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@SensibleSalmon SensibleSalmon released this 05 Apr 22:22
· 236 commits to master since this release
v0.8
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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.

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 in dib-lab/khmer#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, see dib-lab/khmer#633)
  • Screed now has a Changelog, developer documentation and a code of conduct (from @ctb, @mr-c, @bocajnotnef in dib-lab/khmer#625)
  • Versions are now autogenerated using git tags via Versioneer (from
    @bocajnotnef in cadceb5)
  • Documentation is now autogenerated using Doxygen (from @mr-c in d8ed05b)

Notable bugs fixed/issues closed:

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 dib-lab/khmer#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 dib-lab/khmer#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 dib-lab/khmer#700
  • Screed is overly tolerant of spaces in fast{a,q} which is against spec. This is being tracked in dib-lab/khmer#108

Contributors

@bocajnotnef @mr-c @brtaylor92 @wrightmhw @kdmurray91 @luizirber @ctb

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