[khmer-announce] the khmer project v0.8 is released

[Michael R. Crusoe]

Dear colleagues,

I am happy to announce version 0.8 of the khmer project.

89 changed files with 11,223 additions and 6,171 deletions.

## New functionality

Sparse graph labeling @camillescott ( sweep-reads-by-partition-buffered.py )
Initial support for Galaxy integration (for normalize-by-median and
abund-filter) @mr-c
Normalization of arguments across the scripts @camillescott

Note: The default branch on GitHub is now the 'master' branch. Our
unmaintained tutorials that install khmer with a plain git clone have a
warning added to them and potential user are directed to the
khmer-protocols: http://khmer-protocols.readthedocs.org

## Notable bugs fixed

load-graph gives erroneous memory estimate #279 @camillescott
If loadhash is specified, do not complain about hashsize #278 @RamRS
@humberto-ortiz
test_Hashbits case sensitivity #265 @luizirber
Installation fails: cannot find argparse >= 1.2.1 #258 @mr-c & @standage
Bugs found by coverity #256 @camillescott

## Minor updates

abundance-dist-single.py, abundance-dist.py, do-partition.py,
interleave-reads.py, load-graph.py, load-into-counting.py
normalize-by-median.py now exit with return code 1 instead of 255 as is
standard.
Program arguments that have default values are disclosed @mr-c
Developer documentation updates: contribution guidelines, coding standards,
code review hints (with checklist). Release instruction completely
rewritten.
Installation instructions tweaks including specific commands for Debian
derivatives and RHEL6.
Update to the latest versioneer.py & ez_setup.py
The latest version of setuptools is no longer required: version 0.6c11
appears to be just fine.
Many code cleanups. Python namespace usage was tidied. Type safety was
strengthened in the C++/Python integration.
Testing coverage measures the scripts properly.

## Known Issues

All of these are pre-existing.

Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in
https://github.com/ged-lab/khmer/issues/266

Some FASTQ files confuse our parser when running with more than one thread.
For example, while using load-into-counting.py. If you experience this then
add "--threads=1" to your command line. This issue is being tracked in
https://github.com/ged-lab/khmer/issues/249

If your hashfile gets truncated, perhaps from a full filesystem, then our
tools currently will get stuck. This is being tracked in
https://github.com/ged-lab/khmer/issues/247

Paired-end reads from Casava 1.8 currently require renaming for use in
normalize-by-median and abund-filter when used in paired mode. The
integration of a fix for this is being tracked in
https://github.com/ged-lab/khmer/issues/23

A user has reported a floating point exception when running
count-overlap.py. There is no workaround at this time.
https://github.com/ged-lab/khmer/issues/282

## Contributors

@camillescott, @mr-c, @ctb, @luizirber, @RamRS, @humberto-ortiz, and
@standage
Special thanks to the new contributors!


-- 
Michael R. Crusoe:  Programmer & Bioinformatician   mcrusoe at msu.edu
 @ the Genomics, Evolution, and Development lab; Michigan State U
http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670
@biocrusoe<http://twitter.com/biocrusoe>
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