diff --git a/biopython-1.73.tar.gz b/biopython-1.73.tar.gz deleted file mode 100644 index c633614..0000000 --- a/biopython-1.73.tar.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:70c5cc27dc61c23d18bb33b6d38d70edc4b926033aea3b7434737c731c94a5e0 -size 15715102 diff --git a/biopython-1.74.tar.gz b/biopython-1.74.tar.gz new file mode 100644 index 0000000..bd152cf --- /dev/null +++ b/biopython-1.74.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:25152c1be2c9205bf80901fc49adf2c2efff49f0dddbcf6e6b2ce31dfa6590c0 +size 16129257 diff --git a/python-biopython.changes b/python-biopython.changes index 22a45ef..4adc658 100644 --- a/python-biopython.changes +++ b/python-biopython.changes @@ -1,3 +1,53 @@ +------------------------------------------------------------------- +Tue Jul 23 01:23:01 UTC 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. + ------------------------------------------------------------------- Fri Jan 4 17:31:38 UTC 2019 - Todd R diff --git a/python-biopython.spec b/python-biopython.spec index f770f45..64de3f3 100644 --- a/python-biopython.spec +++ b/python-biopython.spec @@ -21,10 +21,10 @@ %{?!python_module:%define python_module() python-%{**} python3-%{**}} Name: python-biopython -Version: 1.73 +Version: 1.74 Release: 0 Summary: Python Tools for Computational Molecular Biology -License: MIT +License: MIT AND BSD-3-Clause Group: Development/Libraries/Python Url: http://www.biopython.org Source0: https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz @@ -47,7 +47,6 @@ Recommends: python-pydot Recommends: python-pygraphviz Recommends: python-rdflib Recommends: python-reportlab -BuildRoot: %{_tmppath}/%{name}-%{version}-build %python_subpackages %description