Changelog for python312-biopython-1.83-1.3.x86_64.rpm :

* Sat Jan 20 2024 Dirk Müller - update to 1.83:
* This release reverts the removal of the .strand, .ref, and .ref_db attributes of the SeqFeature which was done without a deprecation period. They are again aliases for .location.strand etc, but trigger deprecation warnings.
* Wed Dec 27 2023 Dirk Müller - 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 2023 Dirk Müller - update to 1.81:
* The API documentation and the `Biopython Tutorial and Cookbook` have been updated to better annotate use and application of the ``Bio.PDB.internal_coords`` module.
* ``Bio.Phylo`` now supports ``Alignment`` and ``MultipleSeqAlignment`` objects as input.
* Several improvements and bug fixes to the snapgene parser
* Wed Jan 04 2023 Dirk Müller - update to 1.80:
* This release of Biopython supports Python 3.7, 3.8, 3.9, 3.10, 3.11. It has also been tested on PyPy3.7 v7.3.5.
* Functions ``read``, ``parse``, and ``write`` were added to ``Bio.Align`` to read and write ``Alignment`` objects.
* Because dict retains the item order by default since Python3.6, all instances of ``collections.OrderedDict`` have been replaced by either standard ``dict`` or where appropriate by ``collections.defaultsdict``.
* The ``Bio.motifs.jaspar.db`` now returns ``tf_family`` and ``tf_class`` as a string array since the JASPAR 2018 release.
* The Local Composition Complexity functions from ``Bio.SeqUtils`` now uses base 4 log instead of 2 as stated in the original reference Konopka (2005),
* Sequence Complexity and Composition. https://doi.org/10.1038/npg.els.0005260
* Append mode is now supported in ``Bio.bgzf`` (and a bug parsing blocked GZIP files with an internal empty block fixed).
* The experimental warning was dropped from ``Bio.phenotype`` (which was new in Biopython 1.67).
* Sequences now have a ``defined`` attribute that returns a boolean indicating if the underlying data is defined or not.
* The ``Bio.PDB`` module now includes a structural alignment module, using the combinatorial extension algorithm of Shindyalov and Bourne, commonly known as CEAlign. The module allows for two structures to be aligned based solely on their 3D conformation, ie. in a sequence-independent manner. The method is particularly powerful when the structures shared a very low degree of sequence similarity. The new module is available in ``Bio.PDB.CEAligner`` with an interface similar to other 3D superimposition modules.
* A new module ``Bio.PDB.qcprot`` implements the QCP superposition algorithm in pure Python, deprecating the existing C implementation. This leads to a slight performance improvement and to much better maintainability. The refactored ``qcprot.QCPSuperimposer`` class has small changes to its API, to better mirror that of ``Bio.PDB.Superimposer``.
* The ``Bio.PDB.PDBList`` module now allows downloading biological assemblies, for one or more entries of the wwPDB.
* In the ``Bio.Restriction`` module, each restriction enzyme now includes an `id` property giving the numerical identifier for the REBASE database identifier from which the enzyme object was created, and a `uri` property with a canonical `identifiers.org` link to the database, for use in linked-data representations.
* Add new ``gc_fraction`` function in ``SeqUtils`` and marks ``GC`` for future deprecation.
* Support for the old format (dating back to 2004) of the GN line in SwissProt files was dropped in ``Bio.SwissProt``.
* Additionally, a number of small bugs and typos have been fixed with additions to the test suite.
* Sun Mar 27 2022 Dirk Müller - update to 1.79:
* This is intended to be our final release supporting Python 3.6. It also supports Python 3.7, 3.8 and 3.9, and has also been tested on PyPy3.6.1 v7.1.1.
* Detailed list of changes see https://github.com/biopython/biopython/blob/biopython-179/NEWS.rst#1-june-2021-biopython-179
* Sat Feb 20 2021 andy great - Update to version 1.7.8.
* The main change is that Bio.Alphabet is no longer used. In some cases you will now have to specify expected letters, molecule type (DNA, RNA, protein), or gap character explicitly.
