[med-svn] [python-pbcore] branch master updated (0bf210c -> 620c3bb)
Afif Elghraoui
afif at moszumanska.debian.org
Sun Oct 9 18:38:06 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository python-pbcore.
from 0bf210c releasing package python-pbcore version 1.2.9+dfsg-1
new a06a1f0 Imported Upstream version 1.2.10+dfsg
new 06db5ad Merge tag 'upstream/1.2.10+dfsg'
new a454197 Drop patch applied upstream
new b51022d Don't raise exception if pyxb version does not exactly match
new 8d32cb4 Bump Standards-Version to 3.9.8
new 620c3bb releasing package python-pbcore version 1.2.10+dfsg-1
The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
CHANGELOG.org | 5 +
debian/changelog | 10 +
debian/control | 2 +-
debian/patches/ignore-pyxb.patch | 88 ++++++
debian/patches/pysam-0.9.0.patch | 27 --
debian/patches/remove-unnecessary-cython-dep.patch | 2 +-
debian/patches/series | 2 +-
pbcore/__init__.py | 2 +-
pbcore/chemistry/resources/mapping.xml | 71 ++++-
pbcore/io/align/BamAlignment.py | 2 +-
pbcore/io/align/PacBioBamIndex.py | 17 +
pbcore/io/dataset/DataSetErrors.py | 17 +
pbcore/io/dataset/DataSetIO.py | 313 +++++++++++++-----
pbcore/io/dataset/DataSetMembers.py | 185 +++++++----
pbcore/io/dataset/DataSetReader.py | 44 ++-
pbcore/io/dataset/utils.py | 81 ++++-
requirements.txt | 2 +-
tests/test_pbcore_io_AlnFileReaders.py | 19 ++
tests/test_pbdataset.py | 348 ++++++++++++++++++++-
tests/test_pbdataset_subtypes.py | 129 +++++++-
20 files changed, 1174 insertions(+), 192 deletions(-)
create mode 100644 debian/patches/ignore-pyxb.patch
delete mode 100644 debian/patches/pysam-0.9.0.patch
create mode 100644 pbcore/io/dataset/DataSetErrors.py
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