Release 4.1.1

3 files changed, 27 insertions, 6 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 3e2332aad725..f2c21eaa676f 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = python-pyteomics
 	pkgdesc = A framework for proteomics data analysis.
-	pkgver = 4.1
+	pkgver = 4.1.1
 	pkgrel = 1
 	url = https://pyteomics.readthedocs.io
 	changelog = CHANGELOG
@@ -14,9 +14,10 @@ pkgbase = python-pyteomics
 	optdepends = python-lxml: for XML parsing modules
 	optdepends = python-numpy: for most of features, highly recommended
 	optdepends = python-dill: needed for multiprocessing when pickle is not enough
+	optdepends = python-pynumpress: for Numpress support
 	options = !emptydirs
-	source = https://pypi.io/packages/source/p/pyteomics/pyteomics-4.1.tar.gz
-	sha256sums = d7eaa5a1c6f25a39a42c4846e8c39e23cd3ba6f1aeeeedb730c3911c82bf6633
+	source = https://pypi.io/packages/source/p/pyteomics/pyteomics-4.1.1.tar.gz
+	sha256sums = 384e4e5eabdbfec39d7c38369278e386a074c7066f33052d7c313af40f1aa45e
 
 pkgname = python-pyteomics
 
diff --git a/CHANGELOG b/CHANGELOG
index 7f415978efda..72f042ff3daf 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,22 @@
+4.1.1
+-----
+
+ - Add `numpress <https://dx.doi.org/10.1074%2Fmcp.O114.037879>`_ support for mzML and mzXML files.
+   To read files compressed with Numpress, install `pynumpress`
+   (`PyPI <https://pypi.org/project/pynumpress/>`_, `GitHub <https://github.com/mobiusklein/pynumpress>`_).
+
+   .. note:: There is a `known issue
+      <https://bitbucket.org/levitsky/pyteomics/issues/37/add-numpress-support-in-mzml#comment-51540079>`_
+      with `pynumpress` on Linux and Python 2.7, which is contingent on a fix in Cython.
+
+ - Bugfixes.
+
+API changes
+...........
+
+ - In :py:func:`ms1.read` and :py:func:`ms2.read`, the default value for `use_index` is now :py:const:`False`.
+   Using the indexed parsers may result in incorrect behavior if the "first" scan number in S-lines is not unique.
+
 4.1
 ---
 
diff --git a/PKGBUILD b/PKGBUILD
index c1025ff0e9ef..6c76b940cb89 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,6 +1,6 @@
 # Maintainer: Lev Levitsky <levlev at mail dot ru>
 pkgname=python-pyteomics
-pkgver=4.1
+pkgver=4.1.1
 pkgrel=1
 pkgdesc="A framework for proteomics data analysis."
 arch=('any')
@@ -12,10 +12,11 @@ optdepends=('python-matplotlib: for pylab_aux module'
             'python-pandas: for convenient filtering of CSV tables from search engines'
             'python-lxml: for XML parsing modules'
             'python-numpy: for most of features, highly recommended'
-            'python-dill: needed for multiprocessing when pickle is not enough')
+            'python-dill: needed for multiprocessing when pickle is not enough'
+            'python-pynumpress: for Numpress support')
 options=(!emptydirs)
 source=("https://pypi.io/packages/source/p/pyteomics/pyteomics-${pkgver}.tar.gz")
-sha256sums=('d7eaa5a1c6f25a39a42c4846e8c39e23cd3ba6f1aeeeedb730c3911c82bf6633')
+sha256sums=('384e4e5eabdbfec39d7c38369278e386a074c7066f33052d7c313af40f1aa45e')
 changelog="CHANGELOG"
 package() {
   cd "${srcdir}/pyteomics-${pkgver}"