* Bio.SeqIO.parse() is faster with \"fastq\" format due to small improvements in the Bio.SeqIO.QualityIO module.
* The SeqFeature object\'s .extract() method can now be used for trans-spliced locations via an optional dictionary of references.
* As in recent releases, more of our code is now explicitly available under either our original \"Biopython License Agreement\", or the very similar but more commonly used \"3-Clause BSD License\". See the LICENSE.rst file for more details.
* Additionally, a number of small bugs and typos have been fixed with additions to the test suite. There has been further work to follow the Python PEP8, PEP257 and best practice standard coding style, and all of the tests have been reformatted with the black tool to match the main code base.- Skip python36 because numpy no longer support it.
* Tue Nov 03 2020 Matej Cepl - Remove ridiculously wide find commands in %prep, which break a lot (binary) files.
* Wed Jul 08 2020 Marketa Calabkova - Update to version 1.77
*
*
*We have dropped support for Python 2 now.
*
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* ``pairwise2`` now allows the input of parameters with keywords and returns the alignments as a list of ``namedtuples``.
* The codon tables have been updated to NCBI genetic code table version 4.5, which adds Cephalodiscidae mitochondrial as table 33.
* Updated ``Bio.Restriction`` to the January 2020 release of REBASE.
* A major contribution by Rob Miller to ``Bio.PDB`` provides new methods to handle protein structure transformations using dihedral angles (internal coordinates). The new framework supports lossless interconversion between internal and cartesian coordinates, which, among other uses, simplifies the analysis and manipulation of coordinates of proteins structures.
* ``PDBParser`` and ``PDBIO`` now support PQR format file parsing and input/ output.
* In addition to the mainstream ``x86_64`` aka ``AMD64`` CPU architecture, we now also test every contribution on the ``ARM64``, ``ppc64le``, and ``s390x`` CPUs under Linux thanks to Travis CI. Further post-release testing done by Debian and other packagers and distributors of Biopython also covers these CPUs.
* ``Bio.motifs.PositionSpecificScoringMatrix.search()`` method has been re-written: it now applies ``.calculate()`` to chunks of the sequence to maintain a low memory footprint for long sequences.
* Additionally, a number of small bugs and typos have been fixed with further additions to the test suite. There has been further work to follow the Python PEP8, PEP257 and best practice standard coding style, and more of the code style has been reformatted with the ``black`` tool.
* Wed Nov 20 2019 Todd R - Update to version 1.75
* The restriction enzyme list in Bio.Restriction has been updated to the August 2019 release of REBASE.
* ``Bio.SeqIO`` now supports reading and writing files in the native format of Christian Marck\'s DNA Strider program (\"xdna\" format, also used by Serial Cloner), as well as reading files in the native formats of GSL Biotech\'s SnapGene (\"snapgene\") and Textco Biosoftware\'s Gene Construction Kit (\"gck\").
* ``Bio.AlignIO`` now supports GCG MSF multiple sequence alignments as the \"msf\" format (work funded by the National Marrow Donor Program).
* The main ``Seq`` object now has string-like ``.index()`` and ``.rindex()`` methods, matching the existing ``.find()`` and ``.rfind()`` implementations. The ``MutableSeq`` object retains its more list-like ``.index()`` behaviour.
* The ``MMTFIO`` class has been added that allows writing of MMTF file format files from a Biopython structure object. ``MMTFIO`` has a similar interface to ``PDBIO`` and ``MMCIFIO``, including the use of a ``Select`` class to write out a specified selection. This final addition to read/write support for PDB/mmCIF/MMTF in Biopython allows conversion between all three file formats.
* Values from mmCIF files are now read in as a list even when they consist of a single value. This change improves consistency and reduces the likelihood of making an error, but will require user code to be updated accordingly.
* ``Bio.PDB`` has been updated to support parsing REMARK 99 header entries from PDB-style Astral files.
