From 107ec3bb847711e04e053a93b84fc76a114d9380 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Konrad=20F=C3=B6rstner?= Date: Mon, 31 Mar 2014 23:12:33 +0200 Subject: [PATCH 1/3] Add missing comma --- setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 3ef091d6..621c9b96 100644 --- a/setup.py +++ b/setup.py @@ -18,8 +18,8 @@ license='LICENSE.txt', long_description=open('README.rst').read(), classifiers=[ - 'License :: OSI Approved :: ISC License (ISCL)' - 'Operating System :: POSIX' + 'License :: OSI Approved :: ISC License (ISCL)', + 'Operating System :: POSIX', 'Programming Language :: Python :: 3', 'Topic :: Scientific/Engineering :: Bio-Informatics', ] From 52a5a65769cc1a36145ba7ec477c5ebe7e83b8fa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Konrad=20F=C3=B6rstner?= Date: Mon, 31 Mar 2014 23:12:45 +0200 Subject: [PATCH 2/3] Fix typo --- README.md | 2 +- README.rst | 66 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 67 insertions(+), 1 deletion(-) create mode 100644 README.rst diff --git a/README.md b/README.md index de12f258..0b8f8f01 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ About READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed at the IMIB/ZINF to process dRNA-Seq -reads (as introduced by Sharma et al., Nature, 2010 originating from +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 diff --git a/README.rst b/README.rst new file mode 100644 index 00000000..5b5fb28d --- /dev/null +++ b/README.rst @@ -0,0 +1,66 @@ +About +----- + +READemption is a pipeline for the computational evaluation of RNA-Seq +data. It was originally developed at the IMIB/ZINF to process dRNA-Seq +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 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 +READemption follows the principal of "convention over configuration": +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 `__. + +Installation +------------ + +Short version (if you have all the requirements installed): + +:: + + $ pip install READemption + +`Long version `__ +(what are the requirements and how do you get them) + +License +------- + +`ICSL `__ - see LICENSE.txt + +Development +----------- + +- If possible follow the principal of "convention over configuration". + This means input file are into a fixed location and the result file + are placed in fixed location. + +- The classes should be path agnostic as far a possible. The controller + is taking care of that and calls them adequately. + +- The git braching model is very close to the one proposed + `here `__. + There two main branches: + + - master + - dev(elopment) + + And there are further supporting branches: + + - feature branches - branched off and back to the dev branch + - release branches - branched off from dev and merged back into dev + and master + - hotfix branches - branched off from master and merged back into + dev and master + From 28a08040f2e62046f08d8aec679eba4d1ea3217d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Konrad=20F=C3=B6rstner?= Date: Mon, 31 Mar 2014 23:18:10 +0200 Subject: [PATCH 3/3] Set version to 0.2.2 --- CHANGELOG.txt | 3 +++ bin/reademption | 2 +- docs/source/conf.py | 2 +- setup.py | 2 +- 4 files changed, 6 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.txt b/CHANGELOG.txt index 5e11b424..51ea2a2a 100644 --- a/CHANGELOG.txt +++ b/CHANGELOG.txt @@ -1,3 +1,6 @@ +v0.2.2 (2014-03-31) +- Fix setup.py +- Typos fixing v0.2.1 (2014-03-31) - Improve documentation - Add badges and further info to Readme diff --git a/bin/reademption b/bin/reademption index bd7f708c..a2ab3f01 100755 --- a/bin/reademption +++ b/bin/reademption @@ -9,7 +9,7 @@ __author__ = "Konrad Foerstner " __copyright__ = "2011-2013 by Konrad Foerstner " __license__ = "ISC license" __email__ = "konrad@foerstner.org" -__version__ = "0.2.1" +__version__ = "0.2.2" def main(): parser = argparse.ArgumentParser() diff --git a/docs/source/conf.py b/docs/source/conf.py index 88a092a8..d2e3351b 100644 --- a/docs/source/conf.py +++ b/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 = '0.2.1' +release = '0.2.2' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/setup.py b/setup.py index 621c9b96..53c2d33c 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setup( name='READemption', - version='0.2.1', + version='0.2.2', packages=['reademptionlib', 'tests'], author='Konrad U. Förstner', author_email='konrad@foerstner.org',