Version 3.1

3 files changed, 52 insertions, 10 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 7af7e9639d9a..5d5dbf64c902 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,20 +1,19 @@
-# Generated by makepkg 4.2.1
-# Wed Apr 15 22:17:40 UTC 2015
 pkgbase = python2-pyteomics
 	pkgdesc = A framework for proteomics data analysis.
-	pkgver = 3.0.1
-	pkgrel = 1
+	pkgver = 3.1
+	pkgrel = 2
 	url = http://pythonhosted.org/pyteomics
 	changelog = CHANGELOG
 	arch = any
 	license = Apache
 	depends = python2
+	depends = python2-setuptools
 	optdepends = python2-matplotlib: for pylab_aux module, optional
 	optdepends = python2-lxml: for XML parsing modules, recommended
 	optdepends = python2-numpy: for lots of features, highly recommended
 	options = !emptydirs
-	source = https://pypi.python.org/packages/source/p/pyteomics/pyteomics-3.0.1.tar.gz
-	md5sums = 2c838cc1c16dce69148662b883c755b9
+	source = https://pypi.python.org/packages/source/p/pyteomics/pyteomics-3.1.tar.gz
+	md5sums = 5e4c8d38f0891e82b8ec30515ce6718f
 
 pkgname = python2-pyteomics
 
diff --git a/CHANGELOG b/CHANGELOG
index a9f2bb997e99..7dcb0ee07f39 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,45 @@
+3.1
+---
+
+This release offers integration with the great :py:mod:`pandas` library.
+Working with :py:func:`qvalues` and :py:func:`!filter` functions
+is now much easier if you have your PSMs in a :py:class:`DataFrame`.
+Many search engines use CSV as their output format, allowing direct
+creation of :py:class:`DataFrame` objects. New functions
+:py:func:`pyteomics.tandem.DataFrame` and :py:func:`pyteomics.pepxml.DataFrame`
+faciliatate creation of DataFrames from corresponding formats.
+
+Also, :py:func:`qvalues`, :py:func:`!filter` and :py:func:`fdr` functions can now use
+posterior error probabilities (PEPs) instead of using decoys for q-value calculation.
+
+ - In :py:func:`qvalues` and :py:func:`!filter` functions,
+   `key` and `is_decoy` can now be array-like objects or strings
+   (as well as functions and iterators).
+   If a string is given, it is used as a field name in the PSM array
+   or :py:class:`DataFrame`. :py:func:`fdr` functions also support strings
+   and iterables as arguments.
+
+ - New parameter `pep` in :py:func:`qvalues`, :py:func:`!filter` and :py:func:`fdr` functions.
+   It can be callable, array-like, or iterator. Conflicts with decoy-related
+   parameters. Compatible with `key`, but makes it optional.
+
+ - Fixed the behavior of :py:func:`filter.chain` functions. They now treat
+   the `full_output` argument the same way as :py:func:`!filter` functions.
+
+ - Fixed the issue that caused exceptions when calling :py:func:`fasta.decoy_db`
+   and :py:func:`fasta.write_decoy_db` with explicitly given `mode` (signature
+   for creation of :py:class:`pyteomics.auxiliary.FileReader` objects slightly changed).
+
+ - Pyteomics now uses `setuptools` and is a namespace package.
+
+ - Minor fixes.
+
+
+API changes
+...........
+
+- Default value of `remove_decoy` in :py:func:`qvalues` is now :py:const:`False`.
+
 3.0.1
 -----
 
@@ -8,6 +50,7 @@
 
 3.0.0
 -----
+
  - XML parsers are now implemented as objects, each format has its own class.
    Those classes can be instantiated using the same arguments as :py:func:`read`
    functions accepted, and support direct iteration and the ``with`` syntax.
diff --git a/PKGBUILD b/PKGBUILD
index 811249bb4941..cac75f4d731e 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,18 +1,18 @@
 # Maintainer: Lev Levitsky <levlev at mail dot ru>
 pkgname=python2-pyteomics
-pkgver=3.0.1
-pkgrel=1
+pkgver=3.1
+pkgrel=2
 pkgdesc="A framework for proteomics data analysis."
 arch=('any')
 url="http://pythonhosted.org/pyteomics"
 license=('Apache')
-depends=('python2')
+depends=('python2' 'python2-setuptools')
 optdepends=('python2-matplotlib: for pylab_aux module, optional' \
             'python2-lxml: for XML parsing modules, recommended' \
             'python2-numpy: for lots of features, highly recommended')
 options=(!emptydirs)
 source=("https://pypi.python.org/packages/source/p/pyteomics/pyteomics-${pkgver}.tar.gz")
-md5sums=('2c838cc1c16dce69148662b883c755b9')
+md5sums=('5e4c8d38f0891e82b8ec30515ce6718f')
 changelog="CHANGELOG"
 package() {
   cd "${srcdir}/pyteomics-${pkgver}"