* A new keyword parameter ``full_sequences`` was added to ``Bio.pairwise2``\'s pretty print method ``format_alignment`` to restore the output of local alignments to the \'old\' format (showing the whole sequences including the un-aligned parts instead of only showing the aligned parts).
* A new function ``charge_at_pH(pH)`` has been added to ``ProtParam`` and ``IsoelectricPoint`` in ``Bio.SeqUtils``.
* The ``PairwiseAligner`` in ``Bio.Align`` was extended to allow generalized pairwise alignments, i.e. alignments of any Python object, for example three-letter amino acid sequences, three-nucleotide codons, and arrays of integers.
* A new module ``substitution_matrices`` was added to ``Bio.Align``, which includes an ``Array`` class that can be used as a substitution matrix. As the ``Array`` class is a subclass of a numpy array, mathematical operations can be applied to it directly, and C code that makes use of substitution matrices can directly access the numerical values stored in the substitution matrices. This module is intended as a replacement of ``Bio.SubsMat``, which is currently unmaintained.
* As in recent releases, more of our code is now explicitly available under either our original \"Biopython License Agreement\", or the very similar but more commonly used \"3-Clause BSD License\". See the ``LICENSE.rst`` file for more details.
* Additionally, a number of small bugs and typos have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8, PEP257 and best practice standard coding style. We have also started to use the ``black`` Python code formatting tool.
* Tue Jul 23 2019 Todd R - Update to version 1.74
* Our core sequence objects (``Seq``, ``UnknownSeq``, and ``MutableSeq``) now have a string-like ``.join()`` method.
* The NCBI now allows longer accessions in the GenBank file LOCUS line, meaning the fields may not always follow the historical column based positions. We no longer give a warning when parsing these. We now allow writing such files (although with a warning as support for reading them is not yet widespread).
* Support for the ``mysqlclient`` package, a fork of MySQLdb, has been added.
* We now capture the IDcode field from PDB Header records.
* ``Bio.pairwise2``\'s pretty-print output from ``format_alignment`` has been optimized for local alignments: If they do not consist of the whole sequences, only the aligned section of the sequences are shown, together with the start positions of the sequences (in 1-based notation). Alignments of lists will now also be prettily printed.
* ``Bio.SearchIO`` now supports parsing the text output of the HHsuite protein sequence search tool. The format name is ``hhsuite2-text`` and ``hhsuite3-text``, for versions 2 and 3 of HHsuite, respectively.
* ``Bio.SearchIO`` HSP objects has a new attribute called ``output_index``. This attribute is meant for capturing the order by which the HSP were output in the parsed file and is set with a default value of -1 for all HSP objects. It is also used for sorting the output of ``QueryResult.hsps``.
* ``Bio.SeqIO.AbiIO`` has been updated to preserve bytes value when parsing. The goal of this change is make the parser more robust by being able to extract string-values that are not utf-8-encoded. This affects all tag values, except for ID and description values, where they need to be extracted as strings to conform to the ``SeqRecord`` interface. In this case, the parser will attempt to decode using ``utf-8`` and fall back to the system encoding if that fails. This change affects Python 3 only.
* ``Bio.motifs.mast`` has been updated to parse XML output files from MAST over the plain-text output file. The goal of this change is to parse a more structured data source with minimal loss of functionality upon future MAST releases. Class structure remains the same plus an additional attribute ``Record.strand_handling`` required for diagram parsing.
* ``Bio.Entrez`` now automatically retries HTTP requests on failure. The maximum number of tries and the sleep between them can be configured by changing ``Bio.Entrez.max_tries`` and ``Bio.Entrez.sleep_between_tries``. (The defaults are 3 tries and 15 seconds, respectively.)
* All tests using the older print-and-compare approach have been replaced by unittests following Python\'s standard testing framework.
* On the documentation side, all the public modules, classes, methods and functions now have docstrings (built in help strings). Furthermore, the PDF version of the
*Biopython Tutorial and Cookbook
* now uses syntax coloring for code snippets.
* Additionally, a number of small bugs and typos have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8, PEP257 and best practice standard coding style.