This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository python-pbcore.
commit f80c7e4f7f1605de3856fa770cfb7be769b5fd51 Merge: b642087 4a2399d Author: Afif Elghraoui <[email protected]> Date: Sun Jan 7 01:09:09 2018 -0500 Merge tag 'upstream/1.4.2+dfsg' Upstream version 1.4.2+dfsg .pylintrc | 15 + CHANGELOG.org | 8 + Makefile | 6 +- README.md | 12 + bamboo_build.sh | 23 + bin/dataset.py | 13 - bin/updateXSDs.py | 18 +- pbcore/__init__.py | 2 +- pbcore/chemistry/chemistry.py | 9 +- pbcore/chemistry/resources/mapping.xml | 170 +- pbcore/data/__init__.py | 3 + pbcore/data/chemistry.xml | 9 + pbcore/data/datasets/hdfsubread_dataset.xml | 9 +- pbcore/data/datasets/subread.dataset.xml | 25 +- .../datasets/transformed_rs_subread.dataset.xml | 16 +- pbcore/io/BarcodeH5Reader.py | 22 +- pbcore/io/BasH5IO.py | 16 +- pbcore/io/VcfIO.py | 179 ++ pbcore/io/__init__.py | 1 + pbcore/io/_utils.py | 12 +- pbcore/io/align/BamIO.py | 7 +- pbcore/io/align/CmpH5IO.py | 10 +- pbcore/io/dataset/DataSetIO.py | 649 ++++-- pbcore/io/dataset/DataSetMembers.py | 720 ++++--- pbcore/io/dataset/DataSetReader.py | 60 +- pbcore/io/dataset/DataSetValidator.py | 7 +- pbcore/io/dataset/DataSetWriter.py | 111 +- pbcore/io/dataset/pyxb/DataSetXsd.py | 2148 ++++++++++++++++++++ pbcore/io/dataset/pyxb/__init__.py | 0 pbcore/io/dataset/{ => pyxb}/_pbbase.py | 1983 +++++++++++------- pbcore/io/dataset/{DataSetXsd.py => pyxb/_pbds.py} | 908 +++++---- pbcore/io/dataset/{ => pyxb}/_pbmeta.py | 1087 ++++++---- pbcore/io/dataset/pyxb/_pbpn.py | 941 +++++++++ pbcore/io/dataset/{ => pyxb}/_pbrk.py | 414 ++-- pbcore/io/dataset/{ => pyxb}/_pbsample.py | 318 +-- pbcore/io/dataset/utils.py | 321 +-- pbcore/io/opener.py | 2 +- pbcore/io/rangeQueries.py | 17 +- pbcore/util/__init__.py | 4 + requirements-dev.txt | 4 +- requirements.txt | 1 - setup.py | 2 +- tests/test_pbcore_extract_bam_sequence.py | 5 +- tests/test_pbcore_io_AlnFileReaders.py | 23 +- tests/test_pbcore_io_VcfIO.py | 64 + tests/test_pbcore_io_lossless_bam.py | 5 +- tests/test_pbdataset.py | 577 +++++- tests/test_pbdataset_filters.py | 274 ++- tests/test_pbdataset_metadata.py | 59 +- tests/test_pbdataset_split.py | 348 +++- tests/test_pbdataset_subtypes.py | 108 +- tests/test_pbdataset_utils.py | 75 +- tests/utils.py | 22 +- 53 files changed, 8943 insertions(+), 2899 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
