--- Begin Message ---
Source: pybel
Version: 0.15.5-1
Severity: important
Tags: upstream patch forky sid
Control: block 1108453 by -1
Dear Maintainer,
Please drop the python3-click-plugins (build) dependency, the package will be
removed during the forky development cycle.
Upstream ended maintenance of click-plugins and now recommends users to vendor
it, the attached patch does so.
Kind Regards,
Bas
diff -Nru pybel-0.15.5/debian/control pybel-0.15.5/debian/control
--- pybel-0.15.5/debian/control 2024-11-30 02:49:02.000000000 +0100
+++ pybel-0.15.5/debian/control 2025-06-29 08:53:24.000000000 +0200
@@ -9,7 +9,6 @@
pybuild-plugin-pyproject,
python3-all,
python3-setuptools,
- python3-click-plugins,
python3-humanize,
python3-jinja2,
python3-jsonschema,
@@ -38,7 +37,6 @@
${misc:Depends},
libjs-jquery,
libjs-d3,
- python3-click-plugins,
python3-networkx,
python3-pyparsing,
python3-ratelimit,
diff -Nru pybel-0.15.5/debian/patches/pr503-click-plugins.patch
pybel-0.15.5/debian/patches/pr503-click-plugins.patch
--- pybel-0.15.5/debian/patches/pr503-click-plugins.patch 1970-01-01
01:00:00.000000000 +0100
+++ pybel-0.15.5/debian/patches/pr503-click-plugins.patch 2025-06-29
08:53:16.000000000 +0200
@@ -0,0 +1,279 @@
+Description: Vendor click-plugins, PyPI package no longer maintained.
+Author: Bas Couwenberg <[email protected]>
+Bug: https://github.com/pybel/pybel/pull/503
+
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -57,7 +57,6 @@ install_requires =
+ networkx>=2.4
+ sqlalchemy
+ click
+- click-plugins
+ bel_resources>=0.0.3
+ more_itertools
+ requests
+--- a/src/pybel/cli.py
++++ b/src/pybel/cli.py
+@@ -21,11 +21,11 @@ import time
+ from typing import List, Optional
+
+ import click
+-from click_plugins import with_plugins
+ from pkg_resources import iter_entry_points
+ from tqdm.autonotebook import tqdm
+
+ from .canonicalize import to_bel_script
++from .click_plugins import with_plugins
+ from .constants import get_cache_connection
+ from .examples import (
+ braf_graph,
+--- /dev/null
++++ b/src/pybel/click_plugins.py
+@@ -0,0 +1,247 @@
++# This file is part of 'click-plugins':
https://github.com/click-contrib/click-plugins
++#
++# New BSD License
++#
++# Copyright (c) 2015-2025, Kevin D. Wurster, Sean C. Gillies
++# All rights reserved.
++#
++# Redistribution and use in source and binary forms, with or without
++# modification, are permitted provided that the following conditions are met:
++#
++# * Redistributions of source code must retain the above copyright notice,
this
++# list of conditions and the following disclaimer.
++#
++# * Redistributions in binary form must reproduce the above copyright notice,
++# this list of conditions and the following disclaimer in the documentation
++# and/or other materials provided with the distribution.
++#
++# * Neither click-plugins nor the names of its contributors may not be used to
++# endorse or promote products derived from this software without specific
prior
++# written permission.
++#
++# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
++# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
++# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE
++# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
++# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
++# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
++# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
++# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY,
++# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
USE
++# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
++
++
++"""Support CLI plugins with click and entry points.
++
++See :func:`with_plugins`.
++"""
++
++
++import importlib.metadata
++import os
++import sys
++import traceback
++
++import click
++
++
++__version__ = '2.0'
++
++
++def with_plugins(entry_points):
++
++ """Decorator for loading and attaching plugins to a ``click.Group()``.
++
++ Plugins are loaded from an ``importlib.metadata.EntryPoint()``. Each entry
++ point must point to a ``click.Command()``. An entry point that fails to
++ load will be wrapped in a ``BrokenCommand()`` to allow the CLI user to
++ discover and potentially debug the problem.
++
++ >>> from importlib.metadata import entry_points
++ >>>
++ >>> import click
++ >>> from click_plugins import with_plugins
++ >>>
++ >>> @with_plugins('group_name')
++ >>> @click.group()
++ >>> def group():
++ ... '''Group'''
++ >>>
++ >>> @with_plugins(entry_points('group_name'))
++ >>> @click.group()
++ >>> def group():
++ ... '''Group'''
++ >>>
++ >>> @with_plugins(importlib.metadata.EntryPoint(...))
++ >>> @click.group()
++ >>> def group():
++ ... '''Group'''
++ >>>
++ >>> @with_plugins("group1")
++ >>> @with_plugins("group2")
++ >>> def group():
++ ... '''Group'''
++
++ :param str or EntryPoint or sequence[EntryPoint] entry_points:
++ Entry point group name, a single ``importlib.metadata.EntryPoint()``,
++ or a sequence of ``EntryPoint()``s.
