diff options
author | Lev Levitsky | 2016-06-02 15:53:01 +0300 |
---|---|---|
committer | Lev Levitsky | 2016-06-02 15:53:01 +0300 |
commit | be69b00dd429dfbfd267a34f96ff14bd604445df (patch) | |
tree | 94d3040c4cf52027d9cabf735492269683b69afc | |
parent | 9f820c62e6d9074b085101e749c54bd4bbe0e1b0 (diff) | |
download | aur-be69b00dd429dfbfd267a34f96ff14bd604445df.tar.gz |
Version 3.3.1
-rw-r--r-- | .SRCINFO | 8 | ||||
-rw-r--r-- | CHANGELOG | 38 | ||||
-rw-r--r-- | PKGBUILD | 6 |
3 files changed, 45 insertions, 7 deletions
@@ -1,8 +1,8 @@ # Generated by mksrcinfo v8 -# Thu Feb 18 15:25:40 UTC 2016 +# Thu Jun 2 12:51:18 UTC 2016 pkgbase = python2-pyteomics pkgdesc = A framework for proteomics data analysis. - pkgver = 3.2 + pkgver = 3.3.1 pkgrel = 1 url = http://pythonhosted.org/pyteomics changelog = CHANGELOG @@ -16,8 +16,8 @@ pkgbase = python2-pyteomics optdepends = python2-lxml: for XML parsing modules optdepends = python2-numpy: for most of features, highly recommended options = !emptydirs - source = https://pypi.python.org/packages/source/p/pyteomics/pyteomics-3.2.tar.gz - md5sums = 3fd5bc228d248d085a7bf9a461e5c62c + source = https://pypi.io/packages/source/p/pyteomics/pyteomics-3.3.1.tar.gz + md5sums = 0b81c096944334c53ee52c213a42edee pkgname = python2-pyteomics diff --git a/CHANGELOG b/CHANGELOG index 985854c56860..f6c6d142edfc 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,3 +1,41 @@ +3.3.1 +----- + +New submodule :py:mod:`pyteomics.featurexml` with a parser for OpenMS **featureXML** files. + +3.3 +--- + + - mzML and mzIdentML parsers can now create an index of element offsets. + This allows quick random access to elements by unique ID. + + - mzML parsers now come in two flavors: :py:class:`pyteomics.mzml.MzML` and + :py:class:`pyteomics.mzml.PreIndexedMzML`. The latter uses the byte offsets + listed at the end of the file. + + - New parameters `convert_arrays` and `read_charges` in :py:func:`mgf.read` + allow using it without :py:mod:`numpy` and possibly improve performance. + The default behavior is retained. + + - Performance optimizations in :py:func:`mgf.read` and :py:func:`parser.cleave`. + + - New decoy generation mode called "fused decoy", described in the paper accepted to JASMS. + +API changes +........... + + - :py:func:`pyteomics.parser.cleave` no longer accepts the `labels` argument. + It is emphasized that the input sequences are expected to be in plain one-letter + notation, but no checks are performed. + + - :py:func:`DataFrame` functions in :py:mod:`pepxml` and :py:mod:`tandem` now + extract more protein-related information. The list-like protein-related values + can be reported as lists or packed into strings, depending on the optional + paramter `sep`. Some column names have changed as a result. + + - Call signatures of :py:func:`pyteomics.fasta.decoy_sequence` and the functions using it + are slightly changed. Standard modes are now also exposed as individual functions. + 3.2 --- @@ -1,6 +1,6 @@ # Maintainer: Lev Levitsky <levlev at mail dot ru> pkgname=python2-pyteomics -pkgver=3.2 +pkgver=3.3.1 pkgrel=1 pkgdesc="A framework for proteomics data analysis." arch=('any') @@ -13,8 +13,8 @@ optdepends=('python2-matplotlib: for pylab_aux module' 'python2-lxml: for XML parsing modules' 'python2-numpy: for most of features, highly recommended') options=(!emptydirs) -source=("https://pypi.python.org/packages/source/p/pyteomics/pyteomics-${pkgver}.tar.gz") -md5sums=('3fd5bc228d248d085a7bf9a461e5c62c') +source=("https://pypi.io/packages/source/p/pyteomics/pyteomics-${pkgver}.tar.gz") +md5sums=('0b81c096944334c53ee52c213a42edee') changelog="CHANGELOG" package() { cd "${srcdir}/pyteomics-${pkgver}" |