diff --git a/biopython-1.74.tar.gz b/biopython-1.74.tar.gz deleted file mode 100644 index bd152cf..0000000 --- a/biopython-1.74.tar.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:25152c1be2c9205bf80901fc49adf2c2efff49f0dddbcf6e6b2ce31dfa6590c0 -size 16129257 diff --git a/biopython-1.75.tar.gz b/biopython-1.75.tar.gz new file mode 100644 index 0000000..ce10457 --- /dev/null +++ b/biopython-1.75.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5060e4ef29c2bc214749733634051be5b8d11686c6590fa155c3443dcaa89906 +size 16449672 diff --git a/python-biopython.changes b/python-biopython.changes index 4adc658..a80955d 100644 --- a/python-biopython.changes +++ b/python-biopython.changes @@ -1,3 +1,55 @@ +------------------------------------------------------------------- +Wed Nov 20 20:17:31 UTC 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 01:23:01 UTC 2019 - Todd R diff --git a/python-biopython.spec b/python-biopython.spec index 64de3f3..50ad625 100644 --- a/python-biopython.spec +++ b/python-biopython.spec @@ -16,17 +16,15 @@ # +%{?!python_module:%define python_module() python-%{**} python3-%{**}} # Tests require a network connection %bcond_with test - -%{?!python_module:%define python_module() python-%{**} python3-%{**}} Name: python-biopython -Version: 1.74 +Version: 1.75 Release: 0 Summary: Python Tools for Computational Molecular Biology License: MIT AND BSD-3-Clause -Group: Development/Libraries/Python -Url: http://www.biopython.org +URL: http://www.biopython.org Source0: https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz Source100: python-biopython-rpmlintrc BuildRequires: %{python_module devel} @@ -54,7 +52,7 @@ The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. %prep -%setup -n biopython-%{version} +%setup -q -n biopython-%{version} # remove all execute bits from documentation and fix line endings find -type f -exec chmod -x {} 2>/dev/null ';' find -type f -exec sed -i 's/\r//' {} 2>/dev/null ';' @@ -74,7 +72,7 @@ export LANG=en_US.UTF-8 %if %{with test} %check export LANG=en_US.UTF-8 -%python_exec setup.py test +%pytest %endif %files %{python_files}