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broadinstitute / viral-ngs / 4523
23%

Build:
DEFAULT BRANCH: master
Ran 03 Oct 2017 11:31PM UTC
Jobs 2
Files 45
Run time 3min
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improve newline handling (#675)

* replace deprecated universal newline 'U' with py3-compatible

Using the mode ‘U’ to tell Python to open text files with universal
newline support is deprecated in py3, and may be removed in the future.
This commit alters open_or_gzopen to set newline=None (universal
newline) under py3 when ‘U’ is given in the mode, and changes a few
open() calls to use open_or_gzopen(). Add a few test cases for
tab-delimited sample sheets with various line endings. Also replace the
deprecated “py.test” with “pytest”.

* extend open_or_gzopen() to support universal newlines in gzipped text files

extend open_or_gzopen() to support universal newlines in gzipped text
files using TextIOWrapper around a BufferedReader; add a test case with
gzipped samplesheet with windows line endings; allow
illumina.SampleSheet() to accept gzipped samplesheets

* .rstrip('\n').rstrip('\r') -> rstrip('\r\n')

* .rstrip('\n').rstrip('\r') -> .rstrip('\r\n')

* condense rstrip elsewhere

* 'r' mode as default for open_or_gzopen

* remove bufferedreader args not supported under python 2

31 of 31 new or added lines in 4 files covered. (100.0%)

5616 of 8230 relevant lines covered (68.24%)

1.36 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
2
100.0
ncbi.py

Uncovered Existing Lines

Lines Coverage ∆ File
3
100.0
util/misc.py
Jobs
ID Job ID Ran Files Coverage
1 4523.1 03 Oct 2017 11:31PM UTC 0
68.1
Travis Job 4523.1
2 4523.2 03 Oct 2017 11:35PM UTC 0
67.88
Travis Job 4523.2
Source Files on build 4523
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