[khmer] Screed v0.8 Released

[Jake Fenton]

Release v0.8

We are pleased to announce the release of Screed v0.8. Screed is a database
engine capable of storing and retrieving short-read sequence data and is
designed to be fast and adaptable to different sequence file formats.

This version of Screed contains developer documentation for contributing to
the
Screed project and a code of conduct for interacting with other contributors
and project maintainers. Documentation is available at
http://screed.readthedocs.org/en/v0.8/
New items of note:

This release successfully installs and passes its unit tests on Ubuntu
14.04 and the latest release of Mac OS X 10 "Yosemite". It also passes the
khmer acceptance tests as per the eelpond testing protocol.
<https://github.com/ged-lab/literate-resting/blob/master/kp/README.txt>

This release of screed has renamed the 'accuracy' attribute of read records
to 'quality;' this API change will need to be adopted by all users wanting
to upgrade to this version. Unlike the khmer project, Screed is not
currently under semantic versioning. It will be with the 1.0 release.

   - Screed now has automatic compression detection via magic bit sniffing
   for gzip and bzip2 compressed files (from @mr-c <https://github.com/mr-c>
    in ged-lab/khmer#432 <https://github.com/ged-lab/khmer/issues/432>)
   - Screed now supports streaming of uncompressed FASTA and FASTQ
   formatted nucleotide sequence data. bzip2 compressed FASTA and FASTQ
   formatted nucleotide sequence data can also be streamed but not gzip
   compressed FASTA and FASTQ formatted nucleotide sequence data. (from
   @mr-c <https://github.com/mr-c>, see ged-lab/khmer#633
   <https://github.com/ged-lab/khmer/issues/633>)
   - Screed now has a Changelog, developer documentation and a code of
   conduct (from @ctb <https://github.com/ctb>, at mr-c
   <https://github.com/mr-c>, @bocajnotnef <https://github.com/bocajnotnef>
    in ged-lab/khmer#625 <https://github.com/ged-lab/khmer/issues/625>)
   - Versions are now autogenerated using git tags via Versioneer (from
   @bocajnotnef <https://github.com/bocajnotnef> incadceb5
   <https://github.com/ged-lab/screed/commit/cadceb52b062f9c7fb85015f948df76c8acbc965>
   )
   - Documentation is now autogenerated using Doxygen (from @mr-c
   <https://github.com/mr-c> in d8ed05b
   <https://github.com/ged-lab/screed/commit/d8ed05b537f7ac0131ea1003713a8f15a611251f>
   )

Notable bugs fixed/issues closed:

   - A khmer script was not accepting reads on the stdin ged-lab/khmer#633
   <https://github.com/ged-lab/khmer/issues/633> by @mr-c
   <https://github.com/mr-c>
   - screed returning the wrong version and breaking dev installs
   ged-lab/khmer#803 <https://github.com/ged-lab/khmer/issues/803> by @mr-c
   <https://github.com/mr-c>

Known Issues

These are all pre-existing

   - Screed records cannot be sliced requiring un-Pythonic techniques to
   achieve the same behavior. This will be included in a future release. This
   is being tracked in ged-lab/khmer#768
   <https://github.com/ged-lab/khmer/issues/768>
   - Screed self-tests do not use a temporary directory which causes tests
   run from package-based installs to fail. This is being tracked in
   ged-lab/khmer#748 <https://github.com/ged-lab/khmer/issues/748>
   - Screed does not support gzip file streaming. This is an issue with
   Python 2.x and will likely*not* be fixed in future releases. This is
   being tracked in ged-lab/khmer#700
   <https://github.com/ged-lab/khmer/issues/700>
   - Screed is overly tolerant of spaces in fast{a,q} which is against
   spec. This is being tracked inged-lab/khmer#108
   <https://github.com/ged-lab/khmer/issues/108>

Contributors

@bocajnotnef <https://github.com/bocajnotnef> @mr-c
<https://github.com/mr-c> @brtaylor92 <https://github.com/brtaylor92>
@wrightmhw <https://github.com/wrightmhw> @kdmurray91
<https://github.com/kdmurray91> @luizirber <https://github.com/luizirber>
@ctb <https://github.com/ctb>
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