Merge branch 'release'

CHANGELOG.txt

@@ -1,3 +1,7 @@
+v0.2.1 (2014-03-31)
+- Improve documentation
+- Add badges and further info to Readme
+- Extend Makefile
 v0.2.0 (2014-03-29)
 - Switch to DESeq
 - Renaming from TRAPL to READemption (yes, another name change)

Makefile

@@ -8,14 +8,22 @@ coverage:
 package:
 	python3.3 setup.py sdist
 
+package_to_pypi:
+	python setup.py sdist upload
+	@echo "Go to https://pypi.python.org/pypi/READemption/"
+
 html_doc:
 	cd docs && make html && cd ..
 
+upload_doc:
+	cd docs/build/html/ && zip -r READemption_docs.zip * && cd ../../.. && mv docs/build/html/READemption_docs.zip .
+	@echo "Upload at https://pypi.python.org/pypi?%3Aaction=pkg_edit&name=READemption"
+
 show_html_docs:
 	firefox docs/build/html/index.html &
 
 readme_txt:
-	pandoc --from=markdown --to=plain README.md -o README.tex
+	pandoc --from=markdown --to=plain README.md -o README.txt
 
 readme_html:
 	pandoc --from=markdown --to=html README.md -o README.html
@@ -25,6 +33,19 @@ readme_rst:
 
 readme_clean:
 	rm -f README.tex README.html README.rst
+	rm -f README.tex README.html README.txt
 
 pylint:
 	pylint bin/reademption reademptionlib/* tests/*
+
+new_release:
+	@echo "* Please do this manually:"
+	@echo "* ------------------------"
+	@echo "* Change bin/reademption"
+	@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 "* After pushing generate a new release based on this tag at"
+	@echo "  https://github.com/konrad/READemption/releases/new"

README.md

@@ -1,3 +1,7 @@
+[![Latest Version](https://pypip.in/version/READemption/badge.png)](https://pypi.python.org/pypi/READemption/)
+[![License](https://pypip.in/license/READemption/badge.png)](https://pypi.python.org/pypi/READemption/)
+[![Downloads](https://pypip.in/d/READemption/badge.png)](https://pypi.python.org/pypi/READemption/)
+
 About
 -----
 
@@ -7,7 +11,7 @@ reads (as introduced by Sharma et al., Nature, 2010 originating from
 bacterial samples. Meanwhile is has been extended to process data
 generated in different experimental setups and originating from all
 domains of life and is under active development. The subcommands which
-are provided by command-line interface cover read processing and
+are accessible viaq command-line interface cover read processing and
 aligning, coverage plot generation, gene expression quantification as
 well as differential gene expression analysis. READemption was applied
 to analyze numerous data sets. In order to set up analyses quickly
@@ -16,6 +20,21 @@ Once the input files are copied into defined folders no further
 parameters have to be given. Still, READemption's behavior can be
 adapted to specific needs of the user.
 
+Documentation
+-------------
+
+Documentation can be found on [here](http://pythonhosted.org/READemption/).
+
+Installation
+------------
+
+Short version (if you have all the requirements installed):
+
+    $ pip install READemption
+
+[Long version](http://pythonhosted.org/READemption/installation.html)
+(what are the requirements and how do you get them)
+
 License
 -------
 

bin/reademption

@@ -9,7 +9,7 @@ __author__ = "Konrad Foerstner <[email protected]>"
 __copyright__ = "2011-2013 by Konrad Foerstner <[email protected]>"
 __license__ = "ISC license"
 __email__ = "[email protected]"
-__version__ = "0.2.0"
+__version__ = "0.2.1"
 
 def main():
     parser = argparse.ArgumentParser()

docs/source/conf.py

@@ -48,9 +48,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.1'
+version = '0.2'
 # The full version, including alpha/beta/rc tags.
-release = '0.1'
+release = '0.2.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.