[med-svn] [python-pbcommand] 02/10: Merge tag 'upstream/0.3.22'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository python-pbcommand.

commit 613721ea50444f85a46e5bf5e8885592b4c9fa62
Merge: 0c93df8 3ad18d1
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sat Apr 23 19:27:22 2016 -0700

    Merge tag 'upstream/0.3.22'
    
    Upstream version 0.3.22

 Makefile                                           |   4 +-
 README.md                                          |  10 +-
 REQUIREMENTS.txt                                   |   2 +
 REQUIREMENTS_TEST.txt                              |  10 +-
 docs/source/conf.py                                |   9 +-
 docs/source/index.rst                              |   9 +-
 docs/source/services.rst                           |   9 +
 pbcommand/__init__.py                              |   2 +-
 pbcommand/cli/__init__.py                          |   4 +-
 pbcommand/cli/core.py                              | 197 ++++---
 pbcommand/cli/examples/dev_app.py                  |   4 +-
 pbcommand/cli/examples/dev_gather_fasta_app.py     |   2 +-
 pbcommand/cli/examples/dev_mixed_app.py            |   4 +-
 pbcommand/cli/examples/dev_quick_hello_world.py    |  13 +-
 pbcommand/cli/examples/dev_scatter_fasta_app.py    |   2 +-
 pbcommand/cli/examples/dev_txt_app.py              |   4 +-
 pbcommand/cli/examples/template_simple.py          |  49 ++
 pbcommand/cli/quick.py                             | 119 +++--
 pbcommand/cli/utils.py                             | 139 +++++
 pbcommand/common_options.py                        |  90 +++-
 pbcommand/interactive_resolver.py                  |   2 +-
 pbcommand/models/__init__.py                       |   4 +-
 pbcommand/models/common.py                         | 102 +++-
 pbcommand/models/parser.py                         |  39 +-
 pbcommand/models/report.py                         |  49 +-
 pbcommand/models/tool_contract.py                  |  24 +-
 pbcommand/pb_io/report.py                          |  35 +-
 pbcommand/pb_io/tool_contract_io.py                |  21 +-
 pbcommand/resolver.py                              |  34 +-
 pbcommand/schemas/__init__.py                      |   2 +-
 pbcommand/schemas/resolved_tool_contract.avsc      |   6 +-
 pbcommand/services/__init__.py                     |   4 +
 pbcommand/services/cli.py                          | 505 ++++++++++++++++++
 pbcommand/services/models.py                       | 163 ++++++
 pbcommand/services/service_access_layer.py         | 585 +++++++++++++++++++++
 pbcommand/services/utils.py                        | 114 ++++
 pbcommand/testkit/core.py                          |  25 +-
 pbcommand/utils.py                                 | 345 +++++++++++-
 pbcommand/validators.py                            |  76 +--
 setup.py                                           |   3 +-
 .../dev_example_dev_txt_app_tool_contract.json     |   2 +-
 tests/data/dev_example_resolved_tool_contract.json |   3 +-
 tests/data/dev_example_tool_contract.json          |   2 +-
 tests/data/dev_gather_fasta_app_tool_contract.json |   2 +-
 .../data/dev_scatter_fasta_app_tool_contract.json  |   2 +-
 tests/data/example-reports/overview.json           |   4 +-
 ...ommand.tasks.dev_fastq2fasta_tool_contract.json |  55 +-
 ...mmand.tasks.dev_qhello_world_tool_contract.json |   4 +-
 ...nd.tasks.dev_txt_custom_outs_tool_contract.json |   6 +-
 ...bcommand.tasks.dev_txt_hello_tool_contract.json |   6 +-
 tests/data/resolved_contract_01.json               |   5 +-
 tests/data/resolved_tool_contract_dev_app.json     |   5 +-
 tests/test_common_cmdline_core.py                  |   2 +-
 tests/test_e2e_example_apps.py                     |   4 +
 tests/test_load_resolved_tool_contract.py          |   2 +-
 tests/test_models_report.py                        | 206 +++++++-
 tests/test_models_report_attribute.py              |  53 ++
 tests/test_models_report_column.py                 |  76 +++
 tests/test_models_report_plot.py                   |  43 ++
 tests/test_models_report_plotgroup.py              |  58 ++
 tests/test_models_report_table.py                  | 121 +++++
 tests/test_parsers.py                              |  20 +-
 tests/test_pb_io_report.py                         |   3 +
 tests/test_resolver.py                             |   6 +-
 tests/test_utils.py                                |  44 +-
 tox.ini                                            |   2 +
 66 files changed, 3189 insertions(+), 367 deletions(-)

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