Merge branch 'release'

CHANGELOG.txt

@@ -1,3 +1,5 @@
+v0.2.5 (2014-04-05)
+- Add troubleshooting page to docs
 v0.2.4 (2014-04-05)
 - Add logo       
 v0.2.3 (2014-04-01)

Makefile

@@ -48,8 +48,11 @@ new_release:
 	@echo "* Change setup.py"
 	@echo "* Change docs/source/conf.py"
 	@echo "* Change CHANGELOG.txt"
-	@echo "* Commit changes e.g. 'git commit -m 'Set version to 0.2.0'"	
-	@echo "* Tag the commit e.g. 'git tag -a v0.1.9 -m 'version v0.1.9''"
+	@echo "* Create new docs"
+	@echo "* Test package creation"
+	@echo "* Test doc creation"
+	@echo "* Commit changes e.g. 'git commit -m 'Set version to 0.2.X'"	
+	@echo "* Tag the commit e.g. 'git tag -a v0.2.X -m 'version v0.2.X''"
 	@echo "* Merge release into dev and master"
 	@echo "* After pushing generate a new release based on this tag at"
 	@echo "  https://github.com/konrad/READemption/releases/new"

bin/reademption

@@ -9,7 +9,7 @@ __author__ = "Konrad Foerstner <[email protected]>"
 __copyright__ = "2011-2014 by Konrad Foerstner <[email protected]>"
 __license__ = "ISC license"
 __email__ = "[email protected]"
-__version__ = "0.2.4"
+__version__ = "0.2.5"
 
 def main():
     parser = argparse.ArgumentParser()

docs/source/conf.py

@@ -50,7 +50,7 @@
 # The short X.Y version.
 version = '0.2'
 # The full version, including alpha/beta/rc tags.
-release = '0.2.4'
+release = '0.2.5'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/index.rst

@@ -10,6 +10,7 @@ Table of content
    installation
    subcommands      
    example_analysis
+   troubleshooting
    license
    versions	      
 

docs/source/installation.rst

@@ -4,16 +4,13 @@ Installation
 Requirements
 ------------
 
-READemption was developed using Python 3.3 and for best performance
-the user is advised to run READemption with this or a higher
-version. Also Python 2.7 or earlier Python 3 version can be used if
-the backported library `futures
-<https://pypi.python.org/pypi/futures>`_ is installed. In any case,
-the third party packages `pysam <https://code.google.com/p/pysam>`_ as
-well as `setuptools <https://pypi.python.org/pypi/setuptools>`_ and
-`pip <http://www.pip-installer.org>`_ should be available on the
-system in order to make the installation easy. READemption uses the
-short read mapper `segemehl
+READemption was developed using Python 3.3 and the user is advised to
+run READemption with this or a higher version. In any case, the third
+party packages `pysam <https://code.google.com/p/pysam>`_ as well as
+`setuptools <https://pypi.python.org/pypi/setuptools>`_ and `pip
+<http://www.pip-installer.org>`_ should be available on the system in
+order to make the installation easy. READemption uses the short read
+mapper `segemehl
 <http://www.bioinf.uni-leipzig.de/Software/segemehl/>`_ for the
 mapping and this software needs to be installed. The subcommands
 ``viz_align``, ``viz_gene_quanti``, ``viz_deseq`` require the Python

docs/source/troubleshooting.rst

@@ -0,0 +1,20 @@
+Troubleshooting
+===============
+
+Pickling Error
+--------------
+
+Problem
+~~~~~~~
+
+When running reademption (e.g. with Python 3.2) you get an error like this:
+::
+   Traceback (most recent call last):
+     File "/usr/lib/python3.2/multiprocessing/queues.py", line 272, in _feed
+      send(obj)
+   _pickle.PicklingError: Can't pickle <class 'method'>: attribute lookup builtins.method failed
+
+Solution
+~~~~~~~~
+
+Switch to Python 3.3 or higher. The newer versions can handle this.

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='READemption',
-    version='0.2.4',
+    version='0.2.5',
     packages=['reademptionlib', 'tests'],
     author='Konrad U. Förstner',
     author_email='[email protected]',