Accepting request 1135235 from devel:languages:python:numeric

- update to 1.82:
  * The ``inplace`` argument of ``complement`` and
    ``reverse_complement`` in ``Bio.Seq`` now always default to
    ``False`` both for ``Seq`` and ``MutableSeq`` objects.
    To modify a ``MutableSeq`` in-place, use ``inplace=True``.
  * A new class ``CodonAligner`` was added to ``Bio.Align``. A
    ``CodonAligner`` object can align a nucleotide sequence to the
    amino acid sequence it encodes, using a dynamic programming
    algorithm modeled on ``PairwiseAligner`` to take frame shifts
    into account. The ``CodonAligner`` returns ``Alignment``
    objects.
  * By calling the new ``mapall`` method on an ``Alignment``
    object storing a multiple sequence alignment of amino acid
    sequences, with nucleotide-to-amino acid alignments generated
    by ``CodonAligner`` as the argument, a codon-by-codon
    multiple sequence alignment of nucleotide sequences can be
    obtained. The new submodule ``Bio.Align.analysis`` provides
    functions to estimate synonymous and nonsynonymous mutations
    and to perform the McDonald-Kreitman test on the codon
    multiple sequence alignments. Together, this provides the
    same functionality as the ``Bio.codonalign`` module, but uses
    the standard ``Alignment`` class, and does not rely on regular
    expression searching to align a nucleotide sequence to
    an amino acid sequence.
  * The ``hmmer3-text`` SearchIO format now also extracts the
    similarity string of the parsed alignments.
  * HMMER results with the full path to the hmmer executable in
    the banner are now parsed correctly.
  * We now have basic type hint annotations in various modules
    including ``Seq``, ``SeqRecord``, and ``SeqIO``.

OBS-URL: https://build.opensuse.org/request/show/1135235
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=11

biopython-1.81.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0
-size 19324875

biopython-1.82.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a9b10d959ae88a9744a91c6ce3601f4c86e7ec41679bc93c29f679218f6167bb
+size 19432124

python-biopython.changes

@@ -1,3 +1,50 @@
+-------------------------------------------------------------------
+Wed Dec 27 09:23:42 UTC 2023 - Dirk Müller <dmueller@suse.com>
+
+- update to 1.82:
+  * The ``inplace`` argument of ``complement`` and
+    ``reverse_complement`` in ``Bio.Seq`` now always default to
+    ``False`` both for ``Seq`` and ``MutableSeq`` objects.
+    To modify a ``MutableSeq`` in-place, use ``inplace=True``.
+  * A new class ``CodonAligner`` was added to ``Bio.Align``. A
+    ``CodonAligner`` object can align a nucleotide sequence to the
+    amino acid sequence it encodes, using a dynamic programming
+    algorithm modeled on ``PairwiseAligner`` to take frame shifts
+    into account. The ``CodonAligner`` returns ``Alignment``
+    objects.
+  * By calling the new ``mapall`` method on an ``Alignment``
+    object storing a multiple sequence alignment of amino acid
+    sequences, with nucleotide-to-amino acid alignments generated
+    by ``CodonAligner`` as the argument, a codon-by-codon
+    multiple sequence alignment of nucleotide sequences can be
+    obtained. The new submodule ``Bio.Align.analysis`` provides
+    functions to estimate synonymous and nonsynonymous mutations
+    and to perform the McDonald-Kreitman test on the codon
+    multiple sequence alignments. Together, this provides the
+    same functionality as the ``Bio.codonalign`` module, but uses
+    the standard ``Alignment`` class, and does not rely on regular
+    expression searching to align a nucleotide sequence to
+    an amino acid sequence.
+  * The ``hmmer3-text`` SearchIO format now also extracts the
+    similarity string of the parsed alignments.
+  * HMMER results with the full path to the hmmer executable in
+    the banner are now parsed correctly.
+  * We now have basic type hint annotations in various modules
+    including ``Seq``, ``SeqRecord``, and ``SeqIO``.
+  * Calling ``iter`` on a ``PairwiseAlignments`` object returned
+    by a ``PairwiseAigner`` previously reset the iterator
+    such that it will start from the first alignment when iterating.
+  * The MMCIFParser now ignores '.' header values.
+  * Calling ``set_angle()`` on a residue dihedral angle
+    previously set only the specified angle, now the default
+    behavior is to update overlapping angles as well.
+  * Generating a structure with default internal coordinates,
+    e.g. from a sequence with ``read_PIC_seq()``,  previously
+    selected wrong default values in many cases.
+  * Added ``make_extended()`` to set a chain to an extended beta
+    strand conformation, as the default backbone values reflect
+    the more popular alpha helix in most cases.
+
 -------------------------------------------------------------------
 Wed Feb 15 14:03:39 UTC 2023 - Dirk Müller <dmueller@suse.com>
 

python-biopython.spec

@@ -22,7 +22,7 @@
 %define skip_python2 1
 %define skip_python36 1
 Name:           python-biopython
-Version:        1.81
+Version:        1.82
 Release:        0
 Summary:        Python Tools for Computational Molecular Biology
 License:        BSD-3-Clause AND MIT