Version 3.2

3 files changed, 56 insertions, 11 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 8cdabbd9a225..4497d831250f 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,8 @@
+# Generated by mksrcinfo v8
+# Thu Feb 18 15:21:41 UTC 2016
 pkgbase = python-pyteomics
 	pkgdesc = A framework for proteomics data analysis.
-	pkgver = 3.1.1
+	pkgver = 3.2
 	pkgrel = 1
 	url = http://pythonhosted.org/pyteomics
 	changelog = CHANGELOG
@@ -8,13 +10,14 @@ pkgbase = python-pyteomics
 	license = Apache
 	depends = python
 	depends = python-setuptools
-	optdepends = python-matplotlib: for pylab_aux module, optional
+	optdepends = python-matplotlib: for pylab_aux module
+	optdepends = python-sqlalchemy: for mass.unimod module
 	optdepends = python-pandas: for convenient filtering of CSV tables from search engines
-	optdepends = python-lxml: for XML parsing modules, recommended
+	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-3.1.1.tar.gz
-	md5sums = e367dc7eb11fd7d589183ec7e9b15650
+	source = https://pypi.python.org/packages/source/p/pyteomics/pyteomics-3.2.tar.gz
+	md5sums = 3fd5bc228d248d085a7bf9a461e5c62c
 
 pkgname = python-pyteomics
 
diff --git a/CHANGELOG b/CHANGELOG
index 94f5eae040c7..985854c56860 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,42 @@
+3.2
+---
+
+New submodule :py:mod:`pyteomics.mass.unimod` contains rewritten machinery
+for handling of Unimod relational databases (contributed by Joshua Klein).
+This is a substitution and extension for the old :py:class:`mass.Unimod` class.
+:py:mod:`pyteomics.mass.unimod` requires SQLAlchemy.
+
+Other changes:
+
+ - New function :py:func:`pyteomics.auxiliary.linear_regression_perpendicular`
+   provides a linear fit minimizing distances from data points to the fit line
+   (as opposed to :py:func:`pyteomics.auxiliary.linear_regression`, which
+   minimizes vertical distances).
+
+ - Both new and old linear regression functions now accept a single array of shape (N, 2).
+
+ - :py:func:`pyteomics.pylab_aux.scatter_trend` now has an optional parameter
+   `regression` which can be a callable performing the regression.
+   Also, the regression equation is now the label of the regression line, not
+   the scatter plot.
+
+ - Another two new parameters for :py:func:`pyteomics.pylab_aux.scatter_trend`
+   are `sigma_kwargs` and `sigma_values`.
+
+ - :py:mod:`pyteomics.pylab_aux` functions :py:func:`plot_line` and
+   :py:func:`scatter_trend` now return the objects they create.
+
+ - Writer functions (:py:func:`pyteomics.mgf.write`, :py:func:`pyteomics.fasta.write`,
+   :py:func:`pyteomics.fasta.write_decoy_db`) now accept a `file_mode` argument that
+   overrides the mode in which the file is opened.
+
+ - In :py:func:`pyteomics.mgf.write` one can now override the format spec for fragment m/z,
+   intensity and charge values using the optinal `fragment_format` argument. Key order and
+   key-value parameter formatters are now also handled via optional arguments.
+
+ - :py:func:`pyteomics.fasta.decoy_db` now supports `ignore_comments` and `parser` arguments.
+
+
 3.1.1
 -----
 
@@ -176,8 +215,10 @@ Fix for a memory leak in :py:func:`pyteomics.mzid.get_by_id`, which affects
 -----
 
  - Bugfixes in :py:func:`pyteomics.parser.isoforms`:
-  - handling of the `labels` argument is now in accordance with new policy
-  - solved memory problems when using `max_mods`
+
+   - handling of the `labels` argument is now in accordance with new policy
+   - solved memory problems when using `max_mods`
+
  - :py:func:`pyteomics.parser.cleave` does not require a valid *modX* sequence
    by default.
 
diff --git a/PKGBUILD b/PKGBUILD
index 9d116430e60f..46c8a9d1c7b1 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,19 +1,20 @@
 # Maintainer: Lev Levitsky <levlev at mail dot ru>
 pkgname=python-pyteomics
-pkgver=3.1.1
+pkgver=3.2
 pkgrel=1
 pkgdesc="A framework for proteomics data analysis."
 arch=('any')
 url="http://pythonhosted.org/pyteomics"
 license=('Apache')
 depends=('python' 'python-setuptools')
-optdepends=('python-matplotlib: for pylab_aux module, optional'
+optdepends=('python-matplotlib: for pylab_aux module'
+            'python-sqlalchemy: for mass.unimod module'
             'python-pandas: for convenient filtering of CSV tables from search engines'
-            'python-lxml: for XML parsing modules, recommended'
+            '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-${pkgver}.tar.gz")
-md5sums=('e367dc7eb11fd7d589183ec7e9b15650')
+md5sums=('3fd5bc228d248d085a7bf9a461e5c62c')
 changelog="CHANGELOG"
 package() {
   cd "${srcdir}/pyteomics-${pkgver}"