Bump the python-root group across 1 directory with 3 updates (#1268)

Bumps the python-root group with 3 updates in the / directory:
[flake8](https://github.com/pycqa/flake8),
[setuptools](https://github.com/pypa/setuptools) and
[protobuf](https://github.com/protocolbuffers/protobuf).

Updates `flake8` from 7.1.2 to 7.2.0
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/PyCQA/flake8/commit/16f5f28a384f0781bebb37a08aa45e65b9526c50"><code>16f5f28</code></a>
Release 7.2.0</li>
<li><a
href="https://github.com/PyCQA/flake8/commit/ebad305769bbf62d92901a1b9c9121c1b4fec00b"><code>ebad305</code></a>
Merge pull request <a
href="https://redirect.github.com/pycqa/flake8/issues/1974">#1974</a>
from PyCQA/update-plugins</li>
<li><a
href="https://github.com/PyCQA/flake8/commit/d56d569ce40a623a17c212ea7f2b306714f27f31"><code>d56d569</code></a>
update versions of pycodestyle / pyflakes</li>
<li><a
href="https://github.com/PyCQA/flake8/commit/a7e8f6250c23e71546ca4cc35322bc06fe90f9f4"><code>a7e8f62</code></a>
Merge pull request <a
href="https://redirect.github.com/pycqa/flake8/issues/1973">#1973</a>
from PyCQA/py39-plus</li>
<li><a
href="https://github.com/PyCQA/flake8/commit/9d55ccdb729d1255b9cf09438b6073b05b9ce52c"><code>9d55ccd</code></a>
py39+</li>
<li><a
href="https://github.com/PyCQA/flake8/commit/e492aeb385f87c0520c65d32747763209ed1da21"><code>e492aeb</code></a>
Merge pull request <a
href="https://redirect.github.com/pycqa/flake8/issues/1967">#1967</a>
from PyCQA/unnecessary-mocks</li>
<li><a
href="https://github.com/PyCQA/flake8/commit/fa2ed7145cdf80fd983c2a436226a074f9a9d664"><code>fa2ed71</code></a>
remove a few unnecessary mocks in test_checker_manager</li>
<li>See full diff in <a
href="https://github.com/pycqa/flake8/compare/7.1.2...7.2.0">compare
view</a></li>
</ul>
</details>
<br />

Updates `setuptools` from 76.0.0 to 78.1.0
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a
href="https://github.com/pypa/setuptools/blob/main/NEWS.rst">setuptools's
changelog</a>.</em></p>
<blockquote>
<h1>v78.1.0</h1>
<h2>Features</h2>
<ul>
<li>Restore access to _get_vc_env with a warning. (<a
href="https://redirect.github.com/pypa/setuptools/issues/4874">#4874</a>)</li>
</ul>
<h1>v78.0.2</h1>
<h2>Bugfixes</h2>
<ul>
<li>Postponed removals of deprecated dash-separated and uppercase fields
in <code>setup.cfg</code>.
All packages with deprecated configurations are advised to move before
2026. (<a
href="https://redirect.github.com/pypa/setuptools/issues/4911">#4911</a>)</li>
</ul>
<h1>v78.0.1</h1>
<h2>Misc</h2>
<ul>
<li><a
href="https://redirect.github.com/pypa/setuptools/issues/4909">#4909</a></li>
</ul>
<h1>v78.0.0</h1>
<h2>Bugfixes</h2>
<ul>
<li>Reverted distutils changes that broke the monkey patching of command
classes. (<a
href="https://redirect.github.com/pypa/setuptools/issues/4902">#4902</a>)</li>
</ul>
<h2>Deprecations and Removals</h2>
<ul>
<li>
<p>Setuptools no longer accepts options containing uppercase or dash
characters in <code>setup.cfg</code>.
Please ensure to write the options in <code>setup.cfg</code> using the
:wiki:<code>lower_snake_case &lt;Snake_case&gt;</code> convention
(e.g. <code>Name =&gt; name</code>, <code>install-requires =&gt;
install_requires</code>).
This is a follow-up on deprecations introduced in
<code>v54.1.0
&lt;https://setuptools.pypa.io/en/latest/history.html#v54-1-0&gt;</code>_
(see <a
href="https://redirect.github.com/pypa/setuptools/issues/1608">#1608</a>)
and
<code>v54.1.1
&lt;https://setuptools.pypa.io/en/latest/history.html#v54-1-1&gt;</code>_
(see <a
href="https://redirect.github.com/pypa/setuptools/issues/2592">#2592</a>).</p>
<p>.. note::
This change <em>does not affect configurations in</em>
<code>pyproject.toml</code>
(which uses the :wiki:<code>lower-kebab-case
&lt;Letter_case#Kebab_case&gt;</code> convention following the precedent
set in :pep:<code>517</code>/:pep:<code>518</code>). (<a
href="https://redirect.github.com/pypa/setuptools/issues/4870">#4870</a>)</p>
</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/pypa/setuptools/commit/6ead555c5fb29bc57fe6105b1bffc163f56fd558"><code>6ead555</code></a>
Bump version: 78.0.2 → 78.1.0</li>
<li><a
href="https://github.com/pypa/setuptools/commit/d37cd9ede4c0b529f4239d0c1e26c2a5996131c4"><code>d37cd9e</code></a>
Merge <a
href="https://github.com/pypa/distutils">https://github.com/pypa/distutils</a></li>
<li><a
href="https://github.com/pypa/setuptools/commit/efa2eb231c82f6630468ad358cfe4b65a013b690"><code>efa2eb2</code></a>
Restore access to _get_vc_env with a warning.</li>
<li><a
href="https://github.com/pypa/setuptools/commit/3c88de1c62420c1e0161f48e34af6424ac009aa5"><code>3c88de1</code></a>
Bump version: 78.0.1 → 78.0.2</li>
<li><a
href="https://github.com/pypa/setuptools/commit/a219451f7354816fe479cf2b0fd5bc47de0a57ee"><code>a219451</code></a>
Revert removals introduced in <code>v78.0.0</code> (<a
href="https://redirect.github.com/pypa/setuptools/issues/4911">#4911</a>)</li>
<li><a
href="https://github.com/pypa/setuptools/commit/d4326dd6896caa87dbf928610fa160a536b69323"><code>d4326dd</code></a>
Allow PyPy to fail on CI.</li>
<li><a
href="https://github.com/pypa/setuptools/commit/92e22dd5765b54e1ce7c9f25c419371e666b15dc"><code>92e22dd</code></a>
Manually remove file to try to stop flaky tests on PyPy</li>
<li><a
href="https://github.com/pypa/setuptools/commit/caa48ab040420be2885e9d2a14ce6615bd17f992"><code>caa48ab</code></a>
Add news fragment</li>
<li><a
href="https://github.com/pypa/setuptools/commit/4e9b8caec323aba5b2b3764ef97018a8b1596a4b"><code>4e9b8ca</code></a>
Revert removals introduced in v78.0.0</li>
<li><a
href="https://github.com/pypa/setuptools/commit/5450f57f1cefa44c961fb50fc18e9826c95a5d59"><code>5450f57</code></a>
Bump version: 78.0.0 → 78.0.1</li>
<li>Additional commits viewable in <a
href="https://github.com/pypa/setuptools/compare/v76.0.0...v78.1.0">compare
view</a></li>
</ul>
</details>
<br />

