[med-svn] [kineticstools] 02/10: Merge tag 'upstream/0.5.2+dfsg'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository kineticstools.

commit 9465e34be4ba17632f5f119c6541979100664f24
Merge: d46ddce 5ef124e
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sat Jul 2 15:23:24 2016 -0700

    Merge tag 'upstream/0.5.2+dfsg'
    
    Upstream version 0.5.2+dfsg

 .circleci/installHDF5.sh                          | 14 +++++
 circle.yml                                        | 18 ++++++
 kineticsTools/ipdSummary.py                       | 68 +++++++++++------------
 kineticsTools/summarizeModifications.py           | 18 +++---
 requirements-ci.txt                               | 12 ++++
 requirements-dev.txt                              |  3 +
 setup.py                                          |  6 +-
 test/cram/case-ctrl.t                             |  2 +-
 test/cram/detection.t                             |  2 +-
 test/cram/detection_bam.t                         |  8 +--
 test/cram/detection_bam_dataset.t                 |  8 +--
 test/cram/detection_bam_lossless.t                |  6 +-
 test/cram/identify.t                              |  2 +-
 test/cram/long_running/README.txt                 |  6 +-
 test/cram/long_running/detect_and_identify_Bsub.t |  4 +-
 test/cram/long_running/detect_and_identify_Cagg.t |  2 +-
 test/cram/long_running/detect_and_identify_Hpyl.t |  4 +-
 test/cram/long_running/detect_and_identify_Mjan.t |  2 +-
 test/cram/long_running/run_jenkins.sh             | 19 +++++++
 test/cram/methyl-fraction-case-ctrl.t             |  2 +-
 test/cram/version.t                               |  9 +--
 test/test_ReferenceUtils.py                       |  4 +-
 test/test_inputs.py                               | 60 ++++++++++++++++++--
 test/test_tool_contract.py                        |  6 +-
 24 files changed, 199 insertions(+), 86 deletions(-)

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