect ``case_sensitive=False`` when doing shell completion for ``Choice`` :issue:`1692` - Use ``mkstemp()`` instead of ``mktemp()`` in pager implementation. :issue:`1752` - If ``Option.show_default`` is a string, it is displayed even if ``default`` is ``None``. :issue:`1732` - ``click.get_terminal_size()`` is deprecated and will be removed in 8.1. Use :func:`shutil.get_terminal_size` instead. :issue:`1736` - Control the location of the temporary directory created by ``CLIRunner.isolated_filesystem`` by passing ``temp_dir``. A custom directory will not be removed automatically. :issue:`395` - ``click.confirm()`` will prompt until input is given if called with ``default=None``. :issue:`1381` - Option prompts validate the value with the option's callback in addition to its type. :issue:`457` - ``confirmation_prompt`` can be set to a custom string. :issue:`723` - Allow styled output in Jupyter on Windows. :issue:`1271` - ``style()`` supports the ``strikethrough``, ``italic``, and ``overline`` styles. :issue:`805, 1821` - Multiline marker is removed from short help text. :issue:`1597` - Restore progress bar behavior of echoing only the label if the file is not a TTY. :issue:`1138` - Progress bar output is shown even if execution time is less than 0.5 seconds. :issue:`1648` - Progress bar ``item_show_func`` shows the current item, not the previous item. :issue:`1353` - The ``Path`` param type can be passed ``path_type=pathlib.Path`` to return a path object instead of a string. :issue:`405` - ``TypeError`` is raised when parameter with ``multiple=True`` or ``nargs > 1`` has non-iterable default. :issue:`1749` - Add a ``pass_meta_key`` decorator for passing a key from ``Context.meta``. This is useful for extensions using ``meta`` to store information. :issue:`1739` - ``Path`` ``resolve_path`` resolves symlinks on Windows Python < 3.8. :issue:`1813` - Command deprecation notice appears at the start of the help text, as well as in the short help. The notice is not in all caps. :issue:`1791` - When taking arguments from ``sys.argv`` on Windows, glob patterns, user dir, and env vars are expanded. :issue:`1096` - Marked messages shown by the CLI with ``gettext()`` to allow applications to translate Click's built-in strings. :issue:`303` - Writing invalid characters to ``stderr`` when using the test runner does not raise a ``UnicodeEncodeError``. :issue:`848` - Fix an issue where ``readline`` would clear the entire ``prompt()`` line instead of only the input when pressing backspace. :issue:`665` - Add all kwargs passed to ``Context.invoke()`` to ``ctx.params``. Fixes an inconsistency when nesting ``Context.forward()`` calls. :issue:`1568` - The ``MultiCommand.resultcallback`` decorator is renamed to ``result_callback``. The old name is deprecated. :issue:`1160` - Fix issues with ``CliRunner`` output when using ``echo_stdin=True``. :issue:`1101` - Fix a bug of ``click.utils.make_default_short_help`` for which the returned string could be as long as ``max_width + 3``. :issue:`1849` - When defining a parameter, ``default`` is validated with ``multiple`` and ``nargs``. More validation is done for values being processed as well. :issue:`1806` - ``HelpFormatter.write_text`` uses the full line width when wrapping text. :issue:`1871` ``` ### 7.1.2 ``` ------------- Released 2020-04-27 - Revert applying shell quoting to commands for ``echo_with_pager`` and ``edit``. This was intended to allows spaces in commands, but caused issues if the string was actually a command and arguments, or on Windows. Instead, the string must be quoted manually as it should appear on the command line. :issue:`1514` ``` ### 7.1.1 ``` ------------- Released 2020-03-09 - Fix ``ClickException`` output going to stdout instead of stderr. :issue:`1495` ``` ### 7.1 ``` ----------- Released 2020-03-09 - Fix PyPI package name, "click" is lowercase again. - Fix link in ``unicode_literals`` error message. :pr:`1151` - Add support for colored output on UNIX Jupyter notebooks. :issue:`1185` - Operations that strip ANSI controls will strip the cursor hide/show sequences. :issue:`1216` - Remove unused compat shim for ``bytes``. :pr:`1195` - Expand testing around termui, especially getchar on Windows. :issue:`1116` - Fix output on Windows Python 2.7 built with MSVC 14. :pr:`1342` - Fix ``OSError`` when running in MSYS2. :issue:`1338` - Fix ``OSError`` when redirecting to ``NUL`` stream on Windows. :issue:`1065` - Fix memory leak when parsing Unicode arguments on Windows. :issue:`1136` - Fix error in new AppEngine environments. :issue:`1462` - Always return one of the passed choices for ``click.Choice`` :issue:`1277`, :pr:`1318` - Add ``no_args_is_help`` option to ``click.Command``, defaults to False :pr:`1167` - Add ``show_default`` parameter to ``Context`` to enable showing defaults globally. :issue:`1018` - Handle ``env MYPATH=''`` as though the option were not passed. :issue:`1196` - It is once again possible to call ``next(bar)`` on an active progress bar instance. :issue:`1125` - ``open_file`` with ``atomic=True`` retains permissions of existing files and respects the current umask for new files. :issue:`1376` - When using the test ``CliRunner`` with ``mix_stderr=False``, if ``result.stderr`` is empty it will not raise a ``ValueError``. :issue:`1193` - Remove the unused ``mix_stderr`` parameter from ``CliRunner.invoke``. :issue:`1435` - Fix ``TypeError`` raised when using bool flags and specifying ``type=bool``. :issue:`1287` - Newlines in option help text are replaced with spaces before re-wrapping to avoid uneven line breaks. :issue:`834` - ``MissingParameter`` exceptions are printable in the Python interpreter. :issue:`1139` - Fix how default values for file-type options are shown during prompts. :issue:`914` - Fix environment variable automatic generation for commands containing ``-``. :issue:`1253` - Option help text replaces newlines with spaces when rewrapping, but preserves paragraph breaks, fixing multiline formatting. :issue:`834, 1066, 1397` - Option help text that is wrapped adds an extra newline at the end to distinguish it from the next option. :issue:`1075` - Consider ``sensible-editor`` when determining the editor to use for ``click.edit()``. :pr:`1469` - Arguments to system calls such as the executable path passed to ``click.edit`` can contains spaces. :pr:`1470` - Add ZSH completion autoloading and error handling. :issue:`1348` - Add a repr to ``Command``, ``Group``, ``Option``, and ``Argument``, showing the name for friendlier debugging. :issue:`1267` - Completion doesn't consider option names if a value starts with ``-`` after the ``--`` separator. :issue:`1247` - ZSH completion escapes special characters in values. :pr:`1418` - Add completion support for Fish shell. :pr:`1423` - Decoding bytes option values falls back to UTF-8 in more cases. :pr:`1468` - Make the warning about old 2-arg parameter callbacks a deprecation warning, to be removed in 8.0. This has been a warning since Click 2.0. :pr:`1492` - Adjust error messages to standardize the types of quotes used so they match error messages from Python. ```
Links - PyPI: https://pypi.org/project/click - Changelog: https://pyup.io/changelogs/click/ - Homepage: https://palletsprojects.com/p/click/
pyup-bot commented 1 year ago

Closing this in favor of #156