1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
|
Release v0.9
============
We are pleased to announce the release of Screed v0.9. 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 features Python 3 syntax with compatibility with
Python 2. Additional changes have broken backwards compatibility in
several small ways in preparation for our 1.0 release and adoption of
strict semantic versioning from there on out.
It is also the first release since our move to the University of Davis,
California and also under our new name, the Lab for Data Intensive
Biology.
Documentation is available at http://screed.readthedocs.org/en/v0.9/
New items of note:
------------------
- Now a primarily Python 3 codebase with Python 2 compatibility.
https://github.com/dib-lab/screed/pull/41 @luizirber & @mr-c
- Tests now correctly run using temporary directories and the test data
is now shipped allowing the tests to be run after installation.
https://github.com/dib-lab/screed/pull/30 @bocajnotnef
https://github.com/dib-lab/screed/pull/40 @mr-c
- The private method ``screed/screedRecord._screed_record_dict()`` has
been renamed to ``screed.screedRecord.Record()``. This is **not** a
backwards compatible change.
https://github.com/dib-lab/screed/pull/35 @sguermond
- ``screed.open()`` now accepts ``-`` as a synonym for STDIN and is now
an (optional) context manager. It no longer defaults to parsing out a
separate description from the name. The description field will br
removed altogether from the next release. This is **not** a backwards
compatible change. https://github.com/dib-lab/screed/pull/36
@anotherthomas https://github.com/dib-lab/screed/pull/39
https://github.com/dib-lab/screed/pull/41 @luizirber
https://github.com/dib-lab/screed/pull/43 @ctb
- The FASTQ parser was improved and it no longer hangs in the presence
of empty lines. https://github.com/dib-lab/screed/pull/38 @proteasome
- Screed records now slice correctly
https://github.com/dib-lab/screed/pull/41 @wrightmhw @luizirber
Other bugs fixed/issues closed:
-------------------------------
- Release notes are now a part of the documentation.
https://github.com/dib-lab/screed/pull/33 @bocajnotnef
- A test was made more robust to prevent hangs.
https://github.com/dib-lab/screed/pull/37 @anotherthomas
Known Issues
------------
These are all pre-existing
- 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
- Screed is overly tolerant of spaces in fast{a,q} which is against
spec. This is being tracked in ged-lab/khmer#108
Contributors
------------
@luizirber @mr-c @bocajnotnef @ctb \*@proteasome \*@anotherthomas
\*@sguermond
\* Indicates new contributors
|
