doc/conf.py | 3 1 + 2 - 0 !
1 file changed, 1 insertion(+), 2 deletions(-)

 use default sphinx theme for documentation
 The upstream's original theme includes their corporate
 logo. To be safe, this patch ignores it and configures
 the documentation builder to use the default theme.

setup.cfg | 3 3 + 0 - 0 !
setup.py | 1 1 + 0 - 0 !
2 files changed, 4 insertions(+)

 modify setuptools configuration to use nosetests
 Configure nose setuptools configuration as described in
 https://nose.readthedocs.org/en/latest/setuptools_integration.html
 and the manpage for the executable

requirements.txt | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 remove cython from requirements.txt
 Upstream now reads build dependencies from this file,
 but Cython isn't needed and setup.py therefore tries
 to download it (unsuccessfully).

pbcore/io/dataset/utils.py | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 fix compatibility with pysam 0.9.0