Updates `protobuf` from 6.30.1 to 6.30.2
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/protocolbuffers/protobuf/commit/43e1626812c1b543e56a7bec59dc09eb18248bd2"><code>43e1626</code></a>
Updating version.json and repo version numbers to: 30.2</li>
<li><a
href="https://github.com/protocolbuffers/protobuf/commit/7a4c63bac3451b8adf8dd51e9c16ed74d4cbc662"><code>7a4c63b</code></a>
Fix lite classes in the protobuf-java Maven release to be JDK8
compatible. (#...</li>
<li><a
href="https://github.com/protocolbuffers/protobuf/commit/783166965aa8808ec1b74d4890088e3b0799ac08"><code>7831669</code></a>
Remove dllexport attribute on variable definition. (<a
href="https://redirect.github.com/protocolbuffers/protobuf/issues/20833">#20833</a>)</li>
<li><a
href="https://github.com/protocolbuffers/protobuf/commit/da9cadcb975654e3d158796b642ec27ba5f4509d"><code>da9cadc</code></a>
Restore JDK8 compatibility in Bazel for libraries with dependencies from
Mave...</li>
<li><a
href="https://github.com/protocolbuffers/protobuf/commit/09b5078524d60917d1fa8c635bcee52e608f2f04"><code>09b5078</code></a>
Add protobuf_maven artifacts to protobuf_maven_dev as well so they can
still ...</li>
<li><a
href="https://github.com/protocolbuffers/protobuf/commit/b7f06f1ed07a463a9279f7019653fe6c3e90282d"><code>b7f06f1</code></a>
Add volatile to featuresResolved (<a
href="https://redirect.github.com/protocolbuffers/protobuf/issues/20766">#20766</a>)</li>
<li><a
href="https://github.com/protocolbuffers/protobuf/commit/b69f653d6ebc90d88032b8cc82d626758a74ef77"><code>b69f653</code></a>
Restore generator headers in cmake install until the next breaking C++
releas...</li>
<li><a
href="https://github.com/protocolbuffers/protobuf/commit/f4b0a79783aa1c579bfe005908f723fdc6d68169"><code>f4b0a79</code></a>
Restore custom protobuf maven namespaces to avoid polluting main maven
namesp...</li>
<li><a
href="https://github.com/protocolbuffers/protobuf/commit/2dc9f35e83f4b55e58443421266b0f9a158d91dd"><code>2dc9f35</code></a>
Fix Java concurrency issue in feature resolution for old &lt;=3.25.x
gencode usi...</li>
<li><a
href="https://github.com/protocolbuffers/protobuf/commit/221b2a0081ebdba6cf3b7278bf65528316ba4480"><code>221b2a0</code></a>
Change how we decide which empty string implementation to use. (<a
href="https://redirect.github.com/protocolbuffers/protobuf/issues/20708">#20708</a>)</li>
<li>Additional commits viewable in <a
href="https://github.com/protocolbuffers/protobuf/compare/v6.30.1...v6.30.2">compare
view</a></li>
</ul>
</details>
<br />


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requirements.txt

@@ -1,10 +1,10 @@
 # Requirements for linting, building, and uploading the PGV python package to PyPI.
 # The package's own requirements are in python/setup.cfg (and also in python/requirements.in).
-flake8==7.1.2
+flake8==7.2.0
 isort==6.0.1
 build==1.2.2.post1
 twine==6.1.0
 wheel==0.45.1
-setuptools==76.0.0
-protobuf==6.30.1
+setuptools==80.4.0
+protobuf==6.30.2
 setuptools_scm[toml]>=6.2