DuhaimeLab / VirusHostInteractionPredictor
94%
main: 94%

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LAST BUILD ON BRANCH gh-readonly-queue/main/pr-126-ebe03c5b4d6a7831f4159d46a15b6bb962da0c14
branch: gh-readonly-queue/main/pr-126-ebe03c5b4d6a7831f4159d46a15b6bb962da0c14
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coverage: 93.861%. Remained the same
10148664360

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⬆ Bump biopython from 1.83 to 1.84 (#126)

Bumps [biopython](https://github.com/biopython/biopython) from 1.83 to
1.84.
<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>28 June 2024: Biopython 1.84</h1>
<p>This release of Biopython supports Python 3.9, 3.10, 3.11 and 3.12.
It
has also been tested on PyPy3.9 v7.3.13. Python 3.9 is approaching end
of
life, our support for it is now deprecated.</p>
<p>Our main documentation, the Biopython Tutorial and Cookbook, has been
converted from LaTeX to reStructuredText, and combined with the existing
API
documentation, into a single more modern and navigable HTML output.</p>
<p>Bio.Blast contains a new parser for BLAST XML output as a replacement
for the
old parser in Bio.Blast.NCBIXML. The main differences between the
parsers is
as follows:</p>
<ul>
<li>The old parser stores information in a Bio.Blast.NCBIXML.Blast
object, with
attribute names based on plain-text Blast output. The new parser stores
information in a Bio.Blast.Record object. This class follows the DTD
that
describes the XML in terms of attribute names and dictionary key names,
class structure, and object types. This makes it easier to find the
detailed
description of each field in the NCBI Blast documentation.</li>
<li>The old parser stores alignment information directly as seen in the
BLAST XML
output, i.e. as strings with dashes to represent gaps. The new parser
stores
the alignment information as a Bio.Align.Alignment object, which can
then be
used to e.g. print the alignment in a different format.</li>
</ul>
<p>Bio.Blast also contains a new qblast function as a replacement for
the old
qblast function in Bio.Blast.NCBIWWW. The main difference is that the
old
qblast function in Bio.Blast.NCBIWWW returns the BLAST search results as
Python
strings, while the new qblast returns bytes objects. Note that in
Python, to
p... (continued)

474 of 505 relevant lines covered (93.86%)

1.88 hits per line

Relevant lines Covered
505 RELEVANT LINES 474 COVERED LINES
1.88 HITS PER LINE
Source Files on gh-readonly-queue/main/pr-126-ebe03c5b4d6a7831f4159d46a15b6bb962da0c14

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10148664360 gh-readonly-queue/main/pr-126-ebe03c5b4d6a7831f4159d46a15b6bb962da0c14 ⬆ Bump biopython from 1.83 to 1.84 (#126) Bumps [biopython](https://github.com/biopython/biopython) from 1.83 to 1.84. <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/biopython/biopython/blob/master/NEWS.rst... push web-flow github
93.86
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