Version 3.3.1

3 files changed, 45 insertions, 7 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 4497d831250f..b2f72d51171b 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,8 +1,8 @@
 # Generated by mksrcinfo v8
-# Thu Feb 18 15:21:41 UTC 2016
+# Thu Jun  2 12:48:23 UTC 2016
 pkgbase = python-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 = python-pyteomics
 	optdepends = python-lxml: for XML parsing modules
 	optdepends = python-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 = python-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
 ---
 
diff --git a/PKGBUILD b/PKGBUILD
index 46c8a9d1c7b1..42e0492ea5c1 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,6 +1,6 @@
 # Maintainer: Lev Levitsky <levlev at mail dot ru>
 pkgname=python-pyteomics
-pkgver=3.2
+pkgver=3.3.1
 pkgrel=1
 pkgdesc="A framework for proteomics data analysis."
 arch=('any')
@@ -13,8 +13,8 @@ optdepends=('python-matplotlib: for pylab_aux module'
             'python-lxml: for XML parsing modules'
             'python-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}"