[khmer] the khmer project v1.0 is released

Michael R. Crusoe mcrusoe at msu.edu
Tue Apr 1 13:46:48 PDT 2014

Dear colleagues,

I am very happy to announce the release of version 1.0 of the khmer project.


The team has been hard at work since v0.8 to refine the codebase into a
stable product.

With the 1.0 release we are making a commitment to using Semantic
Versioning[0]: the version number will reflect the impact of the changes
between releases. New major versions will likely require you to change how
you use the project. Minor versions indicate new functionality that doesn't
impact the existing. Patch versions indicate backwards-compatible fixes.
Right now we are limiting this promise to the command-line interface. A
future release will introduce a stable and mature Python API to the khmer
project and at that time we will extend the version system to include that

## New items of note:

CITATION: Each script now outputs information on how to cite it. There is a
new paper to describes the project overall: MR Crusoe et al., 2014. doi:

The documentation for the scripts has undergone an overhaul. The scripts
now output extensive notes and the formal documentation website is
generated from the scripts themselves and will never be out of sync.


## Notable bugs fixed/issues closed:

git clone of the khmer repo reqs > 0.5 GiB #223 @mr-c
new khmer/file module #357 @RamRS
Floating point exception in count-overlap.py #282 @qingpeng
add documentation for sample-reads-randomly #192 @mr-c
only build zlib and bzip2 when needed #168 @mr-c

## Minor updates

khmer tools should output intelligent error messages when fed empty files
#135 @RamRS
set IParser::ParserState::ParserState:fill_id to zero at initialization #356
demote nose & sphinx to extra dependencies. #351 @mr-c
CID 1054792 (Medium) Uninitialized scalar field (UNINIT_CTOR) #179 @mr-c
CID 1077117 (Medium): Division or modulo by zero (DIVIDE_BY_ZERO) #182 @mr-c
if --savehash is specified then don't continue if there is not enough free
disk space #245 @RamRS
finish fixing implicit downcasts #330 @mr-c
Clean up compile warnings in subset.cc #172 @mr-c
all scripts need to output their version #236 @mr-c
environmental variables need documenting #303 @mr-c
C++ code should be consistently formatted #261 @mr-c
Clean up ancillary files #146 @mr-c
squash option not implemented in abundance-dist-single.py #271 @RamRS
Add documentation on how to tie into a particular tagged version #29 @mr-c
pip install -e fails with compile error #352 @mr-c
remove the unused KTable object #337 @luizirber
zlib 1.2.3 -> zlib 1.2.8 #336 @mr-c
CID 1173035: Uninitialized scalar field (UNINIT_CTOR) #311 @mr-c
CID 1153101: Resource leak in object (CTOR_DTOR_LEAK) #309 @mr-c
remove khmer::read_parsers::IParser::ParserState::thread_id #323 @mr-c
several modifications about count-overlap.py script #324 @qingpeng
fixed runscript to handle SystemExit #332 @ctb
CID 1063852: Uninitialized scalar field (UNINIT_CTOR) #313 @mr-c
[infrastructure] update to new Doxyfile format, make version number
autoupdate #315 @mr-c
Removed an extraneous using namespace khmer; in kmer.hh, #276 @fishjord
Minimum and recommended python version #94 @mr-c
KmerCount class appears to be unused #302 @mr-c
If loadhash is specified in e.g. normalize-by-median, don't complain about
default hashsize parameters #117 @RamRS

## 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

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

If your k-mer table (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 and
https://github.com/ged-lab/khmer/issues/96 and

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

annotate-partitions.py only outputs FASTA even if given a FASTQ file. This
issue is being tracked in https://github.com/ged-lab/khmer/issues/46

A user reported that abundance-dist-single.py fails with small files and
threads. This issue is being tracked in

## Contributors

@camillescott, @mr-c, @ctb, @luizirber, @RamRS, @qingpeng

[0] http://semver.org/

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
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