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