Version 3.4

3 files changed, 115 insertions, 13 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 8cdabbd9a225..846d0dc700e2 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,8 @@
+# Generated by mksrcinfo v8
+# Thu Sep  8 19:56:16 UTC 2016
 pkgbase = python-pyteomics
 	pkgdesc = A framework for proteomics data analysis.
-	pkgver = 3.1.1
+	pkgver = 3.4
 	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.io/packages/source/p/pyteomics/pyteomics-3.4.tar.gz
+	md5sums = 3c8d1bcc16c53100e531a10a2853f679
 
 pkgname = python-pyteomics
 
diff --git a/CHANGELOG b/CHANGELOG
index 94f5eae040c7..15672ad90dd2 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,10 +1,106 @@
+3.4
+---
+
+ - New module :py:mod:`pyteomics.mzxml` for parsing of MzXML files.
+
+ - New parameter `dtype` in :py:func:`pyteomics.mgf.read`, :py:func:`pyteomics.mzml.read`
+   and :py:func:`pyteomics.mzxml.read`
+   allows changing the dtype of arrays yielded by the parsers.
+
+ - :py:mod:`pyteomics.featurexml` moved into a subpackage :py:mod:`pyteomics.openms`.
+
+ - New module :py:mod:`pyteomics.openms.trafoxml` for OpenMS transformation files.
+
+ - Bugfix in XML indexing code to make it work on Python 3.x versions prior to 3.5.
+
+ - Bugfix in :py:func:`pyteomics.pylab_aux.scatter_trend` (support for lists and other non-ndarrays).
+
+ - Performance improvements in :py:mod:`pyteomics.achrom` calibration functions.
+
+3.3.1
+-----
+
+New submodule :py:mod:`pyteomics.featurexml` with a parser for OpenMS **featureXML** files.
+
+3.3
+---
+
+ - mzML and mzIdentML parsers can now create an index of element offsets.
+   This allows quick random access to elements by unique ID.
+
+ - mzML parsers now come in two flavors: :py:class:`pyteomics.mzml.MzML` and
+   :py:class:`pyteomics.mzml.PreIndexedMzML`. The latter uses the byte offsets
+   listed at the end of the file.
+
+ - New parameters `convert_arrays` and `read_charges` in :py:func:`mgf.read`
+   allow using it without :py:mod:`numpy` and possibly improve performance.
+   The default behavior is retained.
+
+ - Performance optimizations in :py:func:`mgf.read` and :py:func:`parser.cleave`.
+
+ - New decoy generation mode called "fused decoy", described in the paper accepted to JASMS.
+
+API changes
+...........
+
+ - :py:func:`pyteomics.parser.cleave` no longer accepts the `labels` argument.
+   It is emphasized that the input sequences are expected to be in plain one-letter
+   notation, but no checks are performed.
+
+ - :py:func:`DataFrame` functions in :py:mod:`pepxml` and :py:mod:`tandem` now
+   extract more protein-related information. The list-like protein-related values
+   can be reported as lists or packed into strings, depending on the optional
+   paramter `sep`. Some column names have changed as a result.
+
+ - Call signatures of :py:func:`pyteomics.fasta.decoy_sequence` and the functions using it
+   are slightly changed. Standard modes are now also exposed as individual functions.
+
+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
 -----
 
  - Bugfix in :py:mod:`pyteomics.auxiliary`.
 
  - New parameter `show_legend` in :py:func:`pyteomics.pylab_aux.scatter_trend`.
- 
+
  - Performance improvements in :py:mod:`pyteomics.parser`.
 
 3.1
@@ -176,8 +272,10 @@ 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..5c1b9a7c5cfb 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=3.4
 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-${pkgver}.tar.gz")
-md5sums=('e367dc7eb11fd7d589183ec7e9b15650')
+source=("https://pypi.io/packages/source/p/pyteomics/pyteomics-${pkgver}.tar.gz")
+md5sums=('3c8d1bcc16c53100e531a10a2853f679')
 changelog="CHANGELOG"
 package() {
   cd "${srcdir}/pyteomics-${pkgver}"