3.4.1

3 files changed, 33 insertions, 8 deletions

diff --git a/.SRCINFO b/.SRCINFO
index d0cca085c0b9..11052323a9d3 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,8 +1,8 @@
 # Generated by mksrcinfo v8
-# Thu Sep  8 20:08:35 UTC 2016
+# Sun Mar 12 12:32:18 UTC 2017
 pkgbase = python2-pyteomics
 	pkgdesc = A framework for proteomics data analysis.
-	pkgver = 3.4
+	pkgver = 3.4.1
 	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.io/packages/source/p/pyteomics/pyteomics-3.4.tar.gz
-	md5sums = 3c8d1bcc16c53100e531a10a2853f679
+	source = https://pypi.io/packages/source/p/pyteomics/pyteomics-3.4.1.tar.gz
+	md5sums = 9e1aecc88b7ea6e7bc6e77e6479cbb82
 
 pkgname = python2-pyteomics
 
diff --git a/CHANGELOG b/CHANGELOG
index 15672ad90dd2..26e06e13a1cc 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,28 @@
+3.4.1
+-----
+
+ - Add selenocysteine ("U") and pyrrolysine ("O") to :py:data:`pyteomics.mass.std_aa_mass` and
+   :py:data:`pyteomics.mass.std_aa_comp`.
+
+ - An optional parameter `encoding` is now accepted by text file readers (:py:func:`pyteomics.mgf.read`
+   and :py:func:`pyteomics.fasta.read`). This can be useful for MGF files with non-ASCII spectrum
+   titles or comments.
+
+ - New function :py:func:`pyteomics.mass.mass.isotopologues`.
+
+ - Performance improvements in :py:func:`pyteomics.electrochem.pI`.
+
+ - Fix the issue in :py:mod:`pyteomics.xml` which resulted in very long processing times for indexed XML files
+   with a byte ordering mark (BOM).
+
+ - Support all standard and non-standard data array names in :py:mod:`pyteomics.mzml`.
+
+ - Change default value of ``retrieve_refs`` in :py:func:`pyteomics.mzid.read` to :py:const:`True`.
+
+ - Preserve unit information extracted from cvParam tags in PSI XML files.
+
+ - Fix in :py:mod:`pyteomics.mzxml`, other minor fixes.
+
 3.4
 ---
 
@@ -188,8 +213,8 @@ API changes
 
  - All :py:func:`fdr`, :py:func:`qvalues`, and :py:func:`!filter` functions
    now accept a new parameter `correction`. It is used for more accurate
-   estimation of the number of false positives using TDA (paper with explanation
-   submitted to JPR).
+   estimation of the number of false positives using TDA (`paper with explanation
+   <http://dx.doi.org/10.1021/acs.jproteome.6b00144>`_).
 
  - :py:func:`!filter` functions now support both iterator protocol and context
    manager protocol. They now also accept the `full_output` parameter, which has
diff --git a/PKGBUILD b/PKGBUILD
index 73f3f535cf59..6a614a39585c 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,6 +1,6 @@
 # Maintainer: Lev Levitsky <levlev at mail dot ru>
 pkgname=python2-pyteomics
-pkgver=3.4
+pkgver=3.4.1
 pkgrel=1
 pkgdesc="A framework for proteomics data analysis."
 arch=('any')
@@ -14,7 +14,7 @@ optdepends=('python2-matplotlib: for pylab_aux module'
             'python2-numpy: for most of features, highly recommended')
 options=(!emptydirs)
 source=("https://pypi.io/packages/source/p/pyteomics/pyteomics-${pkgver}.tar.gz")
-md5sums=('3c8d1bcc16c53100e531a10a2853f679')
+md5sums=('9e1aecc88b7ea6e7bc6e77e6479cbb82')
 changelog="CHANGELOG"
 package() {
   cd "${srcdir}/pyteomics-${pkgver}"