[MNT] [Dependabot](deps): Update biopython requirement from >=1.83 to >=1.87 (#572)

Updates the requirements on
[biopython](https://github.com/biopython/biopython) to permit the latest
version.
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a
href="https://github.com/biopython/biopython/blob/master/NEWS.rst">biopython's
changelog</a>.</em></p>
<blockquote>
<h1>30 March 2026: Biopython 1.87</h1>
<p>Migrated from <code>setup.py</code> to <code>pyproject.toml</code>
for packaging configuration.</p>
<p>Addressed security issue CVE-2025-68463 in
<code>Bio.Entrez.Parser</code> if parsing
untrusted files.</p>
<p>Additionally, a number of small bugs and typos have been fixed with
additions
to the test suite and type annotations.</p>
<p>Many thanks to the Biopython developers and community for making this
release
possible, especially the following contributors:</p>
<ul>
<li>Michiel de Hoon</li>
<li>Peter Cock</li>
<li>Timothy Dennis (first contribution)</li>
<li>Ziyan Rao (first contribution)</li>
<li>Manuel Lera-Ramirez</li>
<li>Sebastian Pipping</li>
</ul>
<h1>28 October 2025: Biopython 1.86</h1>
<p>This release of Biopython supports Python 3.10, 3.11, 3.12, 3.13 and
3.14. It
has also been tested on PyPy3.10 v7.3.19.</p>
<p><code>Bio.SearchIO</code> now supports parsing the tabular and plain
text output of
<code>Infernal &lt;http://eddylab.org/infernal/&gt;</code> (v1.0.0+) RNA
search tool. The
format names are <code>infernal-tab</code> and
<code>infernal-text</code>.</p>
<p>The default value of the gap score of a <code>PairwiseAligner</code>
object was changed
in this release. Previously, for consistency with
<code>Bio.pairwise2</code>, the
default value for gap score was 0. However, this means that a mismatch,
an
insertion followed by a deletion, and a deletion followed by an
insertion all
get assigned a score of 0. The aligner then finds a large number of
alignments
that are logically the same, but have trivial differences between them.
For
example, aligning AAACAAA to AAAGAAA previously yielded the following
three
alignments, all with score 6::</p>
<pre><code> AAACAAA        AAAC-AAA        AAA-CAAA
 AAAGAAA        AAA-GAAA        AAAG-AAA
</code></pre>
<p>With the new default parameter for the gap score, only the first
alignment is
returned.</p>
<p><code>Bio.PDB.PDBIO</code> now ensures that b-factor values are
always at most 6 characters to
ensure that we do not violate the wwPDB specification. This should not
have an impact
on the majority of uses, as b-factor values are generally small (less
than 100). When
1000 &lt;= b-factor &lt; 10_000, the value is rounded to a single
decimal place. When,</p>
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</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li>See full diff in <a
href="https://github.com/biopython/biopython/commits">compare
view</a></li>
</ul>
</details>
<br />

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Author: dependabot[bot]

pyproject.toml

@@ -13,7 +13,7 @@ authors = [
 ]
 
 dependencies = [
-    "biopython>=1.83",
+    "biopython>=1.87",
     "datasets>=4.8.5",
     "lightning>=2.6.1",
     "numpy>=2.2.6",