Version 4.6

3 files changed, 34 insertions, 5 deletions

diff --git a/.SRCINFO b/.SRCINFO
index ada2c89254fc..533575546f7f 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = python-pyteomics
 	pkgdesc = A framework for proteomics data analysis.
-	pkgver = 4.5.6
+	pkgver = 4.6
 	pkgrel = 1
 	url = https://pyteomics.readthedocs.io
 	changelog = CHANGELOG
@@ -16,7 +16,7 @@ pkgbase = python-pyteomics
 	optdepends = python-dill: needed for multiprocessing when pickle is not enough
 	optdepends = python-pynumpress: for Numpress support
 	options = !emptydirs
-	source = https://pypi.debian.net/pyteomics/pyteomics-4.5.6-py2.py3-none-any.whl
-	sha256sums = 0e279c085370e8085c84997adb8f9e16425facf2d088ba80f2b7e6bcb59cfebe
+	source = https://pypi.debian.net/pyteomics/pyteomics-4.6-py2.py3-none-any.whl
+	sha256sums = 95fea3ca8c8700d6113e85bf20e627acecdd892821fcc6559d16e18235e631dc
 
 pkgname = python-pyteomics
diff --git a/CHANGELOG b/CHANGELOG
index b9483672c03b..bdb0730ab1b2 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,32 @@
+4.6
+---
+
+ - When passing an existing file (by name) to :py:func:`pyteomics.mgf.write` or :py:func:`pyteomics.fasta.write` and
+   other writing functions, **the file will be opened for writing by default**. Previously, it would be opened for
+   appending with a warning about the upcoming change. Please be aware that existing files will be overwritten
+   if passed by name. The rationale for this is better reproducibility if the same code is run multiple
+   times. You can use the `file_mode` argument of the writing functions to override this behaviour, or pass your own
+   file objects.
+ - Add a special warning when trying to write a single spectrum with :py:func:`pyteomics.mgf.write`.
+   See also: `Writing one or more MGF spectra to a file <https://github.com/levitsky/pyteomics/discussions/109>`_.
+ - In :py:func:`pyteomics.mass.mass.calculate_mass`, the `absolute` parameter is now `True` by default.
+   When calculating *m/z* for negative charges, the returned value will be positive by default.
+ - Fix issue #98 (`#99 <https://github.com/levitsky/pyteomics/pull/99>`_ and
+   `#101 <https://github.com/levitsky/pyteomics/pull/101>`_ by Joshua Klein).
+ - Fix issue #91 (`#92 <https://github.com/levitsky/pyteomics/pull/92>`_ by Joshua Klein).
+ - Fix issue #96.
+ - Update the UniProt header pattern (fix rare parsing errors with
+   :py:class:`pyteomics.fasta.UniProt` and :py:class:`pyteomics.fasta.IndexedUniProt`) in
+   `#93 <https://github.com/levitsky/pyteomics/pull/93>`_.
+ - Update the UniRef header pattern (fix parsing errors with
+   :py:class:`pyteomics.fasta.UniRef` and :py:class:`pyteomics.fasta.IndexedUniRef`) in
+   `#102 <https://github.com/levitsky/pyteomics/pull/102>`_. Some keys are removed from the output.
+ - Fix pickling issues with :py:class:`pyteomics.mgf.IndexedMGF`, :py:class:`pyteomics.ms1.IndexedMS1`,
+   :py:class:`pyteomics.ms2.IndexedMS2` (#108).
+ - Add "charge array" and "resolution array" to the output of MS2 parsers (#108). Add new arguments `read_charges`
+   and `read_resolutions` to disable parsing, and `convert_arrays` to govern the creation of NumPy arrays
+   (and masked arrays).
+
 4.5.6
 -----
 
diff --git a/PKGBUILD b/PKGBUILD
index 51570bc1109f..50745bfa1ac6 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,6 +1,6 @@
 # Maintainer: Lev Levitsky <levlev at mail dot ru>
 pkgname=python-pyteomics
-pkgver=4.5.6
+pkgver=4.6
 pkgrel=1
 pkgdesc="A framework for proteomics data analysis."
 arch=('any')
@@ -16,7 +16,7 @@ optdepends=('python-matplotlib: for pylab_aux module'
             'python-pynumpress: for Numpress support')
 options=(!emptydirs)
 source=("https://pypi.debian.net/pyteomics/pyteomics-${pkgver}-py2.py3-none-any.whl")
-sha256sums=('0e279c085370e8085c84997adb8f9e16425facf2d088ba80f2b7e6bcb59cfebe')
+sha256sums=('95fea3ca8c8700d6113e85bf20e627acecdd892821fcc6559d16e18235e631dc')
 changelog=CHANGELOG
 
 package() {