++
++ :rtype function:
++ """
++
++ # Note that the explicit full path reference to:
++ #
++ # importlib.metadata.entry_points()
++ #
++ # in this function allows the call to be mocked in the tests. Replacing
++ # with:
++ #
++ # from importlib.metadata import entry_points
++ #
++ # breaks this ability.
++
++ def decorator(group):
++ if not isinstance(group, click.Group):
++ raise TypeError(
++ f"plugins can only be attached to an instance of"
++ f" 'click.Group()' not: {repr(group)}")
++
++ # Load 'EntryPoint()' objects.
++ if isinstance(entry_points, str):
++
++ # Older versions of Python do not support filtering.
++ if sys.version_info >= (3, 10):
++ all_entry_points = importlib.metadata.entry_points(
++ group=entry_points)
++
++ else:
++ all_entry_points = importlib.metadata.entry_points()
++ all_entry_points = all_entry_points[entry_points]
++
++ # A single 'importlib.metadata.EntryPoint()'
++ elif isinstance(entry_points, importlib.metadata.EntryPoint):
++ all_entry_points = [entry_points]
++
++ # Sequence of 'EntryPoints()'.
++ else:
++ all_entry_points = entry_points
++
++ for ep in all_entry_points:
++
++ try:
++ group.add_command(ep.load())
++
++ # Catch all exceptions (technically not 'BaseException') and
++ # instead register a special 'BrokenCommand()'. Otherwise, a
single
++ # plugin that fails to load and/or register will make the CLI
++ # inoperable. 'BrokenCommand()' explains the situation to users.
++ except Exception as e:
++ group.add_command(BrokenCommand(ep, e))
++
++ return group
++
++ return decorator
++
++
++class BrokenCommand(click.Command):
++
++ """Represents a plugin ``click.Command()`` that failed to load.
++
++ Can be executed just like a ``click.Command()``, but prints information
++ for debugging and exits with an error code.
++ """
++
++ def __init__(self, entry_point, exception):
++
++ """
++ :param importlib.metadata.EntryPoint entry_point:
++ Entry point that failed to load.
++ :param Exception exception:
++ Raised when attempting to load the entry point associated with
++ this instance.
++ """
++
++ super().__init__(entry_point.name)
++
++ # There are several ways to get a traceback from an exception, but
++ # 'TracebackException()' seems to be the most portable across actively
++ # supported versions of Python.
++ tbe = traceback.TracebackException.from_exception(exception)
++
++ # A message for '$ cli command --help'. Contains full traceback and a
++ # helpful note. The intention is to nudge users to figure out which
++ # project should get a bug report since users are likely to report the
++ # issue to the developers of the CLI utility they are directly
++ # interacting with. These are not necessarily the right developers.
++ self.help = (
++ "{ls}ERROR: entry point '{module}:{name}' could not be loaded."
++ " Contact its author for help.{ls}{ls}{tb}").format(
++ module=_module(entry_point),
++ name=entry_point.name,
++ ls=os.linesep,
++ tb=''.join(tbe.format())
++ )
++
++ # Replace the broken command's summary with a warning about how it
++ # was not loaded successfully. The idea is that '$ cli --help' should
++ # include a clear indicator that a subcommand is not functional, and
++ # a little hint for what to do about it. U+2020 is a "dagger", whose
++ # modern use typically indicates a footnote.
++ self.short_help = (
++ f"\u2020 Warning: could not load plugin. Invoke command with"
++ f" '--help' for traceback."
++ )
++
++ def invoke(self, ctx):
++
++ """Print traceback and debugging message.
++
++ :param click.Context ctx:
++ Active context.
++ """
++
++ click.echo(self.help, color=ctx.color, err=True)
++ ctx.exit(1)
++
++ def parse_args(self, ctx, args):
++
++ """Pass arguments along without parsing.
++
++ :param click.Context ctx:
++ Active context.
++ :param list args:
++ List of command line arguments.
++ """
++
++ # Do not attempt to parse these arguments. We do not know why the
++ # entry point failed to load, but it is reasonable to assume that
++ # argument parsing will not work. Ultimately the goal is to get the
++ # 'Command.invoke()' method (overloaded in this class) to execute
++ # and provide the user with a bit of debugging information.
++
++ return args
++
++
++def _module(ep):
++
++ """Module name for a given entry point.
++
++ Parameters
++ ----------
++ ep : importlib.metadata.EntryPoint
++ Determine parent module for this entry point.
++
++ Returns
++ -------
++ str
++ """
++
++ if sys.version_info >= (3, 10):
++ module = ep.module
++
++ else:
++ # From 'importlib.metadata.EntryPoint.module'.
++ match = ep.pattern.match(ep.value)
++ module = match.group('module')
++
++ return module
diff -Nru pybel-0.15.5/debian/patches/series pybel-0.15.5/debian/patches/series
--- pybel-0.15.5/debian/patches/series 2024-11-30 02:42:01.000000000 +0100
+++ pybel-0.15.5/debian/patches/series 2025-06-29 08:52:29.000000000 +0200
@@ -1,3 +1,4 @@
not_testing_what_fails.patch
more_click_is_not_packaged.patch
remove_psycopg2-binary
+pr503-click-plugins.patch
--- End Message ---
pgpj9hxPX2Reu.pgp
