[med-svn] [kineticstools] branch upstream updated (3aad1ff -> 5ef124e)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository kineticstools.

      from  3aad1ff   Imported Upstream version 0.5.1+20150828+git3aa3d96+dfsg
       new  5ef124e   Imported Upstream version 0.5.2+dfsg

The 1 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
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Summary of changes:
 .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(-)
 create mode 100644 .circleci/installHDF5.sh
 create mode 100644 circle.yml
 create mode 100644 requirements-ci.txt
 create mode 100644 requirements-dev.txt
 create mode 100755 test/cram/long_running/run_jenkins.sh

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