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Commit Graph

5 Commits

Author SHA256 Message Date
Tomáš Chvátal
52977e93ef Accepting request 819377 from home:mcalabkova:branches:devel:languages:python:numeric
- Update to version 1.77
  * **We have dropped support for Python 2 now.**
  * ``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.

OBS-URL: https://build.opensuse.org/request/show/819377
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=9
2020-07-08 10:10:38 +00:00
Todd R
e0e5d221c6 Accepting request 750002 from home:TheBlackCat:branches:devel:languages:python:numeric
Update to version 1.75

OBS-URL: https://build.opensuse.org/request/show/750002
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=7
2019-11-20 20:18:30 +00:00
Todd R
3ca7ac07d1 Accepting request 717710 from home:TheBlackCat:branches:devel:languages:python:numeric
- 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.

OBS-URL: https://build.opensuse.org/request/show/717710
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=5
2019-07-23 01:28:49 +00:00
Dominique Leuenberger
562201f9d3 Accepting request 662924 from devel:languages:python:numeric
OBS-URL: https://build.opensuse.org/request/show/662924
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=2
2019-01-21 09:46:29 +00:00
Dominique Leuenberger
061a2d5331 Accepting request 605802 from devel:languages:python
computational molecular biology for python

OBS-URL: https://build.opensuse.org/request/show/605802
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=1
2018-05-29 14:47:30 +00:00